From cbe496bd92dc01a2ec78f5827a339e6f485c0eeb Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 18:16:07 +0000
Subject: [PATCH 01/19] Add regression tests for the mesh readers

The new CTest suite runs pumgen with 1 to 4 ranks on small gmsh-generated
fixtures and compares the written datasets with h5diff against reference PUML
files. fixtures/generate.py computes the references from the gmsh model
directly, i.e. independently of PUMGen. The element and vertex counts of the
layered fixture do not divide evenly among 3 or 4 ranks. CI now runs the tests
for the Release and the Debug (AddressSanitizer) build.

AI-generated. Model: Claude Opus 5.5
---
 .github/workflows/cmake.yml               |    6 +-
 .pre-commit-config.yaml                   |    2 +
 CMakeLists.txt                            |    5 +
 REUSE.toml                                |   11 +
 tests/CMakeLists.txt                      |   69 +
 tests/RunPumgenTest.cmake                 |   59 +
 tests/fixtures/coarse-binary-v41.msh      |  Bin 0 -> 27978 bytes
 tests/fixtures/coarse-o2-v22.msh          | 1186 +++++++
 tests/fixtures/coarse-o2-v41.msh          | 1921 ++++++++++++
 tests/fixtures/coarse-o2.puml.h5          |  Bin 0 -> 48120 bytes
 tests/fixtures/coarse-offset-v41.msh      |  877 ++++++
 tests/fixtures/coarse-partitioned-v41.msh | 1000 ++++++
 tests/fixtures/coarse-v41.msh             |  877 ++++++
 tests/fixtures/coarse.puml.h5             |  Bin 0 -> 20280 bytes
 tests/fixtures/generate.py                |  246 ++
 tests/fixtures/layered-v22.msh            | 2893 +++++++++++++++++
 tests/fixtures/layered-v41.msh            | 3444 +++++++++++++++++++++
 tests/fixtures/layered.neu                | 3378 ++++++++++++++++++++
 tests/fixtures/layered.puml.h5            |  Bin 0 -> 78656 bytes
 tests/fixtures/tiny-badnode-v22.msh       |   14 +
 tests/fixtures/tiny-badnode-v41.msh       |   24 +
 tests/fixtures/tiny-badnumber-v41.msh     |   24 +
 tests/fixtures/tiny-duplicate-v22.msh     |   14 +
 tests/fixtures/tiny-duplicate-v41.msh     |   24 +
 tests/fixtures/tiny-sparse-v41.msh        |   24 +
 tests/fixtures/tiny-truncated-v41.msh     |   23 +
 tests/fixtures/tiny-unknowntype-v41.msh   |   24 +
 tests/fixtures/tiny-v22.msh               |   14 +
 tests/fixtures/tiny-v40.msh               |   24 +
 tests/fixtures/tiny-v41.msh               |   24 +
 tests/fixtures/tiny.puml.h5               |  Bin 0 -> 4368 bytes
 31 files changed, 16206 insertions(+), 1 deletion(-)
 create mode 100644 REUSE.toml
 create mode 100644 tests/CMakeLists.txt
 create mode 100644 tests/RunPumgenTest.cmake
 create mode 100644 tests/fixtures/coarse-binary-v41.msh
 create mode 100644 tests/fixtures/coarse-o2-v22.msh
 create mode 100644 tests/fixtures/coarse-o2-v41.msh
 create mode 100644 tests/fixtures/coarse-o2.puml.h5
 create mode 100644 tests/fixtures/coarse-offset-v41.msh
 create mode 100644 tests/fixtures/coarse-partitioned-v41.msh
 create mode 100644 tests/fixtures/coarse-v41.msh
 create mode 100644 tests/fixtures/coarse.puml.h5
 create mode 100644 tests/fixtures/generate.py
 create mode 100644 tests/fixtures/layered-v22.msh
 create mode 100644 tests/fixtures/layered-v41.msh
 create mode 100644 tests/fixtures/layered.neu
 create mode 100644 tests/fixtures/layered.puml.h5
 create mode 100644 tests/fixtures/tiny-badnode-v22.msh
 create mode 100644 tests/fixtures/tiny-badnode-v41.msh
 create mode 100644 tests/fixtures/tiny-badnumber-v41.msh
 create mode 100644 tests/fixtures/tiny-duplicate-v22.msh
 create mode 100644 tests/fixtures/tiny-duplicate-v41.msh
 create mode 100644 tests/fixtures/tiny-sparse-v41.msh
 create mode 100644 tests/fixtures/tiny-truncated-v41.msh
 create mode 100644 tests/fixtures/tiny-unknowntype-v41.msh
 create mode 100644 tests/fixtures/tiny-v22.msh
 create mode 100644 tests/fixtures/tiny-v40.msh
 create mode 100644 tests/fixtures/tiny-v41.msh
 create mode 100644 tests/fixtures/tiny.puml.h5

diff --git a/.github/workflows/cmake.yml b/.github/workflows/cmake.yml
index be078f9..a6c4ebb 100644
--- a/.github/workflows/cmake.yml
+++ b/.github/workflows/cmake.yml
@@ -29,12 +29,16 @@ jobs:
         run: |
           git submodule update --init --recursive
           mkdir build_${{ matrix.build_type}} && cd build_${{ matrix.build_type}}
-          cmake .. -DCMAKE_PREFIX_PATH=${{ runner.workspace }}/opt -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
+          cmake .. -DCMAKE_PREFIX_PATH=${{ runner.workspace }}/opt -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DMPIEXEC_PREFLAGS=--oversubscribe
 
       - name: Build
         working-directory: ${{ github.workspace }}/build_${{ matrix.build_type }}
         run: cmake --build .
 
+      - name: Test
+        working-directory: ${{ github.workspace }}/build_${{ matrix.build_type }}
+        run: ctest --output-on-failure
+
   pre-commit-check:
     runs-on: ubuntu-latest
     steps:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index d38090d..4034174 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -59,5 +59,7 @@ repos:
     hooks:
     -   id: end-of-file-fixer
         name: '[GENERIC] newline eof'
+        exclude: ^tests/fixtures/
     -   id: trailing-whitespace
         name: '[GENERIC] remove trailing whitespace'
+        exclude: ^tests/fixtures/
diff --git a/CMakeLists.txt b/CMakeLists.txt
index 58e4d5f..0d40349 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -139,3 +139,8 @@ if(SIMMETRIX)
 endif()
 set_target_properties(pumgen PROPERTIES INSTALL_RPATH "${INSTALL_RPATH}")
 install(TARGETS pumgen RUNTIME DESTINATION bin DESTINATION ${CMAKE_INSTALL_BINDIR})
+
+include(CTest)
+if (BUILD_TESTING)
+  add_subdirectory(tests)
+endif()
diff --git a/REUSE.toml b/REUSE.toml
new file mode 100644
index 0000000..4465d3c
--- /dev/null
+++ b/REUSE.toml
@@ -0,0 +1,11 @@
+# SPDX-FileCopyrightText: 2026 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+version = 1
+
+[[annotations]]
+path = ["tests/fixtures/*.msh", "tests/fixtures/*.neu", "tests/fixtures/*.h5"]
+precedence = "override"
+SPDX-FileCopyrightText = "2026 SeisSol Group"
+SPDX-License-Identifier = "BSD-3-Clause"
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
new file mode 100644
index 0000000..d51db5c
--- /dev/null
+++ b/tests/CMakeLists.txt
@@ -0,0 +1,69 @@
+# SPDX-FileCopyrightText: 2026 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+find_program(H5DIFF_EXECUTABLE NAMES h5diff DOC "h5diff, used to compare the test output")
+if(NOT H5DIFF_EXECUTABLE)
+  message(WARNING "h5diff not found: the tests only check whether pumgen succeeds")
+endif()
+
+set(PUMGEN_TEST_FIXTURES ${CMAKE_CURRENT_SOURCE_DIR}/fixtures)
+set(PUMGEN_TEST_OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/output)
+file(MAKE_DIRECTORY ${PUMGEN_TEST_OUTPUT})
+
+# pumgen_add_test(<name> RANKS <n> SOURCE <source> INPUT <fixture>
+#                 [REFERENCE <fixture> [TOLERANCE <tolerance>]] [EXPECT_ERROR <regex>]
+#                 [ARGS <argument>...])
+function(pumgen_add_test name)
+  cmake_parse_arguments(PARSE_ARGV 1 TEST "" "RANKS;SOURCE;INPUT;REFERENCE;TOLERANCE;EXPECT_ERROR"
+                        "ARGS")
+  set(output ${PUMGEN_TEST_OUTPUT}/${name}.puml.h5)
+  set(command
+      ${MPIEXEC_EXECUTABLE}
+      ${MPIEXEC_NUMPROC_FLAG}
+      ${TEST_RANKS}
+      ${MPIEXEC_PREFLAGS}
+      $<TARGET_FILE:pumgen>
+      ${MPIEXEC_POSTFLAGS}
+      -s
+      ${TEST_SOURCE}
+      ${TEST_ARGS}
+      ${PUMGEN_TEST_FIXTURES}/${TEST_INPUT}
+      ${output})
+  string(REPLACE ";" "|" command "${command}")
+
+  set(script_args -DCOMMAND=${command} -DOUTPUT=${output})
+  if(DEFINED TEST_EXPECT_ERROR)
+    list(APPEND script_args "-DEXPECT_ERROR=${TEST_EXPECT_ERROR}")
+  elseif(DEFINED TEST_REFERENCE AND H5DIFF_EXECUTABLE)
+    list(APPEND script_args -DREFERENCE=${PUMGEN_TEST_FIXTURES}/${TEST_REFERENCE}
+         -DH5DIFF=${H5DIFF_EXECUTABLE})
+    if(DEFINED TEST_TOLERANCE)
+      list(APPEND script_args -DTOLERANCE=${TEST_TOLERANCE})
+    endif()
+  endif()
+
+  add_test(NAME pumgen.${name} COMMAND ${CMAKE_COMMAND} ${script_args} -P
+                                       ${CMAKE_CURRENT_SOURCE_DIR}/RunPumgenTest.cmake)
+  set_tests_properties(
+    pumgen.${name} PROPERTIES PROCESSORS ${TEST_RANKS} TIMEOUT 120 ENVIRONMENT
+                              "ASAN_OPTIONS=detect_leaks=0")
+endfunction()
+
+# The fixtures are created by fixtures/generate.py; the reference files are computed from the
+# gmsh model directly. The layered mesh has element and vertex counts which do not divide evenly
+# among 3 or 4 ranks.
+
+foreach(ranks 1 2 3 4)
+  pumgen_add_test(msh4.layered.np${ranks} RANKS ${ranks} SOURCE msh4 INPUT layered-v41.msh
+                  REFERENCE layered.puml.h5)
+endforeach()
+foreach(ranks 1 2 3)
+  pumgen_add_test(msh2.layered.np${ranks} RANKS ${ranks} SOURCE msh2 INPUT layered-v22.msh
+                  REFERENCE layered.puml.h5)
+endforeach()
+pumgen_add_test(msh4.coarse.np2 RANKS 2 SOURCE msh4 INPUT coarse-v41.msh REFERENCE coarse.puml.h5)
+pumgen_add_test(msh2.coarse-o2.np1 RANKS 1 SOURCE msh2 INPUT coarse-o2-v22.msh
+                REFERENCE coarse-o2.puml.h5 ARGS --order=2)
+pumgen_add_test(msh4.tiny.np1 RANKS 1 SOURCE msh4 INPUT tiny-v41.msh REFERENCE tiny.puml.h5)
+pumgen_add_test(msh2.tiny.np1 RANKS 1 SOURCE msh2 INPUT tiny-v22.msh REFERENCE tiny.puml.h5)
diff --git a/tests/RunPumgenTest.cmake b/tests/RunPumgenTest.cmake
new file mode 100644
index 0000000..19ec71a
--- /dev/null
+++ b/tests/RunPumgenTest.cmake
@@ -0,0 +1,59 @@
+# SPDX-FileCopyrightText: 2026 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+# Runs pumgen for one test case and checks the result.
+#
+# Variables:
+#   COMMAND       pumgen command line, with '|' as the argument separator
+#   OUTPUT        file written by pumgen
+#   REFERENCE     (optional) reference PUML file the output has to match
+#   TOLERANCE     (optional) absolute tolerance for the vertex coordinates
+#   H5DIFF        h5diff executable, required together with REFERENCE
+#   EXPECT_ERROR  (optional) pumgen has to fail with a message matching this regular expression
+
+string(REPLACE "|" ";" command "${COMMAND}")
+file(REMOVE "${OUTPUT}")
+
+execute_process(
+  COMMAND ${command}
+  RESULT_VARIABLE result
+  OUTPUT_VARIABLE log
+  ERROR_VARIABLE log
+  TIMEOUT 100)
+message("${log}")
+
+if(DEFINED EXPECT_ERROR)
+  if(result EQUAL 0)
+    message(FATAL_ERROR "pumgen succeeded, but was expected to fail")
+  endif()
+  if(NOT log MATCHES "${EXPECT_ERROR}")
+    message(FATAL_ERROR "pumgen failed without a message matching \"${EXPECT_ERROR}\"")
+  endif()
+  return()
+endif()
+
+if(NOT result EQUAL 0)
+  message(FATAL_ERROR "pumgen failed: ${result}")
+endif()
+
+if(DEFINED REFERENCE)
+  set(failures "")
+  foreach(dataset connect geometry group boundary)
+    set(options "")
+    if(dataset STREQUAL "geometry" AND DEFINED TOLERANCE)
+      set(options -d ${TOLERANCE})
+    endif()
+    execute_process(
+      COMMAND ${H5DIFF} -n 10 ${options} ${OUTPUT} ${REFERENCE} /${dataset} /${dataset}
+      RESULT_VARIABLE differs
+      OUTPUT_VARIABLE difflog
+      ERROR_VARIABLE difflog)
+    if(NOT differs EQUAL 0)
+      string(APPEND failures "\n/${dataset} differs from the reference:\n${difflog}")
+    endif()
+  endforeach()
+  if(NOT failures STREQUAL "")
+    message(FATAL_ERROR "${failures}")
+  endif()
+endif()
diff --git a/tests/fixtures/coarse-binary-v41.msh b/tests/fixtures/coarse-binary-v41.msh
new file mode 100644
index 0000000000000000000000000000000000000000..26acd2b7230057571f46a02ff4bfa97efd016989
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diff --git a/tests/fixtures/coarse-o2.puml.h5 b/tests/fixtures/coarse-o2.puml.h5
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diff --git a/tests/fixtures/coarse.puml.h5 b/tests/fixtures/coarse.puml.h5
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diff --git a/tests/fixtures/generate.py b/tests/fixtures/generate.py
new file mode 100644
index 0000000..be00377
--- /dev/null
+++ b/tests/fixtures/generate.py
@@ -0,0 +1,246 @@
+# SPDX-FileCopyrightText: 2026 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+"""Generate the mesh fixtures and the reference PUML files for the regression tests.
+
+Run from this directory: python3 generate.py
+Requires the gmsh Python API, numpy and h5py. The reference files are computed
+from the gmsh model directly, i.e. independently of PUMGen.
+"""
+
+import itertools
+
+import gmsh
+import h5py
+import numpy as np
+
+# local face numbering of a tetrahedron as used by SeisSol
+FACE_NODES = [(1, 0, 2), (0, 1, 3), (1, 2, 3), (2, 0, 3)]
+
+WIDTH, DEPTH, LAYER = 2.0, 1.0, 0.25
+# OpenCASCADE enlarges bounding boxes slightly, so classify with a generous tolerance
+TOL = 1e-3
+FREE_SURFACE, INTERFACE, ABSORBING = 101, 103, 105
+
+
+def boundary_offset(tag):
+    return tag - 100 if tag >= 100 else tag
+
+
+def build_model(size_top, size_bottom):
+    gmsh.model.add("layered")
+    top = gmsh.model.occ.addBox(0, 0, -LAYER, WIDTH, WIDTH, LAYER)
+    bottom = gmsh.model.occ.addBox(0, 0, -DEPTH, WIDTH, WIDTH, DEPTH - LAYER)
+    gmsh.model.occ.fragment([(3, top)], [(3, bottom)])
+    gmsh.model.occ.synchronize()
+
+    for dim, tag in gmsh.model.getEntities(3):
+        zmin = gmsh.model.getBoundingBox(dim, tag)[2]
+        gmsh.model.addPhysicalGroup(3, [tag], 1 if zmin > -LAYER - TOL else 2)
+
+    groups = {FREE_SURFACE: [], INTERFACE: [], ABSORBING: []}
+    for dim, tag in gmsh.model.getEntities(2):
+        _, _, zmin, _, _, zmax = gmsh.model.getBoundingBox(dim, tag)
+        if zmin > -TOL:
+            groups[FREE_SURFACE].append(tag)
+        elif abs(zmin + LAYER) < TOL and abs(zmax + LAYER) < TOL:
+            groups[INTERFACE].append(tag)
+        else:
+            groups[ABSORBING].append(tag)
+    for physical, tags in groups.items():
+        gmsh.model.addPhysicalGroup(2, tags, physical)
+
+    for dim, tag in gmsh.model.getEntities(0):
+        z = gmsh.model.getValue(dim, tag, [])[2]
+        gmsh.model.mesh.setSize([(dim, tag)], size_bottom if z < -LAYER - TOL else size_top)
+
+    gmsh.model.mesh.generate(3)
+
+
+def physical_of(dim, tag):
+    physicals = gmsh.model.getPhysicalGroupsForEntity(dim, tag)
+    return int(physicals[0]) if len(physicals) > 0 else 0
+
+
+def reference_data():
+    """Mesh data in the layout PUMGen writes: vertices by node tag, cells in file order."""
+    node_tags, coords, _ = gmsh.model.mesh.getNodes()
+    order = np.argsort(node_tags)
+    node_tags = node_tags[order]
+    assert np.array_equal(node_tags, np.arange(1, len(node_tags) + 1)), "expected dense node tags"
+    vertices = coords.reshape(-1, 3)[order]
+
+    face_bc = {}
+    for dim, tag in gmsh.model.getEntities(2):
+        physical = physical_of(dim, tag)
+        if physical == 0:
+            continue
+        types, _, nodes = gmsh.model.mesh.getElements(dim, tag)
+        for element_type, element_nodes in zip(types, nodes):
+            _, _, _, num_nodes, _, _ = gmsh.model.mesh.getElementProperties(element_type)
+            for tri in np.asarray(element_nodes).reshape(-1, num_nodes):
+                face_bc[frozenset(int(v) for v in tri[:3])] = boundary_offset(physical)
+
+    cells, groups, boundary = [], [], []
+    for dim, tag in gmsh.model.getEntities(3):
+        physical = physical_of(dim, tag)
+        types, _, nodes = gmsh.model.mesh.getElements(dim, tag)
+        for element_type, element_nodes in zip(types, nodes):
+            _, _, _, num_nodes, _, _ = gmsh.model.mesh.getElementProperties(element_type)
+            for tet in np.asarray(element_nodes).reshape(-1, num_nodes):
+                code = 0
+                for face, local in enumerate(FACE_NODES):
+                    bc = face_bc.get(frozenset(int(tet[i]) for i in local), 0)
+                    code |= bc << (8 * face)
+                cells.append(tet - 1)
+                groups.append(physical)
+                boundary.append(code)
+    return vertices, np.asarray(cells), np.asarray(groups), np.asarray(boundary)
+
+
+def write_reference(path, mesh_file):
+    """Reference PUML data from a written mesh file, so coordinates match their text form."""
+    gmsh.clear()
+    gmsh.open(mesh_file)
+    vertices, cells, groups, boundary = reference_data()
+    with h5py.File(path, "w") as out:
+        out.create_dataset("connect", data=cells.astype("<u8"))
+        out.create_dataset("geometry", data=vertices.astype("<f8"))
+        out.create_dataset("group", data=groups.astype("<i4"))
+        out.create_dataset("boundary", data=boundary.astype("<i4"))
+
+
+def write_mesh(path, version, binary=False):
+    gmsh.option.setNumber("Mesh.MshFileVersion", version)
+    gmsh.option.setNumber("Mesh.Binary", 1 if binary else 0)
+    gmsh.write(path)
+    gmsh.option.setNumber("Mesh.Binary", 0)
+
+
+def counts_exercise_chunking(count):
+    # the element/vertex counts are chosen such that the default chunk distribution differs
+    # from a ceil-based one for 3 and for 4 ranks
+    return count % 3 == 1 and count % 4 in (1, 2)
+
+
+def generate_layered():
+    for size_top in itertools.count(0.2, 0.0025):
+        gmsh.clear()
+        build_model(size_top, 2.0 * size_top)
+        vertices, cells, _, _ = reference_data()
+        if counts_exercise_chunking(len(cells)) and counts_exercise_chunking(len(vertices)):
+            break
+    print(f"layered: {len(cells)} cells, {len(vertices)} vertices, size {size_top:.4f}")
+
+    write_mesh("layered-v41.msh", 4.1)
+    write_mesh("layered-v22.msh", 2.2)
+    gmsh.write("layered.neu")
+    write_reference("layered.puml.h5", "layered-v41.msh")
+
+
+def generate_coarse():
+    gmsh.clear()
+    build_model(0.5, 1.0)
+    vertices, cells, _, _ = reference_data()
+    print(f"coarse: {len(cells)} cells, {len(vertices)} vertices")
+
+    write_mesh("coarse-v41.msh", 4.1)
+    write_mesh("coarse-binary-v41.msh", 4.1, binary=True)
+
+    # dense node tags that do not start at 1
+    node_tags, _, _ = gmsh.model.mesh.getNodes()
+    gmsh.model.mesh.renumberNodes(node_tags, node_tags + 1000)
+    write_mesh("coarse-offset-v41.msh", 4.1)
+    gmsh.model.mesh.renumberNodes(node_tags + 1000, node_tags)
+
+    gmsh.model.mesh.setOrder(2)
+    write_mesh("coarse-o2-v41.msh", 4.1)
+    write_mesh("coarse-o2-v22.msh", 2.2)
+    gmsh.model.mesh.setOrder(1)
+
+    gmsh.model.mesh.partition(2)
+    write_mesh("coarse-partitioned-v41.msh", 4.1)
+
+    write_reference("coarse.puml.h5", "coarse-v41.msh")
+    write_reference("coarse-o2.puml.h5", "coarse-o2-v41.msh")
+
+
+TINY_V41 = """$MeshFormat
+4.1 0 8
+$EndMeshFormat
+$Entities
+0 0 0 1
+1 0 0 0 1 1 1 1 7 0
+$EndEntities
+$Nodes
+1 4 1 4
+3 1 0 4
+1
+2
+3
+4
+0 0 0
+1 0 0
+0 1 0
+0 0 1
+$EndNodes
+$Elements
+1 1 1 1
+3 1 4 1
+1 1 2 3 4
+$EndElements
+"""
+
+TINY_V22 = """$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$Nodes
+4
+1 0 0 0
+2 1 0 0
+3 0 1 0
+4 0 0 1
+$EndNodes
+$Elements
+1
+1 4 2 7 1 1 2 3 4
+$EndElements
+"""
+
+
+def generate_tiny():
+    variants = {
+        "tiny-v41.msh": TINY_V41,
+        "tiny-v40.msh": TINY_V41.replace("4.1 0 8", "4 0 8"),
+        "tiny-truncated-v41.msh": TINY_V41.split("$Elements")[0] + "$Elements\n1 1 1 1\n3 1 4 1\n1 1 2\n",
+        "tiny-badnumber-v41.msh": TINY_V41.replace("1 0 0\n0 1 0", "1 abc 0\n0 1 0"),
+        "tiny-unknowntype-v41.msh": TINY_V41.replace("3 1 4 1\n", "3 1 999 1\n"),
+        "tiny-sparse-v41.msh": TINY_V41.replace("1 4 1 4\n", "1 4 1 5\n")
+        .replace("3\n4\n0 0 0", "3\n5\n0 0 0")
+        .replace("1 1 2 3 4\n", "1 1 2 3 5\n"),
+        "tiny-duplicate-v41.msh": TINY_V41.replace("1\n2\n3\n4\n", "1\n2\n2\n4\n"),
+        "tiny-badnode-v41.msh": TINY_V41.replace("1 1 2 3 4\n", "1 1 2 3 9\n"),
+        "tiny-v22.msh": TINY_V22,
+        "tiny-duplicate-v22.msh": TINY_V22.replace("3 0 1 0", "2 0 1 0"),
+        "tiny-badnode-v22.msh": TINY_V22.replace("1 2 3 4\n$EndElements", "1 2 3 9\n$EndElements"),
+    }
+    for name, content in variants.items():
+        with open(name, "w") as out:
+            out.write(content)
+    write_reference("tiny.puml.h5", "tiny-v41.msh")
+
+
+def main():
+    gmsh.initialize()
+    gmsh.option.setNumber("General.Terminal", 0)
+    gmsh.option.setNumber("General.NumThreads", 1)
+    gmsh.option.setNumber("Mesh.Algorithm3D", 1)
+    generate_layered()
+    generate_coarse()
+    generate_tiny()
+    gmsh.finalize()
+
+
+if __name__ == "__main__":
+    main()
diff --git a/tests/fixtures/layered-v22.msh b/tests/fixtures/layered-v22.msh
new file mode 100644
index 0000000..f52bc33
--- /dev/null
+++ b/tests/fixtures/layered-v22.msh
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+$EndElements
diff --git a/tests/fixtures/layered.neu b/tests/fixtures/layered.neu
new file mode 100644
index 0000000..635e33c
--- /dev/null
+++ b/tests/fixtures/layered.neu
@@ -0,0 +1,3378 @@
+        CONTROL INFO 2.0.0
+** GAMBIT NEUTRAL FILE
+Gmsh mesh in GAMBIT neutral file format
+PROGRAM:                  Gmsh     VERSION:  4.15.2
+Tue Sep 22 18:13:50 2026
+     NUMNP     NELEM     NGRPS    NBSETS     NDFCD     NDFVL
+       445      1597         2         3         3         3
+ENDOFSECTION
+   NODAL COORDINATES 2.0.0
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+         2   0.00000000000e+00   0.00000000000e+00   0.00000000000e+00
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+         5   2.00000000000e+00   0.00000000000e+00  -2.50000000000e-01
+         6   2.00000000000e+00   0.00000000000e+00   0.00000000000e+00
+         7   2.00000000000e+00   2.00000000000e+00   0.00000000000e+00
+         8   2.00000000000e+00   2.00000000000e+00  -2.50000000000e-01
+         9   0.00000000000e+00   0.00000000000e+00  -1.00000000000e+00
+        10   0.00000000000e+00   2.00000000000e+00  -1.00000000000e+00
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+       445   1.46442268164e+00   5.16800230128e-01  -4.86833384324e-01
+ENDOFSECTION
+      ELEMENTS/CELLS 2.0.0
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+ENDOFSECTION
+       ELEMENT GROUP 2.0.0
+GROUP:          2 ELEMENTS:        842 MATERIAL:          0 NFLAGS:          1
+                Material group 2
+       0
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+    1586    1587    1588    1589    1590    1591    1592    1593    1594    1595
+    1596    1597
+ENDOFSECTION
+       ELEMENT GROUP 2.0.0
+GROUP:          1 ELEMENTS:        755 MATERIAL:          0 NFLAGS:          1
+                Material group 1
+       0
+       1       2       3       4       5       6       7       8       9      10
+      11      12      13      14      15      16      17      18      19      20
+      21      22      23      24      25      26      27      28      29      30
+      31      32      33      34      35      36      37      38      39      40
+      41      42      43      44      45      46      47      48      49      50
+      51      52      53      54      55      56      57      58      59      60
+      61      62      63      64      65      66      67      68      69      70
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diff --git a/tests/fixtures/layered.puml.h5 b/tests/fixtures/layered.puml.h5
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diff --git a/tests/fixtures/tiny-badnode-v22.msh b/tests/fixtures/tiny-badnode-v22.msh
new file mode 100644
index 0000000..9e459ce
--- /dev/null
+++ b/tests/fixtures/tiny-badnode-v22.msh
@@ -0,0 +1,14 @@
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diff --git a/tests/fixtures/tiny-badnode-v41.msh b/tests/fixtures/tiny-badnode-v41.msh
new file mode 100644
index 0000000..8754070
--- /dev/null
+++ b/tests/fixtures/tiny-badnode-v41.msh
@@ -0,0 +1,24 @@
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diff --git a/tests/fixtures/tiny-badnumber-v41.msh b/tests/fixtures/tiny-badnumber-v41.msh
new file mode 100644
index 0000000..c1d58c9
--- /dev/null
+++ b/tests/fixtures/tiny-badnumber-v41.msh
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+1 1 1 1
+3 1 4 1
+1 1 2 3 4
+$EndElements
diff --git a/tests/fixtures/tiny-duplicate-v22.msh b/tests/fixtures/tiny-duplicate-v22.msh
new file mode 100644
index 0000000..cab31c6
--- /dev/null
+++ b/tests/fixtures/tiny-duplicate-v22.msh
@@ -0,0 +1,14 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$Nodes
+4
+1 0 0 0
+2 1 0 0
+2 0 1 0
+4 0 0 1
+$EndNodes
+$Elements
+1
+1 4 2 7 1 1 2 3 4
+$EndElements
diff --git a/tests/fixtures/tiny-duplicate-v41.msh b/tests/fixtures/tiny-duplicate-v41.msh
new file mode 100644
index 0000000..ce03d45
--- /dev/null
+++ b/tests/fixtures/tiny-duplicate-v41.msh
@@ -0,0 +1,24 @@
+$MeshFormat
+4.1 0 8
+$EndMeshFormat
+$Entities
+0 0 0 1
+1 0 0 0 1 1 1 1 7 0
+$EndEntities
+$Nodes
+1 4 1 4
+3 1 0 4
+1
+2
+2
+4
+0 0 0
+1 0 0
+0 1 0
+0 0 1
+$EndNodes
+$Elements
+1 1 1 1
+3 1 4 1
+1 1 2 3 4
+$EndElements
diff --git a/tests/fixtures/tiny-sparse-v41.msh b/tests/fixtures/tiny-sparse-v41.msh
new file mode 100644
index 0000000..16ffb6f
--- /dev/null
+++ b/tests/fixtures/tiny-sparse-v41.msh
@@ -0,0 +1,24 @@
+$MeshFormat
+4.1 0 8
+$EndMeshFormat
+$Entities
+0 0 0 1
+1 0 0 0 1 1 1 1 7 0
+$EndEntities
+$Nodes
+1 4 1 5
+3 1 0 4
+1
+2
+3
+5
+0 0 0
+1 0 0
+0 1 0
+0 0 1
+$EndNodes
+$Elements
+1 1 1 1
+3 1 4 1
+1 1 2 3 5
+$EndElements
diff --git a/tests/fixtures/tiny-truncated-v41.msh b/tests/fixtures/tiny-truncated-v41.msh
new file mode 100644
index 0000000..906031c
--- /dev/null
+++ b/tests/fixtures/tiny-truncated-v41.msh
@@ -0,0 +1,23 @@
+$MeshFormat
+4.1 0 8
+$EndMeshFormat
+$Entities
+0 0 0 1
+1 0 0 0 1 1 1 1 7 0
+$EndEntities
+$Nodes
+1 4 1 4
+3 1 0 4
+1
+2
+3
+4
+0 0 0
+1 0 0
+0 1 0
+0 0 1
+$EndNodes
+$Elements
+1 1 1 1
+3 1 4 1
+1 1 2
diff --git a/tests/fixtures/tiny-unknowntype-v41.msh b/tests/fixtures/tiny-unknowntype-v41.msh
new file mode 100644
index 0000000..7c7ebdf
--- /dev/null
+++ b/tests/fixtures/tiny-unknowntype-v41.msh
@@ -0,0 +1,24 @@
+$MeshFormat
+4.1 0 8
+$EndMeshFormat
+$Entities
+0 0 0 1
+1 0 0 0 1 1 1 1 7 0
+$EndEntities
+$Nodes
+1 4 1 4
+3 1 0 4
+1
+2
+3
+4
+0 0 0
+1 0 0
+0 1 0
+0 0 1
+$EndNodes
+$Elements
+1 1 1 1
+3 1 999 1
+1 1 2 3 4
+$EndElements
diff --git a/tests/fixtures/tiny-v22.msh b/tests/fixtures/tiny-v22.msh
new file mode 100644
index 0000000..449d58a
--- /dev/null
+++ b/tests/fixtures/tiny-v22.msh
@@ -0,0 +1,14 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$Nodes
+4
+1 0 0 0
+2 1 0 0
+3 0 1 0
+4 0 0 1
+$EndNodes
+$Elements
+1
+1 4 2 7 1 1 2 3 4
+$EndElements
diff --git a/tests/fixtures/tiny-v40.msh b/tests/fixtures/tiny-v40.msh
new file mode 100644
index 0000000..517e8b7
--- /dev/null
+++ b/tests/fixtures/tiny-v40.msh
@@ -0,0 +1,24 @@
+$MeshFormat
+4 0 8
+$EndMeshFormat
+$Entities
+0 0 0 1
+1 0 0 0 1 1 1 1 7 0
+$EndEntities
+$Nodes
+1 4 1 4
+3 1 0 4
+1
+2
+3
+4
+0 0 0
+1 0 0
+0 1 0
+0 0 1
+$EndNodes
+$Elements
+1 1 1 1
+3 1 4 1
+1 1 2 3 4
+$EndElements
diff --git a/tests/fixtures/tiny-v41.msh b/tests/fixtures/tiny-v41.msh
new file mode 100644
index 0000000..c0db8d4
--- /dev/null
+++ b/tests/fixtures/tiny-v41.msh
@@ -0,0 +1,24 @@
+$MeshFormat
+4.1 0 8
+$EndMeshFormat
+$Entities
+0 0 0 1
+1 0 0 0 1 1 1 1 7 0
+$EndEntities
+$Nodes
+1 4 1 4
+3 1 0 4
+1
+2
+3
+4
+0 0 0
+1 0 0
+0 1 0
+0 0 1
+$EndNodes
+$Elements
+1 1 1 1
+3 1 4 1
+1 1 2 3 4
+$EndElements
diff --git a/tests/fixtures/tiny.puml.h5 b/tests/fixtures/tiny.puml.h5
new file mode 100644
index 0000000000000000000000000000000000000000..7b0993b1026c5bcb2b16941f738169c7c7b30185
GIT binary patch
literal 4368
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literal 0
HcmV?d00001


From d5f86bfe9249c6454a23dafbd20b2be20b559c47 Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 18:18:36 +0000
Subject: [PATCH 02/19] Fix the parallel Gambit reader

Vertices and elements were distributed in ceil-sized chunks, while
SerialMeshFile allocates the chunks given by getChunksize. Whenever the counts
do not divide evenly (e.g. 815206 elements on 3 ranks), ranks received more
data than their buffers hold; pumgen then aborted or hung. Group numbers and
boundary conditions were routed to their elements with the same mismatch, and
readBoundaries only read the first nBoundaries/P faces in many cases, so with
2 ranks half of the boundary conditions were silently dropped.

All four readers now use getChunksize/getChunksum, a new getChunkOwner maps
elements to ranks, and groups and boundaries are read completely and ended by
an explicit terminator message. The serial reader no longer reads past a
group section that ends exactly at a chunk boundary or past the last section.

AI-generated. Model: Claude Opus 5.5
---
 src/helper/Distributor.h              |  15 ++
 src/meshreader/GambitReader.h         |   8 +-
 src/meshreader/ParallelGambitReader.h | 250 +++++++++++---------------
 src/meshreader/ParallelMeshReader.h   | 158 +++++++---------
 tests/CMakeLists.txt                  |   4 +
 5 files changed, 185 insertions(+), 250 deletions(-)

diff --git a/src/helper/Distributor.h b/src/helper/Distributor.h
index 02897f2..d583427 100644
--- a/src/helper/Distributor.h
+++ b/src/helper/Distributor.h
@@ -4,7 +4,9 @@
 #ifndef PUMGEN_SRC_HELPER_DISTRIBUTOR_H_
 #define PUMGEN_SRC_HELPER_DISTRIBUTOR_H_
 
+#include <algorithm>
 #include <cmath>
+#include <cstddef>
 #include <cstdlib>
 
 // no namespace for now
@@ -20,4 +22,17 @@ constexpr std::size_t getChunksum(std::size_t total, int until, int size) {
   return base + addon;
 }
 
+/**
+ * The rank whose chunk (as given by getChunksize/getChunksum) contains the item index.
+ */
+constexpr int getChunkOwner(std::size_t total, std::size_t index, int size) {
+  const std::size_t base = total / size;
+  const std::size_t rest = total % size;
+  const std::size_t largeChunks = rest * (base + 1);
+  if (index < largeChunks) {
+    return static_cast<int>(index / (base + 1));
+  }
+  return static_cast<int>(rest + (index - largeChunks) / base);
+}
+
 #endif // PUMGEN_SRC_HELPER_DISTRIBUTOR_H_
diff --git a/src/meshreader/GambitReader.h b/src/meshreader/GambitReader.h
index a00d653..260f649 100644
--- a/src/meshreader/GambitReader.h
+++ b/src/meshreader/GambitReader.h
@@ -393,7 +393,7 @@ class GambitReader : public MeshReader {
 
     // Get the group, were we should start reading
     std::vector<GroupSection>::const_iterator section;
-    for (section = m_groups.begin(); section != m_groups.end() && section->nLines < start;
+    for (section = m_groups.begin(); section != m_groups.end() && section->nLines <= start;
          section++) {
       start -= section->nLines;
     }
@@ -417,7 +417,9 @@ class GambitReader : public MeshReader {
         start = 0;
         section++;
 
-        m_mesh.seekg(section->seekPosition);
+        if (section != m_groups.end()) {
+          m_mesh.seekg(section->seekPosition);
+        }
       } else if (start % ELEMENTS_PER_LINE_GROUP == 0)
         // Skip newline char at end of line
         m_mesh.seekg(section->lineSize - section->elementSize * ELEMENTS_PER_LINE_GROUP,
@@ -456,7 +458,7 @@ class GambitReader : public MeshReader {
 
     // Get the boundary, were we should start reading
     std::vector<BoundarySection>::const_iterator section;
-    for (section = m_boundaries.begin(); section != m_boundaries.end() && section->nLines < start;
+    for (section = m_boundaries.begin(); section != m_boundaries.end() && section->nLines <= start;
          section++) {
       start -= section->nLines;
     }
diff --git a/src/meshreader/ParallelGambitReader.h b/src/meshreader/ParallelGambitReader.h
index bf63ab6..fac8859 100644
--- a/src/meshreader/ParallelGambitReader.h
+++ b/src/meshreader/ParallelGambitReader.h
@@ -9,11 +9,18 @@
 
 #include <mpi.h>
 
+#include <algorithm>
+#include <cstddef>
+#include <cstdint>
+#include <tuple>
+#include <vector>
+
 #include "GambitReader.h"
 #include "ParallelMeshReader.h"
 #include "helper/Distributor.h"
 
 #include "third_party/MPITraits.h"
+#include "utils/logger.h"
 
 namespace puml {
 
@@ -25,180 +32,125 @@ class ParallelGambitReader : public ParallelMeshReader<GambitReader> {
       : ParallelMeshReader<GambitReader>(meshFile, comm) {}
 
   /**
-   * Reads all group numbers.
-   * Each process gets <code>nElements() + processes - 1) / processes</code>
-   * group numbers, except for the last, which gets the remaining
+   * Reads all group numbers. Each process gets the group numbers of its elements (see
+   * ParallelMeshReader::readElements).
    *
    * This is a collective operation.
    */
   void readGroups(int* groups) {
-    std::size_t chunkSize = getChunksize(nElements(), m_rank, m_nProcs);
-
-    if (m_rank == 0) {
-      std::size_t maxChunkSize = chunkSize;
-      std::vector<ElementGroup> map(maxChunkSize);
-
-      std::vector<std::vector<int>> aggregator(m_nProcs - 1);
-      std::vector<std::size_t> sizes(m_nProcs - 1);
-      std::vector<MPI_Request> requests((m_nProcs - 1) * 2, MPI_REQUEST_NULL);
-
-      std::size_t position = 0;
-
-      for (int i = 0; i < m_nProcs; i++) {
-        logInfo() << "Reading group information part" << (i + 1) << "of" << m_nProcs;
-
-        chunkSize = getChunksize(nElements(), i, m_nProcs);
-
-        m_serialReader.readGroups(position, chunkSize, map.data());
-        position += chunkSize;
-
-        // Wait for all sending from last iteration
-        MPI_Waitall((m_nProcs - 1) * 2, requests.data(), MPI_STATUSES_IGNORE);
-        for (int j = 0; j < m_nProcs - 1; j++) {
-          aggregator[j].clear();
-        }
-
-        // Sort group numbers into the corresponding aggregator
-        for (std::size_t j = 0; j < chunkSize; j++) {
-          if (map[j].element < maxChunkSize)
-            // Local element
-            groups[map[j].element] = map[j].group;
-          else {
-            // Element for another processor
-            // Serials the struct to make sending easier
-            unsigned int proc = map[j].element / maxChunkSize;
-            aggregator[proc - 1].push_back(map[j].element % maxChunkSize);
-            aggregator[proc - 1].push_back(map[j].group);
-          }
-        }
-
-        // Send send aggregated mapping
-        for (int j = 0; j < m_nProcs - 1; j++) {
-          if (aggregator[j].empty()) {
-            continue;
-          }
-
-          sizes[j] = aggregator[j].size() / 2; // element id + group number
-          MPI_Isend(&sizes[j], 1, tndm::mpi_type_t<std::size_t>(), j + 1, 0, m_comm,
-                    &requests[j * 2]);
-          MPI_Isend(&aggregator[j][0], aggregator[j].size(), MPI_INT, j + 1, 0, m_comm,
-                    &requests[j * 2 + 1]);
-        }
-      }
-
-      MPI_Waitall((m_nProcs - 1) * 2, requests.data(), MPI_STATUSES_IGNORE);
-    } else {
-      // Allocate enough memory
-      std::vector<int> buf(chunkSize * 2);
-
-      unsigned int recieved = 0;
-
-      while (recieved < chunkSize) {
-        std::size_t size;
-        MPI_Recv(&size, 1, tndm::mpi_type_t<std::size_t>(), 0, 0, m_comm, MPI_STATUS_IGNORE);
-        MPI_Recv(buf.data(), size * 2, MPI_INT, 0, 0, m_comm, MPI_STATUS_IGNORE);
-
-        for (std::size_t i = 0; i < size * 2; i += 2) {
-          groups[buf[i]] = buf[i + 1];
-        }
-
-        recieved += size;
-      }
-    }
+    scatterToElementOwners<ElementGroup>(
+        nElements(), 1, groups, "group information",
+        [&](std::size_t start, std::size_t count, ElementGroup* entries) {
+          m_serialReader.readGroups(start, count, entries);
+        },
+        [](const ElementGroup& entry) {
+          return std::make_tuple(entry.element, std::size_t{0}, entry.group);
+        });
   }
 
   /**
-   * Reads all boundaries.
-   * Each process gets the boundaries for <code>nElements() + processes - 1) /
-   * processes</code> elements. Boundaries not specified in the mesh are not
-   * modified.
+   * Reads all boundaries. Each process gets the boundaries of the faces of its elements (see
+   * ParallelMeshReader::readElements). Boundaries not specified in the mesh are not modified.
    *
-   * This is a collective operation
+   * This is a collective operation.
    *
    * @todo Only tetrahedral meshes are supported
    */
   void readBoundaries(int* boundaries) {
-    std::size_t chunkSize = getChunksize(nElements(), m_rank, m_nProcs);
-
-    if (m_rank == 0) {
-      std::size_t maxChunkSize = chunkSize;
-      std::vector<GambitBoundaryFace> faces(maxChunkSize);
-
-      std::vector<std::vector<int>> aggregator(m_nProcs - 1);
-      std::vector<std::size_t> sizes(m_nProcs - 1);
-      std::vector<MPI_Request> requests((m_nProcs - 1) * 2, MPI_REQUEST_NULL);
-
-      std::size_t nChunks = (nBoundaries() + chunkSize - 1) / chunkSize;
-      std::size_t position = 0;
-      for (std::size_t i = 0; i < nChunks; i++) {
-        logInfo() << "Reading boundary conditions part" << (i + 1) << "of" << nChunks;
-
-        chunkSize = getChunksize(nBoundaries(), i, m_nProcs);
+    scatterToElementOwners<GambitBoundaryFace>(
+        nBoundaries(), 4, boundaries, "boundary conditions",
+        [&](std::size_t start, std::size_t count, GambitBoundaryFace* entries) {
+          m_serialReader.readBoundaries(start, count, entries);
+        },
+        [](const GambitBoundaryFace& entry) {
+          return std::make_tuple(entry.element, static_cast<std::size_t>(entry.face), entry.type);
+        });
+  }
 
-        m_serialReader.readBoundaries(position, chunkSize, faces.data());
-        position += chunkSize;
+  private:
+  /**
+   * Reads per-element entries in chunks on rank 0 and stores the value of each entry at
+   * <code>local[localElement * slotsPerElement + slot]</code> on the process owning the element.
+   *
+   * @param read Callable (start, count, entries) reading <code>count</code> entries starting at
+   * <code>start</code>
+   * @param decode Callable returning the tuple (element, slot, value) for an entry
+   */
+  template <typename Entry, typename ReadF, typename DecodeF>
+  void scatterToElementOwners(std::size_t numEntries, std::size_t slotsPerElement, int* local,
+                              const char* name, ReadF&& read, DecodeF&& decode) {
+    const auto messageType = tndm::mpi_type_t<std::int64_t>();
 
-        // Wait for all sending from last iteration
-        MPI_Waitall((m_nProcs - 1) * 2, requests.data(), MPI_STATUSES_IGNORE);
-        for (int j = 0; j < m_nProcs - 1; j++) {
-          aggregator[j].clear();
+    if (m_rank != 0) {
+      std::vector<std::int64_t> buffer;
+      while (true) {
+        std::size_t size = 0;
+        MPI_Recv(&size, 1, tndm::mpi_type_t<std::size_t>(), 0, 0, m_comm, MPI_STATUS_IGNORE);
+        if (size == 0) {
+          break;
         }
-
-        // Sort boundary conditions into the corresponding aggregator
-        for (std::size_t j = 0; j < chunkSize; j++) {
-          if (faces[j].element < maxChunkSize)
-            // Local element
-            boundaries[faces[j].element * 4 + faces[j].face] = faces[j].type;
-          else {
-            // Face for another processor
-            // Serials the struct to make sending easier
-            unsigned int proc = faces[j].element / maxChunkSize;
-            aggregator[proc - 1].push_back((faces[j].element % maxChunkSize) * 4 + faces[j].face);
-            aggregator[proc - 1].push_back(faces[j].type);
-          }
-        }
-
-        // Send send aggregated values
-        for (int j = 0; j < m_nProcs - 1; j++) {
-          if (aggregator[j].empty()) {
-            continue;
-          }
-
-          sizes[j] = aggregator[j].size() / 2; // element id + face type
-          MPI_Isend(&sizes[j], 1, tndm::mpi_type_t<std::size_t>(), j + 1, 0, m_comm,
-                    &requests[j * 2]);
-          MPI_Isend(&aggregator[j][0], aggregator[j].size(), MPI_INT, j + 1, 0, m_comm,
-                    &requests[j * 2 + 1]);
+        buffer.resize(2 * size);
+        MPI_Recv(buffer.data(), messageSize(buffer.size()), messageType, 0, 0, m_comm,
+                 MPI_STATUS_IGNORE);
+        for (std::size_t i = 0; i < size; ++i) {
+          local[buffer[2 * i]] = static_cast<int>(buffer[2 * i + 1]);
         }
       }
+      return;
+    }
 
-      MPI_Waitall((m_nProcs - 1) * 2, requests.data(), MPI_STATUSES_IGNORE);
-
-      // Send finish signal to all other processes
-      std::fill(sizes.begin(), sizes.end(), 0);
-      for (int i = 0; i < m_nProcs - 1; i++) {
-        MPI_Isend(&sizes[i], 1, tndm::mpi_type_t<std::size_t>(), i + 1, 0, m_comm, &requests[i]);
+    const std::size_t chunkSize = std::max(getChunksize(nElements(), 0, m_nProcs), std::size_t{1});
+    std::vector<Entry> entries(std::min(chunkSize, numEntries));
+    std::vector<std::vector<std::int64_t>> outgoing(m_nProcs);
+    std::vector<std::size_t> sizes(m_nProcs, 0);
+    std::vector<MPI_Request> requests(2 * m_nProcs, MPI_REQUEST_NULL);
+
+    for (std::size_t start = 0; start < numEntries; start += chunkSize) {
+      const std::size_t count = std::min(chunkSize, numEntries - start);
+      logInfo() << "Reading" << name << start << "to" << start + count << "of" << numEntries;
+      read(start, count, entries.data());
+
+      // the send buffers of the previous chunk are reused
+      MPI_Waitall(requests.size(), requests.data(), MPI_STATUSES_IGNORE);
+      for (auto& buffer : outgoing) {
+        buffer.clear();
       }
-      MPI_Waitall(m_nProcs - 1, requests.data(), MPI_STATUSES_IGNORE);
-    } else {
-      // Allocate enough memory
-      std::vector<int> buf(chunkSize * 4);
 
-      while (true) {
-        std::size_t size;
-        MPI_Recv(&size, 1, tndm::mpi_type_t<std::size_t>(), 0, 0, m_comm, MPI_STATUS_IGNORE);
-        if (size == 0) {
-          // Finished
-          break;
+      for (std::size_t i = 0; i < count; ++i) {
+        const auto [element, slot, value] = decode(entries[i]);
+        if (element >= nElements() || slot >= slotsPerElement) {
+          logError() << "Invalid" << name << "entry: element" << element << "slot" << slot;
         }
+        const int owner = getChunkOwner(nElements(), element, m_nProcs);
+        const std::size_t index =
+            (element - getChunksum(nElements(), owner, m_nProcs)) * slotsPerElement + slot;
+        if (owner == 0) {
+          local[index] = value;
+        } else {
+          outgoing[owner].push_back(static_cast<std::int64_t>(index));
+          outgoing[owner].push_back(value);
+        }
+      }
 
-        MPI_Recv(buf.data(), size * 2, MPI_INT, 0, 0, m_comm, MPI_STATUS_IGNORE);
-
-        for (std::size_t i = 0; i < size * 2; i += 2) {
-          boundaries[buf[i]] = buf[i + 1];
+      for (int rank = 1; rank < m_nProcs; ++rank) {
+        if (outgoing[rank].empty()) {
+          continue;
         }
+        sizes[rank] = outgoing[rank].size() / 2;
+        MPI_Isend(&sizes[rank], 1, tndm::mpi_type_t<std::size_t>(), rank, 0, m_comm,
+                  &requests[2 * rank]);
+        MPI_Isend(outgoing[rank].data(), messageSize(outgoing[rank].size()), messageType, rank, 0,
+                  m_comm, &requests[2 * rank + 1]);
       }
     }
+    MPI_Waitall(requests.size(), requests.data(), MPI_STATUSES_IGNORE);
+
+    // an empty message ends the transfer
+    std::fill(sizes.begin(), sizes.end(), 0);
+    for (int rank = 1; rank < m_nProcs; ++rank) {
+      MPI_Isend(&sizes[rank], 1, tndm::mpi_type_t<std::size_t>(), rank, 0, m_comm, &requests[rank]);
+    }
+    MPI_Waitall(requests.size(), requests.data(), MPI_STATUSES_IGNORE);
   }
 };
 
diff --git a/src/meshreader/ParallelMeshReader.h b/src/meshreader/ParallelMeshReader.h
index 205bce8..114f5b5 100644
--- a/src/meshreader/ParallelMeshReader.h
+++ b/src/meshreader/ParallelMeshReader.h
@@ -10,9 +10,13 @@
 #include <mpi.h>
 
 #include <array>
+#include <cstddef>
+#include <limits>
 #include <vector>
 
+#include "helper/Distributor.h"
 #include "third_party/MPITraits.h"
+#include "utils/logger.h"
 
 template <class R> class ParallelMeshReader {
   private:
@@ -77,129 +81,87 @@ template <class R> class ParallelMeshReader {
   std::size_t nBoundaries() const { return m_nBoundaries; }
 
   /**
-   * Reads all vertices
-   * Each process gets <code>nVertices() + processes - 1) / processes</code>
-   * elements, except for the last, which gets the remaining elements
+   * Reads all vertices. Each process gets the chunk given by getChunksize/getChunksum.
    *
-   * This is a collective operation
+   * This is a collective operation.
    *
    * @todo Only 3 dimensional meshes are supported
    */
   void readVertices(double* vertices) {
-    std::size_t chunkSize = (m_nVertices + m_nProcs - 1) / m_nProcs;
-
-    if (m_rank == 0) {
-      // Allocate second buffer so we can read and send in parallel
-      std::vector<double> tempVertices(chunkSize * 3);
-      double* vertices2 = tempVertices.data();
-      if (m_nProcs % 2 == 0) {
-        // swap once so we have the correct buffer at the end
-        swap(vertices, vertices2);
-      }
-
-      MPI_Request request = MPI_REQUEST_NULL;
-      for (int i = 1; i < m_nProcs - 1; i++) {
-        logInfo() << "Reading vertices part" << i << "of" << m_nProcs;
-        m_serialReader.readVertices(i * chunkSize, chunkSize, vertices);
-        MPI_Wait(&request, MPI_STATUS_IGNORE);
-        MPI_Isend(vertices, chunkSize * 3, MPI_DOUBLE, i, 0, m_comm, &request);
-        swap(vertices, vertices2);
-      }
-
-      if (m_nProcs > 1) {
-        // Read last one
-        const std::size_t lastChunkSize = m_nVertices - (m_nProcs - 1) * chunkSize;
-        logInfo() << "Reading vertices part" << (m_nProcs - 1) << "of" << m_nProcs;
-        m_serialReader.readVertices((m_nProcs - 1) * chunkSize, lastChunkSize, vertices);
-        MPI_Wait(&request, MPI_STATUS_IGNORE);
-        MPI_Isend(vertices, lastChunkSize * 3, MPI_DOUBLE, m_nProcs - 1, 0, m_comm, &request);
-        swap(vertices, vertices2);
-      }
-
-      // Finally read the first part
-      logInfo() << "Reading vertices part" << m_nProcs << "of" << m_nProcs;
-      m_serialReader.readVertices(0, chunkSize, vertices);
-      MPI_Wait(&request, MPI_STATUS_IGNORE);
-    } else {
-      if (m_rank == m_nProcs - 1)
-        chunkSize = m_nVertices - (m_nProcs - 1) * chunkSize;
-
-      MPI_Recv(vertices, chunkSize * 3, MPI_DOUBLE, 0, 0, m_comm, MPI_STATUS_IGNORE);
-    }
+    distributeChunks(m_nVertices, 3, vertices, "vertices",
+                     [&](std::size_t start, std::size_t count, double* buffer) {
+                       m_serialReader.readVertices(start, count, buffer);
+                     });
   }
 
   /**
-   * Reads all elements.
-   * Each process gets <code>nElements() + processes - 1) / processes</code>
-   * elements, except for the last, which gets the remaining elements
+   * Reads all elements. Each process gets the chunk given by getChunksize/getChunksum.
    *
    * This is a collective operation.
    *
    * @todo Only tetrahedral meshes are supported
    */
   virtual void readElements(std::size_t* elements) {
-    std::size_t chunkSize = (m_nElements + m_nProcs - 1) / m_nProcs;
+    distributeChunks(m_nElements, 4, elements, "elements",
+                     [&](std::size_t start, std::size_t count, std::size_t* buffer) {
+                       m_serialReader.readElements(start, count, buffer);
+                     });
+  }
 
-    if (m_rank == 0) {
-      // Allocate second buffer so we can read and send in parallel
-      std::vector<std::size_t> tempElements(chunkSize * 4);
-      std::size_t* elements2 = tempElements.data();
-      if (m_nProcs % 2 == 0) {
-        // swap once so we have the correct buffer at the end
-        swap(elements, elements2);
-      }
-
-      MPI_Request request = MPI_REQUEST_NULL;
-
-      for (int i = 1; i < m_nProcs - 1; i++) {
-        logInfo() << "Reading elements part" << i << "of" << m_nProcs;
-        m_serialReader.readElements(i * chunkSize, chunkSize, elements);
-        MPI_Wait(&request, MPI_STATUS_IGNORE);
-        MPI_Isend(elements, chunkSize * 4, tndm::mpi_type_t<std::size_t>(), i, 0, m_comm, &request);
-        swap(elements, elements2);
-      }
-
-      if (m_nProcs > 1) {
-        // Read last one
-        const std::size_t lastChunkSize = m_nElements - (m_nProcs - 1) * chunkSize;
-        logInfo() << "Reading elements part" << (m_nProcs - 1) << "of" << m_nProcs;
-        m_serialReader.readElements((m_nProcs - 1) * chunkSize, lastChunkSize, elements);
-        MPI_Wait(&request, MPI_STATUS_IGNORE);
-        MPI_Isend(elements, lastChunkSize * 4, tndm::mpi_type_t<std::size_t>(), m_nProcs - 1, 0,
-                  m_comm, &request);
-        swap(elements, elements2);
-      }
-
-      // Finally read the first part
-      logInfo() << "Reading elements part" << m_nProcs << "of" << m_nProcs;
-      m_serialReader.readElements(0, chunkSize, elements);
-      MPI_Wait(&request, MPI_STATUS_IGNORE);
-    } else {
-      if (m_rank == m_nProcs - 1)
-        chunkSize = m_nElements - (m_nProcs - 1) * chunkSize;
-
-      MPI_Recv(elements, chunkSize * 4, tndm::mpi_type_t<std::size_t>(), 0, 0, m_comm,
-               MPI_STATUS_IGNORE);
+  protected:
+  static int messageSize(std::size_t count) {
+    if (count > static_cast<std::size_t>(std::numeric_limits<int>::max())) {
+      logError() << "MPI message too large:" << count;
     }
+    return static_cast<int>(count);
   }
 
   private:
   /**
-   * Initialize some parameters
+   * Reads the items on rank 0 and sends each process its chunk.
+   *
+   * @param read Callable (start, count, buffer) reading <code>count</code> items starting at
+   * <code>start</code>
    */
-  void init() {
-    MPI_Comm_rank(m_comm, &m_rank);
-    MPI_Comm_size(m_comm, &m_nProcs);
+  template <typename T, typename ReadF>
+  void distributeChunks(std::size_t total, std::size_t valuesPerItem, T* local, const char* name,
+                        ReadF&& read) {
+    const std::size_t localCount = getChunksize(total, m_rank, m_nProcs);
+
+    if (m_rank != 0) {
+      MPI_Recv(local, messageSize(localCount * valuesPerItem), tndm::mpi_type_t<T>(), 0, 0, m_comm,
+               MPI_STATUS_IGNORE);
+      return;
+    }
+
+    // two send buffers, so that reading the next chunk overlaps with sending the previous one
+    const std::size_t maxCount = getChunksize(total, 0, m_nProcs);
+    std::array<std::vector<T>, 2> buffers;
+    std::array<MPI_Request, 2> requests = {MPI_REQUEST_NULL, MPI_REQUEST_NULL};
+
+    for (int rank = 1; rank < m_nProcs; ++rank) {
+      const auto slot = rank % 2;
+      MPI_Wait(&requests[slot], MPI_STATUS_IGNORE);
+      buffers[slot].resize(maxCount * valuesPerItem);
+
+      const std::size_t count = getChunksize(total, rank, m_nProcs);
+      logInfo() << "Reading" << name << "for rank" << rank << "of" << m_nProcs;
+      read(getChunksum(total, rank, m_nProcs), count, buffers[slot].data());
+      MPI_Isend(buffers[slot].data(), messageSize(count * valuesPerItem), tndm::mpi_type_t<T>(),
+                rank, 0, m_comm, &requests[slot]);
+    }
+
+    logInfo() << "Reading" << name << "for rank 0 of" << m_nProcs;
+    read(0, localCount, local);
+    MPI_Waitall(2, requests.data(), MPI_STATUSES_IGNORE);
   }
 
-  protected:
   /**
-   * Swaps two pointers
+   * Initialize some parameters
    */
-  template <typename T> static void swap(T*& p1, T*& p2) {
-    T* tmp = p1;
-    p1 = p2;
-    p2 = tmp;
+  void init() {
+    MPI_Comm_rank(m_comm, &m_rank);
+    MPI_Comm_size(m_comm, &m_nProcs);
   }
 };
 
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index d51db5c..7be4b01 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -62,6 +62,10 @@ foreach(ranks 1 2 3)
   pumgen_add_test(msh2.layered.np${ranks} RANKS ${ranks} SOURCE msh2 INPUT layered-v22.msh
                   REFERENCE layered.puml.h5)
 endforeach()
+foreach(ranks 1 2 3 4)
+  pumgen_add_test(gambit.layered.np${ranks} RANKS ${ranks} SOURCE gambit INPUT layered.neu
+                  REFERENCE layered.puml.h5 TOLERANCE 1e-9)
+endforeach()
 pumgen_add_test(msh4.coarse.np2 RANKS 2 SOURCE msh4 INPUT coarse-v41.msh REFERENCE coarse.puml.h5)
 pumgen_add_test(msh2.coarse-o2.np1 RANKS 1 SOURCE msh2 INPUT coarse-o2-v22.msh
                 REFERENCE coarse-o2.puml.h5 ARGS --order=2)

From d6b3c948b39f55b7724e5bb596f47a38b4e24ef3 Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 18:21:12 +0000
Subject: [PATCH 03/19] Fix writing with HDF5 filters and with ranks without
 cells

--filter-enable failed for every mesh: the chunk shape of the one-dimensional
datasets (group, boundary) was set with rank 2 and a zero second dimension,
which HDF5 rejects. The chunk rows were also derived from the local size,
although the collective dataset creation needs the same shape on all ranks.
The chunk shape now uses the dataset rank and the global size.

With more ranks than cells, the empty ranks dereferenced the end iterator of
their empty insphere list. They now contribute +inf to the minimum and take
part in the collective writes with an empty selection.

AI-generated. Model: Claude Opus 5.5
---
 src/pumgen.cpp       | 22 ++++++++++++++++------
 tests/CMakeLists.txt | 12 ++++++++++++
 2 files changed, 28 insertions(+), 6 deletions(-)

diff --git a/src/pumgen.cpp b/src/pumgen.cpp
index 39d1f14..77c8d7d 100644
--- a/src/pumgen.cpp
+++ b/src/pumgen.cpp
@@ -120,8 +120,11 @@ static void writeH5Data(const F& handler, hid_t h5file, const std::string& name,
   hid_t h5filter = H5P_DEFAULT;
   if (filterEnable > 0) {
     h5filter = checkH5Err(H5Pcreate(H5P_DATASET_CREATE));
-    hsize_t chunk[2] = {std::min(filterChunksize, bufferSize), secondDim};
-    checkH5Err(H5Pset_chunk(h5filter, 2, chunk));
+    // the dataset creation is collective, so the chunk shape must not depend on the local size
+    const hsize_t chunkRows =
+        std::max(static_cast<hsize_t>(1), std::min<hsize_t>(filterChunksize, globalSize));
+    hsize_t chunk[2] = {chunkRows, secondDim};
+    checkH5Err(H5Pset_chunk(h5filter, dimensions, chunk));
     if (filterEnable == 1 && std::is_integral_v<T>) {
       checkH5Err(H5Pset_scaleoffset(h5filter, H5Z_SO_INT, H5Z_SO_INT_MINBITS_DEFAULT));
     } else if (filterEnable < 11) {
@@ -143,9 +146,15 @@ static void writeH5Data(const F& handler, hid_t h5file, const std::string& name,
 
     std::copy_n(handler.begin() + written * secondSize, count[0] * secondSize, data.begin());
 
-    checkH5Err(H5Sselect_hyperslab(h5memspace, H5S_SELECT_SET, nullstart, nullptr, count, nullptr));
-
-    checkH5Err(H5Sselect_hyperslab(h5space, H5S_SELECT_SET, start, nullptr, count, nullptr));
+    if (count[0] > 0) {
+      checkH5Err(
+          H5Sselect_hyperslab(h5memspace, H5S_SELECT_SET, nullstart, nullptr, count, nullptr));
+      checkH5Err(H5Sselect_hyperslab(h5space, H5S_SELECT_SET, start, nullptr, count, nullptr));
+    } else {
+      // ranks without (further) data still take part in the collective write
+      checkH5Err(H5Sselect_none(h5memspace));
+      checkH5Err(H5Sselect_none(h5space));
+    }
 
     checkH5Err(H5Dwrite(h5data, h5memtype, h5memspace, h5space, h5dxlist, data.data()));
 
@@ -415,7 +424,8 @@ int main(int argc, char* argv[]) {
 
   auto inspheres =
       calculateInsphere(meshInput->connectivity(), meshInput->geometry(), MPI_COMM_WORLD);
-  double min = *std::min_element(inspheres.begin(), inspheres.end());
+  double min = inspheres.empty() ? std::numeric_limits<double>::infinity()
+                                 : *std::min_element(inspheres.begin(), inspheres.end());
   MPI_Reduce((rank == 0 ? MPI_IN_PLACE : &min), &min, 1, MPI_DOUBLE, MPI_MIN, 0, MPI_COMM_WORLD);
   logInfo() << "Minimum insphere found:" << min;
 
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 7be4b01..2b6c488 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -71,3 +71,15 @@ pumgen_add_test(msh2.coarse-o2.np1 RANKS 1 SOURCE msh2 INPUT coarse-o2-v22.msh
                 REFERENCE coarse-o2.puml.h5 ARGS --order=2)
 pumgen_add_test(msh4.tiny.np1 RANKS 1 SOURCE msh4 INPUT tiny-v41.msh REFERENCE tiny.puml.h5)
 pumgen_add_test(msh2.tiny.np1 RANKS 1 SOURCE msh2 INPUT tiny-v22.msh REFERENCE tiny.puml.h5)
+
+# more ranks than cells
+foreach(ranks 2 3)
+  pumgen_add_test(msh4.tiny.np${ranks} RANKS ${ranks} SOURCE msh4 INPUT tiny-v41.msh
+                  REFERENCE tiny.puml.h5)
+endforeach()
+
+# HDF5 filters
+pumgen_add_test(msh4.layered.deflate.np3 RANKS 3 SOURCE msh4 INPUT layered-v41.msh
+                REFERENCE layered.puml.h5 ARGS --filter-enable=deflate1 --filter-chunksize=64)
+pumgen_add_test(msh4.tiny.scaleoffset.np3 RANKS 3 SOURCE msh4 INPUT tiny-v41.msh
+                REFERENCE tiny.puml.h5 ARGS --filter-enable=scaleoffset)

From 8ae310462a3cd97cfe9decbe9cfd7460e10a75d2 Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 18:27:52 +0000
Subject: [PATCH 04/19] Fix the --chunksize, --order and --compactify-datatypes
 options

The write chunk size was read from --filter-chunksize, so --chunksize had no
effect and e.g. --filter-chunksize 4096 shrank the write buffer to 4 KiB.

--order took an optional argument, so "-o 2" left the order empty (read as 0,
reported as "Order too high: 0") and consumed the input file name as a
positional argument; the order is now a required argument and has to be at
least 1. --compactify-datatypes is a flag, but required an argument and thus
swallowed the next command line argument.

AI-generated. Model: Claude Opus 5.5
---
 src/pumgen.cpp       | 9 ++++++---
 tests/CMakeLists.txt | 8 ++++++++
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/src/pumgen.cpp b/src/pumgen.cpp
index 77c8d7d..ec4ff43 100644
--- a/src/pumgen.cpp
+++ b/src/pumgen.cpp
@@ -218,7 +218,7 @@ int main(int argc, char* argv[]) {
                                                 "deflate7", "deflate8",    "deflate9"};
   args.addOption("compactify-datatypes", 0,
                  "Compress index and group data types to minimum byte size (no HDF5 filters)",
-                 utils::Args::Required, false);
+                 utils::Args::No, false);
   args.addEnumOption("filter-enable", filters, 0,
                      "Apply HDF5 filters (i.e. compression). Disabled by default.", false);
   args.addOption("filter-chunksize", 0, "Chunksize for filters (default=4096).",
@@ -251,7 +251,7 @@ int main(int argc, char* argv[]) {
   args.addOption("sim_log", 0, "Create SimModSuite log", utils::Args::Required, false);
   args.addAdditionalOption("input", "Input file (mesh or model)");
   args.addAdditionalOption("output", "Output parallel unstructured mesh file", false);
-  args.addOption("order", 'o', "Mesh order", utils::Args::Optional, false);
+  args.addOption("order", 'o', "Mesh order (default: 1)", utils::Args::Required, false);
 
   if (args.parse(argc, argv, rank == 0) != utils::Args::Success)
     return 1;
@@ -271,7 +271,7 @@ int main(int argc, char* argv[]) {
     outputFile.append(".puml.h5");
   }
 
-  hsize_t chunksize = args.getArgument<hsize_t>("filter-chunksize", static_cast<hsize_t>(1) << 30);
+  hsize_t chunksize = args.getArgument<hsize_t>("chunksize", static_cast<hsize_t>(1) << 30);
 
   bool reduceInts = args.isSet("compactify-datatypes");
   int filterEnable = args.getArgument("filter-enable", 0);
@@ -334,6 +334,9 @@ int main(int argc, char* argv[]) {
   }
 
   const auto meshOrder = args.getArgument<int>("order", 1);
+  if (meshOrder < 1) {
+    logError() << "The mesh order has to be at least 1, got" << meshOrder;
+  }
 
   // Create/read the mesh
   MeshData* meshInput = nullptr;
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 2b6c488..b56ae85 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -83,3 +83,11 @@ pumgen_add_test(msh4.layered.deflate.np3 RANKS 3 SOURCE msh4 INPUT layered-v41.m
                 REFERENCE layered.puml.h5 ARGS --filter-enable=deflate1 --filter-chunksize=64)
 pumgen_add_test(msh4.tiny.scaleoffset.np3 RANKS 3 SOURCE msh4 INPUT tiny-v41.msh
                 REFERENCE tiny.puml.h5 ARGS --filter-enable=scaleoffset)
+
+# command line options
+pumgen_add_test(msh2.coarse-o2.shortopt.np1 RANKS 1 SOURCE msh2 INPUT coarse-o2-v22.msh
+                REFERENCE coarse-o2.puml.h5 ARGS -o 2)
+pumgen_add_test(msh4.layered.chunksize.np3 RANKS 3 SOURCE msh4 INPUT layered-v41.msh
+                REFERENCE layered.puml.h5 ARGS --chunksize=4096)
+pumgen_add_test(msh4.tiny.order0 RANKS 1 SOURCE msh4 INPUT tiny-v41.msh ARGS --order=0
+                EXPECT_ERROR "mesh order has to be at least 1")

From 9c3445a8e9f2140ad924501e6b495587a9b22d81 Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 18:30:13 +0000
Subject: [PATCH 05/19] Fix --compactify-datatypes

Writing with compact types aborted at the geometry: the datatype was closed
whenever the option was set, including the immutable predefined float type.
Besides, the reduced integer size was derived from the number of cells rather
than from the stored values. The bit-packed boundary codes then did not fit
and HDF5 clipped them (306 of 1597 cells in the layered test mesh), and vertex
indices could exceed the reduced range as well.

The size is now the smallest one that holds the global value range of the
dataset, including a sign bit for signed types; data with negative values is
not reduced. Only copied types are closed.

AI-generated. Model: Claude Opus 5.5
---
 src/pumgen.cpp       | 48 +++++++++++++++++++++++++++++++++++---------
 tests/CMakeLists.txt |  6 ++++++
 2 files changed, 45 insertions(+), 9 deletions(-)

diff --git a/src/pumgen.cpp b/src/pumgen.cpp
index ec4ff43..68ed458 100644
--- a/src/pumgen.cpp
+++ b/src/pumgen.cpp
@@ -71,6 +71,33 @@ static int ilog(std::size_t value, int expbase = 1) {
 
 constexpr std::size_t NoSecondDim = 0;
 
+/**
+ * The smallest size in bytes of an integer type with the given signedness which holds all values
+ * of the (distributed) data. Data with negative values is not reduced.
+ */
+template <typename F>
+static std::size_t requiredIntegerBytes(const F& data, std::size_t count, bool isSigned) {
+  using ValueT = typename F::value_type;
+  unsigned long long largest = 0;
+  int negative = 0;
+  for (std::size_t i = 0; i < count; ++i) {
+    if constexpr (std::is_signed_v<ValueT>) {
+      if (data[i] < 0) {
+        negative = 1;
+        continue;
+      }
+    }
+    largest = std::max(largest, static_cast<unsigned long long>(data[i]));
+  }
+  MPI_Allreduce(MPI_IN_PLACE, &largest, 1, MPI_UNSIGNED_LONG_LONG, MPI_MAX, MPI_COMM_WORLD);
+  MPI_Allreduce(MPI_IN_PLACE, &negative, 1, MPI_INT, MPI_MAX, MPI_COMM_WORLD);
+  if (negative != 0) {
+    return sizeof(ValueT);
+  }
+  const std::size_t bits = ilog(largest) + (isSigned ? 1 : 0);
+  return std::max(static_cast<std::size_t>(1), (bits + 7) / 8);
+}
+
 template <typename T, typename F>
 static void writeH5Data(const F& handler, hid_t h5file, const std::string& name, void* mesh,
                         int meshdim, hid_t h5memtype, hid_t h5outtype, std::size_t chunk,
@@ -107,14 +134,17 @@ static void writeH5Data(const F& handler, hid_t h5file, const std::string& name,
   checkH5Err(H5Pset_dxpl_mpio(h5dxlist, H5FD_MPIO_COLLECTIVE));
 
   hid_t h5type = h5outtype;
-  if (reduceInts && std::is_integral_v<T>) {
-    h5type = H5Tcopy(h5outtype);
-    std::size_t bits = ilog(globalSize);
-    std::size_t unsignedSize = (bits + 7) / 8;
-    checkH5Err(h5type);
-    checkH5Err(H5Tset_size(h5type, unsignedSize));
-    checkH5Err(H5Tcommit(h5file, (std::string("/") + name + std::string("Type")).c_str(), h5type,
-                         H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT));
+  if constexpr (std::is_integral_v<T>) {
+    if (reduceInts) {
+      const std::size_t bytes = requiredIntegerBytes(handler, localSize * secondSize,
+                                                     H5Tget_sign(h5outtype) == H5T_SGN_2);
+      if (bytes < H5Tget_size(h5outtype)) {
+        h5type = checkH5Err(H5Tcopy(h5outtype));
+        checkH5Err(H5Tset_size(h5type, bytes));
+        checkH5Err(H5Tcommit(h5file, (std::string("/") + name + std::string("Type")).c_str(),
+                             h5type, H5P_DEFAULT, H5P_DEFAULT, H5P_DEFAULT));
+      }
+    }
   }
 
   hid_t h5filter = H5P_DEFAULT;
@@ -164,7 +194,7 @@ static void writeH5Data(const F& handler, hid_t h5file, const std::string& name,
   if (filterEnable > 0) {
     checkH5Err(H5Pclose(h5filter));
   }
-  if (reduceInts) {
+  if (h5type != h5outtype) {
     checkH5Err(H5Tclose(h5type));
   }
   checkH5Err(H5Sclose(h5space));
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index b56ae85..9eb80e8 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -91,3 +91,9 @@ pumgen_add_test(msh4.layered.chunksize.np3 RANKS 3 SOURCE msh4 INPUT layered-v41
                 REFERENCE layered.puml.h5 ARGS --chunksize=4096)
 pumgen_add_test(msh4.tiny.order0 RANKS 1 SOURCE msh4 INPUT tiny-v41.msh ARGS --order=0
                 EXPECT_ERROR "mesh order has to be at least 1")
+
+# integer types reduced to the value range
+pumgen_add_test(msh4.layered.compact.np3 RANKS 3 SOURCE msh4 INPUT layered-v41.msh
+                REFERENCE layered.puml.h5 ARGS --compactify-datatypes)
+pumgen_add_test(msh2.coarse-o2.compact.np2 RANKS 2 SOURCE msh2 INPUT coarse-o2-v22.msh
+                REFERENCE coarse-o2.puml.h5 ARGS --compactify-datatypes --order=2)

From 283ead12e10a60de05db2bd598e584de93cdcfbf Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 18:34:09 +0000
Subject: [PATCH 06/19] Stop the GMSH parsers at the first error

Parse errors were only appended to a message and parsing continued with the
value 0, e.g. a coordinate "abc" was silently read as 0 and pumgen succeeded;
an erroneous node tag became 0 and wrapped around when shifted to a 0-based
index. Errors now throw, and parseFile returns false with the first error
message.

Further messages and checks:
- binary MSH files are rejected with a hint instead of "Expected 0"
- MSH 4.0 is rejected, since the parser implements the 4.1 layout
- unknown element types are reported instead of indexing past the node count
  table (which aborted with std::out_of_range)
- missing $Entities/$Nodes/$Elements sections are reported
The node buffer is sized by the largest element (up to 1000 nodes) instead of
the number of element types (136), which overflowed the stack in the msh2
parser, and msh2 elements without tags get tag 0 instead of the tag of the
previous element.

AI-generated. Model: Claude Opus 5.5
---
 src/meshreader/GMSH4Parser.cpp  | 44 ++++++++++++++++------------
 src/meshreader/GMSH4Parser.h    |  2 +-
 src/third_party/GMSH2Parser.cpp | 32 +++++++++++++--------
 src/third_party/GMSHParser.cpp  |  6 +++-
 src/third_party/GMSHParser.h    | 51 +++++++++++++++++++++++++++------
 tests/CMakeLists.txt            | 14 +++++++++
 6 files changed, 109 insertions(+), 40 deletions(-)

diff --git a/src/meshreader/GMSH4Parser.cpp b/src/meshreader/GMSH4Parser.cpp
index ab36671..a2da382 100644
--- a/src/meshreader/GMSH4Parser.cpp
+++ b/src/meshreader/GMSH4Parser.cpp
@@ -10,15 +10,18 @@
 
 namespace puml {
 bool GMSH4Parser::parse_() {
-  errorMsg.clear();
   getNextToken();
 
   const double version = parseMeshFormat();
   if (version < 4.0 || version >= 5.0) {
     char buf[128];
-    sprintf(buf, "Unsupported MSH version %.1lf", version);
+    snprintf(buf, sizeof(buf), "Unsupported MSH version %.1lf", version);
     return logError<bool>(buf);
   }
+  if (version < 4.1) {
+    return logError<bool>(
+        "MSH 4.0 is not supported; write the mesh as MSH 4.1 (Mesh.MshFileVersion = 4.1)");
+  }
 
   bool hasEntities = false;
   bool hasNodes = false;
@@ -37,7 +40,7 @@ bool GMSH4Parser::parse_() {
       hasElements = parseElements();
       break;
     case tndm::GMSHToken::periodic:
-      hasPeriodic = parsePeriodic(version >= 4.1);
+      hasPeriodic = parsePeriodic();
       break;
     default:
       getNextToken();
@@ -45,7 +48,16 @@ bool GMSH4Parser::parse_() {
     }
   }
 
-  return hasEntities && hasNodes && hasElements;
+  if (!hasEntities) {
+    return logError<bool>("Missing $Entities section");
+  }
+  if (!hasNodes) {
+    return logError<bool>("Missing $Nodes section");
+  }
+  if (!hasElements) {
+    return logError<bool>("Missing $Elements section");
+  }
+  return true;
 }
 
 bool GMSH4Parser::parseEntities() {
@@ -238,9 +250,7 @@ bool GMSH4Parser::parseElements() {
   [[maybe_unused]] const std::size_t maxElementTag = expectNonNegativeInt();
   builder->setNumElements(numElements);
 
-  constexpr std::size_t MaxNodes = sizeof(NumNodes) / sizeof(std::size_t);
-  std::array<long, MaxNodes> nodes{};
-  builder->setNumElements(numElements);
+  std::array<long, MaxNodesPerElement> nodes{};
 
   for (std::size_t blockIdx = 0; blockIdx < numBlocks; blockIdx++) {
     getNextToken();
@@ -249,6 +259,11 @@ bool GMSH4Parser::parseElements() {
     const std::size_t entityTag = expectNonNegativeInt();
     getNextToken();
     const std::size_t type = expectNonNegativeInt();
+    if (type < 1 || type > NumTypes || NumNodes[type - 1] == 0) {
+      char buf[128];
+      snprintf(buf, sizeof(buf), "Unknown element type %zu", type);
+      return logErrorAnnotated<bool>(buf);
+    }
     getNextToken();
     const std::size_t numElementsInBlock = expectNonNegativeInt();
     for (std::size_t elementIdx = 0; elementIdx < numElementsInBlock; ++elementIdx) {
@@ -256,7 +271,7 @@ bool GMSH4Parser::parseElements() {
       [[maybe_unused]] const std::size_t id = expectNonNegativeInt();
       for (std::size_t nodeIdx = 0; nodeIdx < NumNodes[type - 1]; nodeIdx++) {
         getNextToken();
-        nodes.at(nodeIdx) = expectNonNegativeInt() - 1;
+        nodes[nodeIdx] = expectNonNegativeInt() - 1;
       }
       std::size_t tag = (type == 2) ? physicalSurfaceIds[entityTag] : physicalVolumeIds[entityTag];
       builder->addElement(type, tag, nodes.data(), NumNodes[type - 1]);
@@ -271,7 +286,7 @@ bool GMSH4Parser::parseElements() {
   return true;
 }
 
-bool GMSH4Parser::parsePeriodic(bool variableAffine) {
+bool GMSH4Parser::parsePeriodic() {
   getNextToken();
   const auto numPeriodic = expectNonNegativeInt();
 
@@ -285,15 +300,8 @@ bool GMSH4Parser::parsePeriodic(bool variableAffine) {
     getNextToken();
     [[maybe_unused]] const std::size_t entityIdentifyId = expectNonNegativeInt();
 
-    // for MSH4.1 vs MSH4.0
-    const auto affineSize = [&]() -> std::size_t {
-      if (variableAffine) {
-        getNextToken();
-        return expectNonNegativeInt();
-      } else {
-        return 16;
-      }
-    }();
+    getNextToken();
+    const std::size_t affineSize = expectNonNegativeInt();
     for (std::size_t i = 0; i < affineSize; ++i) {
       getNextToken();
       [[maybe_unused]] const double affineValue = expectNumber();
diff --git a/src/meshreader/GMSH4Parser.h b/src/meshreader/GMSH4Parser.h
index 92f7ff4..73c8d17 100644
--- a/src/meshreader/GMSH4Parser.h
+++ b/src/meshreader/GMSH4Parser.h
@@ -40,7 +40,7 @@ class GMSH4Parser : public tndm::GMSHParser {
   bool parseEntities();
   bool parseNodes();
   bool parseElements();
-  bool parsePeriodic(bool variableAffine);
+  bool parsePeriodic();
   virtual bool parse_() override;
 };
 
diff --git a/src/third_party/GMSH2Parser.cpp b/src/third_party/GMSH2Parser.cpp
index 0da1527..9d57f34 100644
--- a/src/third_party/GMSH2Parser.cpp
+++ b/src/third_party/GMSH2Parser.cpp
@@ -10,13 +10,12 @@
 namespace tndm {
 
 bool GMSH2Parser::parse_() {
-  errorMsg.clear();
   getNextToken();
 
   double version = parseMeshFormat();
   if (version < 2.0 || version >= 3.0) {
     char buf[128];
-    sprintf(buf, "Unsupported MSH version %.1lf", version);
+    snprintf(buf, sizeof(buf), "Unsupported MSH version %.1lf", version);
     return logError<bool>(buf);
   }
 
@@ -40,7 +39,13 @@ bool GMSH2Parser::parse_() {
     }
   }
 
-  return hasNodes && hasElements;
+  if (!hasNodes) {
+    return logError<bool>("Missing $Nodes section");
+  }
+  if (!hasElements) {
+    return logError<bool>("Missing $Elements section");
+  }
+  return true;
 }
 
 bool GMSH2Parser::parseNodes() {
@@ -56,7 +61,7 @@ bool GMSH2Parser::parseNodes() {
     if (curTok != GMSHToken::integer || lexer.getInteger() < 1 ||
         lexer.getInteger() > numVertices) {
       char buf[128];
-      sprintf(buf, "Expected node-tag with 1 <= node-tag <= %zu", numVertices);
+      snprintf(buf, sizeof(buf), "Expected node-tag with 1 <= node-tag <= %zu", numVertices);
       return logErrorAnnotated<bool>(buf);
     }
     std::size_t id = lexer.getInteger() - 1;
@@ -87,9 +92,7 @@ bool GMSH2Parser::parseElements() {
   }
   const auto numElements = lexer.getInteger();
 
-  constexpr std::size_t MaxNodes = sizeof(NumNodes) / sizeof(std::size_t);
-  long tag{};
-  std::array<long, MaxNodes> nodes;
+  std::array<long, MaxNodesPerElement> nodes{};
 
   builder->setNumElements(numElements);
 
@@ -100,18 +103,23 @@ bool GMSH2Parser::parseElements() {
     }
 
     getNextToken();
-    if (curTok != GMSHToken::integer || lexer.getInteger() < 1 || lexer.getInteger() > MaxNodes) {
+    if (curTok != GMSHToken::integer) {
+      return logErrorAnnotated<bool>("Expected element-type");
+    }
+    const long type = lexer.getInteger();
+    if (type < 1 || type > static_cast<long>(NumTypes) || NumNodes[type - 1] == 0) {
       char buf[128];
-      sprintf(buf, "Expected element-type with 1 <= element-type <= %zu", MaxNodes);
+      snprintf(buf, sizeof(buf), "Unknown element type %li", type);
       return logErrorAnnotated<bool>(buf);
     }
-    long type = lexer.getInteger();
 
     getNextToken();
     if (curTok != GMSHToken::integer || lexer.getInteger() < 0) {
       return logErrorAnnotated<bool>("Expected number of tags");
     }
     long numTags = lexer.getInteger();
+    // the physical tag; elements without tags get 0
+    long tag = 0;
     for (long tagIdx = 0; tagIdx < numTags; ++tagIdx) {
       getNextToken();
       if (curTok != GMSHToken::integer) {
@@ -126,8 +134,8 @@ bool GMSH2Parser::parseElements() {
       getNextToken();
       if (curTok != GMSHToken::integer || lexer.getInteger() < 1) {
         char buf[128];
-        sprintf(buf, "Expected node number > 0 (%zu/%zu for type %li)", nodeIdx + 1,
-                NumNodes[type - 1], type);
+        snprintf(buf, sizeof(buf), "Expected node number > 0 (%zu/%zu for type %li)", nodeIdx + 1,
+                 NumNodes[type - 1], type);
         return logErrorAnnotated<bool>(buf);
       }
       nodes[nodeIdx] = lexer.getInteger() - 1;
diff --git a/src/third_party/GMSHParser.cpp b/src/third_party/GMSHParser.cpp
index 92881ee..753176d 100644
--- a/src/third_party/GMSHParser.cpp
+++ b/src/third_party/GMSHParser.cpp
@@ -16,8 +16,12 @@ double GMSHParser::parseMeshFormat() {
     return logErrorAnnotated<double>("Expected version number");
   }
   getNextToken();
+  if (curTok == GMSHToken::integer && lexer.getInteger() == 1) {
+    return logErrorAnnotated<double>(
+        "Binary MSH files are not supported; write the mesh as ASCII (Mesh.Binary = 0)");
+  }
   if (curTok != GMSHToken::integer || lexer.getInteger() != 0) {
-    return logErrorAnnotated<double>("Expected 0");
+    return logErrorAnnotated<double>("Expected file type 0 (ASCII)");
   }
   getNextToken(); // skip data-size
   getNextToken();
diff --git a/src/third_party/GMSHParser.h b/src/third_party/GMSHParser.h
index dbb7974..cbef6b6 100644
--- a/src/third_party/GMSHParser.h
+++ b/src/third_party/GMSHParser.h
@@ -8,6 +8,7 @@
 #include <fstream>
 #include <optional>
 #include <sstream>
+#include <stdexcept>
 #include <string>
 #include <string_view>
 
@@ -16,6 +17,16 @@
 
 namespace tndm {
 
+namespace detail {
+template <std::size_t N> constexpr std::size_t maxEntry(const std::size_t (&values)[N]) {
+  std::size_t result = 0;
+  for (std::size_t i = 0; i < N; ++i) {
+    result = values[i] > result ? values[i] : result;
+  }
+  return result;
+}
+} // namespace detail
+
 class GMSHParser {
   public:
   // Look-up table from gmsh type to number of nodes
@@ -149,33 +160,49 @@ class GMSHParser {
       61,   // MSH_PYR_61
       69,   // MSH_PYR_69
   };
+  static constexpr std::size_t NumTypes = sizeof(NumNodes) / sizeof(NumNodes[0]);
+  static constexpr std::size_t MaxNodesPerElement = detail::maxEntry(NumNodes);
 
   explicit GMSHParser(GMSHMeshBuilder* builder) : builder(builder) {};
   [[nodiscard]] std::string_view getErrorMessage() const { return errorMsg; }
 
+  /**
+   * Parses the file; stops at the first error, whose description getErrorMessage() returns.
+   */
   bool parseFile(std::string const& fileName) {
+    errorMsg.clear();
     std::ifstream in(fileName);
     if (!in.is_open()) {
-      return logError<bool>("Unable to open MSH file");
+      errorMsg = "GMSH parser error:\n\tUnable to open MSH file\n";
+      return false;
     }
     lexer.setIStream(&in);
-    return parse_();
+    try {
+      return parse_();
+    } catch (const ParseError&) {
+      return false;
+    } catch (const std::runtime_error& error) {
+      appendAnnotated(error.what());
+      return false;
+    }
   }
 
   protected:
+  /**
+   * Thrown after an error has been recorded in errorMsg.
+   */
+  struct ParseError {};
+
   template <typename T> T logErrorAnnotated(std::string_view msg) {
-    std::stringstream ss;
-    ss << "GMSH parser error in line " << curLoc.line << " in column " << curLoc.col << ":\n";
-    ss << '\t' << msg << '\n';
-    errorMsg += ss.str();
-    return {};
+    appendAnnotated(msg);
+    throw ParseError{};
   }
 
   template <typename T> T logError(std::string_view msg) {
     errorMsg += "GMSH parser error:\n\t";
     errorMsg += msg;
     errorMsg += '\n';
-    return {};
+    throw ParseError{};
   }
 
   GMSHMeshBuilder* builder;
@@ -201,6 +228,14 @@ class GMSHParser {
   virtual bool parse_() = 0;
 
   double parseMeshFormat();
+
+  private:
+  void appendAnnotated(std::string_view msg) {
+    std::stringstream ss;
+    ss << "GMSH parser error in line " << curLoc.line << " in column " << curLoc.col << ":\n";
+    ss << '\t' << msg << '\n';
+    errorMsg += ss.str();
+  }
 };
 } // namespace tndm
 
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 9eb80e8..cb75cc0 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -97,3 +97,17 @@ pumgen_add_test(msh4.layered.compact.np3 RANKS 3 SOURCE msh4 INPUT layered-v41.m
                 REFERENCE layered.puml.h5 ARGS --compactify-datatypes)
 pumgen_add_test(msh2.coarse-o2.compact.np2 RANKS 2 SOURCE msh2 INPUT coarse-o2-v22.msh
                 REFERENCE coarse-o2.puml.h5 ARGS --compactify-datatypes --order=2)
+
+# malformed or unsupported input
+pumgen_add_test(msh4.tiny-truncated RANKS 1 SOURCE msh4 INPUT tiny-truncated-v41.msh
+                EXPECT_ERROR "GMSH parser error")
+pumgen_add_test(msh4.tiny-badnumber RANKS 1 SOURCE msh4 INPUT tiny-badnumber-v41.msh
+                EXPECT_ERROR "Expected number")
+pumgen_add_test(msh4.tiny-unknowntype RANKS 1 SOURCE msh4 INPUT tiny-unknowntype-v41.msh
+                EXPECT_ERROR "Unknown element type 999")
+pumgen_add_test(msh4.tiny-v40 RANKS 1 SOURCE msh4 INPUT tiny-v40.msh
+                EXPECT_ERROR "MSH 4.0 is not supported")
+pumgen_add_test(msh4.coarse-binary RANKS 1 SOURCE msh4 INPUT coarse-binary-v41.msh
+                EXPECT_ERROR "Binary MSH files are not supported")
+pumgen_add_test(msh2.tiny-as-msh4 RANKS 1 SOURCE msh2 INPUT tiny-v41.msh
+                EXPECT_ERROR "Unsupported MSH version 4.1")

From c155f08ce3d08b4be8e9c62c0c96e37a2080c59e Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 18:40:50 +0000
Subject: [PATCH 07/19] Fix periodic meshes with more than one rank

Only rank 0 parses the GMSH file, but every rank asked its own (empty)
builder whether the mesh has a vertex identification. Rank 0 therefore
scattered and wrote the identification alone, and pumgen hung in the
collective HDF5 write. The flag is now broadcast.

Adds a periodic fixture (a box, periodic in x) whose reference
identification is computed from gmsh's periodic node pairs; the tests
compare the identify dataset as well.

AI-generated. Model: Claude Opus 5.5
---
 src/meshreader/ParallelGMSHReader.h        |    6 +-
 tests/CMakeLists.txt                       |   15 +-
 tests/RunPumgenTest.cmake                  |    7 +-
 tests/fixtures/generate.py                 |   47 +-
 tests/fixtures/periodic-parametric-v41.msh | 2371 ++++++++++++++++++++
 tests/fixtures/periodic-v41.msh            | 2371 ++++++++++++++++++++
 tests/fixtures/periodic.puml.h5            |  Bin 0 -> 60528 bytes
 7 files changed, 4811 insertions(+), 6 deletions(-)
 create mode 100644 tests/fixtures/periodic-parametric-v41.msh
 create mode 100644 tests/fixtures/periodic-v41.msh
 create mode 100644 tests/fixtures/periodic.puml.h5

diff --git a/src/meshreader/ParallelGMSHReader.h b/src/meshreader/ParallelGMSHReader.h
index 19dcb99..0a9ac26 100644
--- a/src/meshreader/ParallelGMSHReader.h
+++ b/src/meshreader/ParallelGMSHReader.h
@@ -47,10 +47,12 @@ template <typename P, std::size_t OrderP> class ParallelGMSHReader {
 
       nVertices_ = builder_.vertices.size();
       nElements_ = builder_.elements.size();
+      hasIdentify_ = builder_.identify.empty() ? 0 : 1;
     }
 
     MPI_Bcast(&nVertices_, 1, tndm::mpi_type_t<decltype(nVertices_)>(), 0, comm_);
     MPI_Bcast(&nElements_, 1, tndm::mpi_type_t<decltype(nElements_)>(), 0, comm_);
+    MPI_Bcast(&hasIdentify_, 1, tndm::mpi_type_t<decltype(hasIdentify_)>(), 0, comm_);
   }
 
   [[nodiscard]] std::size_t nVertices() const { return nVertices_; }
@@ -71,7 +73,7 @@ template <typename P, std::size_t OrderP> class ParallelGMSHReader {
   void readGroups(int* groups) const { scatter(builder_.groups.data(), groups, nElements(), 1); }
 
   constexpr static bool SupportsIdentify = true;
-  bool hasIdentify() const { return !builder_.identify.empty(); }
+  bool hasIdentify() const { return hasIdentify_ != 0; }
   void readIdentify(std::size_t* vertices) const {
     scatter(builder_.identify.data(), vertices, nVertices(), 1);
   }
@@ -175,6 +177,8 @@ template <typename P, std::size_t OrderP> class ParallelGMSHReader {
   std::vector<bc_t> bcs_;
   std::size_t nVertices_ = 0;
   std::size_t nElements_ = 0;
+  // only rank 0 parses the file, so all ranks need this flag for the collective reads and writes
+  int hasIdentify_ = 0;
 };
 
 } // namespace puml
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index cb75cc0..45fe62e 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -12,11 +12,11 @@ set(PUMGEN_TEST_OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/output)
 file(MAKE_DIRECTORY ${PUMGEN_TEST_OUTPUT})
 
 # pumgen_add_test(<name> RANKS <n> SOURCE <source> INPUT <fixture>
-#                 [REFERENCE <fixture> [TOLERANCE <tolerance>]] [EXPECT_ERROR <regex>]
+#                 [REFERENCE <fixture> [TOLERANCE <tolerance>] [IDENTIFY]] [EXPECT_ERROR <regex>]
 #                 [ARGS <argument>...])
 function(pumgen_add_test name)
-  cmake_parse_arguments(PARSE_ARGV 1 TEST "" "RANKS;SOURCE;INPUT;REFERENCE;TOLERANCE;EXPECT_ERROR"
-                        "ARGS")
+  cmake_parse_arguments(PARSE_ARGV 1 TEST "IDENTIFY"
+                        "RANKS;SOURCE;INPUT;REFERENCE;TOLERANCE;EXPECT_ERROR" "ARGS")
   set(output ${PUMGEN_TEST_OUTPUT}/${name}.puml.h5)
   set(command
       ${MPIEXEC_EXECUTABLE}
@@ -41,6 +41,9 @@ function(pumgen_add_test name)
     if(DEFINED TEST_TOLERANCE)
       list(APPEND script_args -DTOLERANCE=${TEST_TOLERANCE})
     endif()
+    if(TEST_IDENTIFY)
+      list(APPEND script_args -DIDENTIFY=ON)
+    endif()
   endif()
 
   add_test(NAME pumgen.${name} COMMAND ${CMAKE_COMMAND} ${script_args} -P
@@ -111,3 +114,9 @@ pumgen_add_test(msh4.coarse-binary RANKS 1 SOURCE msh4 INPUT coarse-binary-v41.m
                 EXPECT_ERROR "Binary MSH files are not supported")
 pumgen_add_test(msh2.tiny-as-msh4 RANKS 1 SOURCE msh2 INPUT tiny-v41.msh
                 EXPECT_ERROR "Unsupported MSH version 4.1")
+
+# periodic meshes
+foreach(ranks 1 2 3)
+  pumgen_add_test(msh4.periodic.np${ranks} RANKS ${ranks} SOURCE msh4 INPUT periodic-v41.msh
+                  REFERENCE periodic.puml.h5 IDENTIFY)
+endforeach()
diff --git a/tests/RunPumgenTest.cmake b/tests/RunPumgenTest.cmake
index 19ec71a..3c88ea2 100644
--- a/tests/RunPumgenTest.cmake
+++ b/tests/RunPumgenTest.cmake
@@ -9,6 +9,7 @@
 #   OUTPUT        file written by pumgen
 #   REFERENCE     (optional) reference PUML file the output has to match
 #   TOLERANCE     (optional) absolute tolerance for the vertex coordinates
+#   IDENTIFY      (optional) also compare the vertex identification of periodic meshes
 #   H5DIFF        h5diff executable, required together with REFERENCE
 #   EXPECT_ERROR  (optional) pumgen has to fail with a message matching this regular expression
 
@@ -39,7 +40,11 @@ endif()
 
 if(DEFINED REFERENCE)
   set(failures "")
-  foreach(dataset connect geometry group boundary)
+  set(datasets connect geometry group boundary)
+  if(IDENTIFY)
+    list(APPEND datasets identify)
+  endif()
+  foreach(dataset ${datasets})
     set(options "")
     if(dataset STREQUAL "geometry" AND DEFINED TOLERANCE)
       set(options -d ${TOLERANCE})
diff --git a/tests/fixtures/generate.py b/tests/fixtures/generate.py
index be00377..f7340fa 100644
--- a/tests/fixtures/generate.py
+++ b/tests/fixtures/generate.py
@@ -99,7 +99,28 @@ def reference_data():
     return vertices, np.asarray(cells), np.asarray(groups), np.asarray(boundary)
 
 
-def write_reference(path, mesh_file):
+def periodic_identification(num_vertices):
+    """Each vertex is identified with the smallest vertex index of its periodic class."""
+    parent = list(range(num_vertices))
+
+    def find(v):
+        while parent[v] != v:
+            parent[v] = parent[parent[v]]
+            v = parent[v]
+        return v
+
+    for dim in range(3):
+        for _, tag in gmsh.model.getEntities(dim):
+            master, nodes, master_nodes, _ = gmsh.model.mesh.getPeriodicNodes(dim, tag)
+            if master == tag:
+                continue
+            for node, master_node in zip(nodes, master_nodes):
+                a, b = find(int(node) - 1), find(int(master_node) - 1)
+                parent[max(a, b)] = min(a, b)
+    return np.array([find(v) for v in range(num_vertices)])
+
+
+def write_reference(path, mesh_file, periodic=False):
     """Reference PUML data from a written mesh file, so coordinates match their text form."""
     gmsh.clear()
     gmsh.open(mesh_file)
@@ -109,6 +130,8 @@ def write_reference(path, mesh_file):
         out.create_dataset("geometry", data=vertices.astype("<f8"))
         out.create_dataset("group", data=groups.astype("<i4"))
         out.create_dataset("boundary", data=boundary.astype("<i4"))
+        if periodic:
+            out.create_dataset("identify", data=periodic_identification(len(vertices)).astype("<u8"))
 
 
 def write_mesh(path, version, binary=False):
@@ -166,6 +189,27 @@ def generate_coarse():
     write_reference("coarse-o2.puml.h5", "coarse-o2-v41.msh")
 
 
+def generate_periodic():
+    gmsh.clear()
+    gmsh.model.add("periodic")
+    gmsh.model.occ.addBox(0, 0, 0, 1, 1, 1)
+    gmsh.model.occ.synchronize()
+    translation = [1, 0, 0, 1, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1]
+    left = [tag for _, tag in gmsh.model.getEntitiesInBoundingBox(-TOL, -TOL, -TOL, TOL, 1 + TOL, 1 + TOL, 2)]
+    right = [tag for _, tag in gmsh.model.getEntitiesInBoundingBox(1 - TOL, -TOL, -TOL, 1 + TOL, 1 + TOL, 1 + TOL, 2)]
+    gmsh.model.mesh.setPeriodic(2, right, left, translation)
+    gmsh.model.addPhysicalGroup(3, [1], 1)
+    others = [tag for _, tag in gmsh.model.getEntities(2) if tag not in left + right]
+    gmsh.model.addPhysicalGroup(2, others, FREE_SURFACE)
+    gmsh.option.setNumber("Mesh.MeshSizeMax", 0.4)
+    gmsh.model.mesh.generate(3)
+    write_mesh("periodic-v41.msh", 4.1)
+    gmsh.option.setNumber("Mesh.SaveParametric", 1)
+    write_mesh("periodic-parametric-v41.msh", 4.1)
+    gmsh.option.setNumber("Mesh.SaveParametric", 0)
+    write_reference("periodic.puml.h5", "periodic-v41.msh", periodic=True)
+
+
 TINY_V41 = """$MeshFormat
 4.1 0 8
 $EndMeshFormat
@@ -238,6 +282,7 @@ def main():
     gmsh.option.setNumber("Mesh.Algorithm3D", 1)
     generate_layered()
     generate_coarse()
+    generate_periodic()
     generate_tiny()
     gmsh.finalize()
 
diff --git a/tests/fixtures/periodic-parametric-v41.msh b/tests/fixtures/periodic-parametric-v41.msh
new file mode 100644
index 0000000..c4d967a
--- /dev/null
+++ b/tests/fixtures/periodic-parametric-v41.msh
@@ -0,0 +1,2371 @@
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diff --git a/tests/fixtures/periodic-v41.msh b/tests/fixtures/periodic-v41.msh
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diff --git a/tests/fixtures/periodic.puml.h5 b/tests/fixtures/periodic.puml.h5
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z{O>CHo?73x>if8Tf2{A7&Hsy7xhLER`;EcVLEpFQdux4PxbI_bhF){f_e}e~SKklo
bdt}?7=lhU-zqId(?tt9)-FAZZJ-+`3sbF$;

literal 0
HcmV?d00001


From 20c86340fca2703389718e9295830810338a62f1 Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 18:44:40 +0000
Subject: [PATCH 08/19] Validate the node tags in the GMSH parsers

The msh4 parser used tag - 1 as the vertex index and only checked it with an
assert, so any file whose tags do not form 1..N wrote out of bounds, e.g.
dense tags starting at 1001. Element and periodic node references were not
checked in either parser, and duplicate tags left vertices undefined.

Now the node tags have to be contiguous; in msh4 files they may start at any
positive tag. Duplicate tags and references to unknown nodes are reported,
and $Nodes has to precede $Elements and $Periodic. Gmsh writes contiguous
tags also for models with volumes outside of any physical group, so
non-contiguous tags are rejected instead of remapped.

Parametric node coordinates (Mesh.SaveParametric = 1) are skipped instead of
being read as the next node, and facet node indices use std::size_t like the
cell node indices.

AI-generated. Model: Claude Opus 5.5
---
 src/meshreader/GMSH4Parser.cpp  | 57 +++++++++++++++++++++++++--------
 src/meshreader/GMSH4Parser.h    | 19 +++++++++++
 src/meshreader/GMSHBuilder.h    |  2 +-
 src/third_party/GMSH2Parser.cpp | 30 +++++++++++------
 src/third_party/GMSH2Parser.h   | 15 +++++++++
 tests/CMakeLists.txt            | 16 +++++++++
 6 files changed, 115 insertions(+), 24 deletions(-)

diff --git a/src/meshreader/GMSH4Parser.cpp b/src/meshreader/GMSH4Parser.cpp
index a2da382..18a2c2b 100644
--- a/src/meshreader/GMSH4Parser.cpp
+++ b/src/meshreader/GMSH4Parser.cpp
@@ -3,7 +3,6 @@
 // SPDX-License-Identifier: BSD-3-Clause
 #include "GMSH4Parser.h"
 
-#include <cassert>
 #include <cstdio>
 
 #include "utils/logger.h"
@@ -24,7 +23,6 @@ bool GMSH4Parser::parse_() {
   }
 
   bool hasEntities = false;
-  bool hasNodes = false;
   bool hasElements = false;
   bool hasPeriodic = false;
 
@@ -34,7 +32,7 @@ bool GMSH4Parser::parse_() {
       hasEntities = parseEntities();
       break;
     case tndm::GMSHToken::nodes:
-      hasNodes = parseNodes();
+      parseNodes();
       break;
     case tndm::GMSHToken::elements:
       hasElements = parseElements();
@@ -199,18 +197,32 @@ bool GMSH4Parser::parseNodes() {
   getNextToken();
   const std::size_t numVertices = expectNonNegativeInt();
   getNextToken();
-  [[maybe_unused]] const std::size_t minNodeTag = expectNonNegativeInt();
+  const std::size_t minNodeTag = expectNonNegativeInt();
   getNextToken();
-  [[maybe_unused]] const std::size_t maxNodeTag = expectNonNegativeInt();
+  const std::size_t maxNodeTag = expectNonNegativeInt();
+  if (numVertices > 0 &&
+      (minNodeTag == 0 || maxNodeTag < minNodeTag || maxNodeTag - minNodeTag + 1 != numVertices)) {
+    char buf[192];
+    snprintf(buf, sizeof(buf),
+             "Non-contiguous node tags are not supported (%zu nodes with tags from %zu to %zu)",
+             numVertices, minNodeTag, maxNodeTag);
+    return logErrorAnnotated<bool>(buf);
+  }
+  hasNodes = true;
+  firstNodeTag = minNodeTag;
+  numNodes = numVertices;
   builder->setNumVertices(numVertices);
 
+  // with as many distinct tags as the tag range is long, every node is defined exactly once
+  std::vector<bool> defined(numVertices, false);
+
   for (std::size_t blockIdx = 0; blockIdx < numBlocks; blockIdx++) {
     getNextToken();
-    [[maybe_unused]] const std::size_t dim = expectNonNegativeInt();
+    const std::size_t dim = expectNonNegativeInt();
     getNextToken();
     [[maybe_unused]] const std::size_t entityTag = expectNonNegativeInt();
     getNextToken();
-    [[maybe_unused]] const std::size_t parametric = expectNonNegativeInt();
+    const std::size_t parametric = expectNonNegativeInt();
     getNextToken();
     const std::size_t numVerticesInBlock = expectNonNegativeInt();
     std::vector<std::size_t> vertexIds;
@@ -218,17 +230,28 @@ bool GMSH4Parser::parseNodes() {
     // first read vertex ids
     for (std::size_t vertexIdx = 0; vertexIdx < numVerticesInBlock; ++vertexIdx) {
       getNextToken();
-      vertexIds.push_back(expectNonNegativeInt() - 1);
+      const std::size_t index = expectNodeIndex();
+      if (defined[index]) {
+        char buf[128];
+        snprintf(buf, sizeof(buf), "Duplicate node tag %zu", firstNodeTag + index);
+        return logErrorAnnotated<bool>(buf);
+      }
+      defined[index] = true;
+      vertexIds.push_back(index);
     }
-    // then read vertex data
+    // then read vertex data; parametric nodes carry dim additional parametric coordinates
+    const std::size_t numParametric = parametric != 0 ? dim : 0;
     for (std::size_t vertexIdx = 0; vertexIdx < numVerticesInBlock; ++vertexIdx) {
       std::array<double, 3> x{};
       for (std::size_t i = 0; i < 3; i++) {
         getNextToken();
         x[i] = expectNumber();
       }
-      assert(vertexIds.at(vertexIdx) < numVertices);
-      builder->setVertex(vertexIds.at(vertexIdx), x);
+      for (std::size_t i = 0; i < numParametric; ++i) {
+        getNextToken();
+        expectNumber();
+      }
+      builder->setVertex(vertexIds[vertexIdx], x);
     }
   }
   getNextToken();
@@ -240,6 +263,9 @@ bool GMSH4Parser::parseNodes() {
 }
 
 bool GMSH4Parser::parseElements() {
+  if (!hasNodes) {
+    return logErrorAnnotated<bool>("Expected $Nodes before $Elements");
+  }
   getNextToken();
   const std::size_t numBlocks = expectNonNegativeInt();
   getNextToken();
@@ -271,7 +297,7 @@ bool GMSH4Parser::parseElements() {
       [[maybe_unused]] const std::size_t id = expectNonNegativeInt();
       for (std::size_t nodeIdx = 0; nodeIdx < NumNodes[type - 1]; nodeIdx++) {
         getNextToken();
-        nodes[nodeIdx] = expectNonNegativeInt() - 1;
+        nodes[nodeIdx] = static_cast<long>(expectNodeIndex());
       }
       std::size_t tag = (type == 2) ? physicalSurfaceIds[entityTag] : physicalVolumeIds[entityTag];
       builder->addElement(type, tag, nodes.data(), NumNodes[type - 1]);
@@ -287,6 +313,9 @@ bool GMSH4Parser::parseElements() {
 }
 
 bool GMSH4Parser::parsePeriodic() {
+  if (!hasNodes) {
+    return logErrorAnnotated<bool>("Expected $Nodes before $Periodic");
+  }
   getNextToken();
   const auto numPeriodic = expectNonNegativeInt();
 
@@ -312,9 +341,9 @@ bool GMSH4Parser::parsePeriodic() {
 
     for (std::size_t i = 0; i < identifySize; ++i) {
       getNextToken();
-      const std::size_t nodeId = expectNonNegativeInt() - 1;
+      const std::size_t nodeId = expectNodeIndex();
       getNextToken();
-      const std::size_t nodeIdentifyId = expectNonNegativeInt() - 1;
+      const std::size_t nodeIdentifyId = expectNodeIndex();
       builder->addVertexLink(nodeId, nodeIdentifyId);
     }
   }
diff --git a/src/meshreader/GMSH4Parser.h b/src/meshreader/GMSH4Parser.h
index 73c8d17..2da26f2 100644
--- a/src/meshreader/GMSH4Parser.h
+++ b/src/meshreader/GMSH4Parser.h
@@ -4,6 +4,7 @@
 #ifndef PUMGEN_SRC_MESHREADER_GMSH4PARSER_H_
 #define PUMGEN_SRC_MESHREADER_GMSH4PARSER_H_
 
+#include <cstdio>
 #include <map>
 #include <string>
 #include <string_view>
@@ -22,6 +23,24 @@ class GMSH4Parser : public tndm::GMSHParser {
   std::map<unsigned long, long> physicalSurfaceIds;
   std::map<unsigned long, long> physicalVolumeIds;
 
+  // the node tags form the contiguous range [firstNodeTag, firstNodeTag + numNodes)
+  bool hasNodes = false;
+  std::size_t firstNodeTag = 0;
+  std::size_t numNodes = 0;
+
+  /**
+   * Reads a node tag and returns the index of the node.
+   */
+  std::size_t expectNodeIndex() {
+    const std::size_t tag = expectNonNegativeInt();
+    if (tag < firstNodeTag || tag - firstNodeTag >= numNodes) {
+      char buf[128];
+      snprintf(buf, sizeof(buf), "Unknown node tag %zu", tag);
+      return logErrorAnnotated<std::size_t>(buf);
+    }
+    return tag - firstNodeTag;
+  }
+
   unsigned long expectNonNegativeInt() {
     if (curTok != tndm::GMSHToken::integer || lexer.getInteger() < 0) {
       return logErrorAnnotated<bool>("Expected non-negative integer");
diff --git a/src/meshreader/GMSHBuilder.h b/src/meshreader/GMSHBuilder.h
index d47cebc..d5935a2 100644
--- a/src/meshreader/GMSHBuilder.h
+++ b/src/meshreader/GMSHBuilder.h
@@ -147,7 +147,7 @@ template <std::size_t D, std::size_t Order> class GMSHBuilder : public tndm::GMS
   public:
   using vertex_t = std::array<double, D>;
   using element_t = std::array<std::size_t, nodeCount(D, Order)>;
-  using facet_t = std::array<int, nodeCount(D - 1u, Order)>;
+  using facet_t = std::array<std::size_t, nodeCount(D - 1u, Order)>;
 
   std::vector<vertex_t> vertices;
   std::vector<std::size_t> identify;
diff --git a/src/third_party/GMSH2Parser.cpp b/src/third_party/GMSH2Parser.cpp
index 9d57f34..0f0965a 100644
--- a/src/third_party/GMSH2Parser.cpp
+++ b/src/third_party/GMSH2Parser.cpp
@@ -6,6 +6,7 @@
 #include "GMSHLexer.h"
 
 #include <cstdio>
+#include <vector>
 
 namespace tndm {
 
@@ -55,6 +56,11 @@ bool GMSH2Parser::parseNodes() {
   }
   std::size_t numVertices = lexer.getInteger();
   builder->setNumVertices(numVertices);
+  hasNodes = true;
+  numNodes = numVertices;
+
+  // with numVertices distinct tags in [1, numVertices], every node is defined exactly once
+  std::vector<bool> defined(numVertices, false);
 
   for (std::size_t i = 0; i < numVertices; ++i) {
     getNextToken();
@@ -65,6 +71,12 @@ bool GMSH2Parser::parseNodes() {
       return logErrorAnnotated<bool>(buf);
     }
     std::size_t id = lexer.getInteger() - 1;
+    if (defined[id]) {
+      char buf[128];
+      snprintf(buf, sizeof(buf), "Duplicate node tag %zu", id + 1);
+      return logErrorAnnotated<bool>(buf);
+    }
+    defined[id] = true;
 
     std::array<double, 3> x;
     for (std::size_t i = 0; i < 3; ++i) {
@@ -86,6 +98,9 @@ bool GMSH2Parser::parseNodes() {
 }
 
 bool GMSH2Parser::parseElements() {
+  if (!hasNodes) {
+    return logErrorAnnotated<bool>("Expected $Nodes before $Elements");
+  }
   getNextToken();
   if (curTok != GMSHToken::integer || lexer.getInteger() < 0) {
     return logErrorAnnotated<bool>("Expected non-negative integer");
@@ -132,13 +147,7 @@ bool GMSH2Parser::parseElements() {
 
     for (std::size_t nodeIdx = 0; nodeIdx < NumNodes[type - 1]; ++nodeIdx) {
       getNextToken();
-      if (curTok != GMSHToken::integer || lexer.getInteger() < 1) {
-        char buf[128];
-        snprintf(buf, sizeof(buf), "Expected node number > 0 (%zu/%zu for type %li)", nodeIdx + 1,
-                 NumNodes[type - 1], type);
-        return logErrorAnnotated<bool>(buf);
-      }
-      nodes[nodeIdx] = lexer.getInteger() - 1;
+      nodes[nodeIdx] = static_cast<long>(expectNodeIndex());
     }
 
     builder->addElement(type, tag, nodes.data(), NumNodes[type - 1]);
@@ -153,6 +162,9 @@ bool GMSH2Parser::parseElements() {
 }
 
 bool GMSH2Parser::parsePeriodic() {
+  if (!hasNodes) {
+    return logErrorAnnotated<bool>("Expected $Nodes before $Periodic");
+  }
   getNextToken();
   const auto numPeriodic = expectNonNegativeInt();
 
@@ -180,9 +192,9 @@ bool GMSH2Parser::parsePeriodic() {
 
     for (std::size_t i = 0; i < identifySize; ++i) {
       getNextToken();
-      const std::size_t nodeId = expectNonNegativeInt() - 1;
+      const std::size_t nodeId = expectNodeIndex();
       getNextToken();
-      const std::size_t nodeIdentifyId = expectNonNegativeInt() - 1;
+      const std::size_t nodeIdentifyId = expectNodeIndex();
       builder->addVertexLink(nodeId, nodeIdentifyId);
     }
   }
diff --git a/src/third_party/GMSH2Parser.h b/src/third_party/GMSH2Parser.h
index 83e33bb..38f9e33 100644
--- a/src/third_party/GMSH2Parser.h
+++ b/src/third_party/GMSH2Parser.h
@@ -37,6 +37,21 @@ class GMSH2Parser : public GMSHParser {
     return num.value();
   }
 
+  // the node tags are 1, ..., numNodes
+  bool hasNodes = false;
+  std::size_t numNodes = 0;
+
+  /**
+   * Reads a node tag and returns the index of the node.
+   */
+  std::size_t expectNodeIndex() {
+    if (curTok != GMSHToken::integer || lexer.getInteger() < 1 ||
+        static_cast<std::size_t>(lexer.getInteger()) > numNodes) {
+      return logErrorAnnotated<std::size_t>("Unknown node tag");
+    }
+    return static_cast<std::size_t>(lexer.getInteger()) - 1;
+  }
+
   bool parseNodes();
   bool parseElements();
   bool parsePeriodic();
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 45fe62e..a436afb 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -120,3 +120,19 @@ foreach(ranks 1 2 3)
   pumgen_add_test(msh4.periodic.np${ranks} RANKS ${ranks} SOURCE msh4 INPUT periodic-v41.msh
                   REFERENCE periodic.puml.h5 IDENTIFY)
 endforeach()
+
+# node tags
+pumgen_add_test(msh4.coarse-offset.np2 RANKS 2 SOURCE msh4 INPUT coarse-offset-v41.msh
+                REFERENCE coarse.puml.h5)
+pumgen_add_test(msh4.periodic-parametric.np2 RANKS 2 SOURCE msh4 INPUT periodic-parametric-v41.msh
+                REFERENCE periodic.puml.h5 IDENTIFY)
+pumgen_add_test(msh4.tiny-sparse RANKS 1 SOURCE msh4 INPUT tiny-sparse-v41.msh
+                EXPECT_ERROR "Non-contiguous node tags are not supported")
+pumgen_add_test(msh4.tiny-duplicate RANKS 1 SOURCE msh4 INPUT tiny-duplicate-v41.msh
+                EXPECT_ERROR "Duplicate node tag 2")
+pumgen_add_test(msh4.tiny-badnode RANKS 1 SOURCE msh4 INPUT tiny-badnode-v41.msh
+                EXPECT_ERROR "Unknown node tag 9")
+pumgen_add_test(msh2.tiny-duplicate RANKS 1 SOURCE msh2 INPUT tiny-duplicate-v22.msh
+                EXPECT_ERROR "Duplicate node tag 2")
+pumgen_add_test(msh2.tiny-badnode RANKS 1 SOURCE msh2 INPUT tiny-badnode-v22.msh
+                EXPECT_ERROR "Unknown node tag")

From 7cea1f7dc037e9fb94ef92b0b11ae13b4d315645 Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 18:50:45 +0000
Subject: [PATCH 09/19] Fix higher-order msh4 meshes and reject partitioned
 files

The msh4 parser picked the physical tag of an element from the surface map
only for element type 2 (linear triangles) and from the volume map for all
other types. The boundary conditions of higher-order meshes were thus looked
up with surface entity tags in the volume map (208 of 320 cells wrong in the
order-2 test mesh). The map is now chosen by the entity dimension of the
element block, and lookups no longer insert entries.

Elements of surfaces or volumes without a physical group still get 0, but
pumgen now warns about them. Partitioned MSH files, whose physical groups
live in $PartitionedEntities, are rejected instead of being read with all
groups and boundary conditions 0.

The minimum insphere assumed 4 nodes per cell and reported 0 for order 2; it
now uses the four vertices of each cell.

AI-generated. Model: Claude Opus 5.5
---
 src/helper/InsphereCalculator.cpp      | 24 +++++++++++++++--------
 src/helper/InsphereCalculator.h        |  7 ++++++-
 src/meshreader/GMSH4Parser.cpp         | 27 +++++++++++++++++++++++---
 src/meshreader/GMSH4Parser.h           |  9 +++++++++
 src/pumgen.cpp                         |  4 ++--
 src/third_party/GMSHLexer.cpp          |  3 +++
 src/third_party/GMSHLexer.h            |  1 +
 tests/CMakeLists.txt                   | 25 +++++++++++++++++++++---
 tests/RunPumgenTest.cmake              |  5 +++++
 tests/fixtures/generate.py             |  1 +
 tests/fixtures/tiny-nophysical-v41.msh | 24 +++++++++++++++++++++++
 11 files changed, 113 insertions(+), 17 deletions(-)
 create mode 100644 tests/fixtures/tiny-nophysical-v41.msh

diff --git a/src/helper/InsphereCalculator.cpp b/src/helper/InsphereCalculator.cpp
index 309e35e..ddc2a0c 100644
--- a/src/helper/InsphereCalculator.cpp
+++ b/src/helper/InsphereCalculator.cpp
@@ -13,7 +13,11 @@
 #include "MPIConvenience.h"
 
 std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivity,
-                                      const std::vector<double>& geometry, MPI_Comm comm) {
+                                      const std::vector<double>& geometry, std::size_t cellSize,
+                                      MPI_Comm comm) {
+  constexpr std::size_t VerticesPerCell = 4;
+  const std::size_t numCells = connectivity.size() / cellSize;
+
   int commsize;
   int commrank;
 
@@ -41,7 +45,11 @@ std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivi
 
   std::vector<std::unordered_map<std::size_t, std::size_t>> outidxmap(commsize);
 
-  for (const auto& vertex : connectivity) {
+  for (std::size_t node = 0; node < connectivity.size(); ++node) {
+    if (node % cellSize >= VerticesPerCell) {
+      continue;
+    }
+    const auto vertex = connectivity[node];
     auto itPosition = std::upper_bound(vertexDist.begin(), vertexDist.end(), vertex);
     auto position = std::distance(vertexDist.begin(), itPosition) - 1;
     auto localVertex = vertex - vertexDist[position];
@@ -84,7 +92,7 @@ std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivi
                     tndm::mpi_type_t<std::size_t>(), comm);
   }
 
-  std::vector<double> outvertices(3 * connectivity.size());
+  std::vector<double> outvertices(3 * outdisp[commsize]);
 
   {
     std::vector<double> invertices(3 * indisp[commsize]);
@@ -102,12 +110,12 @@ std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivi
   }
 
   std::vector<std::size_t> counter(commsize);
-  std::vector<double> inspheres(connectivity.size() / 4);
+  std::vector<double> inspheres(numCells);
 
-  for (std::size_t i = 0; i < connectivity.size() / 4; ++i) {
-    std::array<std::array<double, 3>, 4> vertices;
-    for (int j = 0; j < 4; ++j) {
-      auto vertex = connectivity[i * 4 + j];
+  for (std::size_t i = 0; i < numCells; ++i) {
+    std::array<std::array<double, 3>, VerticesPerCell> vertices;
+    for (std::size_t j = 0; j < VerticesPerCell; ++j) {
+      auto vertex = connectivity[i * cellSize + j];
       auto itPosition = std::upper_bound(vertexDist.begin(), vertexDist.end(), vertex);
       auto position = std::distance(vertexDist.begin(), itPosition) - 1;
       auto localVertex = vertex - vertexDist[position];
diff --git a/src/helper/InsphereCalculator.h b/src/helper/InsphereCalculator.h
index 9a8e548..806e726 100644
--- a/src/helper/InsphereCalculator.h
+++ b/src/helper/InsphereCalculator.h
@@ -10,7 +10,12 @@
 
 // assumes a contiguous distribution of all vertices over all processes
 
+/**
+ * The insphere radius of each tetrahedron. Each cell has cellSize nodes, the first four of which
+ * are its vertices.
+ */
 std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivity,
-                                      const std::vector<double>& geometry, MPI_Comm comm);
+                                      const std::vector<double>& geometry, std::size_t cellSize,
+                                      MPI_Comm comm);
 
 #endif // PUMGEN_SRC_HELPER_INSPHERECALCULATOR_H_
diff --git a/src/meshreader/GMSH4Parser.cpp b/src/meshreader/GMSH4Parser.cpp
index 18a2c2b..e74a118 100644
--- a/src/meshreader/GMSH4Parser.cpp
+++ b/src/meshreader/GMSH4Parser.cpp
@@ -40,6 +40,9 @@ bool GMSH4Parser::parse_() {
     case tndm::GMSHToken::periodic:
       hasPeriodic = parsePeriodic();
       break;
+    case tndm::GMSHToken::partitioned_entities:
+      return logErrorAnnotated<bool>(
+          "Partitioned MSH files are not supported; save the mesh without partitions");
     default:
       getNextToken();
       break;
@@ -55,9 +58,27 @@ bool GMSH4Parser::parse_() {
   if (!hasElements) {
     return logError<bool>("Missing $Elements section");
   }
+  if (!unassignedVolumes.empty() || !unassignedSurfaces.empty()) {
+    logWarning() << "The elements of" << unassignedVolumes.size() << "volume(s) and"
+                 << unassignedSurfaces.size()
+                 << "surface(s) without a physical group get group or boundary condition 0";
+  }
   return true;
 }
 
+long GMSH4Parser::physicalTag(std::size_t dim, unsigned long entityTag) {
+  if (dim != 2 && dim != 3) {
+    return 0;
+  }
+  const auto& physicalIds = dim == 3 ? physicalVolumeIds : physicalSurfaceIds;
+  const auto it = physicalIds.find(entityTag);
+  if (it == physicalIds.end()) {
+    (dim == 3 ? unassignedVolumes : unassignedSurfaces).insert(entityTag);
+    return 0;
+  }
+  return it->second;
+}
+
 bool GMSH4Parser::parseEntities() {
   getNextToken();
   const std::size_t numPoints = expectNonNegativeInt();
@@ -280,7 +301,7 @@ bool GMSH4Parser::parseElements() {
 
   for (std::size_t blockIdx = 0; blockIdx < numBlocks; blockIdx++) {
     getNextToken();
-    [[maybe_unused]] const std::size_t dim = expectNonNegativeInt();
+    const std::size_t dim = expectNonNegativeInt();
     getNextToken();
     const std::size_t entityTag = expectNonNegativeInt();
     getNextToken();
@@ -292,6 +313,7 @@ bool GMSH4Parser::parseElements() {
     }
     getNextToken();
     const std::size_t numElementsInBlock = expectNonNegativeInt();
+    const long tag = numElementsInBlock > 0 ? physicalTag(dim, entityTag) : 0;
     for (std::size_t elementIdx = 0; elementIdx < numElementsInBlock; ++elementIdx) {
       getNextToken();
       [[maybe_unused]] const std::size_t id = expectNonNegativeInt();
@@ -299,8 +321,7 @@ bool GMSH4Parser::parseElements() {
         getNextToken();
         nodes[nodeIdx] = static_cast<long>(expectNodeIndex());
       }
-      std::size_t tag = (type == 2) ? physicalSurfaceIds[entityTag] : physicalVolumeIds[entityTag];
-      builder->addElement(type, tag, nodes.data(), NumNodes[type - 1]);
+      builder->addElement(static_cast<long>(type), tag, nodes.data(), NumNodes[type - 1]);
     }
   }
   getNextToken();
diff --git a/src/meshreader/GMSH4Parser.h b/src/meshreader/GMSH4Parser.h
index 2da26f2..97be825 100644
--- a/src/meshreader/GMSH4Parser.h
+++ b/src/meshreader/GMSH4Parser.h
@@ -6,6 +6,7 @@
 
 #include <cstdio>
 #include <map>
+#include <set>
 #include <string>
 #include <string_view>
 
@@ -22,6 +23,14 @@ class GMSH4Parser : public tndm::GMSHParser {
   private:
   std::map<unsigned long, long> physicalSurfaceIds;
   std::map<unsigned long, long> physicalVolumeIds;
+  // surface and volume entities with elements, but without a physical group
+  std::set<unsigned long> unassignedSurfaces;
+  std::set<unsigned long> unassignedVolumes;
+
+  /**
+   * The physical tag of the elements of an entity; 0 if the entity has no physical group.
+   */
+  long physicalTag(std::size_t dim, unsigned long entityTag);
 
   // the node tags form the contiguous range [firstNodeTag, firstNodeTag + numNodes)
   bool hasNodes = false;
diff --git a/src/pumgen.cpp b/src/pumgen.cpp
index 68ed458..c7651a4 100644
--- a/src/pumgen.cpp
+++ b/src/pumgen.cpp
@@ -455,8 +455,8 @@ int main(int argc, char* argv[]) {
   logInfo() << "Total vertex count:" << globalSize[1];
   logInfo() << "Vertex identification:" << meshInput->hasIdentify();
 
-  auto inspheres =
-      calculateInsphere(meshInput->connectivity(), meshInput->geometry(), MPI_COMM_WORLD);
+  auto inspheres = calculateInsphere(meshInput->connectivity(), meshInput->geometry(),
+                                     meshInput->cellSize(), MPI_COMM_WORLD);
   double min = inspheres.empty() ? std::numeric_limits<double>::infinity()
                                  : *std::min_element(inspheres.begin(), inspheres.end());
   MPI_Reduce((rank == 0 ? MPI_IN_PLACE : &min), &min, 1, MPI_DOUBLE, MPI_MIN, 0, MPI_COMM_WORLD);
diff --git a/src/third_party/GMSHLexer.cpp b/src/third_party/GMSHLexer.cpp
index 65cbef6..059407a 100644
--- a/src/third_party/GMSHLexer.cpp
+++ b/src/third_party/GMSHLexer.cpp
@@ -73,6 +73,9 @@ GMSHToken GMSHLexer::getToken() {
     case "EndPeriodic"_fnv1a:
       token = GMSHToken::end_periodic;
       break;
+    case "PartitionedEntities"_fnv1a:
+      token = GMSHToken::partitioned_entities;
+      break;
     default:
       break;
     }
diff --git a/src/third_party/GMSHLexer.h b/src/third_party/GMSHLexer.h
index 2b9eb67..740f907 100644
--- a/src/third_party/GMSHLexer.h
+++ b/src/third_party/GMSHLexer.h
@@ -25,6 +25,7 @@ enum class GMSHToken {
   end_elements,
   periodic,
   end_periodic,
+  partitioned_entities,
   unknown_section,
   unknown_token
 };
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index a436afb..26ab1de 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -12,11 +12,11 @@ set(PUMGEN_TEST_OUTPUT ${CMAKE_CURRENT_BINARY_DIR}/output)
 file(MAKE_DIRECTORY ${PUMGEN_TEST_OUTPUT})
 
 # pumgen_add_test(<name> RANKS <n> SOURCE <source> INPUT <fixture>
-#                 [REFERENCE <fixture> [TOLERANCE <tolerance>] [IDENTIFY]] [EXPECT_ERROR <regex>]
-#                 [ARGS <argument>...])
+#                 [REFERENCE <fixture> [TOLERANCE <tolerance>] [IDENTIFY]]
+#                 [EXPECT_OUTPUT <regex>] [EXPECT_ERROR <regex>] [ARGS <argument>...])
 function(pumgen_add_test name)
   cmake_parse_arguments(PARSE_ARGV 1 TEST "IDENTIFY"
-                        "RANKS;SOURCE;INPUT;REFERENCE;TOLERANCE;EXPECT_ERROR" "ARGS")
+                        "RANKS;SOURCE;INPUT;REFERENCE;TOLERANCE;EXPECT_OUTPUT;EXPECT_ERROR" "ARGS")
   set(output ${PUMGEN_TEST_OUTPUT}/${name}.puml.h5)
   set(command
       ${MPIEXEC_EXECUTABLE}
@@ -33,6 +33,9 @@ function(pumgen_add_test name)
   string(REPLACE ";" "|" command "${command}")
 
   set(script_args -DCOMMAND=${command} -DOUTPUT=${output})
+  if(DEFINED TEST_EXPECT_OUTPUT)
+    list(APPEND script_args "-DEXPECT_OUTPUT=${TEST_EXPECT_OUTPUT}")
+  endif()
   if(DEFINED TEST_EXPECT_ERROR)
     list(APPEND script_args "-DEXPECT_ERROR=${TEST_EXPECT_ERROR}")
   elseif(DEFINED TEST_REFERENCE AND H5DIFF_EXECUTABLE)
@@ -136,3 +139,19 @@ pumgen_add_test(msh2.tiny-duplicate RANKS 1 SOURCE msh2 INPUT tiny-duplicate-v22
                 EXPECT_ERROR "Duplicate node tag 2")
 pumgen_add_test(msh2.tiny-badnode RANKS 1 SOURCE msh2 INPUT tiny-badnode-v22.msh
                 EXPECT_ERROR "Unknown node tag")
+
+# higher-order meshes (with the inspheres of the linear mesh) and partitioned files
+foreach(ranks 1 2)
+  pumgen_add_test(msh4.coarse-o2.np${ranks} RANKS ${ranks} SOURCE msh4 INPUT coarse-o2-v41.msh
+                  REFERENCE coarse-o2.puml.h5 ARGS --order=2
+                  EXPECT_OUTPUT "Minimum insphere found: 0[.]03184[67]")
+endforeach()
+pumgen_add_test(msh2.coarse-o2.np2 RANKS 2 SOURCE msh2 INPUT coarse-o2-v22.msh
+                REFERENCE coarse-o2.puml.h5 ARGS --order=2
+                EXPECT_OUTPUT "Minimum insphere found: 0[.]03184[67]")
+pumgen_add_test(msh4.coarse.insphere RANKS 1 SOURCE msh4 INPUT coarse-v41.msh
+                EXPECT_OUTPUT "Minimum insphere found: 0[.]03184[67]")
+pumgen_add_test(msh4.coarse-partitioned RANKS 1 SOURCE msh4 INPUT coarse-partitioned-v41.msh
+                EXPECT_ERROR "Partitioned MSH files are not supported")
+pumgen_add_test(msh4.tiny-nophysical RANKS 1 SOURCE msh4 INPUT tiny-nophysical-v41.msh
+                EXPECT_OUTPUT "1 volume[(]s[)] and 0 surface[(]s[)] without a physical group")
diff --git a/tests/RunPumgenTest.cmake b/tests/RunPumgenTest.cmake
index 3c88ea2..df04c6a 100644
--- a/tests/RunPumgenTest.cmake
+++ b/tests/RunPumgenTest.cmake
@@ -12,6 +12,7 @@
 #   IDENTIFY      (optional) also compare the vertex identification of periodic meshes
 #   H5DIFF        h5diff executable, required together with REFERENCE
 #   EXPECT_ERROR  (optional) pumgen has to fail with a message matching this regular expression
+#   EXPECT_OUTPUT (optional) the output of a successful run has to match this regular expression
 
 string(REPLACE "|" ";" command "${COMMAND}")
 file(REMOVE "${OUTPUT}")
@@ -38,6 +39,10 @@ if(NOT result EQUAL 0)
   message(FATAL_ERROR "pumgen failed: ${result}")
 endif()
 
+if(DEFINED EXPECT_OUTPUT AND NOT log MATCHES "${EXPECT_OUTPUT}")
+  message(FATAL_ERROR "The output does not match \"${EXPECT_OUTPUT}\"")
+endif()
+
 if(DEFINED REFERENCE)
   set(failures "")
   set(datasets connect geometry group boundary)
diff --git a/tests/fixtures/generate.py b/tests/fixtures/generate.py
index f7340fa..7315829 100644
--- a/tests/fixtures/generate.py
+++ b/tests/fixtures/generate.py
@@ -256,6 +256,7 @@ def generate_periodic():
 def generate_tiny():
     variants = {
         "tiny-v41.msh": TINY_V41,
+        "tiny-nophysical-v41.msh": TINY_V41.replace("1 0 0 0 1 1 1 1 7 0", "1 0 0 0 1 1 1 0 0"),
         "tiny-v40.msh": TINY_V41.replace("4.1 0 8", "4 0 8"),
         "tiny-truncated-v41.msh": TINY_V41.split("$Elements")[0] + "$Elements\n1 1 1 1\n3 1 4 1\n1 1 2\n",
         "tiny-badnumber-v41.msh": TINY_V41.replace("1 0 0\n0 1 0", "1 abc 0\n0 1 0"),
diff --git a/tests/fixtures/tiny-nophysical-v41.msh b/tests/fixtures/tiny-nophysical-v41.msh
new file mode 100644
index 0000000..e7ffbbc
--- /dev/null
+++ b/tests/fixtures/tiny-nophysical-v41.msh
@@ -0,0 +1,24 @@
+$MeshFormat
+4.1 0 8
+$EndMeshFormat
+$Entities
+0 0 0 1
+1 0 0 0 1 1 1 0 0
+$EndEntities
+$Nodes
+1 4 1 4
+3 1 0 4
+1
+2
+3
+4
+0 0 0
+1 0 0
+0 1 0
+0 0 1
+$EndNodes
+$Elements
+1 1 1 1
+3 1 4 1
+1 1 2 3 4
+$EndElements

From 0e55cff56ffa5f8f9cbe1f3067a807d0ef205bdc Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 19:07:50 +0000
Subject: [PATCH 10/19] Replace the GMSH lexer by a buffered reader

The lexer read the file character by character through std::istream::get and
converted numbers with strtol/strtod; on a mesh with 3.6M cells (170 MB MSH
4.1, 196 MB MSH 2.2) parsing took 2.18 s and 2.82 s. The new MshInput reads
the file in 16 MiB blocks and parses the numbers in place with std::from_chars
(with a strtod fallback for standard libraries without floating-point
from_chars), which brings parsing down to 0.41 s and 0.54 s (5.3x); the
results are identical.

The parsers become part of src/meshreader and read the values they expect
instead of generic tokens. Unneeded sections are skipped as a whole. Errors
are still reported with line and column; binary MSH 2 files get a message of
their own. A new unit test parses the fixtures with a buffer of 256 bytes, so
that tokens and section markers straddle the buffer boundaries.

AI-generated. Model: Claude Opus 5.5
---
 CMakeLists.txt                                |   6 +-
 src/meshreader/GMSH2Parser.cpp                | 156 ++++++
 src/meshreader/GMSH2Parser.h                  |  39 ++
 src/meshreader/GMSH4Parser.cpp                | 443 +++++++-----------
 src/meshreader/GMSH4Parser.h                  |  77 ++-
 src/meshreader/GMSHBuilder.h                  |   4 +-
 .../GMSHMeshBuilder.h                         |  11 +-
 src/meshreader/GMSHParser.cpp                 |  87 ++++
 src/{third_party => meshreader}/GMSHParser.h  | 136 +++---
 src/meshreader/MshInput.cpp                   | 150 ++++++
 src/meshreader/MshInput.h                     | 177 +++++++
 src/pumgen.cpp                                |   4 +-
 src/third_party/GMSH2Parser.cpp               | 211 ---------
 src/third_party/GMSH2Parser.h                 |  63 ---
 src/third_party/GMSHLexer.cpp                 | 130 -----
 src/third_party/GMSHLexer.h                   |  66 ---
 src/third_party/GMSHParser.cpp                |  34 --
 src/third_party/Hash.h                        |  24 -
 src/third_party/README.md                     |   7 +-
 tests/CMakeLists.txt                          |  13 +
 tests/ReaderTest.cpp                          |  97 ++++
 21 files changed, 1000 insertions(+), 935 deletions(-)
 create mode 100644 src/meshreader/GMSH2Parser.cpp
 create mode 100644 src/meshreader/GMSH2Parser.h
 rename src/{third_party => meshreader}/GMSHMeshBuilder.h (73%)
 create mode 100644 src/meshreader/GMSHParser.cpp
 rename src/{third_party => meshreader}/GMSHParser.h (69%)
 create mode 100644 src/meshreader/MshInput.cpp
 create mode 100644 src/meshreader/MshInput.h
 delete mode 100644 src/third_party/GMSH2Parser.cpp
 delete mode 100644 src/third_party/GMSH2Parser.h
 delete mode 100644 src/third_party/GMSHLexer.cpp
 delete mode 100644 src/third_party/GMSHLexer.h
 delete mode 100644 src/third_party/GMSHParser.cpp
 delete mode 100644 src/third_party/Hash.h
 create mode 100644 tests/ReaderTest.cpp

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 0d40349..be1cf15 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -37,11 +37,11 @@ set(CMAKE_CXX_FLAGS_RELEASE "-O2")
 add_executable(pumgen
   ${CMAKE_CURRENT_SOURCE_DIR}/src/pumgen.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/GambitReader.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/GMSHParser.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/GMSH2Parser.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/GMSH4Parser.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/MshInput.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/input/ParallelVertexFilter.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/src/third_party/GMSHLexer.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/src/third_party/GMSHParser.cpp
-  ${CMAKE_CURRENT_SOURCE_DIR}/src/third_party/GMSH2Parser.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/helper/InsphereCalculator.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/helper/MPIConvenience.cpp
   )
diff --git a/src/meshreader/GMSH2Parser.cpp b/src/meshreader/GMSH2Parser.cpp
new file mode 100644
index 0000000..4365f3b
--- /dev/null
+++ b/src/meshreader/GMSH2Parser.cpp
@@ -0,0 +1,156 @@
+// SPDX-FileCopyrightText: 2022 SeisSol Group
+// SPDX-FileCopyrightText: 2020 Ludwig-Maximilians-Universität München
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#include "GMSH2Parser.h"
+
+#include <array>
+#include <cstdio>
+#include <string>
+#include <vector>
+
+namespace puml {
+
+void GMSH2Parser::parse_() {
+  const auto format = parseMeshFormatHeader();
+  if (format.version < 2.0 || format.version >= 3.0) {
+    char buf[128];
+    snprintf(buf, sizeof(buf), "Unsupported MSH version %.1lf", format.version);
+    failFile(buf);
+  }
+  if (format.fileType != 0) {
+    failFile("Binary MSH 2 files are not supported; write the mesh as ASCII (Mesh.Binary = 0)");
+  }
+  expectToken("$EndMeshFormat");
+
+  bool hasElements = false;
+  while (true) {
+    const auto section = nextSection();
+    if (section.empty()) {
+      break;
+    }
+    if (section == "$Nodes") {
+      parseNodes();
+    } else if (section == "$Elements") {
+      parseElements();
+      hasElements = true;
+    } else if (section == "$Periodic") {
+      parsePeriodic();
+    } else {
+      skipSection(section);
+    }
+  }
+
+  if (!hasNodes) {
+    failFile("Missing $Nodes section");
+  }
+  if (!hasElements) {
+    failFile("Missing $Elements section");
+  }
+}
+
+std::size_t GMSH2Parser::readNodeIndex() {
+  input->skipWhitespace();
+  const auto offset = input->offset();
+  const auto tag = input->readInteger<std::size_t>();
+  if (!tag || *tag < 1 || *tag > numNodes) {
+    failAt(offset, "Unknown node tag");
+  }
+  return *tag - 1;
+}
+
+void GMSH2Parser::parseNodes() {
+  const std::size_t numVertices = expectSize();
+  builder->setNumVertices(numVertices);
+  hasNodes = true;
+  numNodes = numVertices;
+
+  // with numVertices distinct tags in [1, numVertices], every node is defined exactly once
+  std::vector<bool> defined(numVertices, false);
+
+  for (std::size_t i = 0; i < numVertices; ++i) {
+    input->skipWhitespace();
+    const auto offset = input->offset();
+    const auto tag = input->readInteger<std::size_t>();
+    if (!tag || *tag < 1 || *tag > numVertices) {
+      failAt(offset, "Expected node-tag with 1 <= node-tag <= " + std::to_string(numVertices));
+    }
+    const std::size_t id = *tag - 1;
+    if (defined[id]) {
+      failAt(offset, "Duplicate node tag " + std::to_string(*tag));
+    }
+    defined[id] = true;
+
+    std::array<double, 3> x{};
+    for (auto& coordinate : x) {
+      coordinate = expectNumber();
+    }
+    builder->setVertex(static_cast<long>(id), x);
+  }
+  expectToken("$EndNodes");
+}
+
+void GMSH2Parser::parseElements() {
+  if (!hasNodes) {
+    fail("Expected $Nodes before $Elements");
+  }
+  const std::size_t numElements = expectSize();
+  builder->setNumElements(numElements);
+
+  std::array<long, MaxNodesPerElement> nodes{};
+
+  for (std::size_t elementIdx = 0; elementIdx < numElements; ++elementIdx) {
+    expectInteger(); // element tag
+    input->skipWhitespace();
+    const auto typeOffset = input->offset();
+    const long type = expectInteger();
+    if (type < 1 || type > static_cast<long>(NumTypes) || NumNodes[type - 1] == 0) {
+      failAt(typeOffset, "Unknown element type " + std::to_string(type));
+    }
+    const std::size_t numTags = expectSize();
+    // the physical tag; elements without tags get 0
+    long tag = 0;
+    for (std::size_t tagIdx = 0; tagIdx < numTags; ++tagIdx) {
+      const long value = expectInteger();
+      if (tagIdx == 0) {
+        tag = value;
+      }
+    }
+    const std::size_t numNodesPerElement = NumNodes[type - 1];
+    for (std::size_t nodeIdx = 0; nodeIdx < numNodesPerElement; ++nodeIdx) {
+      nodes[nodeIdx] = static_cast<long>(readNodeIndex());
+    }
+    builder->addElement(type, tag, nodes.data(), numNodesPerElement);
+  }
+  expectToken("$EndElements");
+}
+
+void GMSH2Parser::parsePeriodic() {
+  if (!hasNodes) {
+    fail("Expected $Nodes before $Periodic");
+  }
+  const std::size_t numPeriodic = expectSize();
+
+  // only the node identification is needed
+  for (std::size_t blockIdx = 0; blockIdx < numPeriodic; ++blockIdx) {
+    expectSize();    // entity dimension
+    expectInteger(); // entity tag
+    expectInteger(); // master entity tag
+    if (input->peek() == 'A') {
+      // "Affine" and 16 values
+      expectToken("Affine");
+      for (int i = 0; i < 16; ++i) {
+        expectNumber();
+      }
+    }
+    const std::size_t numIdentified = expectSize();
+    for (std::size_t i = 0; i < numIdentified; ++i) {
+      const std::size_t node = readNodeIndex();
+      const std::size_t master = readNodeIndex();
+      builder->addVertexLink(node, master);
+    }
+  }
+  expectToken("$EndPeriodic");
+}
+
+} // namespace puml
diff --git a/src/meshreader/GMSH2Parser.h b/src/meshreader/GMSH2Parser.h
new file mode 100644
index 0000000..9b561e6
--- /dev/null
+++ b/src/meshreader/GMSH2Parser.h
@@ -0,0 +1,39 @@
+// SPDX-FileCopyrightText: 2022 SeisSol Group
+// SPDX-FileCopyrightText: 2020 Ludwig-Maximilians-Universität München
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#ifndef PUMGEN_SRC_MESHREADER_GMSH2PARSER_H_
+#define PUMGEN_SRC_MESHREADER_GMSH2PARSER_H_
+
+#include <cstddef>
+
+#include "GMSHParser.h"
+
+namespace puml {
+
+/**
+ * Parser for MSH 2 files (ASCII).
+ */
+class GMSH2Parser : public GMSHParser {
+  public:
+  using GMSHParser::GMSHParser;
+
+  private:
+  void parse_() override;
+  void parseNodes();
+  void parseElements();
+  void parsePeriodic();
+
+  /**
+   * Reads a node tag and returns the index of the node.
+   */
+  std::size_t readNodeIndex();
+
+  // the node tags are 1, ..., numNodes
+  bool hasNodes = false;
+  std::size_t numNodes = 0;
+};
+
+} // namespace puml
+
+#endif // PUMGEN_SRC_MESHREADER_GMSH2PARSER_H_
diff --git a/src/meshreader/GMSH4Parser.cpp b/src/meshreader/GMSH4Parser.cpp
index e74a118..8264b7e 100644
--- a/src/meshreader/GMSH4Parser.cpp
+++ b/src/meshreader/GMSH4Parser.cpp
@@ -3,231 +3,139 @@
 // SPDX-License-Identifier: BSD-3-Clause
 #include "GMSH4Parser.h"
 
+#include <array>
 #include <cstdio>
+#include <string>
+#include <string_view>
+#include <vector>
 
 #include "utils/logger.h"
 
 namespace puml {
-bool GMSH4Parser::parse_() {
-  getNextToken();
 
-  const double version = parseMeshFormat();
-  if (version < 4.0 || version >= 5.0) {
+void GMSH4Parser::parse_() {
+  const auto format = parseMeshFormatHeader();
+  if (format.version < 4.0 || format.version >= 5.0) {
     char buf[128];
-    snprintf(buf, sizeof(buf), "Unsupported MSH version %.1lf", version);
-    return logError<bool>(buf);
+    snprintf(buf, sizeof(buf), "Unsupported MSH version %.1lf", format.version);
+    failFile(buf);
   }
-  if (version < 4.1) {
-    return logError<bool>(
-        "MSH 4.0 is not supported; write the mesh as MSH 4.1 (Mesh.MshFileVersion = 4.1)");
+  if (format.version < 4.1) {
+    failFile("MSH 4.0 is not supported; write the mesh as MSH 4.1 (Mesh.MshFileVersion = 4.1)");
   }
+  if (format.fileType == 1) {
+    failFile("Binary MSH files are not supported; write the mesh as ASCII (Mesh.Binary = 0)");
+  }
+  if (format.fileType != 0) {
+    failFile("Expected file type 0 (ASCII)");
+  }
+  expectToken("$EndMeshFormat");
 
   bool hasEntities = false;
   bool hasElements = false;
-  bool hasPeriodic = false;
-
-  while (curTok != tndm::GMSHToken::eof) {
-    switch (curTok) {
-    case tndm::GMSHToken::entities:
-      hasEntities = parseEntities();
+  while (true) {
+    const auto section = nextSection();
+    if (section.empty()) {
       break;
-    case tndm::GMSHToken::nodes:
+    }
+    if (section == "$Entities") {
+      parseEntities();
+      hasEntities = true;
+    } else if (section == "$Nodes") {
       parseNodes();
-      break;
-    case tndm::GMSHToken::elements:
-      hasElements = parseElements();
-      break;
-    case tndm::GMSHToken::periodic:
-      hasPeriodic = parsePeriodic();
-      break;
-    case tndm::GMSHToken::partitioned_entities:
-      return logErrorAnnotated<bool>(
-          "Partitioned MSH files are not supported; save the mesh without partitions");
-    default:
-      getNextToken();
-      break;
+    } else if (section == "$Elements") {
+      parseElements();
+      hasElements = true;
+    } else if (section == "$Periodic") {
+      parsePeriodic();
+    } else if (section == "$PartitionedEntities") {
+      failFile("Partitioned MSH files are not supported; save the mesh without partitions");
+    } else {
+      skipSection(section);
     }
   }
 
   if (!hasEntities) {
-    return logError<bool>("Missing $Entities section");
+    failFile("Missing $Entities section");
   }
   if (!hasNodes) {
-    return logError<bool>("Missing $Nodes section");
+    failFile("Missing $Nodes section");
   }
   if (!hasElements) {
-    return logError<bool>("Missing $Elements section");
+    failFile("Missing $Elements section");
   }
   if (!unassignedVolumes.empty() || !unassignedSurfaces.empty()) {
     logWarning() << "The elements of" << unassignedVolumes.size() << "volume(s) and"
                  << unassignedSurfaces.size()
                  << "surface(s) without a physical group get group or boundary condition 0";
   }
-  return true;
-}
-
-long GMSH4Parser::physicalTag(std::size_t dim, unsigned long entityTag) {
-  if (dim != 2 && dim != 3) {
-    return 0;
-  }
-  const auto& physicalIds = dim == 3 ? physicalVolumeIds : physicalSurfaceIds;
-  const auto it = physicalIds.find(entityTag);
-  if (it == physicalIds.end()) {
-    (dim == 3 ? unassignedVolumes : unassignedSurfaces).insert(entityTag);
-    return 0;
-  }
-  return it->second;
 }
 
-bool GMSH4Parser::parseEntities() {
-  getNextToken();
-  const std::size_t numPoints = expectNonNegativeInt();
-  getNextToken();
-  const std::size_t numCurves = expectNonNegativeInt();
-  getNextToken();
-  const std::size_t numSurfaces = expectNonNegativeInt();
-  getNextToken();
-  const std::size_t numVolumes = expectNonNegativeInt();
+void GMSH4Parser::parseEntities() {
+  const std::size_t numPoints = readSize();
+  const std::size_t numCurves = readSize();
+  const std::size_t numSurfaces = readSize();
+  const std::size_t numVolumes = readSize();
 
-  // ignore points
   for (std::size_t i = 0; i < numPoints; ++i) {
-    getNextToken();
-    [[maybe_unused]] const std::size_t id = expectNonNegativeInt();
-    getNextToken();
-    [[maybe_unused]] const double x_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double y_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double z_1 = expectNumber();
-    getNextToken();
-    const std::size_t numTags = expectNonNegativeInt();
-    // ignore tags
-    for (std::size_t tagIdx = 0; tagIdx < numTags; tagIdx++) {
-      getNextToken();
-    }
-  }
-
-  //  ignore curves
-  for (std::size_t i = 0; i < numCurves; ++i) {
-    getNextToken();
-    [[maybe_unused]] const std::size_t id = expectNonNegativeInt();
-    getNextToken();
-    [[maybe_unused]] const double x_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double y_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double z_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double x_2 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double y_2 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double z_2 = expectNumber();
-    getNextToken();
-    const std::size_t numPhysicalTags = expectNonNegativeInt();
-    getNextToken();
-    // ignore tags
-    for (std::size_t tagIdx = 0; tagIdx < numPhysicalTags; tagIdx++) {
-      getNextToken();
+    readInt();
+    for (int k = 0; k < 3; ++k) {
+      readDouble();
     }
-    std::size_t numBoundaryTags = expectNonNegativeInt();
-    // ignore boundary
-    for (std::size_t tagIdx = 0; tagIdx < numBoundaryTags; tagIdx++) {
-      getNextToken();
+    const std::size_t numPhysicalTags = readSize();
+    for (std::size_t j = 0; j < numPhysicalTags; ++j) {
+      readInt();
     }
   }
 
-  //  read surfaces
-  for (std::size_t i = 0; i < numSurfaces; ++i) {
-    getNextToken();
-    const std::size_t id = expectNonNegativeInt();
-    getNextToken();
-    [[maybe_unused]] const double x_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double y_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double z_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double x_2 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double y_2 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double z_2 = expectNumber();
-    getNextToken();
-    const std::size_t numPhysicalTags = expectNonNegativeInt();
-    std::vector<std::size_t> tags;
-    for (std::size_t tagIdx = 0; tagIdx < numPhysicalTags; ++tagIdx) {
-      getNextToken();
-      tags.push_back(expectNonNegativeInt());
-    }
-    if (!tags.empty()) {
-      physicalSurfaceIds.insert_or_assign(id, tags.at(0));
-    }
-    getNextToken();
-    std::size_t numBoundaryTags = expectNonNegativeInt();
-    // ignore boundary
-    for (std::size_t curveIdx = 0; curveIdx < numBoundaryTags; ++curveIdx) {
-      getNextToken();
+  const auto readEntities = [&](std::size_t count, std::map<long, long>* physicalIds) {
+    for (std::size_t i = 0; i < count; ++i) {
+      const long tag = readInt();
+      for (int k = 0; k < 6; ++k) {
+        readDouble();
+      }
+      const std::size_t numPhysicalTags = readSize();
+      for (std::size_t j = 0; j < numPhysicalTags; ++j) {
+        const long physical = readInt();
+        if (j == 0 && physicalIds != nullptr) {
+          physicalIds->insert_or_assign(tag, physical);
+        }
+      }
+      const std::size_t numBoundingEntities = readSize();
+      for (std::size_t j = 0; j < numBoundingEntities; ++j) {
+        readInt();
+      }
     }
-  }
+  };
+  readEntities(numCurves, nullptr);
+  readEntities(numSurfaces, &physicalSurfaceIds);
+  readEntities(numVolumes, &physicalVolumeIds);
 
-  //  read volumes
-  for (std::size_t i = 0; i < numVolumes; ++i) {
-    getNextToken();
-    const std::size_t id = expectNonNegativeInt();
-    getNextToken();
-    [[maybe_unused]] const double x_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double y_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double z_1 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double x_2 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double y_2 = expectNumber();
-    getNextToken();
-    [[maybe_unused]] const double z_2 = expectNumber();
-    getNextToken();
-    const std::size_t numPhysicalTags = expectNonNegativeInt();
-    std::vector<std::size_t> tags;
-    for (std::size_t tagIdx = 0; tagIdx < numPhysicalTags; ++tagIdx) {
-      getNextToken();
-      tags.push_back(expectNonNegativeInt());
-    }
-    if (!tags.empty()) {
-      physicalVolumeIds.insert_or_assign(id, tags.at(0));
-    }
-    getNextToken();
-    const std::size_t numBoundaryTags = expectNonNegativeInt();
-    // ignore boundary
-    for (std::size_t curveIdx = 0; curveIdx < numBoundaryTags; ++curveIdx) {
-      getNextToken();
-    }
-  }
-  getNextToken();
-  if (curTok != tndm::GMSHToken::end_entities) {
-    return logErrorAnnotated<bool>("Expected $EndEntities");
+  expectToken("$EndEntities");
+}
+
+std::size_t GMSH4Parser::readNodeIndex() {
+  input->skipWhitespace();
+  const auto offset = input->offset();
+  const std::size_t tag = readSize();
+  if (tag < firstNodeTag || tag - firstNodeTag >= numNodes) {
+    failAt(offset, "Unknown node tag " + std::to_string(tag));
   }
-  getNextToken();
-  return true;
+  return tag - firstNodeTag;
 }
 
-bool GMSH4Parser::parseNodes() {
-  getNextToken();
-  const std::size_t numBlocks = expectNonNegativeInt();
-  getNextToken();
-  const std::size_t numVertices = expectNonNegativeInt();
-  getNextToken();
-  const std::size_t minNodeTag = expectNonNegativeInt();
-  getNextToken();
-  const std::size_t maxNodeTag = expectNonNegativeInt();
+void GMSH4Parser::parseNodes() {
+  const std::size_t numBlocks = readSize();
+  const std::size_t numVertices = readSize();
+  const std::size_t minNodeTag = readSize();
+  const std::size_t maxNodeTag = readSize();
   if (numVertices > 0 &&
       (minNodeTag == 0 || maxNodeTag < minNodeTag || maxNodeTag - minNodeTag + 1 != numVertices)) {
     char buf[192];
     snprintf(buf, sizeof(buf),
              "Non-contiguous node tags are not supported (%zu nodes with tags from %zu to %zu)",
              numVertices, minNodeTag, maxNodeTag);
-    return logErrorAnnotated<bool>(buf);
+    fail(buf);
   }
   hasNodes = true;
   firstNodeTag = minNodeTag;
@@ -236,146 +144,113 @@ bool GMSH4Parser::parseNodes() {
 
   // with as many distinct tags as the tag range is long, every node is defined exactly once
   std::vector<bool> defined(numVertices, false);
+  std::vector<std::size_t> indices;
 
-  for (std::size_t blockIdx = 0; blockIdx < numBlocks; blockIdx++) {
-    getNextToken();
-    const std::size_t dim = expectNonNegativeInt();
-    getNextToken();
-    [[maybe_unused]] const std::size_t entityTag = expectNonNegativeInt();
-    getNextToken();
-    const std::size_t parametric = expectNonNegativeInt();
-    getNextToken();
-    const std::size_t numVerticesInBlock = expectNonNegativeInt();
-    std::vector<std::size_t> vertexIds;
-    vertexIds.reserve(numVerticesInBlock);
-    // first read vertex ids
-    for (std::size_t vertexIdx = 0; vertexIdx < numVerticesInBlock; ++vertexIdx) {
-      getNextToken();
-      const std::size_t index = expectNodeIndex();
+  for (std::size_t blockIdx = 0; blockIdx < numBlocks; ++blockIdx) {
+    const long dim = readInt();
+    readInt(); // entity tag
+    const long parametric = readInt();
+    const std::size_t numVerticesInBlock = readSize();
+
+    indices.resize(numVerticesInBlock);
+    for (auto& index : indices) {
+      input->skipWhitespace();
+      const auto offset = input->offset();
+      index = readNodeIndex();
       if (defined[index]) {
-        char buf[128];
-        snprintf(buf, sizeof(buf), "Duplicate node tag %zu", firstNodeTag + index);
-        return logErrorAnnotated<bool>(buf);
+        failAt(offset, "Duplicate node tag " + std::to_string(firstNodeTag + index));
       }
       defined[index] = true;
-      vertexIds.push_back(index);
     }
-    // then read vertex data; parametric nodes carry dim additional parametric coordinates
-    const std::size_t numParametric = parametric != 0 ? dim : 0;
-    for (std::size_t vertexIdx = 0; vertexIdx < numVerticesInBlock; ++vertexIdx) {
+
+    // parametric nodes carry dim additional parametric coordinates
+    const long numParametric = parametric != 0 ? dim : 0;
+    for (const auto index : indices) {
       std::array<double, 3> x{};
-      for (std::size_t i = 0; i < 3; i++) {
-        getNextToken();
-        x[i] = expectNumber();
+      for (auto& coordinate : x) {
+        coordinate = readDouble();
       }
-      for (std::size_t i = 0; i < numParametric; ++i) {
-        getNextToken();
-        expectNumber();
+      for (long i = 0; i < numParametric; ++i) {
+        readDouble();
       }
-      builder->setVertex(vertexIds[vertexIdx], x);
+      builder->setVertex(static_cast<long>(index), x);
     }
   }
-  getNextToken();
-  if (curTok != tndm::GMSHToken::end_nodes) {
-    return logErrorAnnotated<bool>("Expected $EndNodes");
-  }
-  getNextToken();
-  return true;
+  expectToken("$EndNodes");
 }
 
-bool GMSH4Parser::parseElements() {
+void GMSH4Parser::parseElements() {
   if (!hasNodes) {
-    return logErrorAnnotated<bool>("Expected $Nodes before $Elements");
+    fail("Expected $Nodes before $Elements");
   }
-  getNextToken();
-  const std::size_t numBlocks = expectNonNegativeInt();
-  getNextToken();
-  const std::size_t numElements = expectNonNegativeInt();
-  getNextToken();
-  [[maybe_unused]] const std::size_t minElementTag = expectNonNegativeInt();
-  getNextToken();
-  [[maybe_unused]] const std::size_t maxElementTag = expectNonNegativeInt();
+  const std::size_t numBlocks = readSize();
+  const std::size_t numElements = readSize();
+  readSize(); // minimal element tag
+  readSize(); // maximal element tag
   builder->setNumElements(numElements);
 
   std::array<long, MaxNodesPerElement> nodes{};
 
-  for (std::size_t blockIdx = 0; blockIdx < numBlocks; blockIdx++) {
-    getNextToken();
-    const std::size_t dim = expectNonNegativeInt();
-    getNextToken();
-    const std::size_t entityTag = expectNonNegativeInt();
-    getNextToken();
-    const std::size_t type = expectNonNegativeInt();
-    if (type < 1 || type > NumTypes || NumNodes[type - 1] == 0) {
-      char buf[128];
-      snprintf(buf, sizeof(buf), "Unknown element type %zu", type);
-      return logErrorAnnotated<bool>(buf);
+  for (std::size_t blockIdx = 0; blockIdx < numBlocks; ++blockIdx) {
+    const long dim = readInt();
+    const long entityTag = readInt();
+    input->skipWhitespace();
+    const auto typeOffset = input->offset();
+    const long type = readInt();
+    if (type < 1 || type > static_cast<long>(NumTypes) || NumNodes[type - 1] == 0) {
+      failAt(typeOffset, "Unknown element type " + std::to_string(type));
     }
-    getNextToken();
-    const std::size_t numElementsInBlock = expectNonNegativeInt();
+    const std::size_t numNodesPerElement = NumNodes[type - 1];
+    const std::size_t numElementsInBlock = readSize();
     const long tag = numElementsInBlock > 0 ? physicalTag(dim, entityTag) : 0;
+
     for (std::size_t elementIdx = 0; elementIdx < numElementsInBlock; ++elementIdx) {
-      getNextToken();
-      [[maybe_unused]] const std::size_t id = expectNonNegativeInt();
-      for (std::size_t nodeIdx = 0; nodeIdx < NumNodes[type - 1]; nodeIdx++) {
-        getNextToken();
-        nodes[nodeIdx] = static_cast<long>(expectNodeIndex());
+      readSize(); // element tag
+      for (std::size_t nodeIdx = 0; nodeIdx < numNodesPerElement; ++nodeIdx) {
+        nodes[nodeIdx] = static_cast<long>(readNodeIndex());
       }
-      builder->addElement(static_cast<long>(type), tag, nodes.data(), NumNodes[type - 1]);
+      builder->addElement(type, tag, nodes.data(), numNodesPerElement);
     }
   }
-  getNextToken();
-  if (curTok != tndm::GMSHToken::end_elements) {
-    return logErrorAnnotated<bool>("Expected $EndElements");
-  }
-  getNextToken();
-
-  return true;
+  expectToken("$EndElements");
 }
 
-bool GMSH4Parser::parsePeriodic() {
+void GMSH4Parser::parsePeriodic() {
   if (!hasNodes) {
-    return logErrorAnnotated<bool>("Expected $Nodes before $Periodic");
+    fail("Expected $Nodes before $Periodic");
   }
-  getNextToken();
-  const auto numPeriodic = expectNonNegativeInt();
-
-  // ignore everything but the node identification
+  const std::size_t numPeriodic = readSize();
 
-  for (std::size_t blockIdx = 0; blockIdx < numPeriodic; blockIdx++) {
-    getNextToken();
-    [[maybe_unused]] const std::size_t entityDim = expectNonNegativeInt();
-    getNextToken();
-    [[maybe_unused]] const std::size_t entityId = expectNonNegativeInt();
-    getNextToken();
-    [[maybe_unused]] const std::size_t entityIdentifyId = expectNonNegativeInt();
-
-    getNextToken();
-    const std::size_t affineSize = expectNonNegativeInt();
-    for (std::size_t i = 0; i < affineSize; ++i) {
-      getNextToken();
-      [[maybe_unused]] const double affineValue = expectNumber();
+  // only the node identification is needed
+  for (std::size_t blockIdx = 0; blockIdx < numPeriodic; ++blockIdx) {
+    readInt(); // entity dimension
+    readInt(); // entity tag
+    readInt(); // master entity tag
+    const std::size_t numAffine = readSize();
+    for (std::size_t i = 0; i < numAffine; ++i) {
+      readDouble();
     }
-
-    getNextToken();
-    const std::size_t identifySize = expectNonNegativeInt();
-
-    for (std::size_t i = 0; i < identifySize; ++i) {
-      getNextToken();
-      const std::size_t nodeId = expectNodeIndex();
-      getNextToken();
-      const std::size_t nodeIdentifyId = expectNodeIndex();
-      builder->addVertexLink(nodeId, nodeIdentifyId);
+    const std::size_t numIdentified = readSize();
+    for (std::size_t i = 0; i < numIdentified; ++i) {
+      const std::size_t node = readNodeIndex();
+      const std::size_t master = readNodeIndex();
+      builder->addVertexLink(node, master);
     }
   }
+  expectToken("$EndPeriodic");
+}
 
-  getNextToken();
-  if (curTok != tndm::GMSHToken::end_periodic) {
-    return logErrorAnnotated<bool>("Expected $EndPeriodic");
+long GMSH4Parser::physicalTag(std::size_t dim, long entityTag) {
+  if (dim != 2 && dim != 3) {
+    return 0;
   }
-  getNextToken();
-
-  return true;
+  const auto& physicalIds = dim == 3 ? physicalVolumeIds : physicalSurfaceIds;
+  const auto it = physicalIds.find(entityTag);
+  if (it == physicalIds.end()) {
+    (dim == 3 ? unassignedVolumes : unassignedSurfaces).insert(entityTag);
+    return 0;
+  }
+  return it->second;
 }
 
 } // namespace puml
diff --git a/src/meshreader/GMSH4Parser.h b/src/meshreader/GMSH4Parser.h
index 97be825..7ca1ef7 100644
--- a/src/meshreader/GMSH4Parser.h
+++ b/src/meshreader/GMSH4Parser.h
@@ -4,72 +4,53 @@
 #ifndef PUMGEN_SRC_MESHREADER_GMSH4PARSER_H_
 #define PUMGEN_SRC_MESHREADER_GMSH4PARSER_H_
 
-#include <cstdio>
+#include <cstddef>
 #include <map>
 #include <set>
-#include <string>
-#include <string_view>
 
-#include "meshreader/GMSHBuilder.h"
-#include "third_party/GMSHLexer.h"
-#include "third_party/GMSHParser.h"
+#include "GMSHParser.h"
 
 namespace puml {
 
-class GMSH4Parser : public tndm::GMSHParser {
+/**
+ * Parser for MSH 4.1 files.
+ */
+class GMSH4Parser : public GMSHParser {
   public:
-  using tndm::GMSHParser::GMSHParser;
+  using GMSHParser::GMSHParser;
 
   private:
-  std::map<unsigned long, long> physicalSurfaceIds;
-  std::map<unsigned long, long> physicalVolumeIds;
-  // surface and volume entities with elements, but without a physical group
-  std::set<unsigned long> unassignedSurfaces;
-  std::set<unsigned long> unassignedVolumes;
+  void parse_() override;
+  void parseEntities();
+  void parseNodes();
+  void parseElements();
+  void parsePeriodic();
+
+  // the values of the sections
+  std::size_t readSize() { return expectSize(); }
+  long readInt() { return expectInteger(); }
+  double readDouble() { return expectNumber(); }
+
+  /**
+   * Reads a node tag and returns the index of the node.
+   */
+  std::size_t readNodeIndex();
 
   /**
    * The physical tag of the elements of an entity; 0 if the entity has no physical group.
    */
-  long physicalTag(std::size_t dim, unsigned long entityTag);
+  long physicalTag(std::size_t dim, long entityTag);
+
+  std::map<long, long> physicalSurfaceIds;
+  std::map<long, long> physicalVolumeIds;
+  // surface and volume entities with elements, but without a physical group
+  std::set<long> unassignedSurfaces;
+  std::set<long> unassignedVolumes;
 
   // the node tags form the contiguous range [firstNodeTag, firstNodeTag + numNodes)
   bool hasNodes = false;
   std::size_t firstNodeTag = 0;
   std::size_t numNodes = 0;
-
-  /**
-   * Reads a node tag and returns the index of the node.
-   */
-  std::size_t expectNodeIndex() {
-    const std::size_t tag = expectNonNegativeInt();
-    if (tag < firstNodeTag || tag - firstNodeTag >= numNodes) {
-      char buf[128];
-      snprintf(buf, sizeof(buf), "Unknown node tag %zu", tag);
-      return logErrorAnnotated<std::size_t>(buf);
-    }
-    return tag - firstNodeTag;
-  }
-
-  unsigned long expectNonNegativeInt() {
-    if (curTok != tndm::GMSHToken::integer || lexer.getInteger() < 0) {
-      return logErrorAnnotated<bool>("Expected non-negative integer");
-    }
-    return static_cast<unsigned long>(lexer.getInteger());
-  }
-
-  double expectNumber() {
-    auto num = getNumber();
-    if (!num) {
-      return logErrorAnnotated<bool>("Expected number");
-    }
-    return num.value();
-  }
-
-  bool parseEntities();
-  bool parseNodes();
-  bool parseElements();
-  bool parsePeriodic();
-  virtual bool parse_() override;
 };
 
 } // namespace puml
diff --git a/src/meshreader/GMSHBuilder.h b/src/meshreader/GMSHBuilder.h
index d5935a2..287eda1 100644
--- a/src/meshreader/GMSHBuilder.h
+++ b/src/meshreader/GMSHBuilder.h
@@ -14,7 +14,7 @@
 
 #include "utils/logger.h"
 
-#include "third_party/GMSHMeshBuilder.h"
+#include "GMSHMeshBuilder.h"
 
 namespace puml {
 
@@ -143,7 +143,7 @@ template <> struct GMSHSimplexType<3U, 10U> {
   static constexpr long type = 75;
 };
 
-template <std::size_t D, std::size_t Order> class GMSHBuilder : public tndm::GMSHMeshBuilder {
+template <std::size_t D, std::size_t Order> class GMSHBuilder : public GMSHMeshBuilder {
   public:
   using vertex_t = std::array<double, D>;
   using element_t = std::array<std::size_t, nodeCount(D, Order)>;
diff --git a/src/third_party/GMSHMeshBuilder.h b/src/meshreader/GMSHMeshBuilder.h
similarity index 73%
rename from src/third_party/GMSHMeshBuilder.h
rename to src/meshreader/GMSHMeshBuilder.h
index a66ac2a..d72d1d8 100644
--- a/src/third_party/GMSHMeshBuilder.h
+++ b/src/meshreader/GMSHMeshBuilder.h
@@ -1,12 +1,13 @@
 // SPDX-FileCopyrightText: 2022 SeisSol Group
 //
 // SPDX-License-Identifier: BSD-3-Clause
-#ifndef PUMGEN_SRC_THIRD_PARTY_GMSHMESHBUILDER_H_
-#define PUMGEN_SRC_THIRD_PARTY_GMSHMESHBUILDER_H_
+#ifndef PUMGEN_SRC_MESHREADER_GMSHMESHBUILDER_H_
+#define PUMGEN_SRC_MESHREADER_GMSHMESHBUILDER_H_
 
 #include <array>
+#include <cstddef>
 
-namespace tndm {
+namespace puml {
 
 class GMSHMeshBuilder {
   public:
@@ -19,6 +20,6 @@ class GMSHMeshBuilder {
   virtual void postprocess() = 0;
 };
 
-} // namespace tndm
+} // namespace puml
 
-#endif // PUMGEN_SRC_THIRD_PARTY_GMSHMESHBUILDER_H_
+#endif // PUMGEN_SRC_MESHREADER_GMSHMESHBUILDER_H_
diff --git a/src/meshreader/GMSHParser.cpp b/src/meshreader/GMSHParser.cpp
new file mode 100644
index 0000000..a44488d
--- /dev/null
+++ b/src/meshreader/GMSHParser.cpp
@@ -0,0 +1,87 @@
+// SPDX-FileCopyrightText: 2022 SeisSol Group
+// SPDX-FileCopyrightText: 2020 Ludwig-Maximilians-Universität München
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#include "GMSHParser.h"
+
+#include <exception>
+#include <sstream>
+#include <string>
+
+namespace puml {
+
+bool GMSHParser::parseFile(const std::string& fileName) {
+  errorMsg.clear();
+  try {
+    input = std::make_unique<MshInput>(fileName, bufferSize);
+    parse_();
+    input.reset();
+    return true;
+  } catch (const ParseError&) {
+  } catch (const std::exception& error) {
+    errorMsg += "GMSH parser error:\n\t";
+    errorMsg += error.what();
+    errorMsg += '\n';
+  }
+  input.reset();
+  return false;
+}
+
+void GMSHParser::failAt(std::size_t offset, std::string_view message) {
+  const auto [line, column] = input->location(offset);
+  std::stringstream stream;
+  stream << "GMSH parser error in line " << line << " in column " << column << ":\n";
+  stream << '\t' << message << '\n';
+  errorMsg += stream.str();
+  throw ParseError{};
+}
+
+void GMSHParser::fail(std::string_view message) {
+  input->skipWhitespace();
+  failAt(input->offset(), message);
+}
+
+void GMSHParser::failFile(std::string_view message) {
+  errorMsg += "GMSH parser error:\n\t";
+  errorMsg += message;
+  errorMsg += '\n';
+  throw ParseError{};
+}
+
+void GMSHParser::expectToken(std::string_view token) {
+  input->skipWhitespace();
+  const auto offset = input->offset();
+  if (input->readToken() != token) {
+    failAt(offset, "Expected " + std::string(token));
+  }
+}
+
+GMSHParser::MeshFormat GMSHParser::parseMeshFormatHeader() {
+  expectToken("$MeshFormat");
+  MeshFormat format{};
+  format.version = expectNumber();
+  format.fileType = expectInteger();
+  format.dataSize = expectSize();
+  return format;
+}
+
+std::string_view GMSHParser::nextSection() {
+  if (!input->skipWhitespace()) {
+    return {};
+  }
+  const auto offset = input->offset();
+  const auto section = input->readToken();
+  if (section.empty() || section.front() != '$') {
+    failAt(offset, "Expected a section");
+  }
+  return section;
+}
+
+void GMSHParser::skipSection(std::string_view section) {
+  const std::string endMarker = "$End" + std::string(section.substr(1));
+  if (!input->skipTo(endMarker)) {
+    failFile("Missing " + endMarker);
+  }
+}
+
+} // namespace puml
diff --git a/src/third_party/GMSHParser.h b/src/meshreader/GMSHParser.h
similarity index 69%
rename from src/third_party/GMSHParser.h
rename to src/meshreader/GMSHParser.h
index cbef6b6..9462d06 100644
--- a/src/third_party/GMSHParser.h
+++ b/src/meshreader/GMSHParser.h
@@ -2,20 +2,18 @@
 // SPDX-FileCopyrightText: 2020 Ludwig-Maximilians-Universität München
 //
 // SPDX-License-Identifier: BSD-3-Clause
-#ifndef PUMGEN_SRC_THIRD_PARTY_GMSHPARSER_H_
-#define PUMGEN_SRC_THIRD_PARTY_GMSHPARSER_H_
+#ifndef PUMGEN_SRC_MESHREADER_GMSHPARSER_H_
+#define PUMGEN_SRC_MESHREADER_GMSHPARSER_H_
 
-#include <fstream>
-#include <optional>
-#include <sstream>
-#include <stdexcept>
+#include <cstddef>
+#include <memory>
 #include <string>
 #include <string_view>
 
-#include "GMSHLexer.h"
 #include "GMSHMeshBuilder.h"
+#include "MshInput.h"
 
-namespace tndm {
+namespace puml {
 
 namespace detail {
 template <std::size_t N> constexpr std::size_t maxEntry(const std::size_t (&values)[N]) {
@@ -27,6 +25,9 @@ template <std::size_t N> constexpr std::size_t maxEntry(const std::size_t (&valu
 }
 } // namespace detail
 
+/**
+ * Common parts of the MSH parsers: element types, error handling and reading of text values.
+ */
 class GMSHParser {
   public:
   // Look-up table from gmsh type to number of nodes
@@ -163,80 +164,93 @@ class GMSHParser {
   static constexpr std::size_t NumTypes = sizeof(NumNodes) / sizeof(NumNodes[0]);
   static constexpr std::size_t MaxNodesPerElement = detail::maxEntry(NumNodes);
 
-  explicit GMSHParser(GMSHMeshBuilder* builder) : builder(builder) {};
-  [[nodiscard]] std::string_view getErrorMessage() const { return errorMsg; }
+  explicit GMSHParser(GMSHMeshBuilder* builder,
+                      std::size_t bufferSize = MshInput::DefaultBufferSize)
+      : builder(builder), bufferSize(bufferSize) {}
+  virtual ~GMSHParser() = default;
 
   /**
    * Parses the file; stops at the first error, whose description getErrorMessage() returns.
    */
-  bool parseFile(std::string const& fileName) {
-    errorMsg.clear();
-    std::ifstream in(fileName);
-    if (!in.is_open()) {
-      errorMsg = "GMSH parser error:\n\tUnable to open MSH file\n";
-      return false;
-    }
-    lexer.setIStream(&in);
-    try {
-      return parse_();
-    } catch (const ParseError&) {
-      return false;
-    } catch (const std::runtime_error& error) {
-      appendAnnotated(error.what());
-      return false;
-    }
-  }
+  bool parseFile(const std::string& fileName);
+
+  [[nodiscard]] std::string_view getErrorMessage() const { return errorMsg; }
 
   protected:
+  struct MeshFormat {
+    double version;
+    long fileType;
+    std::size_t dataSize;
+  };
+
   /**
    * Thrown after an error has been recorded in errorMsg.
    */
   struct ParseError {};
 
-  template <typename T> T logErrorAnnotated(std::string_view msg) {
-    appendAnnotated(msg);
-    throw ParseError{};
-  }
+  /**
+   * Records an error at the given file offset and aborts parsing.
+   */
+  [[noreturn]] void failAt(std::size_t offset, std::string_view message);
 
-  template <typename T> T logError(std::string_view msg) {
-    errorMsg += "GMSH parser error:\n\t";
-    errorMsg += msg;
-    errorMsg += '\n';
-    throw ParseError{};
-  }
+  /**
+   * Records an error at the next token and aborts parsing.
+   */
+  [[noreturn]] void fail(std::string_view message);
 
-  GMSHMeshBuilder* builder;
-  GMSHSourceLocation curLoc = {0, 0};
-  GMSHToken curTok;
-  GMSHLexer lexer;
-  std::string errorMsg;
+  /**
+   * Records an error concerning the whole file and aborts parsing.
+   */
+  [[noreturn]] void failFile(std::string_view message);
 
-  GMSHToken getNextToken() {
-    curLoc = lexer.getSourceLoc();
-    return curTok = lexer.getToken();
+  std::size_t expectSize() {
+    if (const auto value = input->readInteger<std::size_t>()) {
+      return *value;
+    }
+    fail("Expected non-negative integer");
   }
 
-  std::optional<double> getNumber() {
-    if (curTok == GMSHToken::integer) {
-      return {lexer.getInteger()};
-    } else if (curTok == GMSHToken::real) {
-      return {lexer.getReal()};
+  long expectInteger() {
+    if (const auto value = input->readInteger<long>()) {
+      return *value;
     }
-    return std::nullopt;
+    fail("Expected integer");
   }
 
-  virtual bool parse_() = 0;
+  double expectNumber() {
+    if (const auto value = input->readReal()) {
+      return *value;
+    }
+    fail("Expected number");
+  }
+
+  void expectToken(std::string_view token);
+
+  /**
+   * Reads the $MeshFormat section up to (and including) the data size.
+   */
+  MeshFormat parseMeshFormatHeader();
+
+  /**
+   * Returns the name of the next section (e.g. "$Nodes"), or an empty view at the end of the file.
+   */
+  std::string_view nextSection();
+
+  /**
+   * Skips the rest of a section which is not needed.
+   */
+  void skipSection(std::string_view section);
 
-  double parseMeshFormat();
+  virtual void parse_() = 0;
+
+  GMSHMeshBuilder* builder;
+  std::unique_ptr<MshInput> input;
 
   private:
-  void appendAnnotated(std::string_view msg) {
-    std::stringstream ss;
-    ss << "GMSH parser error in line " << curLoc.line << " in column " << curLoc.col << ":\n";
-    ss << '\t' << msg << '\n';
-    errorMsg += ss.str();
-  }
+  std::size_t bufferSize;
+  std::string errorMsg;
 };
-} // namespace tndm
 
-#endif // PUMGEN_SRC_THIRD_PARTY_GMSHPARSER_H_
+} // namespace puml
+
+#endif // PUMGEN_SRC_MESHREADER_GMSHPARSER_H_
diff --git a/src/meshreader/MshInput.cpp b/src/meshreader/MshInput.cpp
new file mode 100644
index 0000000..aeee650
--- /dev/null
+++ b/src/meshreader/MshInput.cpp
@@ -0,0 +1,150 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#include "MshInput.h"
+
+#include <algorithm>
+#include <cstring>
+#include <stdexcept>
+
+namespace puml {
+
+MshInput::MshInput(const std::string& fileName, std::size_t bufferSize)
+    : fileName(fileName), buffer(std::max(bufferSize, 2 * MaxTokenLength) + 1) {
+  file = std::fopen(fileName.c_str(), "rb");
+  if (file == nullptr) {
+    throw std::runtime_error("Unable to open MSH file " + fileName);
+  }
+  buffer[0] = '\0';
+}
+
+MshInput::~MshInput() {
+  if (file != nullptr) {
+    std::fclose(file);
+  }
+}
+
+std::string_view MshInput::readToken() {
+  if (!skipWhitespace()) {
+    return {};
+  }
+  ensure(MaxTokenLength);
+  std::size_t stop = begin;
+  while (stop < end && !isSpace(buffer[stop]) && stop - begin < MaxTokenLength) {
+    ++stop;
+  }
+  const std::string_view token(buffer.data() + begin, stop - begin);
+  begin = stop;
+  return token;
+}
+
+bool MshInput::readLineBreak() {
+  ensure(2);
+  if (begin < end && buffer[begin] == '\r') {
+    ++begin;
+  }
+  if (begin < end && buffer[begin] == '\n') {
+    ++begin;
+    return true;
+  }
+  return false;
+}
+
+bool MshInput::readRaw(void* data, std::size_t bytes) {
+  auto* out = static_cast<char*>(data);
+  while (bytes > 0) {
+    if (begin == end && bytes >= (buffer.size() - 1) / 2) {
+      // large reads bypass the (empty) buffer
+      bufferOffset += end;
+      begin = end = 0;
+      const std::size_t read = std::fread(out, 1, bytes, file);
+      bufferOffset += read;
+      if (read < bytes) {
+        eof = true;
+        return false;
+      }
+      return true;
+    }
+    if (begin == end && !refill()) {
+      return false;
+    }
+    const std::size_t count = std::min(bytes, end - begin);
+    std::memcpy(out, buffer.data() + begin, count);
+    begin += count;
+    out += count;
+    bytes -= count;
+  }
+  return true;
+}
+
+bool MshInput::skipTo(std::string_view marker) {
+  while (true) {
+    const std::string_view data(buffer.data() + begin, end - begin);
+    const auto found = data.find(marker);
+    if (found != std::string_view::npos) {
+      begin += found + marker.size();
+      return true;
+    }
+    // the tail may hold the beginning of the marker
+    begin = end - std::min(data.size(), marker.size() - 1);
+    if (!refill()) {
+      begin = end;
+      return false;
+    }
+  }
+}
+
+std::pair<std::size_t, std::size_t> MshInput::location(std::size_t offset) const {
+  std::size_t line = 1;
+  std::size_t column = 1;
+  std::FILE* scan = std::fopen(fileName.c_str(), "rb");
+  if (scan == nullptr) {
+    return {line, column};
+  }
+  std::vector<char> chunk(std::size_t{1} << 20);
+  std::size_t position = 0;
+  while (position < offset) {
+    const std::size_t read =
+        std::fread(chunk.data(), 1, std::min(chunk.size(), offset - position), scan);
+    if (read == 0) {
+      break;
+    }
+    for (std::size_t i = 0; i < read; ++i) {
+      if (chunk[i] == '\n') {
+        ++line;
+        column = 1;
+      } else {
+        ++column;
+      }
+    }
+    position += read;
+  }
+  std::fclose(scan);
+  return {line, column};
+}
+
+bool MshInput::refill() {
+  if (eof) {
+    return false;
+  }
+  const std::size_t remaining = end - begin;
+  if (begin > 0) {
+    std::memmove(buffer.data(), buffer.data() + begin, remaining);
+    bufferOffset += begin;
+    begin = 0;
+    end = remaining;
+  }
+  const std::size_t capacity = buffer.size() - 1;
+  if (end == capacity) {
+    return false;
+  }
+  const std::size_t read = std::fread(buffer.data() + end, 1, capacity - end, file);
+  end += read;
+  buffer[end] = '\0';
+  if (read == 0) {
+    eof = true;
+  }
+  return read > 0;
+}
+
+} // namespace puml
diff --git a/src/meshreader/MshInput.h b/src/meshreader/MshInput.h
new file mode 100644
index 0000000..f00e6eb
--- /dev/null
+++ b/src/meshreader/MshInput.h
@@ -0,0 +1,177 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#ifndef PUMGEN_SRC_MESHREADER_MSHINPUT_H_
+#define PUMGEN_SRC_MESHREADER_MSHINPUT_H_
+
+#include <charconv>
+#include <cstddef>
+#include <cstdio>
+#include <cstdlib>
+#include <optional>
+#include <string>
+#include <string_view>
+#include <utility>
+#include <vector>
+
+namespace puml {
+
+/**
+ * Buffered sequential reading of an MSH file: whitespace-separated text tokens for the ASCII
+ * parts and raw bytes for the binary parts.
+ */
+class MshInput {
+  public:
+  static constexpr std::size_t DefaultBufferSize = std::size_t{16} << 20;
+  // numbers and section names are shorter; the buffer always holds this many bytes ahead
+  static constexpr std::size_t MaxTokenLength = 128;
+
+  /**
+   * @throws std::runtime_error if the file cannot be opened
+   */
+  explicit MshInput(const std::string& fileName, std::size_t bufferSize = DefaultBufferSize);
+  ~MshInput();
+  MshInput(const MshInput&) = delete;
+  MshInput& operator=(const MshInput&) = delete;
+
+  /**
+   * Skips whitespace; returns false at the end of the file.
+   */
+  bool skipWhitespace() {
+    while (true) {
+      while (begin < end && isSpace(buffer[begin])) {
+        ++begin;
+      }
+      if (begin < end) {
+        return true;
+      }
+      if (!refill()) {
+        return false;
+      }
+    }
+  }
+
+  /**
+   * The first character of the next token, or '\0' at the end of the file.
+   */
+  char peek() { return skipWhitespace() ? buffer[begin] : '\0'; }
+
+  /**
+   * The next whitespace-separated token (at most MaxTokenLength characters); empty at the end of
+   * the file. The view is valid until the next read.
+   */
+  std::string_view readToken();
+
+  /**
+   * Reads a whitespace-separated integer; std::nullopt (without consuming anything but
+   * whitespace) if the next token is not an integer of type T.
+   */
+  template <typename T> std::optional<T> readInteger() {
+    if (!skipWhitespace()) {
+      return std::nullopt;
+    }
+    ensure(MaxTokenLength);
+    const char* first = buffer.data() + begin;
+    const char* last = buffer.data() + end;
+    if (*first == '+') {
+      ++first;
+    }
+    T value{};
+    const auto [ptr, ec] = std::from_chars(first, last, value);
+    if (ec != std::errc() || (ptr != last && !isSpace(*ptr))) {
+      return std::nullopt;
+    }
+    begin = static_cast<std::size_t>(ptr - buffer.data());
+    return value;
+  }
+
+  /**
+   * Reads a whitespace-separated floating-point number; std::nullopt (without consuming anything
+   * but whitespace) if the next token is not a number.
+   */
+  std::optional<double> readReal() {
+    if (!skipWhitespace()) {
+      return std::nullopt;
+    }
+    ensure(MaxTokenLength);
+    const char* first = buffer.data() + begin;
+    const char* last = buffer.data() + end;
+    if (*first == '+') {
+      ++first;
+    }
+    double value = 0;
+#if defined(__cpp_lib_to_chars) && __cpp_lib_to_chars >= 201611L
+    const auto [ptr, ec] = std::from_chars(first, last, value);
+    const bool parsed = ec == std::errc();
+#else
+    // the buffer is null-terminated behind the valid data
+    char* ptr = nullptr;
+    value = std::strtod(first, &ptr);
+    const bool parsed = ptr != first;
+#endif
+    if (!parsed || (ptr != last && !isSpace(*ptr))) {
+      return std::nullopt;
+    }
+    begin = static_cast<std::size_t>(ptr - buffer.data());
+    return value;
+  }
+
+  /**
+   * Consumes a single line break ("\n" or "\r\n"), as it separates the header line of a binary
+   * section from its data.
+   */
+  bool readLineBreak();
+
+  /**
+   * Reads the next bytes as they are.
+   */
+  bool readRaw(void* data, std::size_t bytes);
+
+  /**
+   * Skips everything up to and including the next occurrence of the marker.
+   */
+  bool skipTo(std::string_view marker);
+
+  /**
+   * The offset of the next unread byte in the file.
+   */
+  [[nodiscard]] std::size_t offset() const { return bufferOffset + begin; }
+
+  /**
+   * Line and column (both starting at 1) of a byte offset; reads the file up to that offset.
+   */
+  [[nodiscard]] std::pair<std::size_t, std::size_t> location(std::size_t offset) const;
+
+  private:
+  static bool isSpace(char c) { return c == ' ' || (c >= '\t' && c <= '\r'); }
+
+  /**
+   * Moves the unread data to the front of the buffer and appends more data from the file;
+   * returns false if nothing could be appended.
+   */
+  bool refill();
+
+  /**
+   * Makes at least count bytes available unless the end of the file comes first.
+   */
+  void ensure(std::size_t count) {
+    while (end - begin < count && !eof) {
+      refill();
+    }
+  }
+
+  std::string fileName;
+  std::FILE* file = nullptr;
+  // one byte more than the capacity for the terminating null character
+  std::vector<char> buffer;
+  // the unread data is buffer[begin, end)
+  std::size_t begin = 0;
+  std::size_t end = 0;
+  // the file offset of buffer[0]
+  std::size_t bufferOffset = 0;
+  bool eof = false;
+};
+
+} // namespace puml
+
+#endif // PUMGEN_SRC_MESHREADER_MSHINPUT_H_
diff --git a/src/pumgen.cpp b/src/pumgen.cpp
index c7651a4..7227859 100644
--- a/src/pumgen.cpp
+++ b/src/pumgen.cpp
@@ -44,10 +44,10 @@
 #ifdef USE_SIMMOD
 #include "input/SimModSuite.h"
 #endif // USE_SIMMOD
+#include "meshreader/GMSH2Parser.h"
 #include "meshreader/GMSH4Parser.h"
 #include "meshreader/ParallelGMSHReader.h"
 #include "meshreader/ParallelGambitReader.h"
-#include "third_party/GMSH2Parser.h"
 
 #include "helper/InsphereCalculator.h"
 
@@ -217,7 +217,7 @@ void addAttribute(hid_t h5file, const std::string& name, const std::string& valu
 }
 
 template <std::size_t Order>
-using SMF2 = SerialMeshFile<puml::ParallelGMSHReader<tndm::GMSH2Parser, Order>>;
+using SMF2 = SerialMeshFile<puml::ParallelGMSHReader<puml::GMSH2Parser, Order>>;
 template <std::size_t Order>
 using SMF4 = SerialMeshFile<puml::ParallelGMSHReader<puml::GMSH4Parser, Order>>;
 
diff --git a/src/third_party/GMSH2Parser.cpp b/src/third_party/GMSH2Parser.cpp
deleted file mode 100644
index 0f0965a..0000000
--- a/src/third_party/GMSH2Parser.cpp
+++ /dev/null
@@ -1,211 +0,0 @@
-// SPDX-FileCopyrightText: 2022 SeisSol Group
-// SPDX-FileCopyrightText: 2020 Ludwig-Maximilians-Universität München
-//
-// SPDX-License-Identifier: BSD-3-Clause
-#include "GMSH2Parser.h"
-#include "GMSHLexer.h"
-
-#include <cstdio>
-#include <vector>
-
-namespace tndm {
-
-bool GMSH2Parser::parse_() {
-  getNextToken();
-
-  double version = parseMeshFormat();
-  if (version < 2.0 || version >= 3.0) {
-    char buf[128];
-    snprintf(buf, sizeof(buf), "Unsupported MSH version %.1lf", version);
-    return logError<bool>(buf);
-  }
-
-  bool hasNodes = false;
-  bool hasElements = false;
-
-  while (curTok != GMSHToken::eof) {
-    switch (curTok) {
-    case GMSHToken::nodes:
-      hasNodes = parseNodes();
-      break;
-    case GMSHToken::elements:
-      hasElements = parseElements();
-      break;
-    case GMSHToken::periodic:
-      parsePeriodic();
-      break;
-    default:
-      getNextToken();
-      break;
-    }
-  }
-
-  if (!hasNodes) {
-    return logError<bool>("Missing $Nodes section");
-  }
-  if (!hasElements) {
-    return logError<bool>("Missing $Elements section");
-  }
-  return true;
-}
-
-bool GMSH2Parser::parseNodes() {
-  getNextToken();
-  if (curTok != GMSHToken::integer || lexer.getInteger() < 0) {
-    return logErrorAnnotated<bool>("Expected non-zero integer");
-  }
-  std::size_t numVertices = lexer.getInteger();
-  builder->setNumVertices(numVertices);
-  hasNodes = true;
-  numNodes = numVertices;
-
-  // with numVertices distinct tags in [1, numVertices], every node is defined exactly once
-  std::vector<bool> defined(numVertices, false);
-
-  for (std::size_t i = 0; i < numVertices; ++i) {
-    getNextToken();
-    if (curTok != GMSHToken::integer || lexer.getInteger() < 1 ||
-        lexer.getInteger() > numVertices) {
-      char buf[128];
-      snprintf(buf, sizeof(buf), "Expected node-tag with 1 <= node-tag <= %zu", numVertices);
-      return logErrorAnnotated<bool>(buf);
-    }
-    std::size_t id = lexer.getInteger() - 1;
-    if (defined[id]) {
-      char buf[128];
-      snprintf(buf, sizeof(buf), "Duplicate node tag %zu", id + 1);
-      return logErrorAnnotated<bool>(buf);
-    }
-    defined[id] = true;
-
-    std::array<double, 3> x;
-    for (std::size_t i = 0; i < 3; ++i) {
-      getNextToken();
-      auto coord = getNumber();
-      if (!coord) {
-        return logErrorAnnotated<bool>("Expected coordinate");
-      }
-      x[i] = *coord;
-    }
-    builder->setVertex(id, x);
-  }
-  getNextToken();
-  if (curTok != GMSHToken::end_nodes) {
-    return logErrorAnnotated<bool>("Expected $EndNodes");
-  }
-  getNextToken();
-  return true;
-}
-
-bool GMSH2Parser::parseElements() {
-  if (!hasNodes) {
-    return logErrorAnnotated<bool>("Expected $Nodes before $Elements");
-  }
-  getNextToken();
-  if (curTok != GMSHToken::integer || lexer.getInteger() < 0) {
-    return logErrorAnnotated<bool>("Expected non-negative integer");
-  }
-  const auto numElements = lexer.getInteger();
-
-  std::array<long, MaxNodesPerElement> nodes{};
-
-  builder->setNumElements(numElements);
-
-  for (std::size_t elementIdx = 0; elementIdx < numElements; ++elementIdx) {
-    getNextToken();
-    if (curTok != GMSHToken::integer) {
-      return logErrorAnnotated<bool>("Expected element-tag");
-    }
-
-    getNextToken();
-    if (curTok != GMSHToken::integer) {
-      return logErrorAnnotated<bool>("Expected element-type");
-    }
-    const long type = lexer.getInteger();
-    if (type < 1 || type > static_cast<long>(NumTypes) || NumNodes[type - 1] == 0) {
-      char buf[128];
-      snprintf(buf, sizeof(buf), "Unknown element type %li", type);
-      return logErrorAnnotated<bool>(buf);
-    }
-
-    getNextToken();
-    if (curTok != GMSHToken::integer || lexer.getInteger() < 0) {
-      return logErrorAnnotated<bool>("Expected number of tags");
-    }
-    long numTags = lexer.getInteger();
-    // the physical tag; elements without tags get 0
-    long tag = 0;
-    for (long tagIdx = 0; tagIdx < numTags; ++tagIdx) {
-      getNextToken();
-      if (curTok != GMSHToken::integer) {
-        return logErrorAnnotated<bool>("Expected tag (integer)");
-      }
-      if (tagIdx == 0) {
-        tag = lexer.getInteger();
-      }
-    }
-
-    for (std::size_t nodeIdx = 0; nodeIdx < NumNodes[type - 1]; ++nodeIdx) {
-      getNextToken();
-      nodes[nodeIdx] = static_cast<long>(expectNodeIndex());
-    }
-
-    builder->addElement(type, tag, nodes.data(), NumNodes[type - 1]);
-  }
-  getNextToken();
-  if (curTok != GMSHToken::end_elements) {
-    return logErrorAnnotated<bool>("Expected $EndElements");
-  }
-  getNextToken();
-
-  return true;
-}
-
-bool GMSH2Parser::parsePeriodic() {
-  if (!hasNodes) {
-    return logErrorAnnotated<bool>("Expected $Nodes before $Periodic");
-  }
-  getNextToken();
-  const auto numPeriodic = expectNonNegativeInt();
-
-  // ignore everything but the node identification
-
-  for (std::size_t blockIdx = 0; blockIdx < numPeriodic; blockIdx++) {
-    getNextToken();
-    [[maybe_unused]] const std::size_t entityDim = expectNonNegativeInt();
-    getNextToken();
-    [[maybe_unused]] const std::size_t entityId = expectNonNegativeInt();
-    getNextToken();
-    [[maybe_unused]] const std::size_t entityIdentifyId = expectNonNegativeInt();
-
-    getNextToken();
-    if (curTok == GMSHToken::string) {
-      // Gmsh msh2 may write: "Affine a11 a12 ... a44" (16 values)
-      constexpr std::size_t affineSize = 16;
-      for (std::size_t i = 0; i < affineSize; ++i) {
-        getNextToken();
-        [[maybe_unused]] const double affineValue = expectNumber();
-      }
-      getNextToken();
-    }
-    const std::size_t identifySize = expectNonNegativeInt();
-
-    for (std::size_t i = 0; i < identifySize; ++i) {
-      getNextToken();
-      const std::size_t nodeId = expectNodeIndex();
-      getNextToken();
-      const std::size_t nodeIdentifyId = expectNodeIndex();
-      builder->addVertexLink(nodeId, nodeIdentifyId);
-    }
-  }
-
-  getNextToken();
-  if (curTok != tndm::GMSHToken::end_periodic) {
-    return logErrorAnnotated<bool>("Expected $EndPeriodic");
-  }
-  getNextToken();
-
-  return true;
-}
-
-} // namespace tndm
diff --git a/src/third_party/GMSH2Parser.h b/src/third_party/GMSH2Parser.h
deleted file mode 100644
index 38f9e33..0000000
--- a/src/third_party/GMSH2Parser.h
+++ /dev/null
@@ -1,63 +0,0 @@
-// SPDX-FileCopyrightText: 2022 SeisSol Group
-// SPDX-FileCopyrightText: 2020 Ludwig-Maximilians-Universität München
-//
-// SPDX-License-Identifier: BSD-3-Clause
-#ifndef PUMGEN_SRC_THIRD_PARTY_GMSH2PARSER_H_
-#define PUMGEN_SRC_THIRD_PARTY_GMSH2PARSER_H_
-
-#include "GMSHLexer.h"
-#include "GMSHMeshBuilder.h"
-#include "GMSHParser.h"
-
-#include <array>
-#include <optional>
-#include <streambuf>
-#include <string>
-#include <string_view>
-
-namespace tndm {
-
-class GMSH2Parser : public GMSHParser {
-  public:
-  using GMSHParser::GMSHParser;
-
-  private:
-  unsigned long expectNonNegativeInt() {
-    if (curTok != tndm::GMSHToken::integer || lexer.getInteger() < 0) {
-      return logErrorAnnotated<bool>("Expected non-negative integer");
-    }
-    return static_cast<unsigned long>(lexer.getInteger());
-  }
-
-  double expectNumber() {
-    auto num = getNumber();
-    if (!num) {
-      return logErrorAnnotated<bool>("Expected number");
-    }
-    return num.value();
-  }
-
-  // the node tags are 1, ..., numNodes
-  bool hasNodes = false;
-  std::size_t numNodes = 0;
-
-  /**
-   * Reads a node tag and returns the index of the node.
-   */
-  std::size_t expectNodeIndex() {
-    if (curTok != GMSHToken::integer || lexer.getInteger() < 1 ||
-        static_cast<std::size_t>(lexer.getInteger()) > numNodes) {
-      return logErrorAnnotated<std::size_t>("Unknown node tag");
-    }
-    return static_cast<std::size_t>(lexer.getInteger()) - 1;
-  }
-
-  bool parseNodes();
-  bool parseElements();
-  bool parsePeriodic();
-  virtual bool parse_() override;
-};
-
-}; // namespace tndm
-
-#endif // PUMGEN_SRC_THIRD_PARTY_GMSH2PARSER_H_
diff --git a/src/third_party/GMSHLexer.cpp b/src/third_party/GMSHLexer.cpp
deleted file mode 100644
index 059407a..0000000
--- a/src/third_party/GMSHLexer.cpp
+++ /dev/null
@@ -1,130 +0,0 @@
-// SPDX-FileCopyrightText: 2022 SeisSol Group
-// SPDX-FileCopyrightText: 2020 Ludwig-Maximilians-Universität München
-//
-// SPDX-License-Identifier: BSD-3-Clause
-#include "GMSHLexer.h"
-#include "Hash.h"
-
-namespace tndm {
-
-void GMSHLexer::advance() {
-  in->get(lastChar);
-
-  if (lastChar == '\n' || lastChar == '\r') {
-    ++loc.line;
-    loc.col = 1;
-  } else {
-    ++loc.col;
-  }
-}
-
-GMSHToken GMSHLexer::getToken() {
-  if (in == nullptr) {
-    return GMSHToken::eof;
-  }
-  in->peek();
-  if (!in->good()) {
-    return GMSHToken::eof;
-  }
-
-  while (isspace(lastChar) && in->good()) {
-    advance();
-  }
-  if (!in->good()) {
-    return GMSHToken::eof;
-  }
-
-  if (lastChar == '$') {
-    advance();
-    auto hash = fnv1a0();
-    while (isalpha(lastChar)) {
-      hash = fnv1a_step(hash, lastChar);
-      advance();
-    }
-    GMSHToken token = GMSHToken::unknown_section;
-    switch (hash) {
-    case "MeshFormat"_fnv1a:
-      token = GMSHToken::mesh_format;
-      break;
-    case "EndMeshFormat"_fnv1a:
-      token = GMSHToken::end_mesh_format;
-      break;
-    case "Entities"_fnv1a:
-      token = GMSHToken::entities;
-      break;
-    case "EndEntities"_fnv1a:
-      token = GMSHToken::end_entities;
-      break;
-    case "Nodes"_fnv1a:
-      token = GMSHToken::nodes;
-      break;
-    case "EndNodes"_fnv1a:
-      token = GMSHToken::end_nodes;
-      break;
-    case "Elements"_fnv1a:
-      token = GMSHToken::elements;
-      break;
-    case "EndElements"_fnv1a:
-      token = GMSHToken::end_elements;
-      break;
-    case "Periodic"_fnv1a:
-      token = GMSHToken::periodic;
-      break;
-    case "EndPeriodic"_fnv1a:
-      token = GMSHToken::end_periodic;
-      break;
-    case "PartitionedEntities"_fnv1a:
-      token = GMSHToken::partitioned_entities;
-      break;
-    default:
-      break;
-    }
-    return token;
-  }
-
-  auto mustbereal = [](char c) { return c == '.' || c == 'e' || c == 'E'; };
-  auto isnumber = [&mustbereal](char c) {
-    return isdigit(c) || c == '+' || c == '-' || mustbereal(c);
-  };
-
-  if (isnumber(lastChar)) {
-    char buf[MaxNumberLength + 1];
-    int pos = 0;
-    bool isreal = false;
-    do {
-      buf[pos++] = lastChar;
-      isreal = isreal || mustbereal(lastChar);
-      advance();
-    } while (isnumber(lastChar) && pos < MaxNumberLength);
-    buf[pos] = 0;
-    if (pos == MaxNumberLength) {
-      throw std::runtime_error("Too large number encountered in GMSHLexer: " + std::string(buf));
-    }
-    if (isreal) {
-      real = std::strtod(buf, 0);
-      return GMSHToken::real;
-    }
-    integer = std::strtol(buf, 0, 10);
-    return GMSHToken::integer;
-  }
-
-  if (lastChar == '"') {
-    do {
-      advance();
-    } while (lastChar != '"');
-    advance();
-    return GMSHToken::string;
-  }
-  if (isalpha(lastChar)) {
-    do {
-      advance();
-    } while (isalpha(lastChar));
-    return GMSHToken::string;
-  }
-  // Always consume at least one character for unknown tokens to avoid
-  // getting stuck in an infinite tokenization loop.
-  advance();
-  return GMSHToken::unknown_token;
-}
-
-} // namespace tndm
diff --git a/src/third_party/GMSHLexer.h b/src/third_party/GMSHLexer.h
deleted file mode 100644
index 740f907..0000000
--- a/src/third_party/GMSHLexer.h
+++ /dev/null
@@ -1,66 +0,0 @@
-// SPDX-FileCopyrightText: 2022 SeisSol Group
-// SPDX-FileCopyrightText: 2020 Ludwig-Maximilians-Universität München
-//
-// SPDX-License-Identifier: BSD-3-Clause
-#ifndef PUMGEN_SRC_THIRD_PARTY_GMSHLEXER_H_
-#define PUMGEN_SRC_THIRD_PARTY_GMSHLEXER_H_
-
-#include <cstdint>
-#include <fstream>
-
-namespace tndm {
-
-enum class GMSHToken {
-  eof,
-  integer,
-  real,
-  string,
-  mesh_format,
-  end_mesh_format,
-  entities,
-  end_entities,
-  nodes,
-  end_nodes,
-  elements,
-  end_elements,
-  periodic,
-  end_periodic,
-  partitioned_entities,
-  unknown_section,
-  unknown_token
-};
-
-struct GMSHSourceLocation {
-  std::size_t line;
-  std::size_t col;
-};
-
-class GMSHLexer {
-  private:
-  uint64_t identifier;
-  long integer;
-  double real;
-  char lastChar = ' ';
-  std::istream* in = nullptr;
-  GMSHSourceLocation loc = {1, 1};
-
-  protected:
-  void advance();
-
-  public:
-  static constexpr std::size_t MaxNumberLength = 128;
-
-  void setIStream(std::istream* istream) {
-    in = istream;
-    loc = {1, 1};
-  }
-
-  GMSHToken getToken();
-  uint64_t getIdentifier() const { return identifier; }
-  long getInteger() const { return integer; }
-  double getReal() const { return real; }
-  GMSHSourceLocation getSourceLoc() const { return loc; }
-};
-} // namespace tndm
-
-#endif // PUMGEN_SRC_THIRD_PARTY_GMSHLEXER_H_
diff --git a/src/third_party/GMSHParser.cpp b/src/third_party/GMSHParser.cpp
deleted file mode 100644
index 753176d..0000000
--- a/src/third_party/GMSHParser.cpp
+++ /dev/null
@@ -1,34 +0,0 @@
-// SPDX-FileCopyrightText: 2022 SeisSol Group
-// SPDX-FileCopyrightText: 2020 Ludwig-Maximilians-Universität München
-//
-// SPDX-License-Identifier: BSD-3-Clause
-#include "GMSHParser.h"
-
-namespace tndm {
-
-double GMSHParser::parseMeshFormat() {
-  if (curTok != GMSHToken::mesh_format) {
-    return logErrorAnnotated<double>("Expected $MeshFormat");
-  }
-  getNextToken();
-  auto version = getNumber();
-  if (!version) {
-    return logErrorAnnotated<double>("Expected version number");
-  }
-  getNextToken();
-  if (curTok == GMSHToken::integer && lexer.getInteger() == 1) {
-    return logErrorAnnotated<double>(
-        "Binary MSH files are not supported; write the mesh as ASCII (Mesh.Binary = 0)");
-  }
-  if (curTok != GMSHToken::integer || lexer.getInteger() != 0) {
-    return logErrorAnnotated<double>("Expected file type 0 (ASCII)");
-  }
-  getNextToken(); // skip data-size
-  getNextToken();
-  if (curTok != GMSHToken::end_mesh_format) {
-    return logErrorAnnotated<double>("Expected $EndMeshFormat");
-  }
-  getNextToken();
-  return *version;
-}
-} // namespace tndm
diff --git a/src/third_party/Hash.h b/src/third_party/Hash.h
deleted file mode 100644
index 11c328a..0000000
--- a/src/third_party/Hash.h
+++ /dev/null
@@ -1,24 +0,0 @@
-// SPDX-FileCopyrightText: 2025 SeisSol Group
-// SPDX-FileCopyrightText: 2020 Ludwig-Maximilians-Universität München
-//
-// SPDX-License-Identifier: BSD-3-Clause
-#ifndef PUMGEN_SRC_THIRD_PARTY_HASH_H_
-#define PUMGEN_SRC_THIRD_PARTY_HASH_H_
-
-#include <cstdint>
-#include <string>
-
-namespace tndm {
-
-// https://de.wikipedia.org/wiki/FNV_(Informatik)
-constexpr uint64_t fnv1a0() { return 0xcbf29ce484222325; }
-constexpr uint64_t fnv1a_step(uint64_t hash, char c) { return (hash ^ c) * 0x00000100000001b3; }
-constexpr uint64_t fnv1a(char const* s, std::size_t len) {
-  return len > 0 ? fnv1a_step(fnv1a(s, len - 1), s[len - 1]) : fnv1a0();
-}
-uint64_t fnv1a(std::string const& s) { return fnv1a(s.data(), s.size()); }
-constexpr uint64_t operator""_fnv1a(char const* s, std::size_t len) { return tndm::fnv1a(s, len); }
-
-} // namespace tndm
-
-#endif // PUMGEN_SRC_THIRD_PARTY_HASH_H_
diff --git a/src/third_party/README.md b/src/third_party/README.md
index 55b51fd..3721c9a 100644
--- a/src/third_party/README.md
+++ b/src/third_party/README.md
@@ -6,5 +6,8 @@
 
 # Third party sources
 
-Taken from <https://github.com/TEAR-ERC/tandem/commit/555bbfa06aad688d609cfa2fae6b5bc2e2315589>;
-one further addition from <https://github.com/TEAR-ERC/tandem/commit/565ba7ba8aeb02eba2c5773f68119d01d41a82de>.
+`MPITraits.h` is taken from tandem, commit
+<https://github.com/TEAR-ERC/tandem/commit/555bbfa06aad688d609cfa2fae6b5bc2e2315589>.
+The GMSH parsers in `src/meshreader` are derived from the tandem GMSH
+parser of that commit and of commit
+<https://github.com/TEAR-ERC/tandem/commit/565ba7ba8aeb02eba2c5773f68119d01d41a82de>.
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 26ab1de..e901b9b 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -56,6 +56,19 @@ function(pumgen_add_test name)
                               "ASAN_OPTIONS=detect_leaks=0")
 endfunction()
 
+# the GMSH parsers with a tiny read buffer
+add_executable(
+  pumgen_reader_test
+  ReaderTest.cpp ${PROJECT_SOURCE_DIR}/src/meshreader/MshInput.cpp
+  ${PROJECT_SOURCE_DIR}/src/meshreader/GMSHParser.cpp
+  ${PROJECT_SOURCE_DIR}/src/meshreader/GMSH2Parser.cpp
+  ${PROJECT_SOURCE_DIR}/src/meshreader/GMSH4Parser.cpp)
+target_include_directories(pumgen_reader_test PRIVATE ${PROJECT_SOURCE_DIR}/src
+                                                      ${PROJECT_SOURCE_DIR}/submodules)
+target_compile_definitions(pumgen_reader_test PRIVATE LOG_LEVEL=${LOG_LEVEL})
+add_test(NAME reader.buffer-boundaries COMMAND pumgen_reader_test ${PUMGEN_TEST_FIXTURES})
+set_tests_properties(reader.buffer-boundaries PROPERTIES ENVIRONMENT "ASAN_OPTIONS=detect_leaks=0")
+
 # The fixtures are created by fixtures/generate.py; the reference files are computed from the
 # gmsh model directly. The layered mesh has element and vertex counts which do not divide evenly
 # among 3 or 4 ranks.
diff --git a/tests/ReaderTest.cpp b/tests/ReaderTest.cpp
new file mode 100644
index 0000000..75efd93
--- /dev/null
+++ b/tests/ReaderTest.cpp
@@ -0,0 +1,97 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+
+// Parses the fixtures with a tiny read buffer, so that tokens and section markers straddle buffer
+// boundaries, and compares the result with the one of the default buffer.
+
+#include <cstdio>
+#include <fstream>
+#include <sstream>
+#include <string>
+
+#include "meshreader/GMSH2Parser.h"
+#include "meshreader/GMSH4Parser.h"
+#include "meshreader/GMSHBuilder.h"
+#include "meshreader/MshInput.h"
+
+namespace {
+
+constexpr std::size_t TinyBuffer = 2 * puml::MshInput::MaxTokenLength;
+
+template <typename Parser, typename Builder>
+bool parse(const std::string& file, std::size_t bufferSize, Builder& builder) {
+  Parser parser(&builder, bufferSize);
+  if (!parser.parseFile(file)) {
+    std::fprintf(stderr, "%s (buffer %zu): %s", file.c_str(), bufferSize,
+                 std::string(parser.getErrorMessage()).c_str());
+    return false;
+  }
+  builder.postprocess();
+  return true;
+}
+
+template <typename Parser, std::size_t Order> bool check(const std::string& file) {
+  puml::GMSHBuilder<3, Order> reference;
+  puml::GMSHBuilder<3, Order> tiny;
+  if (!parse<Parser>(file, puml::MshInput::DefaultBufferSize, reference) ||
+      !parse<Parser>(file, TinyBuffer, tiny)) {
+    return false;
+  }
+  const bool same = reference.vertices == tiny.vertices && reference.elements == tiny.elements &&
+                    reference.groups == tiny.groups && reference.facets == tiny.facets &&
+                    reference.bcs == tiny.bcs && reference.identify == tiny.identify &&
+                    !reference.elements.empty();
+  std::printf("%s: %s\n", file.c_str(), same ? "ok" : "DIFFERENT");
+  return same;
+}
+
+std::string readFile(const std::string& file) {
+  std::ifstream in(file, std::ios::binary);
+  std::stringstream content;
+  content << in.rdbuf();
+  return content.str();
+}
+
+// a section to be skipped, longer than the tiny buffer and with partial end markers
+bool checkSkippedSection(const std::string& fixtures) {
+  std::string content = readFile(fixtures + "/tiny-v41.msh");
+  std::string junk = "$Comments\n";
+  for (int i = 0; i < 200; ++i) {
+    junk += "$EndComment $EndCommentz ";
+  }
+  junk += "\n$EndComments\n";
+  content.insert(content.find("$Nodes"), junk);
+  const std::string file = "reader-test-skipped-section.msh";
+  std::ofstream(file, std::ios::binary) << content;
+
+  puml::GMSHBuilder<3, 1> reference;
+  puml::GMSHBuilder<3, 1> skipped;
+  const bool ok = parse<puml::GMSH4Parser>(fixtures + "/tiny-v41.msh",
+                                           puml::MshInput::DefaultBufferSize, reference) &&
+                  parse<puml::GMSH4Parser>(file, TinyBuffer, skipped) &&
+                  reference.vertices == skipped.vertices &&
+                  reference.elements == skipped.elements && reference.groups == skipped.groups;
+  std::remove(file.c_str());
+  std::printf("skipped section: %s\n", ok ? "ok" : "DIFFERENT");
+  return ok;
+}
+
+} // namespace
+
+int main(int argc, char** argv) {
+  if (argc != 2) {
+    std::fprintf(stderr, "Usage: %s <fixture directory>\n", argv[0]);
+    return 2;
+  }
+  const std::string fixtures = argv[1];
+  bool ok = true;
+  ok &= check<puml::GMSH4Parser, 1>(fixtures + "/layered-v41.msh");
+  ok &= check<puml::GMSH2Parser, 1>(fixtures + "/layered-v22.msh");
+  ok &= check<puml::GMSH4Parser, 1>(fixtures + "/periodic-v41.msh");
+  ok &= check<puml::GMSH4Parser, 1>(fixtures + "/periodic-parametric-v41.msh");
+  ok &= check<puml::GMSH4Parser, 2>(fixtures + "/coarse-o2-v41.msh");
+  ok &= check<puml::GMSH2Parser, 2>(fixtures + "/coarse-o2-v22.msh");
+  ok &= checkSkippedSection(fixtures);
+  return ok ? 0 : 1;
+}

From 7a5f13c9534473d3f98718a13da2a98a53fc138c Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 19:24:32 +0000
Subject: [PATCH 11/19] Read binary MSH 4.1 files

Binary files are parsed as the ASCII ones, but with the values read as raw
4-byte ints, doubles and data-size integers; node tags, coordinates and
element nodes are read in bulk. Other byte orders (detected by the marker in
$MeshFormat) and a data size of 4 are supported as well. On the mesh with
3.6M cells, parsing the binary file takes 0.18 s instead of 0.43 s for the
ASCII file (and 2.18 s for the ASCII file before the buffered reader).

Errors in binary data are reported with their byte offset. The binary
fixtures are written by gmsh; fixtures/generate.py derives big-endian and
4-byte-size variants and first checks that its converter reproduces gmsh's
file byte for byte. The references of the binary tests are compared with a
tolerance, since they are built from the ASCII files (%.16g).

AI-generated. Model: Claude Opus 5.5
---
 src/meshreader/GMSH4Parser.cpp                | 214 ++++++++++++++----
 src/meshreader/GMSH4Parser.h                  |  35 ++-
 src/meshreader/GMSHParser.cpp                 |  13 +-
 src/meshreader/GMSHParser.h                   |   2 +
 tests/CMakeLists.txt                          |  18 +-
 tests/ReaderTest.cpp                          |   5 +
 .../fixtures/coarse-binary-bigendian-v41.msh  | Bin 0 -> 27978 bytes
 tests/fixtures/coarse-binary-size4-v41.msh    | Bin 0 -> 16918 bytes
 .../fixtures/coarse-binary-truncated-v41.msh  | Bin 0 -> 7966 bytes
 tests/fixtures/coarse-o2-binary-v41.msh       | Bin 0 -> 65530 bytes
 tests/fixtures/generate.py                    |  97 ++++++++
 tests/fixtures/layered-binary-v41.msh         | Bin 0 -> 109538 bytes
 tests/fixtures/periodic-binary-v41.msh        | Bin 0 -> 73486 bytes
 13 files changed, 334 insertions(+), 50 deletions(-)
 create mode 100644 tests/fixtures/coarse-binary-bigendian-v41.msh
 create mode 100644 tests/fixtures/coarse-binary-size4-v41.msh
 create mode 100644 tests/fixtures/coarse-binary-truncated-v41.msh
 create mode 100644 tests/fixtures/coarse-o2-binary-v41.msh
 create mode 100644 tests/fixtures/layered-binary-v41.msh
 create mode 100644 tests/fixtures/periodic-binary-v41.msh

diff --git a/src/meshreader/GMSH4Parser.cpp b/src/meshreader/GMSH4Parser.cpp
index 8264b7e..6e1b53c 100644
--- a/src/meshreader/GMSH4Parser.cpp
+++ b/src/meshreader/GMSH4Parser.cpp
@@ -3,8 +3,11 @@
 // SPDX-License-Identifier: BSD-3-Clause
 #include "GMSH4Parser.h"
 
+#include <algorithm>
 #include <array>
+#include <cstdint>
 #include <cstdio>
+#include <cstring>
 #include <string>
 #include <string_view>
 #include <vector>
@@ -13,6 +16,19 @@
 
 namespace puml {
 
+namespace {
+template <typename T> T swapBytesOf(T value) {
+  std::array<unsigned char, sizeof(T)> bytes{};
+  std::memcpy(bytes.data(), &value, sizeof(T));
+  std::reverse(bytes.begin(), bytes.end());
+  std::memcpy(&value, bytes.data(), sizeof(T));
+  return value;
+}
+
+// blocks of binary element data are read in pieces of this many elements
+constexpr std::size_t ElementChunk = 1 << 16;
+} // namespace
+
 void GMSH4Parser::parse_() {
   const auto format = parseMeshFormatHeader();
   if (format.version < 4.0 || format.version >= 5.0) {
@@ -24,10 +40,21 @@ void GMSH4Parser::parse_() {
     failFile("MSH 4.0 is not supported; write the mesh as MSH 4.1 (Mesh.MshFileVersion = 4.1)");
   }
   if (format.fileType == 1) {
-    failFile("Binary MSH files are not supported; write the mesh as ASCII (Mesh.Binary = 0)");
-  }
-  if (format.fileType != 0) {
-    failFile("Expected file type 0 (ASCII)");
+    binary = true;
+    dataSize = format.dataSize;
+    if (dataSize != 4 && dataSize != 8) {
+      failFile("Unsupported data size " + std::to_string(dataSize) + " (expected 4 or 8)");
+    }
+    beginSectionData();
+    std::int32_t one = 0;
+    readBinary(&one, sizeof(one));
+    if (swapBytesOf(one) == 1) {
+      swapBytes = true;
+    } else if (one != 1) {
+      failFile("Invalid byte order mark in the binary MSH file");
+    }
+  } else if (format.fileType != 0) {
+    failFile("Expected file type 0 (ASCII) or 1 (binary)");
   }
   expectToken("$EndMeshFormat");
 
@@ -71,7 +98,99 @@ void GMSH4Parser::parse_() {
   }
 }
 
+void GMSH4Parser::beginSectionData() {
+  if (binary) {
+    if (!input->readLineBreak()) {
+      fail("Expected a line break before the binary data");
+    }
+    binaryData = true;
+  }
+}
+
+void GMSH4Parser::readBinary(void* data, std::size_t bytes) {
+  if (!input->readRaw(data, bytes)) {
+    failFile("Unexpected end of file in binary data");
+  }
+}
+
+std::size_t GMSH4Parser::readSize() {
+  if (!binary) {
+    return expectSize();
+  }
+  std::size_t value = 0;
+  readSizes(&value, 1);
+  return value;
+}
+
+long GMSH4Parser::readInt() {
+  if (!binary) {
+    return expectInteger();
+  }
+  std::int32_t value = 0;
+  readBinary(&value, sizeof(value));
+  return swapBytes ? swapBytesOf(value) : value;
+}
+
+double GMSH4Parser::readDouble() {
+  if (!binary) {
+    return expectNumber();
+  }
+  double value = 0;
+  readDoubles(&value, 1);
+  return value;
+}
+
+void GMSH4Parser::readSizes(std::size_t* values, std::size_t count) {
+  if (!binary) {
+    for (std::size_t i = 0; i < count; ++i) {
+      values[i] = expectSize();
+    }
+    return;
+  }
+  if (dataSize == sizeof(std::uint64_t)) {
+    static_assert(sizeof(std::size_t) == sizeof(std::uint64_t));
+    readBinary(values, count * sizeof(std::uint64_t));
+    if (swapBytes) {
+      std::transform(values, values + count, values, swapBytesOf<std::size_t>);
+    }
+  } else {
+    narrowSizes.resize(count);
+    readBinary(narrowSizes.data(), count * sizeof(std::uint32_t));
+    for (std::size_t i = 0; i < count; ++i) {
+      values[i] = swapBytes ? swapBytesOf(narrowSizes[i]) : narrowSizes[i];
+    }
+  }
+}
+
+void GMSH4Parser::readDoubles(double* values, std::size_t count) {
+  if (!binary) {
+    for (std::size_t i = 0; i < count; ++i) {
+      values[i] = expectNumber();
+    }
+    return;
+  }
+  readBinary(values, count * sizeof(double));
+  if (swapBytes) {
+    std::transform(values, values + count, values, swapBytesOf<double>);
+  }
+}
+
+std::size_t GMSH4Parser::position() {
+  if (!binary) {
+    input->skipWhitespace();
+  }
+  return input->offset();
+}
+
+std::size_t GMSH4Parser::nodeIndex(std::size_t tag, std::size_t offset) {
+  if (tag < firstNodeTag || tag - firstNodeTag >= numNodes) {
+    failAt(offset, "Unknown node tag " + std::to_string(tag));
+  }
+  return tag - firstNodeTag;
+}
+
 void GMSH4Parser::parseEntities() {
+  beginSectionData();
   const std::size_t numPoints = readSize();
   const std::size_t numCurves = readSize();
   const std::size_t numSurfaces = readSize();
@@ -114,17 +233,8 @@ void GMSH4Parser::parseEntities() {
   expectToken("$EndEntities");
 }
 
-std::size_t GMSH4Parser::readNodeIndex() {
-  input->skipWhitespace();
-  const auto offset = input->offset();
-  const std::size_t tag = readSize();
-  if (tag < firstNodeTag || tag - firstNodeTag >= numNodes) {
-    failAt(offset, "Unknown node tag " + std::to_string(tag));
-  }
-  return tag - firstNodeTag;
-}
-
 void GMSH4Parser::parseNodes() {
+  beginSectionData();
   const std::size_t numBlocks = readSize();
   const std::size_t numVertices = readSize();
   const std::size_t minNodeTag = readSize();
@@ -145,6 +255,7 @@ void GMSH4Parser::parseNodes() {
   // with as many distinct tags as the tag range is long, every node is defined exactly once
   std::vector<bool> defined(numVertices, false);
   std::vector<std::size_t> indices;
+  std::vector<double> coordinates;
 
   for (std::size_t blockIdx = 0; blockIdx < numBlocks; ++blockIdx) {
     const long dim = readInt();
@@ -153,27 +264,31 @@ void GMSH4Parser::parseNodes() {
     const std::size_t numVerticesInBlock = readSize();
 
     indices.resize(numVerticesInBlock);
-    for (auto& index : indices) {
-      input->skipWhitespace();
-      const auto offset = input->offset();
-      index = readNodeIndex();
+    const auto tagsOffset = input->offset();
+    if (binary) {
+      readSizes(indices.data(), numVerticesInBlock);
+    }
+    for (std::size_t i = 0; i < numVerticesInBlock; ++i) {
+      auto offset = tagsOffset + i * dataSize;
+      if (!binary) {
+        offset = position();
+        indices[i] = expectSize();
+      }
+      const std::size_t index = nodeIndex(indices[i], offset);
       if (defined[index]) {
-        failAt(offset, "Duplicate node tag " + std::to_string(firstNodeTag + index));
+        failAt(offset, "Duplicate node tag " + std::to_string(indices[i]));
       }
       defined[index] = true;
+      indices[i] = index;
     }
 
     // parametric nodes carry dim additional parametric coordinates
-    const long numParametric = parametric != 0 ? dim : 0;
-    for (const auto index : indices) {
-      std::array<double, 3> x{};
-      for (auto& coordinate : x) {
-        coordinate = readDouble();
-      }
-      for (long i = 0; i < numParametric; ++i) {
-        readDouble();
-      }
-      builder->setVertex(static_cast<long>(index), x);
+    const std::size_t valuesPerNode = 3 + (parametric != 0 ? static_cast<std::size_t>(dim) : 0);
+    coordinates.resize(numVerticesInBlock * valuesPerNode);
+    readDoubles(coordinates.data(), coordinates.size());
+    for (std::size_t i = 0; i < numVerticesInBlock; ++i) {
+      const double* x = &coordinates[i * valuesPerNode];
+      builder->setVertex(static_cast<long>(indices[i]), {x[0], x[1], x[2]});
     }
   }
   expectToken("$EndNodes");
@@ -183,6 +298,7 @@ void GMSH4Parser::parseElements() {
   if (!hasNodes) {
     fail("Expected $Nodes before $Elements");
   }
+  beginSectionData();
   const std::size_t numBlocks = readSize();
   const std::size_t numElements = readSize();
   readSize(); // minimal element tag
@@ -190,12 +306,12 @@ void GMSH4Parser::parseElements() {
   builder->setNumElements(numElements);
 
   std::array<long, MaxNodesPerElement> nodes{};
+  std::vector<std::size_t> values;
 
   for (std::size_t blockIdx = 0; blockIdx < numBlocks; ++blockIdx) {
     const long dim = readInt();
     const long entityTag = readInt();
-    input->skipWhitespace();
-    const auto typeOffset = input->offset();
+    const auto typeOffset = position();
     const long type = readInt();
     if (type < 1 || type > static_cast<long>(NumTypes) || NumNodes[type - 1] == 0) {
       failAt(typeOffset, "Unknown element type " + std::to_string(type));
@@ -204,12 +320,31 @@ void GMSH4Parser::parseElements() {
     const std::size_t numElementsInBlock = readSize();
     const long tag = numElementsInBlock > 0 ? physicalTag(dim, entityTag) : 0;
 
-    for (std::size_t elementIdx = 0; elementIdx < numElementsInBlock; ++elementIdx) {
-      readSize(); // element tag
-      for (std::size_t nodeIdx = 0; nodeIdx < numNodesPerElement; ++nodeIdx) {
-        nodes[nodeIdx] = static_cast<long>(readNodeIndex());
+    // each element consists of its tag and its node tags
+    const std::size_t valuesPerElement = 1 + numNodesPerElement;
+    for (std::size_t first = 0; first < numElementsInBlock; first += ElementChunk) {
+      const std::size_t count = std::min(ElementChunk, numElementsInBlock - first);
+      const auto chunkOffset = input->offset();
+      if (binary) {
+        values.resize(count * valuesPerElement);
+        readSizes(values.data(), values.size());
+      }
+      for (std::size_t element = 0; element < count; ++element) {
+        if (!binary) {
+          readSize(); // element tag
+        }
+        for (std::size_t node = 0; node < numNodesPerElement; ++node) {
+          if (binary) {
+            const std::size_t valueIdx = element * valuesPerElement + 1 + node;
+            nodes[node] =
+                static_cast<long>(nodeIndex(values[valueIdx], chunkOffset + valueIdx * dataSize));
+          } else {
+            const auto offset = position();
+            nodes[node] = static_cast<long>(nodeIndex(expectSize(), offset));
+          }
+        }
+        builder->addElement(type, tag, nodes.data(), numNodesPerElement);
       }
-      builder->addElement(type, tag, nodes.data(), numNodesPerElement);
     }
   }
   expectToken("$EndElements");
@@ -219,6 +354,7 @@ void GMSH4Parser::parsePeriodic() {
   if (!hasNodes) {
     fail("Expected $Nodes before $Periodic");
   }
+  beginSectionData();
   const std::size_t numPeriodic = readSize();
 
   // only the node identification is needed
@@ -232,8 +368,10 @@ void GMSH4Parser::parsePeriodic() {
     }
     const std::size_t numIdentified = readSize();
     for (std::size_t i = 0; i < numIdentified; ++i) {
-      const std::size_t node = readNodeIndex();
-      const std::size_t master = readNodeIndex();
+      const auto nodeOffset = position();
+      const std::size_t node = nodeIndex(readSize(), nodeOffset);
+      const auto masterOffset = position();
+      const std::size_t master = nodeIndex(readSize(), masterOffset);
       builder->addVertexLink(node, master);
     }
   }
diff --git a/src/meshreader/GMSH4Parser.h b/src/meshreader/GMSH4Parser.h
index 7ca1ef7..77f8c5b 100644
--- a/src/meshreader/GMSH4Parser.h
+++ b/src/meshreader/GMSH4Parser.h
@@ -5,15 +5,17 @@
 #define PUMGEN_SRC_MESHREADER_GMSH4PARSER_H_
 
 #include <cstddef>
+#include <cstdint>
 #include <map>
 #include <set>
+#include <vector>
 
 #include "GMSHParser.h"
 
 namespace puml {
 
 /**
- * Parser for MSH 4.1 files.
+ * Parser for MSH 4.1 files, ASCII or binary.
  */
 class GMSH4Parser : public GMSHParser {
   public:
@@ -26,15 +28,34 @@ class GMSH4Parser : public GMSHParser {
   void parseElements();
   void parsePeriodic();
 
-  // the values of the sections
-  std::size_t readSize() { return expectSize(); }
-  long readInt() { return expectInteger(); }
-  double readDouble() { return expectNumber(); }
+  /**
+   * Starts the data of a section; in binary files, the data begins after the line break.
+   */
+  void beginSectionData();
+
+  // the values of the sections: text, or binary with sizeof(size_t) == dataSize and 4-byte ints
+  std::size_t readSize();
+  long readInt();
+  double readDouble();
+  // bulk reading of binary sizes and doubles
+  void readSizes(std::size_t* values, std::size_t count);
+  void readDoubles(double* values, std::size_t count);
+  void readBinary(void* data, std::size_t bytes);
 
   /**
-   * Reads a node tag and returns the index of the node.
+   * The offset of the next value, e.g. for error messages.
    */
-  std::size_t readNodeIndex();
+  std::size_t position();
+
+  /**
+   * The index of the node with the given tag; the tag started at the given file offset.
+   */
+  std::size_t nodeIndex(std::size_t tag, std::size_t offset);
+
+  bool binary = false;
+  bool swapBytes = false;
+  std::size_t dataSize = 8;
+  std::vector<std::uint32_t> narrowSizes;
 
   /**
    * The physical tag of the elements of an entity; 0 if the entity has no physical group.
diff --git a/src/meshreader/GMSHParser.cpp b/src/meshreader/GMSHParser.cpp
index a44488d..5c0c3bd 100644
--- a/src/meshreader/GMSHParser.cpp
+++ b/src/meshreader/GMSHParser.cpp
@@ -28,16 +28,22 @@ bool GMSHParser::parseFile(const std::string& fileName) {
 }
 
 void GMSHParser::failAt(std::size_t offset, std::string_view message) {
-  const auto [line, column] = input->location(offset);
   std::stringstream stream;
-  stream << "GMSH parser error in line " << line << " in column " << column << ":\n";
+  if (binaryData) {
+    stream << "GMSH parser error at byte " << offset << ":\n";
+  } else {
+    const auto [line, column] = input->location(offset);
+    stream << "GMSH parser error in line " << line << " in column " << column << ":\n";
+  }
   stream << '\t' << message << '\n';
   errorMsg += stream.str();
   throw ParseError{};
 }
 
 void GMSHParser::fail(std::string_view message) {
-  input->skipWhitespace();
+  if (!binaryData) {
+    input->skipWhitespace();
+  }
   failAt(input->offset(), message);
 }
 
@@ -49,6 +55,7 @@ void GMSHParser::failFile(std::string_view message) {
 }
 
 void GMSHParser::expectToken(std::string_view token) {
+  binaryData = false;
   input->skipWhitespace();
   const auto offset = input->offset();
   if (input->readToken() != token) {
diff --git a/src/meshreader/GMSHParser.h b/src/meshreader/GMSHParser.h
index 9462d06..f71f32c 100644
--- a/src/meshreader/GMSHParser.h
+++ b/src/meshreader/GMSHParser.h
@@ -245,6 +245,8 @@ class GMSHParser {
 
   GMSHMeshBuilder* builder;
   std::unique_ptr<MshInput> input;
+  // errors in binary data are located by byte offset instead of line and column
+  bool binaryData = false;
 
   private:
   std::size_t bufferSize;
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index e901b9b..066b0ff 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -126,8 +126,6 @@ pumgen_add_test(msh4.tiny-unknowntype RANKS 1 SOURCE msh4 INPUT tiny-unknowntype
                 EXPECT_ERROR "Unknown element type 999")
 pumgen_add_test(msh4.tiny-v40 RANKS 1 SOURCE msh4 INPUT tiny-v40.msh
                 EXPECT_ERROR "MSH 4.0 is not supported")
-pumgen_add_test(msh4.coarse-binary RANKS 1 SOURCE msh4 INPUT coarse-binary-v41.msh
-                EXPECT_ERROR "Binary MSH files are not supported")
 pumgen_add_test(msh2.tiny-as-msh4 RANKS 1 SOURCE msh2 INPUT tiny-v41.msh
                 EXPECT_ERROR "Unsupported MSH version 4.1")
 
@@ -168,3 +166,19 @@ pumgen_add_test(msh4.coarse-partitioned RANKS 1 SOURCE msh4 INPUT coarse-partiti
                 EXPECT_ERROR "Partitioned MSH files are not supported")
 pumgen_add_test(msh4.tiny-nophysical RANKS 1 SOURCE msh4 INPUT tiny-nophysical-v41.msh
                 EXPECT_OUTPUT "1 volume[(]s[)] and 0 surface[(]s[)] without a physical group")
+
+# binary MSH 4.1; the coordinates of the references come from the ASCII files
+foreach(ranks 1 2 3)
+  pumgen_add_test(msh4.layered-binary.np${ranks} RANKS ${ranks} SOURCE msh4
+                  INPUT layered-binary-v41.msh REFERENCE layered.puml.h5 TOLERANCE 1e-12)
+endforeach()
+foreach(variant binary binary-bigendian binary-size4)
+  pumgen_add_test(msh4.coarse-${variant}.np2 RANKS 2 SOURCE msh4 INPUT coarse-${variant}-v41.msh
+                  REFERENCE coarse.puml.h5 TOLERANCE 1e-12)
+endforeach()
+pumgen_add_test(msh4.coarse-o2-binary.np2 RANKS 2 SOURCE msh4 INPUT coarse-o2-binary-v41.msh
+                REFERENCE coarse-o2.puml.h5 TOLERANCE 1e-12 ARGS --order=2)
+pumgen_add_test(msh4.periodic-binary.np2 RANKS 2 SOURCE msh4 INPUT periodic-binary-v41.msh
+                REFERENCE periodic.puml.h5 TOLERANCE 1e-12 IDENTIFY)
+pumgen_add_test(msh4.coarse-binary-truncated RANKS 1 SOURCE msh4
+                INPUT coarse-binary-truncated-v41.msh EXPECT_ERROR "Unexpected end of file")
diff --git a/tests/ReaderTest.cpp b/tests/ReaderTest.cpp
index 75efd93..ae43e60 100644
--- a/tests/ReaderTest.cpp
+++ b/tests/ReaderTest.cpp
@@ -92,6 +92,11 @@ int main(int argc, char** argv) {
   ok &= check<puml::GMSH4Parser, 1>(fixtures + "/periodic-parametric-v41.msh");
   ok &= check<puml::GMSH4Parser, 2>(fixtures + "/coarse-o2-v41.msh");
   ok &= check<puml::GMSH2Parser, 2>(fixtures + "/coarse-o2-v22.msh");
+  ok &= check<puml::GMSH4Parser, 1>(fixtures + "/layered-binary-v41.msh");
+  ok &= check<puml::GMSH4Parser, 1>(fixtures + "/periodic-binary-v41.msh");
+  ok &= check<puml::GMSH4Parser, 1>(fixtures + "/coarse-binary-bigendian-v41.msh");
+  ok &= check<puml::GMSH4Parser, 1>(fixtures + "/coarse-binary-size4-v41.msh");
+  ok &= check<puml::GMSH4Parser, 2>(fixtures + "/coarse-o2-binary-v41.msh");
   ok &= checkSkippedSection(fixtures);
   return ok ? 0 : 1;
 }
diff --git a/tests/fixtures/coarse-binary-bigendian-v41.msh b/tests/fixtures/coarse-binary-bigendian-v41.msh
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diff --git a/tests/fixtures/generate.py b/tests/fixtures/generate.py
index 7315829..3ae5a2f 100644
--- a/tests/fixtures/generate.py
+++ b/tests/fixtures/generate.py
@@ -10,6 +10,8 @@
 """
 
 import itertools
+import os
+import struct
 
 import gmsh
 import h5py
@@ -141,6 +143,86 @@ def write_mesh(path, version, binary=False):
     gmsh.option.setNumber("Mesh.Binary", 0)
 
 
+# nodes per element type, for the element types in the fixtures
+ELEMENT_NODES = {15: 1, 1: 2, 2: 3, 4: 4, 8: 3, 9: 6, 11: 10}
+
+
+def convert_binary(source, target, byte_order, size_bytes):
+    """Rewrites a binary MSH 4.1 file (as written by gmsh: little endian, 8-byte sizes) with
+    another byte order ("<" or ">") and size of size_t (4 or 8)."""
+    with open(source, "rb") as f:
+        data = f.read()
+    pos = 0
+    out = bytearray()
+    size_format = "Q" if size_bytes == 8 else "I"
+
+    def line():
+        nonlocal pos
+        end = data.index(b"\n", pos)
+        text = data[pos:end]
+        pos = end + 1
+        return text
+
+    def get(fmt, count=1):
+        nonlocal pos
+        fmt = f"<{count}{fmt}"
+        values = struct.unpack_from(fmt, data, pos)
+        pos += struct.calcsize(fmt)
+        out.extend(struct.pack(byte_order + fmt[1:].replace("Q", size_format), *values))
+        return values
+
+    def sizes(count=1):
+        return get("Q", count)
+
+    assert line() == b"$MeshFormat" and line() == b"4.1 1 8"
+    out.extend(f"$MeshFormat\n4.1 1 {size_bytes}\n".encode())
+    assert get("i")[0] == 1
+    assert line() == b""
+    out.extend(b"\n")
+    while pos < len(data):
+        text = line()
+        out.extend(text + b"\n")
+        if text == b"$MeshFormat":
+            continue
+        if text == b"$Entities":
+            counts = sizes(4)
+            for kind, count in enumerate(counts):
+                for _ in range(count):
+                    get("i")
+                    get("d", 3 if kind == 0 else 6)
+                    get("i", sizes()[0])
+                    if kind > 0:
+                        get("i", sizes()[0])
+        elif text == b"$Nodes":
+            num_blocks = sizes(4)[0]
+            for _ in range(num_blocks):
+                dim, _, parametric = get("i", 3)
+                count = sizes()[0]
+                sizes(count)
+                get("d", count * (3 + (dim if parametric else 0)))
+        elif text == b"$Elements":
+            num_blocks = sizes(4)[0]
+            for _ in range(num_blocks):
+                _, _, element_type = get("i", 3)
+                count = sizes()[0]
+                sizes(count * (1 + ELEMENT_NODES[element_type]))
+        elif text == b"$Periodic":
+            for _ in range(sizes()[0]):
+                get("i", 3)
+                get("d", sizes()[0])
+                sizes(2 * sizes()[0])
+        elif text.startswith(b"$End"):
+            continue
+        else:
+            raise ValueError(f"unexpected section {text}")
+        assert line() == b""
+        end = line()
+        assert end == b"$End" + text[1:]
+        out.extend(b"\n" + end + b"\n")
+    with open(target, "wb") as f:
+        f.write(out)
+
+
 def counts_exercise_chunking(count):
     # the element/vertex counts are chosen such that the default chunk distribution differs
     # from a ceil-based one for 3 and for 4 ranks
@@ -157,6 +239,7 @@ def generate_layered():
     print(f"layered: {len(cells)} cells, {len(vertices)} vertices, size {size_top:.4f}")
 
     write_mesh("layered-v41.msh", 4.1)
+    write_mesh("layered-binary-v41.msh", 4.1, binary=True)
     write_mesh("layered-v22.msh", 2.2)
     gmsh.write("layered.neu")
     write_reference("layered.puml.h5", "layered-v41.msh")
@@ -179,12 +262,25 @@ def generate_coarse():
 
     gmsh.model.mesh.setOrder(2)
     write_mesh("coarse-o2-v41.msh", 4.1)
+    write_mesh("coarse-o2-binary-v41.msh", 4.1, binary=True)
     write_mesh("coarse-o2-v22.msh", 2.2)
     gmsh.model.mesh.setOrder(1)
 
     gmsh.model.mesh.partition(2)
     write_mesh("coarse-partitioned-v41.msh", 4.1)
 
+    # the converter reproduces gmsh's layout exactly before it is used for other layouts
+    convert_binary("coarse-binary-v41.msh", "coarse-binary-copy.msh", "<", 8)
+    with open("coarse-binary-v41.msh", "rb") as a, open("coarse-binary-copy.msh", "rb") as b:
+        assert a.read() == b.read()
+    os.remove("coarse-binary-copy.msh")
+    convert_binary("coarse-binary-v41.msh", "coarse-binary-bigendian-v41.msh", ">", 8)
+    convert_binary("coarse-binary-v41.msh", "coarse-binary-size4-v41.msh", "<", 4)
+    with open("coarse-binary-v41.msh", "rb") as f:
+        data = f.read()
+    with open("coarse-binary-truncated-v41.msh", "wb") as f:
+        f.write(data[: data.index(b"$Elements") + 400])
+
     write_reference("coarse.puml.h5", "coarse-v41.msh")
     write_reference("coarse-o2.puml.h5", "coarse-o2-v41.msh")
 
@@ -204,6 +300,7 @@ def generate_periodic():
     gmsh.option.setNumber("Mesh.MeshSizeMax", 0.4)
     gmsh.model.mesh.generate(3)
     write_mesh("periodic-v41.msh", 4.1)
+    write_mesh("periodic-binary-v41.msh", 4.1, binary=True)
     gmsh.option.setNumber("Mesh.SaveParametric", 1)
     write_mesh("periodic-parametric-v41.msh", 4.1)
     gmsh.option.setNumber("Mesh.SaveParametric", 0)
diff --git a/tests/fixtures/layered-binary-v41.msh b/tests/fixtures/layered-binary-v41.msh
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diff --git a/tests/fixtures/periodic-binary-v41.msh b/tests/fixtures/periodic-binary-v41.msh
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zS1*j&x$@?JyPo`SpUMC2y#C+Ljr-V#nqXJ37T67}4c-sd0lR~B!5*OR+&z))HG3g9
z0DFTC!3V%bpzo}Wk$o3!g4`Eu3ibn=f&Ibe;6q>w@L{keH~_o@d<3*79*FF_+@r{?
zz(Jtj2nHj!0Ura~f_^i;8+j<$4jcyF13nJk3l0a{gCoEW;7G6|I120pjs`n}W56!p
K+1@#&WBxz$B~F0=

literal 0
HcmV?d00001


From e720b2269d759c666b04e1bb2a89f0eb222f405e Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 19:36:42 +0000
Subject: [PATCH 12/19] Run the single-rank error tests without mpiexec

In one of about 90 runs, a test expecting an error did not see pumgen's error
message: mpiexec may drop the output of a process which ends with MPI_Abort.
The tests expecting an error on one rank now start pumgen as MPI singleton,
which also shortens them from about 2.3 s to 0.35 s each.

AI-generated. Model: Claude Opus 5.5
---
 tests/CMakeLists.txt | 27 +++++++++++++++------------
 1 file changed, 15 insertions(+), 12 deletions(-)

diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 066b0ff..eb510a5 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -18,18 +18,21 @@ function(pumgen_add_test name)
   cmake_parse_arguments(PARSE_ARGV 1 TEST "IDENTIFY"
                         "RANKS;SOURCE;INPUT;REFERENCE;TOLERANCE;EXPECT_OUTPUT;EXPECT_ERROR" "ARGS")
   set(output ${PUMGEN_TEST_OUTPUT}/${name}.puml.h5)
-  set(command
-      ${MPIEXEC_EXECUTABLE}
-      ${MPIEXEC_NUMPROC_FLAG}
-      ${TEST_RANKS}
-      ${MPIEXEC_PREFLAGS}
-      $<TARGET_FILE:pumgen>
-      ${MPIEXEC_POSTFLAGS}
-      -s
-      ${TEST_SOURCE}
-      ${TEST_ARGS}
-      ${PUMGEN_TEST_FIXTURES}/${TEST_INPUT}
-      ${output})
+  if(DEFINED TEST_EXPECT_ERROR AND TEST_RANKS EQUAL 1)
+    # started as MPI singleton, since mpiexec may drop the output of a process ending with
+    # MPI_Abort
+    set(command $<TARGET_FILE:pumgen>)
+  else()
+    set(command
+        ${MPIEXEC_EXECUTABLE}
+        ${MPIEXEC_NUMPROC_FLAG}
+        ${TEST_RANKS}
+        ${MPIEXEC_PREFLAGS}
+        $<TARGET_FILE:pumgen>
+        ${MPIEXEC_POSTFLAGS})
+  endif()
+  list(APPEND command -s ${TEST_SOURCE} ${TEST_ARGS} ${PUMGEN_TEST_FIXTURES}/${TEST_INPUT}
+       ${output})
   string(REPLACE ";" "|" command "${command}")
 
   set(script_args -DCOMMAND=${command} -DOUTPUT=${output})

From a7cf1b990abb9e783a0463e71b5c06536889b7fb Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 19:42:02 +0000
Subject: [PATCH 13/19] Speed up the boundary condition matching of GMSH meshes

The matching kept a list of adjacent surface facets for every vertex and
intersected these lists for each face of each cell. It now marks the vertices
of the surface mesh and looks up only the faces of cells with at least three
such vertices, in the surface faces sorted by their vertices. On the mesh with
3.6M cells (151016 boundary faces), 161886 faces remain to be looked up; the
matching takes 0.105 s instead of 0.21 s, and the peak memory of reading the
mesh drops from 230 MB to 215 MB. The results are identical.

Adds a test for a surface face given twice, which remains an error.

AI-generated. Model: Claude Opus 5.5
---
 src/meshreader/ParallelGMSHReader.h       | 96 +++++++++++++----------
 tests/CMakeLists.txt                      |  4 +
 tests/fixtures/generate.py                |  3 +
 tests/fixtures/tiny-duplicateface-v22.msh | 16 ++++
 4 files changed, 78 insertions(+), 41 deletions(-)
 create mode 100644 tests/fixtures/tiny-duplicateface-v22.msh

diff --git a/src/meshreader/ParallelGMSHReader.h b/src/meshreader/ParallelGMSHReader.h
index 0a9ac26..6e6d8b7 100644
--- a/src/meshreader/ParallelGMSHReader.h
+++ b/src/meshreader/ParallelGMSHReader.h
@@ -12,7 +12,9 @@
 #include <mpi.h>
 
 #include <algorithm>
+#include <array>
 #include <cstddef>
+#include <cstdint>
 #include <iostream>
 #include <vector>
 
@@ -86,53 +88,65 @@ template <typename P, std::size_t OrderP> class ParallelGMSHReader {
    * with the surface mesh.
    */
   void convertBoundaryConditions() {
-    const auto nVerts = builder_.vertices.size();
-    const auto nFacets = builder_.facets.size();
-    const auto nElements = builder_.elements.size();
-
-    bcs_.clear();
-    bcs_.resize(nElements);
-
-    constexpr auto nFacetsPerTet = Dim + 1u;
-    constexpr auto nVertsPerTri = Dim;
-
-    // vertex to triangle map
-    std::vector<std::vector<std::size_t>> vertex2facets(nVerts);
-    for (std::size_t fctNo = 0; fctNo < nFacets; ++fctNo) {
-      for (auto const& vtxNo : builder_.facets[fctNo]) {
-        vertex2facets[vtxNo].push_back(fctNo);
+    using Face = std::array<std::size_t, Dim>;
+    struct BoundaryFace {
+      Face vertices;
+      int bc;
+    };
+    const auto sortedFace = [](Face face) {
+      std::sort(face.begin(), face.end());
+      return face;
+    };
+
+    // the surface mesh as sorted vertex triples; the vertices of a facet come first
+    std::vector<std::uint8_t> onBoundary(builder_.vertices.size(), 0);
+    std::vector<BoundaryFace> boundaryFaces(builder_.facets.size());
+    for (std::size_t fctNo = 0; fctNo < builder_.facets.size(); ++fctNo) {
+      Face face{};
+      for (std::size_t i = 0; i < Dim; ++i) {
+        face[i] = builder_.facets[fctNo][i];
+        onBoundary[face[i]] = 1;
       }
+      boundaryFaces[fctNo] = {sortedFace(face), builder_.bcs[fctNo]};
     }
-    for (auto& v2f : vertex2facets) {
-      std::sort(v2f.begin(), v2f.end());
-    }
+    const auto byVertices = [](const BoundaryFace& a, const BoundaryFace& b) {
+      return a.vertices < b.vertices;
+    };
+    std::sort(boundaryFaces.begin(), boundaryFaces.end(), byVertices);
 
+    const auto nElements = builder_.elements.size();
+    bcs_.assign(nElements, bc_t{});
     for (std::size_t elNo = 0; elNo < nElements; ++elNo) {
-      for (int localFctNo = 0; localFctNo < nFacetsPerTet; ++localFctNo) {
-        std::array<std::size_t, nVertsPerTri> nodes;
-        for (int localNo = 0; localNo < nVertsPerTri; ++localNo) {
-          const auto localNoElement = Facet2Nodes[localFctNo][localNo];
-          nodes[localNo] = builder_.elements[elNo][localNoElement];
+      const auto& element = builder_.elements[elNo];
+      // only faces with all vertices on the surface mesh can be part of it
+      std::array<bool, Dim + 1> vertexOnBoundary{};
+      std::size_t verticesOnBoundary = 0;
+      for (std::size_t i = 0; i < Dim + 1; ++i) {
+        vertexOnBoundary[i] = onBoundary[element[i]] != 0;
+        verticesOnBoundary += vertexOnBoundary[i] ? 1 : 0;
+      }
+      if (verticesOnBoundary < Dim) {
+        continue;
+      }
+      for (std::size_t localFctNo = 0; localFctNo < Dim + 1; ++localFctNo) {
+        Face face{};
+        bool candidate = true;
+        for (std::size_t i = 0; i < Dim; ++i) {
+          const auto localVertex = Facet2Nodes[localFctNo][i];
+          candidate = candidate && vertexOnBoundary[localVertex];
+          face[i] = element[localVertex];
+        }
+        if (!candidate) {
+          continue;
         }
-        std::array<std::vector<std::size_t>, nVertsPerTri - 1> intersect;
-        std::set_intersection(vertex2facets[nodes[0]].begin(), vertex2facets[nodes[0]].end(),
-                              vertex2facets[nodes[1]].begin(), vertex2facets[nodes[1]].end(),
-                              std::back_inserter(intersect[0]));
-        for (int node = 2; node < nVertsPerTri; ++node) {
-          std::set_intersection(intersect[node - 2].begin(), intersect[node - 2].end(),
-                                vertex2facets[nodes[node]].begin(),
-                                vertex2facets[nodes[node]].end(),
-                                std::back_inserter(intersect[node - 1]));
+        const BoundaryFace key{sortedFace(face), 0};
+        const auto [first, last] =
+            std::equal_range(boundaryFaces.begin(), boundaryFaces.end(), key, byVertices);
+        if (last - first > 1) {
+          logError() << "A face of an element exists multiple times in the surface mesh.";
         }
-        if (!intersect[nVertsPerTri - 2].empty()) {
-          if (intersect[nVertsPerTri - 2].size() > 1) {
-            logError() << "A face of an element exists multiple times in the "
-                          "surface mesh.";
-          }
-          const auto fctNo = intersect[nVertsPerTri - 2][0];
-          bcs_[elNo][localFctNo] = adjustBoundaryCondition(builder_.bcs[fctNo]);
-        } else {
-          bcs_[elNo][localFctNo] = 0;
+        if (first != last) {
+          bcs_[elNo][localFctNo] = adjustBoundaryCondition(first->bc);
         }
       }
     }
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index eb510a5..117e837 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -185,3 +185,7 @@ pumgen_add_test(msh4.periodic-binary.np2 RANKS 2 SOURCE msh4 INPUT periodic-bina
                 REFERENCE periodic.puml.h5 TOLERANCE 1e-12 IDENTIFY)
 pumgen_add_test(msh4.coarse-binary-truncated RANKS 1 SOURCE msh4
                 INPUT coarse-binary-truncated-v41.msh EXPECT_ERROR "Unexpected end of file")
+
+# a face of the surface mesh given twice
+pumgen_add_test(msh2.tiny-duplicateface RANKS 1 SOURCE msh2 INPUT tiny-duplicateface-v22.msh
+                EXPECT_ERROR "exists multiple times in the surface mesh")
diff --git a/tests/fixtures/generate.py b/tests/fixtures/generate.py
index 3ae5a2f..c75b460 100644
--- a/tests/fixtures/generate.py
+++ b/tests/fixtures/generate.py
@@ -366,6 +366,9 @@ def generate_tiny():
         "tiny-v22.msh": TINY_V22,
         "tiny-duplicate-v22.msh": TINY_V22.replace("3 0 1 0", "2 0 1 0"),
         "tiny-badnode-v22.msh": TINY_V22.replace("1 2 3 4\n$EndElements", "1 2 3 9\n$EndElements"),
+        "tiny-duplicateface-v22.msh": TINY_V22.replace(
+            "1\n1 4 2 7 1 1 2 3 4\n", "3\n1 4 2 7 1 1 2 3 4\n2 2 2 101 1 1 3 2\n3 2 2 105 1 2 1 3\n"
+        ),
     }
     for name, content in variants.items():
         with open(name, "w") as out:
diff --git a/tests/fixtures/tiny-duplicateface-v22.msh b/tests/fixtures/tiny-duplicateface-v22.msh
new file mode 100644
index 0000000..7d9288e
--- /dev/null
+++ b/tests/fixtures/tiny-duplicateface-v22.msh
@@ -0,0 +1,16 @@
+$MeshFormat
+2.2 0 8
+$EndMeshFormat
+$Nodes
+4
+1 0 0 0
+2 1 0 0
+3 0 1 0
+4 0 0 1
+$EndNodes
+$Elements
+3
+1 4 2 7 1 1 2 3 4
+2 2 2 101 1 1 3 2
+3 2 2 105 1 2 1 3
+$EndElements

From 6db9f7a7bf474988e0328dd4bbf0ed4d18e921c8 Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 19:45:44 +0000
Subject: [PATCH 14/19] Release the GMSH mesh on rank 0 once it is distributed

Rank 0 kept the complete parsed mesh until pumgen ended, i.e. also while
computing the inspheres and writing. Each part (vertices, elements, groups,
boundary conditions, identification) is now released right after it has been
scattered, and the surface mesh right after the boundary conditions have been
matched. On the mesh with 3.6M cells and one rank, the memory after reading
drops from 392 MB to 192 MB and the peak of the whole run from 534 MB to
388 MB; the peak is now reached while the elements are scattered.

The scatter no longer dereferences the data of empty vectors on the other
ranks.

AI-generated. Model: Claude Opus 5.5
---
 src/meshreader/ParallelGMSHReader.h | 38 +++++++++++++++++++++++------
 1 file changed, 30 insertions(+), 8 deletions(-)

diff --git a/src/meshreader/ParallelGMSHReader.h b/src/meshreader/ParallelGMSHReader.h
index 6e6d8b7..718cca8 100644
--- a/src/meshreader/ParallelGMSHReader.h
+++ b/src/meshreader/ParallelGMSHReader.h
@@ -46,6 +46,8 @@ template <typename P, std::size_t OrderP> class ParallelGMSHReader {
       }
       builder_.postprocess();
       convertBoundaryConditions();
+      release(builder_.facets);
+      release(builder_.bcs);
 
       nVertices_ = builder_.vertices.size();
       nElements_ = builder_.elements.size();
@@ -59,28 +61,48 @@ template <typename P, std::size_t OrderP> class ParallelGMSHReader {
 
   [[nodiscard]] std::size_t nVertices() const { return nVertices_; }
   [[nodiscard]] std::size_t nElements() const { return nElements_; }
-  void readElements(std::size_t* elements) const {
+
+  // Each read function distributes one part of the mesh and releases it on rank 0 afterwards, so
+  // it can be called only once.
+
+  void readElements(std::size_t* elements) {
     static_assert(sizeof(typename GMSHBuilder<Dim, Order>::element_t) ==
                   nodeCount(Dim, Order) * sizeof(std::size_t));
-    scatter(builder_.elements.data()->data(), elements, nElements(), nodeCount(Dim, Order));
+    scatter(flatData(builder_.elements), elements, nElements(), nodeCount(Dim, Order));
+    release(builder_.elements);
   }
-  void readVertices(double* vertices) const {
+  void readVertices(double* vertices) {
     static_assert(sizeof(typename GMSHBuilder<Dim, Order>::vertex_t) == Dim * sizeof(double));
-    scatter(builder_.vertices.data()->data(), vertices, nVertices(), Dim);
+    scatter(flatData(builder_.vertices), vertices, nVertices(), Dim);
+    release(builder_.vertices);
   }
-  void readBoundaries(int* boundaries) const {
+  void readBoundaries(int* boundaries) {
     static_assert(sizeof(bc_t) == (Dim + 1) * sizeof(int));
-    scatter(bcs_.data()->data(), boundaries, nElements(), Dim + 1);
+    scatter(flatData(bcs_), boundaries, nElements(), Dim + 1);
+    release(bcs_);
+  }
+  void readGroups(int* groups) {
+    scatter(builder_.groups.data(), groups, nElements(), 1);
+    release(builder_.groups);
   }
-  void readGroups(int* groups) const { scatter(builder_.groups.data(), groups, nElements(), 1); }
 
   constexpr static bool SupportsIdentify = true;
   bool hasIdentify() const { return hasIdentify_ != 0; }
-  void readIdentify(std::size_t* vertices) const {
+  void readIdentify(std::size_t* vertices) {
     scatter(builder_.identify.data(), vertices, nVertices(), 1);
+    release(builder_.identify);
   }
 
   private:
+  template <typename T, std::size_t N>
+  static const T* flatData(const std::vector<std::array<T, N>>& values) {
+    return values.empty() ? nullptr : values.front().data();
+  }
+
+  template <typename T> static void release(std::vector<T>& values) {
+    std::vector<T>().swap(values);
+  }
+
   /**
    * GMSH stores boundary conditions on a surface mesh whereas SeisSol expects
    * boundary conditions to be stored per element. In the following we convert

From 7f29207a83cb6b3f29a8009ea1072599a4a37242 Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 19:56:33 +0000
Subject: [PATCH 15/19] Separate the velocity-aware mesh size from SimModSuite

The settings of velocity-aware meshing (refinement cuboids, frequency, easi
file, elements per wavelength) and their XML parsing move from MeshAttributes
to src/sizing, as does the mesh size computation from EasiMeshSize, which now
evaluates the easi model for many points at once. EasiMeshSize keeps only the
SimModSuite part, i.e. finding the region of a point, and passes single points
to the shared computation; the settings and the size formula stay the same.

easi becomes a dependency of its own (option EASI, implied by SIMMETRIX), so
that tools without SimModSuite can use the same settings and sizes.

AI-generated. Model: Claude Opus 5.5
---
 CMakeLists.txt                       |  24 ++++-
 src/input/EasiMeshSize.cpp           |  90 +++----------------
 src/input/EasiMeshSize.h             |  25 ++----
 src/input/MeshAttributes.cpp         |  89 +-----------------
 src/input/MeshAttributes.h           |  41 +--------
 src/sizing/VelocityAwareMeshSize.cpp |  98 ++++++++++++++++++++
 src/sizing/VelocityAwareMeshSize.h   |  54 +++++++++++
 src/sizing/VelocityAwareSettings.cpp | 129 +++++++++++++++++++++++++++
 src/sizing/VelocityAwareSettings.h   |  74 +++++++++++++++
 9 files changed, 398 insertions(+), 226 deletions(-)
 create mode 100644 src/sizing/VelocityAwareMeshSize.cpp
 create mode 100644 src/sizing/VelocityAwareMeshSize.h
 create mode 100644 src/sizing/VelocityAwareSettings.cpp
 create mode 100644 src/sizing/VelocityAwareSettings.h

diff --git a/CMakeLists.txt b/CMakeLists.txt
index be1cf15..4333aa5 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -13,6 +13,7 @@ set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fno-omit-frame-pointer -fsa
 set(CMAKE_LINKER_FLAGS_DEBUG "${CMAKE_LINKER_FLAGS_DEBUG} -fno-omit-frame-pointer -fsanitize=address")
 
 option(SIMMETRIX "Use simmetrix libraries" OFF)
+option(EASI "Build the velocity-aware sizing with easi (always on with SIMMETRIX)" OFF)
 set(SIMMETRIX_ROOT "" CACHE STRING "Root directory of simmetrix dev files")
 set(SIM_MPI "" CACHE STRING "MPI version used by simmetrix")
 option(NETCDF "Use netcdf" OFF)
@@ -93,10 +94,6 @@ target_link_libraries(pumgen PUBLIC tinyxml2)
 if (SIMMETRIX)
     find_package(SIMMETRIX REQUIRED)
 
-    # easi
-    find_package(easi 1.0.0 REQUIRED)
-    target_link_libraries(pumgen PUBLIC easi::easi)
-
     target_sources(pumgen PUBLIC
       ${CMAKE_CURRENT_SOURCE_DIR}/src/input/AnalysisAttributes.cpp
       ${CMAKE_CURRENT_SOURCE_DIR}/src/input/EasiMeshSize.cpp
@@ -134,6 +131,25 @@ endfunction()
 
 cast_log_level_to_int(LOG_LEVEL LOG_LEVEL)
 target_compile_definitions(pumgen PUBLIC LOG_LEVEL=${LOG_LEVEL})
+
+if (SIMMETRIX)
+  set(EASI ON)
+endif()
+if (EASI)
+  find_package(easi 1.0.0 REQUIRED)
+  add_library(pumgen_sizing STATIC
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/sizing/VelocityAwareSettings.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/sizing/VelocityAwareMeshSize.cpp
+  )
+  target_include_directories(pumgen_sizing PUBLIC
+    ${CMAKE_CURRENT_SOURCE_DIR}/src
+    ${CMAKE_CURRENT_SOURCE_DIR}/submodules
+  )
+  target_compile_definitions(pumgen_sizing PRIVATE LOG_LEVEL=${LOG_LEVEL})
+  target_link_libraries(pumgen_sizing PUBLIC easi::easi tinyxml2)
+  target_link_libraries(pumgen PUBLIC pumgen_sizing)
+  target_compile_definitions(pumgen PUBLIC USE_EASI)
+endif()
 if(SIMMETRIX)
   set(INSTALL_RPATH "${SIM_PS_KRNL_LIB_DIR}:${INSTALL_RPATH}")
 endif()
diff --git a/src/input/EasiMeshSize.cpp b/src/input/EasiMeshSize.cpp
index 6c82a96..d4a9e82 100644
--- a/src/input/EasiMeshSize.cpp
+++ b/src/input/EasiMeshSize.cpp
@@ -2,20 +2,15 @@
 //
 // SPDX-License-Identifier: BSD-3-Clause
 #include "EasiMeshSize.h"
-#include <unordered_map>
-#include <utils/logger.h>
 
-#include <tuple>
+#include <cassert>
+#include <limits>
 #include <utility>
 
-EasiMeshSize::EasiMeshSize() : parser(nullptr), model(nullptr) {}
-
-EasiMeshSize::EasiMeshSize(VelocityAwareRefinementSettings refinementSettings, pGModel simModel,
-                           std::unordered_map<pGRegion, int> groupMap)
-    : refinementSettings(refinementSettings), simModel(simModel), parser(new easi::YAMLParser(3)),
-      groupMap(std::move(groupMap)) {
-  model = parser->parse(refinementSettings.getEasiFileName());
-}
+EasiMeshSize::EasiMeshSize(const VelocityAwareRefinementSettings& refinementSettings,
+                           pGModel simModel, std::unordered_map<pGRegion, int> groupMap)
+    : meshSize(std::make_shared<VelocityAwareMeshSize>(refinementSettings)), simModel(simModel),
+      groupMap(std::move(groupMap)) {}
 
 int EasiMeshSize::findGroup(std::array<double, 3> point) {
   // GR_containsPoint can be expensive for large geometry,
@@ -34,77 +29,20 @@ int EasiMeshSize::findGroup(std::array<double, 3> point) {
   return -1;
 }
 
-std::tuple<const double, const int>
-EasiMeshSize::getTargetedFrequencyAndRegion(const std::array<double, 3>& point) {
-  const auto& refinementRegions = refinementSettings.getRefinementRegions();
-  double targetedFrequency = 0.0;
-  int bypassFindRegionAndUseGroup = 0;
-  for (const auto& refinementCube : refinementRegions) {
-    auto& cuboid = refinementCube.cuboid;
-    bool isInCuboid = true;
-
-    double u0 = (point[0] - cuboid.center[0]) * cuboid.cosSinRotationZ[0] +
-                (point[1] - cuboid.center[1]) * cuboid.cosSinRotationZ[1];
-    isInCuboid &= std::abs(u0) <= cuboid.halfSize[0];
-    double u1 = (point[0] - cuboid.center[0]) * -cuboid.cosSinRotationZ[1] +
-                (point[1] - cuboid.center[1]) * cuboid.cosSinRotationZ[0];
-    isInCuboid &= std::abs(u1) <= cuboid.halfSize[1];
-    double u2 = (point[2] - cuboid.center[2]);
-    isInCuboid &= std::abs(u2) <= cuboid.halfSize[2];
-
-    if (isInCuboid) {
-      if (refinementCube.targetedFrequency >= targetedFrequency) {
-        bypassFindRegionAndUseGroup = refinementCube.bypassFindRegionAndUseGroup;
-      }
-      targetedFrequency = std::max(targetedFrequency, refinementCube.targetedFrequency);
-    }
-  }
-  return std::make_tuple(targetedFrequency, bypassFindRegionAndUseGroup);
-}
-
 double EasiMeshSize::getMeshSize(const std::array<double, 3>& point) {
-  if (!model) {
-    logError() << "Model was not parsed correctly";
-  }
-
-  constexpr double defaultMeshSize = std::numeric_limits<double>::max();
+  constexpr double DefaultMeshSize = std::numeric_limits<double>::max();
   const auto [targetedFrequency, bypassFindRegionAndUseGroup] =
-      getTargetedFrequencyAndRegion(point);
-
+      meshSize->targetedFrequencyAndGroup(point);
   if (targetedFrequency == 0.0) {
-    return defaultMeshSize;
+    return DefaultMeshSize;
   }
 
-  easi::Query query(1, 3);
-  query.x(0, 0) = point[0];
-  query.x(0, 1) = point[1];
-  query.x(0, 2) = point[2];
-  query.group(0) = bypassFindRegionAndUseGroup ? bypassFindRegionAndUseGroup : findGroup(point);
-
+  const int group =
+      bypassFindRegionAndUseGroup != 0 ? bypassFindRegionAndUseGroup : findGroup(point);
   // This means the point is slightly outside the geometry
-  if (query.group(0) <= 0) {
-    return defaultMeshSize;
-  }
-
-  // Need array for easi interface
-  auto materials = std::array<ElasticMaterial, 1>();
-  auto& material = materials[0];
-  auto adapter = easi::ArrayOfStructsAdapter<ElasticMaterial>(materials.data());
-  adapter.addBindingPoint("lambda", &ElasticMaterial::lambda);
-  adapter.addBindingPoint("mu", &ElasticMaterial::mu);
-  adapter.addBindingPoint("rho", &ElasticMaterial::rho);
-
-  model->evaluate(query, adapter);
-
-  double waveSpeed = 0.0;
-  if (material.mu < 10e-14) {
-    // acoustic
-    waveSpeed = std::sqrt((material.lambda + 2 * material.mu) / material.rho);
-  } else {
-    // elastic
-    waveSpeed = std::sqrt(material.mu / material.rho);
+  if (group <= 0) {
+    return DefaultMeshSize;
   }
 
-  const auto waveLength = waveSpeed / targetedFrequency;
-  return waveLength / refinementSettings.getElementsPerWaveLength();
+  return meshSize->meshSizes({point}, {group}, {targetedFrequency})[0];
 }
diff --git a/src/input/EasiMeshSize.h b/src/input/EasiMeshSize.h
index a9fa62e..1df68ea 100644
--- a/src/input/EasiMeshSize.h
+++ b/src/input/EasiMeshSize.h
@@ -4,37 +4,26 @@
 #ifndef PUMGEN_SRC_INPUT_EASIMESHSIZE_H_
 #define PUMGEN_SRC_INPUT_EASIMESHSIZE_H_
 
-#include "MeshAttributes.h"
+#include "sizing/VelocityAwareMeshSize.h"
 #include <MeshTypes.h>
 #include <SimModel.h>
 #include <array>
-#include <easi/Component.h>
-#include <easi/YAMLParser.h>
 #include <memory>
-#include <string>
-
-struct ElasticMaterial {
-  double lambda, mu, rho;
-};
+#include <unordered_map>
 
+/**
+ * Velocity-aware mesh size for SimModSuite, which asks for one point at a time.
+ */
 class EasiMeshSize {
   private:
-  VelocityAwareRefinementSettings refinementSettings;
-
-  easi::YAMLParser* parser;
-  easi::Component* model; // Unique ptr to model leads to segfault
+  std::shared_ptr<VelocityAwareMeshSize> meshSize;
   pGModel simModel;
   std::unordered_map<pGRegion, int> groupMap;
 
   int findGroup(std::array<double, 3> point);
 
-  std::tuple<const double, const int>
-  getTargetedFrequencyAndRegion(const std::array<double, 3>& point);
-
   public:
-  EasiMeshSize();
-  ;
-  EasiMeshSize(VelocityAwareRefinementSettings refinementSettings, pGModel simModel,
+  EasiMeshSize(const VelocityAwareRefinementSettings& refinementSettings, pGModel simModel,
                std::unordered_map<pGRegion, int> groupMap);
 
   double getMeshSize(const std::array<double, 3>& point);
diff --git a/src/input/MeshAttributes.cpp b/src/input/MeshAttributes.cpp
index 4559e6f..500e40a 100644
--- a/src/input/MeshAttributes.cpp
+++ b/src/input/MeshAttributes.cpp
@@ -3,31 +3,6 @@
 // SPDX-License-Identifier: BSD-3-Clause
 #include "MeshAttributes.h"
 
-VelocityAwareRefinementSettings::VelocityAwareRefinementSettings(double elementsPerWaveLength,
-                                                                 std::string easiFileName)
-    : elementsPerWaveLength(elementsPerWaveLength), easiFileName(std::move(easiFileName)) {}
-
-void VelocityAwareRefinementSettings::addRefinementRegion(SimpleCuboid cuboid,
-                                                          double targetedFrequency,
-                                                          int bypassFindRegionAndUseGroup) {
-  refinementRegions.emplace_back(cuboid, targetedFrequency, bypassFindRegionAndUseGroup);
-}
-
-bool VelocityAwareRefinementSettings::isVelocityAwareRefinementOn() const {
-  return !refinementRegions.empty();
-}
-
-const std::string& VelocityAwareRefinementSettings::getEasiFileName() const { return easiFileName; }
-
-double VelocityAwareRefinementSettings::getElementsPerWaveLength() const {
-  return elementsPerWaveLength;
-}
-
-const std::vector<VelocityRefinementCube>&
-VelocityAwareRefinementSettings::getRefinementRegions() const {
-  return refinementRegions;
-}
-
 MeshAttributes::MeshAttributes()
     : lpair_lVertexId_MSize(), lpair_lEdgeId_MSize(), lpair_lFaceId_MSize(),
       lpair_lRegionId_MSize() {}
@@ -168,69 +143,7 @@ void MeshAttributes::set_regionMSize() {
 }
 
 void MeshAttributes::set_velocity_aware_meshing() {
-  int numChilds = 0;
-  const auto name = "VelocityAwareMeshing";
-  for (auto velocityAwareMeshingElement = doc.FirstChildElement(name); velocityAwareMeshingElement;
-       velocityAwareMeshingElement = velocityAwareMeshingElement->NextSiblingElement(name)) {
-    const auto easiFileName = velocityAwareMeshingElement->Attribute("easiFile");
-    const auto elementsPerWaveLength =
-        std::stof(velocityAwareMeshingElement->Attribute("elementsPerWaveLength"));
-    velocityAwareRefinementSettings =
-        VelocityAwareRefinementSettings(elementsPerWaveLength, easiFileName);
-    constexpr auto cuboidName = "VelocityRefinementCuboid";
-    logInfo() << "Activating velocity aware meshing, using" << elementsPerWaveLength
-              << "elements per wavelength and easi file" << easiFileName;
-    for (auto child = velocityAwareMeshingElement->FirstChildElement(cuboidName); child;
-         child = child->NextSiblingElement(cuboidName)) {
-
-      const char* attr = child->Attribute("rotationZAnticlockwiseFromX");
-      double rotationZAnticlockwiseFromX = 0.0;
-      if (attr != nullptr) {
-        rotationZAnticlockwiseFromX = std::stof(attr);
-      }
-      attr = child->Attribute("bypassFindRegionAndUseGroup");
-      int bypassFindRegionAndUseGroup = 0;
-      if (attr != nullptr) {
-        bypassFindRegionAndUseGroup = std::stoi(attr);
-      }
-      auto cuboid = SimpleCuboid{{
-                                     std::stof(child->Attribute("centerX")),
-                                     std::stof(child->Attribute("centerY")),
-                                     std::stof(child->Attribute("centerZ")),
-                                 },
-                                 {
-                                     std::stof(child->Attribute("halfSizeX")),
-                                     std::stof(child->Attribute("halfSizeY")),
-                                     std::stof(child->Attribute("halfSizeZ")),
-                                 },
-                                 {std::cos(rotationZAnticlockwiseFromX * toRadians),
-                                  std::sin(rotationZAnticlockwiseFromX * toRadians)},
-                                 rotationZAnticlockwiseFromX};
-      const auto targetedFrequency = std::stof(child->Attribute("frequency"));
-
-      velocityAwareRefinementSettings.addRefinementRegion(cuboid, targetedFrequency,
-                                                          bypassFindRegionAndUseGroup);
-      logInfo() << "Adding velocity aware refinement region targeting" << targetedFrequency
-                << "Hz, centered at x =" << cuboid.center[0] << "y=" << cuboid.center[1]
-                << "z=" << cuboid.center[2] << "with half sizes"
-                << "x =" << cuboid.halfSize[0] << "y =" << cuboid.halfSize[1]
-                << "z =" << cuboid.halfSize[2];
-      if (std::abs(cuboid.rotationZ) > 0.0) {
-        logInfo() << "rotated around z axis by " << cuboid.rotationZ
-                  << "degree(s) counterclockwise from x axis.";
-      }
-      if (bypassFindRegionAndUseGroup) {
-        logInfo() << "bypass findRegion and use group =" << bypassFindRegionAndUseGroup;
-      }
-    }
-    if (!velocityAwareRefinementSettings.isVelocityAwareRefinementOn()) {
-      logWarning() << "Activated velocity aware meshing but did not specify any refinement region!";
-    }
-    ++numChilds;
-  }
-  if (numChilds > 1) {
-    logError() << "Multiple definitions of velocityAwareMeshing";
-  }
+  velocityAwareRefinementSettings = readVelocityAwareSettings(doc);
 }
 
 void MeshAttributes::set_global_mesh_attributes() {
diff --git a/src/input/MeshAttributes.h b/src/input/MeshAttributes.h
index cac7e40..337e743 100644
--- a/src/input/MeshAttributes.h
+++ b/src/input/MeshAttributes.h
@@ -10,6 +10,7 @@
 #include <list>
 #include <string>
 
+#include "sizing/VelocityAwareSettings.h"
 #include "split.h"
 #include "tinyxml2/tinyxml2.h"
 #include "utils/logger.h"
@@ -25,46 +26,6 @@ struct Cube {
   double CubeMSize = 0, CubeCenter[3], CubeWidth[3], CubeHeight[3], CubeDepth[3];
 };
 
-struct SimpleCuboid {
-  std::array<double, 3> center;
-  std::array<double, 3> halfSize;
-  std::array<double, 2> cosSinRotationZ;
-  double rotationZ;
-};
-
-struct VelocityRefinementCube {
-  VelocityRefinementCube(SimpleCuboid cuboid, double targetedFrequency,
-                         int bypassFindRegionAndUseGroup)
-      : cuboid(cuboid), targetedFrequency(targetedFrequency),
-        bypassFindRegionAndUseGroup(bypassFindRegionAndUseGroup) {};
-
-  SimpleCuboid cuboid;
-  double targetedFrequency;
-  int bypassFindRegionAndUseGroup;
-};
-
-class VelocityAwareRefinementSettings {
-  public:
-  VelocityAwareRefinementSettings() = default;
-  VelocityAwareRefinementSettings(double elementsPerWaveLength, std::string easiFileName);
-
-  void addRefinementRegion(SimpleCuboid cuboid, double targetedFrequency,
-                           int bypassFindRegionAndUseGroup);
-
-  [[nodiscard]] bool isVelocityAwareRefinementOn() const;
-
-  [[nodiscard]] const std::string& getEasiFileName() const;
-
-  [[nodiscard]] double getElementsPerWaveLength() const;
-
-  [[nodiscard]] const std::vector<VelocityRefinementCube>& getRefinementRegions() const;
-
-  private:
-  double elementsPerWaveLength{};
-  std::string easiFileName;
-  std::vector<VelocityRefinementCube> refinementRegions{};
-};
-
 enum class ElementType { vertex = 0, edge = 1, face = 2, region = 3 };
 
 using namespace tinyxml2;
diff --git a/src/sizing/VelocityAwareMeshSize.cpp b/src/sizing/VelocityAwareMeshSize.cpp
new file mode 100644
index 0000000..dfbfae9
--- /dev/null
+++ b/src/sizing/VelocityAwareMeshSize.cpp
@@ -0,0 +1,98 @@
+// SPDX-FileCopyrightText: 2021 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#include "VelocityAwareMeshSize.h"
+
+#include <algorithm>
+#include <cmath>
+#include <limits>
+#include <utility>
+
+#include <easi/Component.h>
+#include <easi/Query.h>
+#include <easi/ResultAdapter.h>
+#include <easi/YAMLParser.h>
+
+#include "utils/logger.h"
+
+namespace {
+struct ElasticMaterial {
+  double lambda;
+  double mu;
+  double rho;
+};
+
+// the material model is evaluated in batches of this many points
+constexpr std::size_t QueryBatch = std::size_t{1} << 20;
+} // namespace
+
+VelocityAwareMeshSize::VelocityAwareMeshSize(VelocityAwareRefinementSettings settings)
+    : settings(std::move(settings)), parser(std::make_unique<easi::YAMLParser>(3)) {
+  model = parser->parse(this->settings.getEasiFileName());
+  if (model == nullptr) {
+    logError() << "Could not parse the easi file" << this->settings.getEasiFileName();
+  }
+}
+
+VelocityAwareMeshSize::~VelocityAwareMeshSize() { delete model; }
+
+std::pair<double, int>
+VelocityAwareMeshSize::targetedFrequencyAndGroup(const std::array<double, 3>& point) const {
+  double targetedFrequency = 0.0;
+  int bypassFindRegionAndUseGroup = 0;
+  for (const auto& refinementCube : settings.getRefinementRegions()) {
+    if (refinementCube.cuboid.contains(point)) {
+      if (refinementCube.targetedFrequency >= targetedFrequency) {
+        bypassFindRegionAndUseGroup = refinementCube.bypassFindRegionAndUseGroup;
+      }
+      targetedFrequency = std::max(targetedFrequency, refinementCube.targetedFrequency);
+    }
+  }
+  return {targetedFrequency, bypassFindRegionAndUseGroup};
+}
+
+std::vector<double>
+VelocityAwareMeshSize::meshSizes(const std::vector<std::array<double, 3>>& points,
+                                 const std::vector<int>& groups,
+                                 const std::vector<double>& frequencies) const {
+  std::vector<double> sizes(points.size(), std::numeric_limits<double>::max());
+
+  std::vector<std::size_t> evaluated;
+  for (std::size_t i = 0; i < points.size(); ++i) {
+    if (frequencies[i] > 0.0 && groups[i] > 0) {
+      evaluated.push_back(i);
+    }
+  }
+
+  std::vector<ElasticMaterial> materials;
+  for (std::size_t first = 0; first < evaluated.size(); first += QueryBatch) {
+    const std::size_t count = std::min(QueryBatch, evaluated.size() - first);
+    easi::Query query(count, 3);
+    for (std::size_t j = 0; j < count; ++j) {
+      const auto i = evaluated[first + j];
+      for (int k = 0; k < 3; ++k) {
+        query.x(j, k) = points[i][k];
+      }
+      query.group(j) = groups[i];
+    }
+
+    materials.assign(count, ElasticMaterial{});
+    easi::ArrayOfStructsAdapter<ElasticMaterial> adapter(materials.data());
+    adapter.addBindingPoint("lambda", &ElasticMaterial::lambda);
+    adapter.addBindingPoint("mu", &ElasticMaterial::mu);
+    adapter.addBindingPoint("rho", &ElasticMaterial::rho);
+    model->evaluate(query, adapter);
+
+    for (std::size_t j = 0; j < count; ++j) {
+      const auto& material = materials[j];
+      // the shear wave speed, or the P wave speed in acoustic material
+      const double waveSpeed = material.mu < 10e-14
+                                   ? std::sqrt((material.lambda + 2 * material.mu) / material.rho)
+                                   : std::sqrt(material.mu / material.rho);
+      const auto i = evaluated[first + j];
+      const double waveLength = waveSpeed / frequencies[i];
+      sizes[i] = waveLength / settings.getElementsPerWaveLength();
+    }
+  }
+  return sizes;
+}
diff --git a/src/sizing/VelocityAwareMeshSize.h b/src/sizing/VelocityAwareMeshSize.h
new file mode 100644
index 0000000..2036175
--- /dev/null
+++ b/src/sizing/VelocityAwareMeshSize.h
@@ -0,0 +1,54 @@
+// SPDX-FileCopyrightText: 2021 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#ifndef PUMGEN_SRC_SIZING_VELOCITYAWAREMESHSIZE_H_
+#define PUMGEN_SRC_SIZING_VELOCITYAWAREMESHSIZE_H_
+
+#include <array>
+#include <memory>
+#include <utility>
+#include <vector>
+
+#include "VelocityAwareSettings.h"
+
+namespace easi {
+class Component;
+class YAMLParser;
+} // namespace easi
+
+/**
+ * Mesh sizes from the wave speeds of an easi material model: the wavelength of the targeted
+ * frequency divided by the number of elements per wavelength.
+ */
+class VelocityAwareMeshSize {
+  public:
+  explicit VelocityAwareMeshSize(VelocityAwareRefinementSettings settings);
+  ~VelocityAwareMeshSize();
+  VelocityAwareMeshSize(const VelocityAwareMeshSize&) = delete;
+  VelocityAwareMeshSize& operator=(const VelocityAwareMeshSize&) = delete;
+
+  /**
+   * The highest targeted frequency of the refinement regions containing the point (0 if there is
+   * none) and the group fixed by that region (0 if the region does not fix one).
+   */
+  [[nodiscard]] std::pair<double, int>
+  targetedFrequencyAndGroup(const std::array<double, 3>& point) const;
+
+  /**
+   * The mesh sizes at the points for the given frequencies, with the material of the given
+   * groups; points with a frequency of 0 or a group <= 0 get std::numeric_limits<double>::max().
+   * The material model is evaluated for all points at once.
+   */
+  [[nodiscard]] std::vector<double> meshSizes(const std::vector<std::array<double, 3>>& points,
+                                              const std::vector<int>& groups,
+                                              const std::vector<double>& frequencies) const;
+
+  [[nodiscard]] const VelocityAwareRefinementSettings& getSettings() const { return settings; }
+
+  private:
+  VelocityAwareRefinementSettings settings;
+  std::unique_ptr<easi::YAMLParser> parser;
+  easi::Component* model = nullptr;
+};
+
+#endif // PUMGEN_SRC_SIZING_VELOCITYAWAREMESHSIZE_H_
diff --git a/src/sizing/VelocityAwareSettings.cpp b/src/sizing/VelocityAwareSettings.cpp
new file mode 100644
index 0000000..98c9406
--- /dev/null
+++ b/src/sizing/VelocityAwareSettings.cpp
@@ -0,0 +1,129 @@
+// SPDX-FileCopyrightText: 2020 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#include "VelocityAwareSettings.h"
+
+#include <algorithm>
+#include <cmath>
+#include <string>
+#include <utility>
+
+#include "tinyxml2/tinyxml2.h"
+#include "utils/logger.h"
+
+namespace {
+const double ToRadians = std::acos(-1) / 180.0;
+} // namespace
+
+bool SimpleCuboid::contains(const std::array<double, 3>& point, double margin) const {
+  const double u0 =
+      (point[0] - center[0]) * cosSinRotationZ[0] + (point[1] - center[1]) * cosSinRotationZ[1];
+  const double u1 =
+      (point[0] - center[0]) * -cosSinRotationZ[1] + (point[1] - center[1]) * cosSinRotationZ[0];
+  const double u2 = point[2] - center[2];
+  return std::abs(u0) <= halfSize[0] + margin && std::abs(u1) <= halfSize[1] + margin &&
+         std::abs(u2) <= halfSize[2] + margin;
+}
+
+std::array<std::array<double, 3>, 2> SimpleCuboid::boundingBox(double margin) const {
+  const double hx = halfSize[0] + margin;
+  const double hy = halfSize[1] + margin;
+  const double hz = halfSize[2] + margin;
+  const double c = std::abs(cosSinRotationZ[0]);
+  const double s = std::abs(cosSinRotationZ[1]);
+  const double ex = hx * c + hy * s;
+  const double ey = hx * s + hy * c;
+  return {{{center[0] - ex, center[1] - ey, center[2] - hz},
+           {center[0] + ex, center[1] + ey, center[2] + hz}}};
+}
+
+VelocityAwareRefinementSettings::VelocityAwareRefinementSettings(double elementsPerWaveLength,
+                                                                 std::string easiFileName)
+    : elementsPerWaveLength(elementsPerWaveLength), easiFileName(std::move(easiFileName)) {}
+
+void VelocityAwareRefinementSettings::addRefinementRegion(SimpleCuboid cuboid,
+                                                          double targetedFrequency,
+                                                          int bypassFindRegionAndUseGroup) {
+  refinementRegions.emplace_back(cuboid, targetedFrequency, bypassFindRegionAndUseGroup);
+}
+
+bool VelocityAwareRefinementSettings::isVelocityAwareRefinementOn() const {
+  return !refinementRegions.empty();
+}
+
+const std::string& VelocityAwareRefinementSettings::getEasiFileName() const { return easiFileName; }
+
+double VelocityAwareRefinementSettings::getElementsPerWaveLength() const {
+  return elementsPerWaveLength;
+}
+
+const std::vector<VelocityRefinementCube>&
+VelocityAwareRefinementSettings::getRefinementRegions() const {
+  return refinementRegions;
+}
+
+VelocityAwareRefinementSettings readVelocityAwareSettings(const tinyxml2::XMLDocument& doc) {
+  VelocityAwareRefinementSettings settings;
+  int numChilds = 0;
+  const auto name = "VelocityAwareMeshing";
+  for (auto velocityAwareMeshingElement = doc.FirstChildElement(name); velocityAwareMeshingElement;
+       velocityAwareMeshingElement = velocityAwareMeshingElement->NextSiblingElement(name)) {
+    const auto easiFileName = velocityAwareMeshingElement->Attribute("easiFile");
+    const auto elementsPerWaveLength =
+        std::stof(velocityAwareMeshingElement->Attribute("elementsPerWaveLength"));
+    settings = VelocityAwareRefinementSettings(elementsPerWaveLength, easiFileName);
+    constexpr auto cuboidName = "VelocityRefinementCuboid";
+    logInfo() << "Activating velocity aware meshing, using" << elementsPerWaveLength
+              << "elements per wavelength and easi file" << easiFileName;
+    for (auto child = velocityAwareMeshingElement->FirstChildElement(cuboidName); child;
+         child = child->NextSiblingElement(cuboidName)) {
+
+      const char* attr = child->Attribute("rotationZAnticlockwiseFromX");
+      double rotationZAnticlockwiseFromX = 0.0;
+      if (attr != nullptr) {
+        rotationZAnticlockwiseFromX = std::stof(attr);
+      }
+      attr = child->Attribute("bypassFindRegionAndUseGroup");
+      int bypassFindRegionAndUseGroup = 0;
+      if (attr != nullptr) {
+        bypassFindRegionAndUseGroup = std::stoi(attr);
+      }
+      auto cuboid = SimpleCuboid{{
+                                     std::stof(child->Attribute("centerX")),
+                                     std::stof(child->Attribute("centerY")),
+                                     std::stof(child->Attribute("centerZ")),
+                                 },
+                                 {
+                                     std::stof(child->Attribute("halfSizeX")),
+                                     std::stof(child->Attribute("halfSizeY")),
+                                     std::stof(child->Attribute("halfSizeZ")),
+                                 },
+                                 {std::cos(rotationZAnticlockwiseFromX * ToRadians),
+                                  std::sin(rotationZAnticlockwiseFromX * ToRadians)},
+                                 rotationZAnticlockwiseFromX};
+      const auto targetedFrequency = std::stof(child->Attribute("frequency"));
+
+      settings.addRefinementRegion(cuboid, targetedFrequency, bypassFindRegionAndUseGroup);
+      logInfo() << "Adding velocity aware refinement region targeting" << targetedFrequency
+                << "Hz, centered at x =" << cuboid.center[0] << "y=" << cuboid.center[1]
+                << "z=" << cuboid.center[2] << "with half sizes"
+                << "x =" << cuboid.halfSize[0] << "y =" << cuboid.halfSize[1]
+                << "z =" << cuboid.halfSize[2];
+      if (std::abs(cuboid.rotationZ) > 0.0) {
+        logInfo() << "rotated around z axis by " << cuboid.rotationZ
+                  << "degree(s) counterclockwise from x axis.";
+      }
+      if (bypassFindRegionAndUseGroup) {
+        logInfo() << "bypass findRegion and use group =" << bypassFindRegionAndUseGroup;
+      }
+    }
+    if (!settings.isVelocityAwareRefinementOn()) {
+      logWarning() << "Activated velocity aware meshing but did not specify any refinement region!";
+    }
+    ++numChilds;
+  }
+  if (numChilds > 1) {
+    logError() << "Multiple definitions of velocityAwareMeshing";
+  }
+  return settings;
+}
diff --git a/src/sizing/VelocityAwareSettings.h b/src/sizing/VelocityAwareSettings.h
new file mode 100644
index 0000000..7a9b798
--- /dev/null
+++ b/src/sizing/VelocityAwareSettings.h
@@ -0,0 +1,74 @@
+// SPDX-FileCopyrightText: 2020 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#ifndef PUMGEN_SRC_SIZING_VELOCITYAWARESETTINGS_H_
+#define PUMGEN_SRC_SIZING_VELOCITYAWARESETTINGS_H_
+
+#include <array>
+#include <string>
+#include <vector>
+
+namespace tinyxml2 {
+class XMLDocument;
+} // namespace tinyxml2
+
+/**
+ * A cuboid, rotated around the z axis.
+ */
+struct SimpleCuboid {
+  std::array<double, 3> center;
+  std::array<double, 3> halfSize;
+  std::array<double, 2> cosSinRotationZ;
+  double rotationZ;
+
+  /**
+   * Whether the point lies in the cuboid, enlarged by margin in each direction.
+   */
+  [[nodiscard]] bool contains(const std::array<double, 3>& point, double margin = 0) const;
+
+  /**
+   * The axis-aligned bounding box (minimum and maximum corner) of the enlarged cuboid.
+   */
+  [[nodiscard]] std::array<std::array<double, 3>, 2> boundingBox(double margin = 0) const;
+};
+
+struct VelocityRefinementCube {
+  VelocityRefinementCube(SimpleCuboid cuboid, double targetedFrequency,
+                         int bypassFindRegionAndUseGroup)
+      : cuboid(cuboid), targetedFrequency(targetedFrequency),
+        bypassFindRegionAndUseGroup(bypassFindRegionAndUseGroup) {}
+
+  SimpleCuboid cuboid;
+  double targetedFrequency;
+  int bypassFindRegionAndUseGroup;
+};
+
+class VelocityAwareRefinementSettings {
+  public:
+  VelocityAwareRefinementSettings() = default;
+  VelocityAwareRefinementSettings(double elementsPerWaveLength, std::string easiFileName);
+
+  void addRefinementRegion(SimpleCuboid cuboid, double targetedFrequency,
+                           int bypassFindRegionAndUseGroup);
+
+  [[nodiscard]] bool isVelocityAwareRefinementOn() const;
+
+  [[nodiscard]] const std::string& getEasiFileName() const;
+
+  [[nodiscard]] double getElementsPerWaveLength() const;
+
+  [[nodiscard]] const std::vector<VelocityRefinementCube>& getRefinementRegions() const;
+
+  private:
+  double elementsPerWaveLength{};
+  std::string easiFileName;
+  std::vector<VelocityRefinementCube> refinementRegions{};
+};
+
+/**
+ * Reads the VelocityAwareMeshing element of a mesh attributes document; the settings are empty
+ * (isVelocityAwareRefinementOn() is false) if the document has none.
+ */
+VelocityAwareRefinementSettings readVelocityAwareSettings(const tinyxml2::XMLDocument& doc);
+
+#endif // PUMGEN_SRC_SIZING_VELOCITYAWARESETTINGS_H_

From b18ea60baaadaed7cd90912b23be74ee7434b00d Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 20:06:09 +0000
Subject: [PATCH 16/19] Separate the gathering of cell vertices from the
 insphere computation

CellVertices fetches the coordinates of the vertices of the local cells which
are owned by other ranks once and provides the vertices per cell, so that
further per-cell computations can share them with the insphere calculation.

AI-generated. Model: Claude Opus 5.5
---
 src/helper/InsphereCalculator.cpp | 70 ++++++++++++++++---------------
 src/helper/InsphereCalculator.h   | 37 +++++++++++++---
 src/pumgen.cpp                    |  5 ++-
 3 files changed, 70 insertions(+), 42 deletions(-)

diff --git a/src/helper/InsphereCalculator.cpp b/src/helper/InsphereCalculator.cpp
index ddc2a0c..cad62b7 100644
--- a/src/helper/InsphereCalculator.cpp
+++ b/src/helper/InsphereCalculator.cpp
@@ -12,15 +12,10 @@
 
 #include "MPIConvenience.h"
 
-std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivity,
-                                      const std::vector<double>& geometry, std::size_t cellSize,
-                                      MPI_Comm comm) {
-  constexpr std::size_t VerticesPerCell = 4;
-  const std::size_t numCells = connectivity.size() / cellSize;
-
+CellVertices::CellVertices(const std::vector<std::size_t>& connectivity,
+                           const std::vector<double>& geometry, std::size_t cellSize, MPI_Comm comm)
+    : connectivity(connectivity), geometry(geometry), cellSize(cellSize) {
   int commsize;
-  int commrank;
-
   MPI_Comm_size(comm, &commsize);
   MPI_Comm_rank(comm, &commrank);
 
@@ -34,7 +29,7 @@ std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivi
 
   std::size_t localVertices = geometry.size() / 3;
 
-  std::vector<std::size_t> vertexDist(commsize + 1);
+  vertexDist.resize(commsize + 1);
 
   MPI_Allgather(&localVertices, 1, tndm::mpi_type_t<std::size_t>(), vertexDist.data() + 1, 1,
                 tndm::mpi_type_t<std::size_t>(), comm);
@@ -43,7 +38,7 @@ std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivi
     vertexDist[i + 1] += vertexDist[i];
   }
 
-  std::vector<std::unordered_map<std::size_t, std::size_t>> outidxmap(commsize);
+  outidxmap.resize(commsize);
 
   for (std::size_t node = 0; node < connectivity.size(); ++node) {
     if (node % cellSize >= VerticesPerCell) {
@@ -65,7 +60,7 @@ std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivi
   MPI_Alltoall(outrequests.data(), 1, tndm::mpi_type_t<std::size_t>(), inrequests.data(), 1,
                tndm::mpi_type_t<std::size_t>(), comm);
 
-  std::vector<std::size_t> outdisp(commsize + 1);
+  outdisp.resize(commsize + 1);
   std::vector<std::size_t> indisp(commsize + 1);
   for (std::size_t i = 1; i < commsize + 1; ++i) {
     outdisp[i] = outdisp[i - 1] + outrequests[i - 1];
@@ -92,7 +87,7 @@ std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivi
                     tndm::mpi_type_t<std::size_t>(), comm);
   }
 
-  std::vector<double> outvertices(3 * outdisp[commsize]);
+  outvertices.resize(3 * outdisp[commsize]);
 
   {
     std::vector<double> invertices(3 * indisp[commsize]);
@@ -109,27 +104,36 @@ std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivi
                     outvertices.data(), outrequests.data(), outdisp.data(), vertexType, comm);
   }
 
-  std::vector<std::size_t> counter(commsize);
-  std::vector<double> inspheres(numCells);
-
-  for (std::size_t i = 0; i < numCells; ++i) {
-    std::array<std::array<double, 3>, VerticesPerCell> vertices;
-    for (std::size_t j = 0; j < VerticesPerCell; ++j) {
-      auto vertex = connectivity[i * cellSize + j];
-      auto itPosition = std::upper_bound(vertexDist.begin(), vertexDist.end(), vertex);
-      auto position = std::distance(vertexDist.begin(), itPosition) - 1;
-      auto localVertex = vertex - vertexDist[position];
-      if (position == commrank) {
-        vertices[j][0] = geometry[localVertex * 3 + 0];
-        vertices[j][1] = geometry[localVertex * 3 + 1];
-        vertices[j][2] = geometry[localVertex * 3 + 2];
-      } else {
-        auto transferidx = outidxmap[position][localVertex] + outdisp[position];
-        vertices[j][0] = outvertices[transferidx * 3 + 0];
-        vertices[j][1] = outvertices[transferidx * 3 + 1];
-        vertices[j][2] = outvertices[transferidx * 3 + 2];
-      }
+  MPI_Type_free(&vertexType);
+}
+
+std::array<std::array<double, 3>, CellVertices::VerticesPerCell>
+CellVertices::operator()(std::size_t cell) const {
+  std::array<std::array<double, 3>, VerticesPerCell> vertices;
+  for (std::size_t j = 0; j < VerticesPerCell; ++j) {
+    auto vertex = connectivity[cell * cellSize + j];
+    auto itPosition = std::upper_bound(vertexDist.begin(), vertexDist.end(), vertex);
+    auto position = std::distance(vertexDist.begin(), itPosition) - 1;
+    auto localVertex = vertex - vertexDist[position];
+    if (position == commrank) {
+      vertices[j][0] = geometry[localVertex * 3 + 0];
+      vertices[j][1] = geometry[localVertex * 3 + 1];
+      vertices[j][2] = geometry[localVertex * 3 + 2];
+    } else {
+      auto transferidx = outidxmap[position].at(localVertex) + outdisp[position];
+      vertices[j][0] = outvertices[transferidx * 3 + 0];
+      vertices[j][1] = outvertices[transferidx * 3 + 1];
+      vertices[j][2] = outvertices[transferidx * 3 + 2];
     }
+  }
+  return vertices;
+}
+
+std::vector<double> calculateInsphere(const CellVertices& cells) {
+  std::vector<double> inspheres(cells.numCells());
+
+  for (std::size_t i = 0; i < cells.numCells(); ++i) {
+    const auto vertices = cells(i);
     double a11 = vertices[1][0] - vertices[0][0];
     double a12 = vertices[1][1] - vertices[0][1];
     double a13 = vertices[1][2] - vertices[0][2];
@@ -170,7 +174,5 @@ std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivi
     inspheres[i] = gram / faces;
   }
 
-  MPI_Type_free(&vertexType);
-
   return inspheres;
 }
diff --git a/src/helper/InsphereCalculator.h b/src/helper/InsphereCalculator.h
index 806e726..94feb2d 100644
--- a/src/helper/InsphereCalculator.h
+++ b/src/helper/InsphereCalculator.h
@@ -4,18 +4,43 @@
 #ifndef PUMGEN_SRC_HELPER_INSPHERECALCULATOR_H_
 #define PUMGEN_SRC_HELPER_INSPHERECALCULATOR_H_
 
+#include <array>
 #include <cstddef>
 #include <mpi.h>
+#include <unordered_map>
 #include <vector>
 
-// assumes a contiguous distribution of all vertices over all processes
+/**
+ * The vertex coordinates of the local cells; the coordinates of vertices owned by other ranks are
+ * fetched once. Assumes a contiguous distribution of all vertices over all processes. Each cell
+ * has cellSize nodes, the first four of which are its vertices.
+ */
+class CellVertices {
+  public:
+  static constexpr std::size_t VerticesPerCell = 4;
+
+  CellVertices(const std::vector<std::size_t>& connectivity, const std::vector<double>& geometry,
+               std::size_t cellSize, MPI_Comm comm);
+
+  [[nodiscard]] std::size_t numCells() const { return connectivity.size() / cellSize; }
+
+  [[nodiscard]] std::array<std::array<double, 3>, VerticesPerCell>
+  operator()(std::size_t cell) const;
+
+  private:
+  const std::vector<std::size_t>& connectivity;
+  const std::vector<double>& geometry;
+  std::size_t cellSize;
+  int commrank = 0;
+  std::vector<std::size_t> vertexDist;
+  std::vector<std::unordered_map<std::size_t, std::size_t>> outidxmap;
+  std::vector<std::size_t> outdisp;
+  std::vector<double> outvertices;
+};
 
 /**
- * The insphere radius of each tetrahedron. Each cell has cellSize nodes, the first four of which
- * are its vertices.
+ * The insphere radius of each tetrahedron.
  */
-std::vector<double> calculateInsphere(const std::vector<std::size_t>& connectivity,
-                                      const std::vector<double>& geometry, std::size_t cellSize,
-                                      MPI_Comm comm);
+std::vector<double> calculateInsphere(const CellVertices& cells);
 
 #endif // PUMGEN_SRC_HELPER_INSPHERECALCULATOR_H_
diff --git a/src/pumgen.cpp b/src/pumgen.cpp
index 7227859..cd67a80 100644
--- a/src/pumgen.cpp
+++ b/src/pumgen.cpp
@@ -455,8 +455,9 @@ int main(int argc, char* argv[]) {
   logInfo() << "Total vertex count:" << globalSize[1];
   logInfo() << "Vertex identification:" << meshInput->hasIdentify();
 
-  auto inspheres = calculateInsphere(meshInput->connectivity(), meshInput->geometry(),
-                                     meshInput->cellSize(), MPI_COMM_WORLD);
+  const CellVertices cellVertices(meshInput->connectivity(), meshInput->geometry(),
+                                  meshInput->cellSize(), MPI_COMM_WORLD);
+  auto inspheres = calculateInsphere(cellVertices);
   double min = inspheres.empty() ? std::numeric_limits<double>::infinity()
                                  : *std::min_element(inspheres.begin(), inspheres.end());
   MPI_Reduce((rank == 0 ? MPI_IN_PLACE : &min), &min, 1, MPI_DOUBLE, MPI_MIN, 0, MPI_COMM_WORLD);

From 7e32225b6aa68f12f1d9bfb618eb57e50611edea Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 20:07:45 +0000
Subject: [PATCH 17/19] Add pumgen-sizefield for velocity-aware meshing with
 gmsh

pumgen-sizefield reads the VelocityAwareMeshing element of a mesh attributes
file and writes, for each refinement cuboid, a binary grid for gmsh's
Structured field with the mesh size of the cuboid's group (given by
bypassFindRegionAndUseGroup, which is required here). The easi model is
evaluated for all grid nodes at once, distributed over the ranks in x slabs;
each rank writes its slab with MPI-IO.

Each node takes the minimum of its 3x3x3 neighbourhood, so that gmsh's
trilinear interpolation never exceeds the smallest size sampled at the
corners of a grid cell; the grid covers the cuboid with a margin of two
spacings, so that all grid cells which intersect the cuboid have defined
corners. A .geo file restricts each field to the physical volume of its group
and uses their minimum as background field; it refers to the grids relative
to its own directory.

On the layered test model (20 x 20 x 10 km, 2 km sediment), gmsh's HXT
meshes with these fields have the same edge length distribution as meshes
from the exact per-point size callback (816945 vs. 815206 cells).

AI-generated. Model: Claude Opus 5.5
---
 CMakeLists.txt                           |   7 +
 REUSE.toml                               |   3 +-
 src/sizefield.cpp                        | 189 +++++++++++++++++++++++
 src/sizing/SizeField.cpp                 |  73 +++++++++
 src/sizing/SizeField.h                   |  53 +++++++
 tests/CMakeLists.txt                     |  20 +++
 tests/RunSizefieldTest.cmake             |  36 +++++
 tests/fixtures/velocity-material.yaml    |  21 +++
 tests/fixtures/velocity-sizefield-0.bin  | Bin 0 -> 8172 bytes
 tests/fixtures/velocity-sizefield-1.bin  | Bin 0 -> 14396 bytes
 tests/fixtures/velocity-sizefield.xml.in |  16 ++
 11 files changed, 417 insertions(+), 1 deletion(-)
 create mode 100644 src/sizefield.cpp
 create mode 100644 src/sizing/SizeField.cpp
 create mode 100644 src/sizing/SizeField.h
 create mode 100644 tests/RunSizefieldTest.cmake
 create mode 100644 tests/fixtures/velocity-material.yaml
 create mode 100644 tests/fixtures/velocity-sizefield-0.bin
 create mode 100644 tests/fixtures/velocity-sizefield-1.bin
 create mode 100644 tests/fixtures/velocity-sizefield.xml.in

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 4333aa5..930b740 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -140,6 +140,7 @@ if (EASI)
   add_library(pumgen_sizing STATIC
     ${CMAKE_CURRENT_SOURCE_DIR}/src/sizing/VelocityAwareSettings.cpp
     ${CMAKE_CURRENT_SOURCE_DIR}/src/sizing/VelocityAwareMeshSize.cpp
+    ${CMAKE_CURRENT_SOURCE_DIR}/src/sizing/SizeField.cpp
   )
   target_include_directories(pumgen_sizing PUBLIC
     ${CMAKE_CURRENT_SOURCE_DIR}/src
@@ -149,6 +150,12 @@ if (EASI)
   target_link_libraries(pumgen_sizing PUBLIC easi::easi tinyxml2)
   target_link_libraries(pumgen PUBLIC pumgen_sizing)
   target_compile_definitions(pumgen PUBLIC USE_EASI)
+
+  add_executable(pumgen-sizefield ${CMAKE_CURRENT_SOURCE_DIR}/src/sizefield.cpp)
+  target_compile_definitions(pumgen-sizefield PRIVATE LOG_LEVEL=${LOG_LEVEL})
+  target_link_libraries(pumgen-sizefield PRIVATE pumgen_sizing MPI::MPI_CXX)
+  set_target_properties(pumgen-sizefield PROPERTIES INSTALL_RPATH "${INSTALL_RPATH}")
+  install(TARGETS pumgen-sizefield RUNTIME DESTINATION bin)
 endif()
 if(SIMMETRIX)
   set(INSTALL_RPATH "${SIM_PS_KRNL_LIB_DIR}:${INSTALL_RPATH}")
diff --git a/REUSE.toml b/REUSE.toml
index 4465d3c..c2f58e0 100644
--- a/REUSE.toml
+++ b/REUSE.toml
@@ -5,7 +5,8 @@
 version = 1
 
 [[annotations]]
-path = ["tests/fixtures/*.msh", "tests/fixtures/*.neu", "tests/fixtures/*.h5"]
+path = ["tests/fixtures/*.msh", "tests/fixtures/*.neu", "tests/fixtures/*.h5",
+        "tests/fixtures/*.bin"]
 precedence = "override"
 SPDX-FileCopyrightText = "2026 SeisSol Group"
 SPDX-License-Identifier = "BSD-3-Clause"
diff --git a/src/sizefield.cpp b/src/sizefield.cpp
new file mode 100644
index 0000000..dcbea2d
--- /dev/null
+++ b/src/sizefield.cpp
@@ -0,0 +1,189 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+
+// Writes gmsh Structured fields for velocity-aware meshing (one per refinement cuboid) and a .geo
+// file which combines them into the background mesh size.
+
+#include <mpi.h>
+
+#include <algorithm>
+#include <cstdint>
+#include <cstring>
+#include <fstream>
+#include <limits>
+#include <string>
+#include <vector>
+
+#include "helper/Distributor.h"
+#include "sizing/SizeField.h"
+#include "sizing/VelocityAwareMeshSize.h"
+#include "sizing/VelocityAwareSettings.h"
+#include "tinyxml2/tinyxml2.h"
+#include "utils/args.h"
+#include "utils/logger.h"
+
+namespace {
+
+/**
+ * Writes the binary format of gmsh's Structured field: origin and spacing (3 doubles each), node
+ * counts (3 4-byte ints), then the values. Each rank writes the nodes with x index from first.
+ */
+void writeGrid(const std::string& fileName, const StructuredGrid& grid,
+               const std::vector<double>& values, std::size_t first, MPI_Comm comm) {
+  MPI_File file;
+  if (MPI_File_open(comm, fileName.c_str(), MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL,
+                    &file) != MPI_SUCCESS) {
+    logError() << "Could not open" << fileName;
+  }
+  MPI_File_set_size(file, 0);
+
+  constexpr std::size_t HeaderSize = 6 * sizeof(double) + 3 * sizeof(std::int32_t);
+  int rank = 0;
+  MPI_Comm_rank(comm, &rank);
+  if (rank == 0) {
+    char header[HeaderSize];
+    const double spacing[3] = {grid.spacing, grid.spacing, grid.spacing};
+    std::int32_t count[3];
+    for (int d = 0; d < 3; ++d) {
+      count[d] = static_cast<std::int32_t>(grid.count[d]);
+    }
+    std::memcpy(header, grid.origin.data(), 3 * sizeof(double));
+    std::memcpy(header + 3 * sizeof(double), spacing, 3 * sizeof(double));
+    std::memcpy(header + 6 * sizeof(double), count, 3 * sizeof(std::int32_t));
+    MPI_File_write_at(file, 0, header, HeaderSize, MPI_BYTE, MPI_STATUS_IGNORE);
+  }
+
+  // in pieces, since MPI counts are ints
+  constexpr std::size_t Piece = std::size_t{1} << 26;
+  const MPI_Offset offset = HeaderSize + first * grid.count[1] * grid.count[2] * sizeof(double);
+  for (std::size_t done = 0; done < values.size(); done += Piece) {
+    const auto count = static_cast<int>(std::min(Piece, values.size() - done));
+    MPI_File_write_at(file, offset + static_cast<MPI_Offset>(done * sizeof(double)),
+                      values.data() + done, count, MPI_DOUBLE, MPI_STATUS_IGNORE);
+  }
+  MPI_File_close(&file);
+}
+
+std::string baseName(const std::string& path) {
+  const auto slash = path.find_last_of('/');
+  return slash == std::string::npos ? path : path.substr(slash + 1);
+}
+
+void writeGeo(const std::string& fileName, const std::string& settingsFile,
+              const std::vector<std::string>& gridFiles, const std::vector<int>& groups,
+              int firstField) {
+  std::ofstream geo(fileName);
+  geo << "// Velocity-aware mesh size written by pumgen-sizefield from " << settingsFile << ":\n"
+      << "// one Structured field per refinement cuboid, restricted to the physical volume of\n"
+      << "// the cuboid's group, and their minimum as background field. The grid files are\n"
+      << "// expected next to this file. Recommended options:\n"
+      << "// Mesh.MeshSizeExtendFromBoundary = 0; Mesh.MeshSizeFromPoints = 0;\n"
+      << "// Mesh.MeshSizeFromCurvature = 0;\n";
+  std::string restricted;
+  for (std::size_t c = 0; c < gridFiles.size(); ++c) {
+    const int grid = firstField + 2 * static_cast<int>(c);
+    const int restrict = grid + 1;
+    geo << "Field[" << grid << "] = Structured;\n"
+        << "Field[" << grid << "].FileName = StrCat(CurrentDirectory, \"" << baseName(gridFiles[c])
+        << "\");\n"
+        << "Field[" << grid << "].TextFormat = 0;\n"
+        << "Field[" << grid << "].SetOutsideValue = 1;\n"
+        << "Field[" << grid << "].OutsideValue = " << UnconstrainedSize << ";\n"
+        << "Field[" << restrict << "] = Restrict;\n"
+        << "Field[" << restrict << "].InField = " << grid << ";\n"
+        << "Field[" << restrict << "].VolumesList = {Physical Volume{" << groups[c] << "}};\n"
+        << "Field[" << restrict << "].IncludeBoundary = 1;\n";
+    restricted += (c == 0 ? "" : ", ") + std::to_string(restrict);
+  }
+  const int minimum = firstField + 2 * static_cast<int>(gridFiles.size());
+  geo << "Field[" << minimum << "] = Min;\n"
+      << "Field[" << minimum << "].FieldsList = {" << restricted << "};\n"
+      << "Background Field = " << minimum << ";\n";
+}
+
+} // namespace
+
+int main(int argc, char* argv[]) {
+  MPI_Init(&argc, &argv);
+  int rank = 0;
+  int size = 1;
+  MPI_Comm_rank(MPI_COMM_WORLD, &rank);
+  MPI_Comm_size(MPI_COMM_WORLD, &size);
+  utils::Logger::setRank(rank);
+
+  utils::Args args("Writes gmsh Structured fields for velocity-aware meshing, one per refinement "
+                   "cuboid, and a .geo file which restricts each field to the physical volume of "
+                   "the cuboid's group (bypassFindRegionAndUseGroup) and uses their minimum as "
+                   "background field.");
+  args.addOption("spacing", 0, "Grid spacing; about the smallest mesh size", utils::Args::Required,
+                 true);
+  args.addOption("first-field", 0, "Number of the first gmsh field (default: 1000)",
+                 utils::Args::Required, false);
+  args.addAdditionalOption("settings", "Mesh attributes (XML) with a VelocityAwareMeshing element");
+  args.addAdditionalOption("output", "Prefix of the output files");
+  if (args.parse(argc, argv, rank == 0) != utils::Args::Success) {
+    MPI_Finalize();
+    return 1;
+  }
+  const auto settingsFile = args.getAdditionalArgument<std::string>("settings");
+  const auto prefix = args.getAdditionalArgument<std::string>("output");
+  const auto spacing = args.getArgument<double>("spacing");
+  const auto firstField = args.getArgument<int>("first-field", 1000);
+  if (!(spacing > 0)) {
+    logError() << "The grid spacing has to be positive";
+  }
+
+  tinyxml2::XMLDocument doc;
+  if (doc.LoadFile(settingsFile.c_str()) != tinyxml2::XML_SUCCESS) {
+    logError() << "Could not read" << settingsFile;
+  }
+  const auto settings = readVelocityAwareSettings(doc);
+  const auto& regions = settings.getRefinementRegions();
+  if (regions.empty()) {
+    logError() << "No refinement cuboid in" << settingsFile;
+  }
+  for (std::size_t c = 0; c < regions.size(); ++c) {
+    if (regions[c].bypassFindRegionAndUseGroup <= 0) {
+      logError() << "Refinement cuboid" << c
+                 << "has no group; pumgen-sizefield needs bypassFindRegionAndUseGroup";
+    }
+  }
+
+  const VelocityAwareMeshSize meshSize(settings);
+  std::vector<std::string> gridFiles;
+  std::vector<int> groups;
+  for (std::size_t c = 0; c < regions.size(); ++c) {
+    const auto grid = gridForCuboid(regions[c].cuboid, spacing);
+    for (const auto count : grid.count) {
+      if (count > static_cast<std::size_t>(std::numeric_limits<std::int32_t>::max())) {
+        logError() << "Too many grid nodes for refinement cuboid" << c;
+      }
+    }
+    logInfo() << "Refinement cuboid" << c << "(group" << regions[c].bypassFindRegionAndUseGroup
+              << ", " << regions[c].targetedFrequency << "Hz): grid of" << grid.count[0] << "x"
+              << grid.count[1] << "x" << grid.count[2] << "nodes";
+
+    const std::size_t first = getChunksum(grid.count[0], rank, size);
+    const std::size_t last = first + getChunksize(grid.count[0], rank, size);
+    const auto values = cuboidMeshSizes(meshSize, regions[c], grid, first, last);
+
+    double smallest =
+        values.empty() ? UnconstrainedSize : *std::min_element(values.begin(), values.end());
+    MPI_Allreduce(MPI_IN_PLACE, &smallest, 1, MPI_DOUBLE, MPI_MIN, MPI_COMM_WORLD);
+    logInfo() << "Refinement cuboid" << c << ": smallest mesh size" << smallest;
+
+    const std::string gridFile = prefix + "-" + std::to_string(c) + ".bin";
+    writeGrid(gridFile, grid, values, first, MPI_COMM_WORLD);
+    gridFiles.push_back(gridFile);
+    groups.push_back(regions[c].bypassFindRegionAndUseGroup);
+  }
+
+  if (rank == 0) {
+    writeGeo(prefix + ".geo", settingsFile, gridFiles, groups, firstField);
+    logInfo() << "Wrote" << (prefix + ".geo").c_str();
+  }
+
+  MPI_Finalize();
+  return 0;
+}
diff --git a/src/sizing/SizeField.cpp b/src/sizing/SizeField.cpp
new file mode 100644
index 0000000..93d3600
--- /dev/null
+++ b/src/sizing/SizeField.cpp
@@ -0,0 +1,73 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#include "SizeField.h"
+
+#include <algorithm>
+#include <cmath>
+
+StructuredGrid gridForCuboid(const SimpleCuboid& cuboid, double spacing) {
+  const auto box = cuboid.boundingBox(2 * spacing);
+  StructuredGrid grid{box[0], spacing, {}};
+  for (int d = 0; d < 3; ++d) {
+    grid.count[d] = static_cast<std::size_t>(std::ceil((box[1][d] - box[0][d]) / spacing)) + 1;
+  }
+  return grid;
+}
+
+std::vector<double> cuboidMeshSizes(const VelocityAwareMeshSize& meshSize,
+                                    const VelocityRefinementCube& region,
+                                    const StructuredGrid& grid, std::size_t first,
+                                    std::size_t last) {
+  const std::size_t ny = grid.count[1];
+  const std::size_t nz = grid.count[2];
+  const std::size_t layer = ny * nz;
+  // one layer more on each side for the neighbourhood minimum
+  const std::size_t haloFirst = first > 0 ? first - 1 : first;
+  const std::size_t haloLast = std::min(last + 1, grid.count[0]);
+  const std::size_t numLayers = haloLast - haloFirst;
+
+  std::vector<double> sizes(numLayers * layer, UnconstrainedSize);
+  std::vector<std::array<double, 3>> points;
+  std::vector<std::size_t> indices;
+  for (std::size_t i = haloFirst; i < haloLast; ++i) {
+    for (std::size_t j = 0; j < ny; ++j) {
+      for (std::size_t k = 0; k < nz; ++k) {
+        const auto point = grid.node(i, j, k);
+        if (region.cuboid.contains(point, 2 * grid.spacing)) {
+          points.push_back(point);
+          indices.push_back(((i - haloFirst) * ny + j) * nz + k);
+        }
+      }
+    }
+  }
+  const std::vector<int> groups(points.size(), region.bypassFindRegionAndUseGroup);
+  const std::vector<double> frequencies(points.size(), region.targetedFrequency);
+  const auto values = meshSize.meshSizes(points, groups, frequencies);
+  for (std::size_t p = 0; p < points.size(); ++p) {
+    sizes[indices[p]] = std::min(values[p], UnconstrainedSize);
+  }
+
+  // the minimum over the 3x3x3 neighbourhood, one direction after the other
+  std::vector<double> previous;
+  const auto minimumAlong = [&](std::size_t count, std::size_t stride) {
+    previous = sizes;
+    for (std::size_t index = 0; index < sizes.size(); ++index) {
+      const std::size_t position = (index / stride) % count;
+      if (position > 0) {
+        sizes[index] = std::min(sizes[index], previous[index - stride]);
+      }
+      if (position + 1 < count) {
+        sizes[index] = std::min(sizes[index], previous[index + stride]);
+      }
+    }
+  };
+  minimumAlong(nz, 1);
+  minimumAlong(ny, nz);
+  minimumAlong(numLayers, layer);
+
+  // drop the halo layers
+  const std::size_t offset = (first - haloFirst) * layer;
+  return {sizes.begin() + static_cast<std::ptrdiff_t>(offset),
+          sizes.begin() + static_cast<std::ptrdiff_t>(offset + (last - first) * layer)};
+}
diff --git a/src/sizing/SizeField.h b/src/sizing/SizeField.h
new file mode 100644
index 0000000..c5b0758
--- /dev/null
+++ b/src/sizing/SizeField.h
@@ -0,0 +1,53 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#ifndef PUMGEN_SRC_SIZING_SIZEFIELD_H_
+#define PUMGEN_SRC_SIZING_SIZEFIELD_H_
+
+#include <array>
+#include <cstddef>
+#include <vector>
+
+#include "VelocityAwareMeshSize.h"
+
+/**
+ * A regular grid for gmsh's Structured field: the value of node (i, j, k) is stored at
+ * (i * count[1] + j) * count[2] + k.
+ */
+struct StructuredGrid {
+  std::array<double, 3> origin;
+  double spacing;
+  std::array<std::size_t, 3> count;
+
+  [[nodiscard]] std::array<double, 3> node(std::size_t i, std::size_t j, std::size_t k) const {
+    return {origin[0] + static_cast<double>(i) * spacing,
+            origin[1] + static_cast<double>(j) * spacing,
+            origin[2] + static_cast<double>(k) * spacing};
+  }
+};
+
+/**
+ * The value of grid nodes which do not constrain the mesh size.
+ */
+constexpr double UnconstrainedSize = 1e22;
+
+/**
+ * The grid covering a cuboid with a margin of two grid spacings, so that all grid cells which
+ * intersect the cuboid have their corners within the margin.
+ */
+StructuredGrid gridForCuboid(const SimpleCuboid& cuboid, double spacing);
+
+/**
+ * The mesh sizes of the grid nodes with x index in [first, last) for one refinement cuboid.
+ *
+ * The nodes within the margin of the cuboid get the mesh size of the material of the given group;
+ * the others get UnconstrainedSize. Each node then takes the minimum of its 3x3x3 neighbourhood,
+ * so that the trilinear interpolation in a grid cell never exceeds the smallest size sampled at the
+ * cell's corners.
+ */
+std::vector<double> cuboidMeshSizes(const VelocityAwareMeshSize& meshSize,
+                                    const VelocityRefinementCube& region,
+                                    const StructuredGrid& grid, std::size_t first,
+                                    std::size_t last);
+
+#endif // PUMGEN_SRC_SIZING_SIZEFIELD_H_
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 117e837..ebf9e56 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -189,3 +189,23 @@ pumgen_add_test(msh4.coarse-binary-truncated RANKS 1 SOURCE msh4
 # a face of the surface mesh given twice
 pumgen_add_test(msh2.tiny-duplicateface RANKS 1 SOURCE msh2 INPUT tiny-duplicateface-v22.msh
                 EXPECT_ERROR "exists multiple times in the surface mesh")
+
+# velocity-aware sizing, with a material of shear wave speed 1 in group 1 and 2 in group 2
+if(EASI)
+  configure_file(fixtures/velocity-sizefield.xml.in
+                 ${CMAKE_CURRENT_BINARY_DIR}/velocity-sizefield.xml @ONLY)
+
+  # the expected grids are verified independently; they must not depend on the number of ranks
+  foreach(ranks 1 3)
+    set(prefix ${PUMGEN_TEST_OUTPUT}/sizefield-np${ranks})
+    set(command ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${ranks} ${MPIEXEC_PREFLAGS}
+                $<TARGET_FILE:pumgen-sizefield> ${MPIEXEC_POSTFLAGS} --spacing 0.25
+                ${CMAKE_CURRENT_BINARY_DIR}/velocity-sizefield.xml ${prefix})
+    string(REPLACE ";" "|" command "${command}")
+    add_test(NAME sizefield.np${ranks}
+             COMMAND ${CMAKE_COMMAND} -DCOMMAND=${command} -DPREFIX=${prefix}
+                     -DEXPECTED=${PUMGEN_TEST_FIXTURES}/velocity-sizefield -DGRIDS=2 -P
+                     ${CMAKE_CURRENT_SOURCE_DIR}/RunSizefieldTest.cmake)
+    set_tests_properties(sizefield.np${ranks} PROPERTIES PROCESSORS ${ranks} TIMEOUT 120)
+  endforeach()
+endif()
diff --git a/tests/RunSizefieldTest.cmake b/tests/RunSizefieldTest.cmake
new file mode 100644
index 0000000..8be34df
--- /dev/null
+++ b/tests/RunSizefieldTest.cmake
@@ -0,0 +1,36 @@
+# SPDX-FileCopyrightText: 2026 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+# Runs pumgen-sizefield and compares the written grids with the expected ones.
+#
+# Variables:
+#   COMMAND   pumgen-sizefield command line, with '|' as the argument separator
+#   PREFIX    output prefix of the command
+#   EXPECTED  prefix of the expected grids
+#   GRIDS     number of grids
+
+string(REPLACE "|" ";" command "${COMMAND}")
+file(REMOVE "${PREFIX}.geo")
+execute_process(
+  COMMAND ${command}
+  RESULT_VARIABLE result
+  OUTPUT_VARIABLE log
+  ERROR_VARIABLE log
+  TIMEOUT 100)
+message("${log}")
+if(NOT result EQUAL 0)
+  message(FATAL_ERROR "pumgen-sizefield failed: ${result}")
+endif()
+
+math(EXPR last "${GRIDS} - 1")
+foreach(grid RANGE ${last})
+  execute_process(COMMAND ${CMAKE_COMMAND} -E compare_files "${PREFIX}-${grid}.bin"
+                          "${EXPECTED}-${grid}.bin" RESULT_VARIABLE differs)
+  if(NOT differs EQUAL 0)
+    message(FATAL_ERROR "${PREFIX}-${grid}.bin differs from ${EXPECTED}-${grid}.bin")
+  endif()
+endforeach()
+if(NOT EXISTS "${PREFIX}.geo")
+  message(FATAL_ERROR "${PREFIX}.geo was not written")
+endif()
diff --git a/tests/fixtures/velocity-material.yaml b/tests/fixtures/velocity-material.yaml
new file mode 100644
index 0000000..d8214c1
--- /dev/null
+++ b/tests/fixtures/velocity-material.yaml
@@ -0,0 +1,21 @@
+# SPDX-FileCopyrightText: 2026 SeisSol Group
+#
+# SPDX-License-Identifier: BSD-3-Clause
+
+# shear wave speed 1 in group 1 and 2 in group 2
+!Any
+components:
+  - !GroupFilter
+    groups: [1]
+    components: !ConstantMap
+      map:
+        rho: 1.0
+        mu: 1.0
+        lambda: 2.0
+  - !GroupFilter
+    groups: [2]
+    components: !ConstantMap
+      map:
+        rho: 1.0
+        mu: 4.0
+        lambda: 8.0
diff --git a/tests/fixtures/velocity-sizefield-0.bin b/tests/fixtures/velocity-sizefield-0.bin
new file mode 100644
index 0000000000000000000000000000000000000000..8b7bbbf3d65ce232a1271a066815b411ed131ba2
GIT binary patch
literal 8172
zcmeIyyA8k~3<W@{beW0KvqDCoWDGDyVS;pr1W$Y_%Umfj+Oy)zzV~m<^ON^Hh<WA3
zT-$ylvn1-E4p9Mppbzwcf4~6_aDW3G-~b0WzyS_$fCC)h00%h00S<70103K02RQJb
F0|Q9Pc{u<8

literal 0
HcmV?d00001

diff --git a/tests/fixtures/velocity-sizefield-1.bin b/tests/fixtures/velocity-sizefield-1.bin
new file mode 100644
index 0000000000000000000000000000000000000000..f8a5dda4f04f730b7f2705f045ba6429147500a1
GIT binary patch
literal 14396
zcmeI3Ar8Vo5Jjs9if|(g5<G%i;7|xI0LS0}1lJ>g;RG0Pl}Hxa1ixSWPWLt0Y#^D;
z?)z`3qT1}&m&2<*EmqI%`B7KD=iTkMS^N3FPtzBZw8m*2@5|A(+0EJWIJ9h=j&XTA
z-sE{R6mF&aAN~GA@z8aT==pR0F9F|s+vROv`r@D0Klp3>`!Ywl=OBMAfB1R%<$B+j
zI{fka1Ai}n_Z*VHH-Gqh`Mc*&?T<fRf8g)sug;HJPyXKg;UAm7I)7?C{>1i&{IvYk
z`BCf1Ps<N}vH7X<<F3cQ*#4ECpL>4X{Y%fE`)j{nZhxcq$3M-#==`GlTl)E<`{zD?
V>Hctk?f)Zgf7SlvujQ}u`v9eZP$&QZ

literal 0
HcmV?d00001

diff --git a/tests/fixtures/velocity-sizefield.xml.in b/tests/fixtures/velocity-sizefield.xml.in
new file mode 100644
index 0000000..4ce36ee
--- /dev/null
+++ b/tests/fixtures/velocity-sizefield.xml.in
@@ -0,0 +1,16 @@
+<!--
+    SPDX-FileCopyrightText: 2026 SeisSol Group
+
+    SPDX-License-Identifier: BSD-3-Clause
+-->
+
+<!-- an axis-aligned cuboid (group 1, mesh size 0.5) and a rotated one (group 2, mesh size 1) -->
+<VelocityAwareMeshing easiFile="@PUMGEN_TEST_FIXTURES@/velocity-material.yaml"
+                      elementsPerWaveLength="2">
+    <VelocityRefinementCuboid frequency="1" centerX="1" centerY="1" centerZ="-0.125"
+                              halfSizeX="1" halfSizeY="1" halfSizeZ="0.125"
+                              bypassFindRegionAndUseGroup="1"/>
+    <VelocityRefinementCuboid frequency="1" centerX="1" centerY="1" centerZ="-0.625"
+                              halfSizeX="1" halfSizeY="0.5" halfSizeZ="0.375"
+                              rotationZAnticlockwiseFromX="30" bypassFindRegionAndUseGroup="2"/>
+</VelocityAwareMeshing>

From 8adbbc5699a01011427e371d44eb50d006781081 Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 20:10:10 +0000
Subject: [PATCH 18/19] Add a velocity check of the cell sizes

With --velocity-check <mesh attributes>, pumgen compares the edge lengths of
the cells in the refinement regions of the VelocityAwareMeshing settings with
the mesh size at their barycentre, for the material of the cell's group. It
logs the distribution of the mean and of the longest edge length over the mesh
size (quantiles from a histogram with 0.23 % wide bins, the maximum, and the
number of cells above 1). This works for meshes from any source, so that
meshes of different generators can be compared by the same measure.

For the layered test model, meshed by gmsh with a size callback, the check
reproduces the independently computed quantiles (mean edge: p50 1.37, p90
1.57, p99 1.71, max 2.14).

AI-generated. Model: Claude Opus 5.5
---
 CMakeLists.txt                          |   1 +
 src/pumgen.cpp                          |  30 +++++
 src/sizing/VelocityCheck.cpp            | 143 ++++++++++++++++++++++++
 src/sizing/VelocityCheck.h              |  21 ++++
 tests/CMakeLists.txt                    |  14 +++
 tests/fixtures/velocity-settings.xml.in |  16 +++
 6 files changed, 225 insertions(+)
 create mode 100644 src/sizing/VelocityCheck.cpp
 create mode 100644 src/sizing/VelocityCheck.h
 create mode 100644 tests/fixtures/velocity-settings.xml.in

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 930b740..269e851 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -149,6 +149,7 @@ if (EASI)
   target_compile_definitions(pumgen_sizing PRIVATE LOG_LEVEL=${LOG_LEVEL})
   target_link_libraries(pumgen_sizing PUBLIC easi::easi tinyxml2)
   target_link_libraries(pumgen PUBLIC pumgen_sizing)
+  target_sources(pumgen PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/src/sizing/VelocityCheck.cpp)
   target_compile_definitions(pumgen PUBLIC USE_EASI)
 
   add_executable(pumgen-sizefield ${CMAKE_CURRENT_SOURCE_DIR}/src/sizefield.cpp)
diff --git a/src/pumgen.cpp b/src/pumgen.cpp
index cd67a80..cb83b58 100644
--- a/src/pumgen.cpp
+++ b/src/pumgen.cpp
@@ -51,6 +51,13 @@
 
 #include "helper/InsphereCalculator.h"
 
+#ifdef USE_EASI
+#include "sizing/VelocityAwareMeshSize.h"
+#include "sizing/VelocityAwareSettings.h"
+#include "sizing/VelocityCheck.h"
+#include "tinyxml2/tinyxml2.h"
+#endif
+
 template <typename TT> static TT _checkH5Err(TT&& status, const char* file, int line) {
   if (status < 0) {
     logError() << utils::nospace << "An HDF5 error occurred (" << file << ": " << line << ")";
@@ -282,6 +289,10 @@ int main(int argc, char* argv[]) {
   args.addAdditionalOption("input", "Input file (mesh or model)");
   args.addAdditionalOption("output", "Output parallel unstructured mesh file", false);
   args.addOption("order", 'o', "Mesh order (default: 1)", utils::Args::Required, false);
+  args.addOption("velocity-check", 0,
+                 "Compare the cell sizes with the velocity-aware mesh size of the "
+                 "VelocityAwareMeshing element of a mesh attributes file (XML)",
+                 utils::Args::Required, false);
 
   if (args.parse(argc, argv, rank == 0) != utils::Args::Success)
     return 1;
@@ -463,6 +474,25 @@ int main(int argc, char* argv[]) {
   MPI_Reduce((rank == 0 ? MPI_IN_PLACE : &min), &min, 1, MPI_DOUBLE, MPI_MIN, 0, MPI_COMM_WORLD);
   logInfo() << "Minimum insphere found:" << min;
 
+  if (args.isSet("velocity-check")) {
+#ifdef USE_EASI
+    const auto* settingsFile = args.getArgument<const char*>("velocity-check");
+    tinyxml2::XMLDocument doc;
+    if (doc.LoadFile(settingsFile) != tinyxml2::XML_SUCCESS) {
+      logError() << "Could not read" << settingsFile;
+    }
+    const auto settings = readVelocityAwareSettings(doc);
+    if (!settings.isVelocityAwareRefinementOn()) {
+      logError() << "No refinement cuboid in" << settingsFile;
+    }
+    const VelocityAwareMeshSize meshSize(settings);
+    checkVelocityAwareMeshSize(meshSize, cellVertices, meshInput->group(), MPI_COMM_WORLD);
+#else
+    logError() << "This version of PUMGen has been compiled without easi; hence, --velocity-check "
+                  "is not available.";
+#endif
+  }
+
   // Get offsets
   std::size_t offsets[2] = {localSize[0], localSize[1]};
   MPI_Scan(MPI_IN_PLACE, offsets, 2, tndm::mpi_type_t<std::size_t>(), MPI_SUM, MPI_COMM_WORLD);
diff --git a/src/sizing/VelocityCheck.cpp b/src/sizing/VelocityCheck.cpp
new file mode 100644
index 0000000..04f6a59
--- /dev/null
+++ b/src/sizing/VelocityCheck.cpp
@@ -0,0 +1,143 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#include "VelocityCheck.h"
+
+#include <algorithm>
+#include <array>
+#include <cmath>
+#include <cstdint>
+#include <iomanip>
+#include <limits>
+#include <sstream>
+#include <string>
+
+#include "utils/logger.h"
+
+namespace {
+
+// log-spaced histogram of the ratios between MinRatio and MaxRatio
+constexpr double MinRatio = 1e-3;
+constexpr double MaxRatio = 1e3;
+constexpr std::size_t NumBins = 6000;
+constexpr std::size_t Batch = std::size_t{1} << 20;
+
+std::size_t binOf(double ratio) {
+  const double position =
+      std::log(ratio / MinRatio) / std::log(MaxRatio / MinRatio) * static_cast<double>(NumBins);
+  return static_cast<std::size_t>(std::clamp(position, 0.0, static_cast<double>(NumBins - 1)));
+}
+
+double upperEdgeOf(std::size_t bin) {
+  return MinRatio * std::pow(MaxRatio / MinRatio, static_cast<double>(bin + 1) / NumBins);
+}
+
+struct RatioStatistics {
+  std::vector<std::uint64_t> histogram = std::vector<std::uint64_t>(NumBins, 0);
+  std::uint64_t above = 0;
+  double maximum = 0;
+
+  void add(double ratio) {
+    ++histogram[binOf(ratio)];
+    above += ratio > 1 ? 1 : 0;
+    maximum = std::max(maximum, ratio);
+  }
+
+  void reduce(MPI_Comm comm) {
+    MPI_Allreduce(MPI_IN_PLACE, histogram.data(), NumBins, MPI_UINT64_T, MPI_SUM, comm);
+    MPI_Allreduce(MPI_IN_PLACE, &above, 1, MPI_UINT64_T, MPI_SUM, comm);
+    MPI_Allreduce(MPI_IN_PLACE, &maximum, 1, MPI_DOUBLE, MPI_MAX, comm);
+  }
+
+  /**
+   * The quantile, rounded up to the next bin edge (0.23 % apart).
+   */
+  [[nodiscard]] double quantile(double q, std::uint64_t total) const {
+    const auto target = static_cast<std::uint64_t>(std::ceil(q * static_cast<double>(total)));
+    std::uint64_t cumulative = 0;
+    for (std::size_t bin = 0; bin < NumBins; ++bin) {
+      cumulative += histogram[bin];
+      if (cumulative >= target && cumulative > 0) {
+        return std::min(upperEdgeOf(bin), maximum);
+      }
+    }
+    return maximum;
+  }
+
+  [[nodiscard]] std::string summary(std::uint64_t total) const {
+    std::stringstream stream;
+    stream << std::setprecision(3) << "p50 " << quantile(0.5, total) << ", p90 "
+           << quantile(0.9, total) << ", p99 " << quantile(0.99, total) << ", max " << maximum
+           << "; " << above << " cells above 1";
+    return stream.str();
+  }
+};
+
+double distance(const std::array<double, 3>& a, const std::array<double, 3>& b) {
+  return std::sqrt((a[0] - b[0]) * (a[0] - b[0]) + (a[1] - b[1]) * (a[1] - b[1]) +
+                   (a[2] - b[2]) * (a[2] - b[2]));
+}
+
+} // namespace
+
+void checkVelocityAwareMeshSize(const VelocityAwareMeshSize& meshSize, const CellVertices& cells,
+                                const std::vector<int>& groups, MPI_Comm comm) {
+  RatioStatistics meanEdge;
+  RatioStatistics longestEdge;
+  std::uint64_t checked = 0;
+
+  std::vector<std::array<double, 3>> barycenters;
+  std::vector<int> cellGroups;
+  std::vector<double> frequencies;
+  std::vector<std::array<double, 2>> edges;
+  for (std::size_t first = 0; first < cells.numCells(); first += Batch) {
+    const std::size_t count = std::min(Batch, cells.numCells() - first);
+    barycenters.resize(count);
+    cellGroups.resize(count);
+    frequencies.resize(count);
+    edges.resize(count);
+    for (std::size_t c = 0; c < count; ++c) {
+      const auto vertices = cells(first + c);
+      std::array<double, 3> barycenter{};
+      double sum = 0;
+      double longest = 0;
+      for (std::size_t a = 0; a < vertices.size(); ++a) {
+        for (int d = 0; d < 3; ++d) {
+          barycenter[d] += vertices[a][d] / static_cast<double>(vertices.size());
+        }
+        for (std::size_t b = a + 1; b < vertices.size(); ++b) {
+          const double length = distance(vertices[a], vertices[b]);
+          sum += length;
+          longest = std::max(longest, length);
+        }
+      }
+      barycenters[c] = barycenter;
+      cellGroups[c] = groups[first + c];
+      frequencies[c] = meshSize.targetedFrequencyAndGroup(barycenter).first;
+      edges[c] = {sum / 6, longest};
+    }
+
+    const auto sizes = meshSize.meshSizes(barycenters, cellGroups, frequencies);
+    for (std::size_t c = 0; c < count; ++c) {
+      if (sizes[c] == std::numeric_limits<double>::max()) {
+        continue;
+      }
+      ++checked;
+      meanEdge.add(edges[c][0] / sizes[c]);
+      longestEdge.add(edges[c][1] / sizes[c]);
+    }
+  }
+
+  std::uint64_t total = cells.numCells();
+  MPI_Allreduce(MPI_IN_PLACE, &checked, 1, MPI_UINT64_T, MPI_SUM, comm);
+  MPI_Allreduce(MPI_IN_PLACE, &total, 1, MPI_UINT64_T, MPI_SUM, comm);
+  meanEdge.reduce(comm);
+  longestEdge.reduce(comm);
+
+  logInfo() << "Velocity check:" << checked << "of" << total
+            << "cells lie in refinement regions (ratios of edge length and mesh size)";
+  if (checked > 0) {
+    logInfo() << "Velocity check, mean edge:" << meanEdge.summary(checked).c_str();
+    logInfo() << "Velocity check, longest edge:" << longestEdge.summary(checked).c_str();
+  }
+}
diff --git a/src/sizing/VelocityCheck.h b/src/sizing/VelocityCheck.h
new file mode 100644
index 0000000..202a3b3
--- /dev/null
+++ b/src/sizing/VelocityCheck.h
@@ -0,0 +1,21 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#ifndef PUMGEN_SRC_SIZING_VELOCITYCHECK_H_
+#define PUMGEN_SRC_SIZING_VELOCITYCHECK_H_
+
+#include <mpi.h>
+#include <vector>
+
+#include "VelocityAwareMeshSize.h"
+#include "helper/InsphereCalculator.h"
+
+/**
+ * Compares the edge lengths of the cells in the refinement regions with the velocity-aware mesh
+ * size at their barycentre (for the material of the cell's group) and logs the distribution of the
+ * ratios, as mean and as longest edge length over mesh size.
+ */
+void checkVelocityAwareMeshSize(const VelocityAwareMeshSize& meshSize, const CellVertices& cells,
+                                const std::vector<int>& groups, MPI_Comm comm);
+
+#endif // PUMGEN_SRC_SIZING_VELOCITYCHECK_H_
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index ebf9e56..5e342e3 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -192,9 +192,19 @@ pumgen_add_test(msh2.tiny-duplicateface RANKS 1 SOURCE msh2 INPUT tiny-duplicate
 
 # velocity-aware sizing, with a material of shear wave speed 1 in group 1 and 2 in group 2
 if(EASI)
+  configure_file(fixtures/velocity-settings.xml.in ${CMAKE_CURRENT_BINARY_DIR}/velocity-settings.xml
+                 @ONLY)
   configure_file(fixtures/velocity-sizefield.xml.in
                  ${CMAKE_CURRENT_BINARY_DIR}/velocity-sizefield.xml @ONLY)
 
+  # the counts are computed independently from the reference of the coarse mesh
+  pumgen_add_test(
+    msh4.coarse.velocity-check RANKS 2 SOURCE msh4 INPUT coarse-v41.msh
+    ARGS --velocity-check=${CMAKE_CURRENT_BINARY_DIR}/velocity-settings.xml
+    EXPECT_OUTPUT
+      "320 of 320 cells lie in refinement regions.*mean edge:[^\n]*; 4 cells above 1.*longest edge:[^\n]*; 143 cells above 1"
+  )
+
   # the expected grids are verified independently; they must not depend on the number of ranks
   foreach(ranks 1 3)
     set(prefix ${PUMGEN_TEST_OUTPUT}/sizefield-np${ranks})
@@ -209,3 +219,7 @@ if(EASI)
     set_tests_properties(sizefield.np${ranks} PROPERTIES PROCESSORS ${ranks} TIMEOUT 120)
   endforeach()
 endif()
+if(NOT EASI)
+  pumgen_add_test(msh4.tiny.velocity-check-without-easi RANKS 1 SOURCE msh4 INPUT tiny-v41.msh
+                  ARGS --velocity-check=unused.xml EXPECT_ERROR "compiled without easi")
+endif()
diff --git a/tests/fixtures/velocity-settings.xml.in b/tests/fixtures/velocity-settings.xml.in
new file mode 100644
index 0000000..0c56141
--- /dev/null
+++ b/tests/fixtures/velocity-settings.xml.in
@@ -0,0 +1,16 @@
+<!--
+    SPDX-FileCopyrightText: 2026 SeisSol Group
+
+    SPDX-License-Identifier: BSD-3-Clause
+-->
+
+<!-- mesh sizes 0.5 in the upper layer (group 1) and 1 below (group 2) of the coarse fixture -->
+<VelocityAwareMeshing easiFile="@PUMGEN_TEST_FIXTURES@/velocity-material.yaml"
+                      elementsPerWaveLength="2">
+    <VelocityRefinementCuboid frequency="1" centerX="1" centerY="1" centerZ="-0.125"
+                              halfSizeX="1" halfSizeY="1" halfSizeZ="0.125"
+                              bypassFindRegionAndUseGroup="1"/>
+    <VelocityRefinementCuboid frequency="1" centerX="1" centerY="1" centerZ="-0.625"
+                              halfSizeX="1" halfSizeY="1" halfSizeZ="0.375"
+                              bypassFindRegionAndUseGroup="2"/>
+</VelocityAwareMeshing>

From db7c86ac679f4c24d03a35a419b0df6b30352a95 Mon Sep 17 00:00:00 2001
From: David Schneller <david.schneller@tum.de>
Date: Tue, 22 Sep 2026 20:33:55 +0000
Subject: [PATCH 19/19] Read binary MSH 4.1 files with all ranks

For binary MSH 4.1 files, rank 0 now only reads the structure of the file
(entities, block headers, periodic nodes) and skips the node and element
data. With the resulting offsets, every rank reads a share of the nodes,
cells and boundary faces. The nodes are sent to the ranks owning them in the
chunk distribution; the cells are read directly by their owners, in file
order as before. The boundary faces go to the ranks given by a hash of their
vertices, their vertices are marked in a bit set shared by all ranks, and
only cell faces whose vertices all lie on the surface mesh are looked up.
Periodic nodes are joined into classes on rank 0 and sent to the owners.

On the mesh with 3.6M cells, the output is identical to the one of the
serial reader for 1, 2, 4 and 8 ranks. The highest peak memory of a rank
drops from 255 MB to 161 MB with 4 ranks and from 235 MB to 129 MB with 8
ranks; with one rank, time and memory stay about the same (1.07 s vs.
1.11 s, 404 MB vs. 378 MB).

--gmsh-reader=serial keeps reading on rank 0; ASCII files are always read
there.

AI-generated. Model: Claude Opus 5.5
---
 CMakeLists.txt                               |   2 +
 src/meshreader/DistributedGMSHReader.cpp     |  79 +++
 src/meshreader/DistributedGMSHReader.h       | 482 +++++++++++++++++++
 src/meshreader/GMSH4Parser.h                 |   9 +-
 src/meshreader/Msh4Index.cpp                 | 139 ++++++
 src/meshreader/Msh4Index.h                   |  82 ++++
 src/meshreader/MshInput.cpp                  |  19 +
 src/meshreader/MshInput.h                    |   6 +
 src/pumgen.cpp                               |  25 +-
 tests/CMakeLists.txt                         |  20 +
 tests/fixtures/generate.py                   |  22 +
 tests/fixtures/tiny-binary-badnode-v41.msh   | Bin 0 -> 482 bytes
 tests/fixtures/tiny-binary-duplicate-v41.msh | Bin 0 -> 482 bytes
 tests/fixtures/tiny-binary-sparse-v41.msh    | Bin 0 -> 482 bytes
 tests/fixtures/tiny-binary-v41.msh           | Bin 0 -> 482 bytes
 15 files changed, 878 insertions(+), 7 deletions(-)
 create mode 100644 src/meshreader/DistributedGMSHReader.cpp
 create mode 100644 src/meshreader/DistributedGMSHReader.h
 create mode 100644 src/meshreader/Msh4Index.cpp
 create mode 100644 src/meshreader/Msh4Index.h
 create mode 100644 tests/fixtures/tiny-binary-badnode-v41.msh
 create mode 100644 tests/fixtures/tiny-binary-duplicate-v41.msh
 create mode 100644 tests/fixtures/tiny-binary-sparse-v41.msh
 create mode 100644 tests/fixtures/tiny-binary-v41.msh

diff --git a/CMakeLists.txt b/CMakeLists.txt
index 269e851..3ae9833 100644
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -42,6 +42,8 @@ add_executable(pumgen
   ${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/GMSH2Parser.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/GMSH4Parser.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/MshInput.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/Msh4Index.cpp
+  ${CMAKE_CURRENT_SOURCE_DIR}/src/meshreader/DistributedGMSHReader.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/input/ParallelVertexFilter.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/helper/InsphereCalculator.cpp
   ${CMAKE_CURRENT_SOURCE_DIR}/src/helper/MPIConvenience.cpp
diff --git a/src/meshreader/DistributedGMSHReader.cpp b/src/meshreader/DistributedGMSHReader.cpp
new file mode 100644
index 0000000..238030b
--- /dev/null
+++ b/src/meshreader/DistributedGMSHReader.cpp
@@ -0,0 +1,79 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#include "DistributedGMSHReader.h"
+
+#include <algorithm>
+#include <array>
+#include <cstring>
+
+namespace puml::distributed {
+
+namespace {
+template <typename T> T swapBytesOf(T value) {
+  std::array<unsigned char, sizeof(T)> bytes{};
+  std::memcpy(bytes.data(), &value, sizeof(T));
+  std::reverse(bytes.begin(), bytes.end());
+  std::memcpy(&value, bytes.data(), sizeof(T));
+  return value;
+}
+
+std::uint64_t mix(std::uint64_t value) {
+  // splitmix64 finalizer
+  value ^= value >> 30;
+  value *= 0xbf58476d1ce4e5b9ULL;
+  value ^= value >> 27;
+  value *= 0x94d049bb133111ebULL;
+  value ^= value >> 31;
+  return value;
+}
+} // namespace
+
+RawMshFile::RawMshFile(const std::string& fileName, const Msh4Index& index)
+    : dataSize(index.dataSize), swapBytes(index.swapBytes) {
+  file = std::fopen(fileName.c_str(), "rb");
+  if (file == nullptr) {
+    logError() << "Unable to open MSH file" << fileName;
+  }
+}
+
+RawMshFile::~RawMshFile() {
+  if (file != nullptr) {
+    std::fclose(file);
+  }
+}
+
+void RawMshFile::readBytes(std::uint64_t offset, std::size_t bytes, void* data) {
+  if (std::fseek(file, static_cast<long>(offset), SEEK_SET) != 0 ||
+      std::fread(data, 1, bytes, file) != bytes) {
+    logError() << "Unexpected end of file in binary data";
+  }
+}
+
+void RawMshFile::readSizes(std::uint64_t offset, std::size_t count, std::uint64_t* values) {
+  if (dataSize == sizeof(std::uint64_t)) {
+    readBytes(offset, count * sizeof(std::uint64_t), values);
+    if (swapBytes) {
+      std::transform(values, values + count, values, swapBytesOf<std::uint64_t>);
+    }
+  } else {
+    narrowSizes.resize(count);
+    readBytes(offset, count * sizeof(std::uint32_t), narrowSizes.data());
+    for (std::size_t i = 0; i < count; ++i) {
+      values[i] = swapBytes ? swapBytesOf(narrowSizes[i]) : narrowSizes[i];
+    }
+  }
+}
+
+void RawMshFile::readDoubles(std::uint64_t offset, std::size_t count, double* values) {
+  readBytes(offset, count * sizeof(double), values);
+  if (swapBytes) {
+    std::transform(values, values + count, values, swapBytesOf<double>);
+  }
+}
+
+std::uint64_t hashFace(const std::array<std::uint64_t, 3>& face) {
+  return mix(mix(mix(face[0]) ^ face[1]) ^ face[2]);
+}
+
+} // namespace puml::distributed
diff --git a/src/meshreader/DistributedGMSHReader.h b/src/meshreader/DistributedGMSHReader.h
new file mode 100644
index 0000000..c390cd3
--- /dev/null
+++ b/src/meshreader/DistributedGMSHReader.h
@@ -0,0 +1,482 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#ifndef PUMGEN_SRC_MESHREADER_DISTRIBUTEDGMSHREADER_H_
+#define PUMGEN_SRC_MESHREADER_DISTRIBUTEDGMSHREADER_H_
+
+#include <mpi.h>
+
+#include <algorithm>
+#include <array>
+#include <cstddef>
+#include <cstdint>
+#include <cstdio>
+#include <numeric>
+#include <string>
+#include <type_traits>
+#include <unordered_map>
+#include <vector>
+
+#include "GMSHBuilder.h"
+#include "Msh4Index.h"
+#include "helper/Distributor.h"
+#include "helper/MPIConvenience.h"
+#include "third_party/MPITraits.h"
+#include "utils/logger.h"
+
+namespace puml {
+
+namespace distributed {
+
+/**
+ * Reads values of a binary MSH 4.1 file at given offsets.
+ */
+class RawMshFile {
+  public:
+  RawMshFile(const std::string& fileName, const Msh4Index& index);
+  ~RawMshFile();
+  RawMshFile(const RawMshFile&) = delete;
+  RawMshFile& operator=(const RawMshFile&) = delete;
+
+  void readSizes(std::uint64_t offset, std::size_t count, std::uint64_t* values);
+  void readDoubles(std::uint64_t offset, std::size_t count, double* values);
+
+  private:
+  void readBytes(std::uint64_t offset, std::size_t bytes, void* data);
+
+  std::FILE* file = nullptr;
+  std::uint64_t dataSize;
+  bool swapBytes;
+  std::vector<std::uint32_t> narrowSizes;
+};
+
+/**
+ * Sends outgoing[r] to rank r; returns what each rank has sent to this one.
+ */
+template <typename T>
+std::vector<std::vector<T>> exchange(const std::vector<std::vector<T>>& outgoing, MPI_Comm comm) {
+  static_assert(std::is_trivially_copyable_v<T>);
+  int size = 1;
+  MPI_Comm_size(comm, &size);
+  std::vector<std::size_t> sendCounts(size);
+  std::vector<std::size_t> recvCounts(size);
+  for (int r = 0; r < size; ++r) {
+    sendCounts[r] = outgoing[r].size();
+  }
+  MPI_Alltoall(sendCounts.data(), 1, tndm::mpi_type_t<std::size_t>(), recvCounts.data(), 1,
+               tndm::mpi_type_t<std::size_t>(), comm);
+  std::vector<std::size_t> sendDisp(size + 1, 0);
+  std::vector<std::size_t> recvDisp(size + 1, 0);
+  for (int r = 0; r < size; ++r) {
+    sendDisp[r + 1] = sendDisp[r] + sendCounts[r];
+    recvDisp[r + 1] = recvDisp[r] + recvCounts[r];
+  }
+  std::vector<T> sendBuffer(sendDisp[size]);
+  for (int r = 0; r < size; ++r) {
+    std::copy(outgoing[r].begin(), outgoing[r].end(), sendBuffer.begin() + sendDisp[r]);
+  }
+  std::vector<T> recvBuffer(recvDisp[size]);
+
+  MPI_Datatype type;
+  MPI_Type_contiguous(sizeof(T), MPI_BYTE, &type);
+  MPI_Type_commit(&type);
+  sparseAlltoallv(sendBuffer.data(), sendCounts.data(), sendDisp.data(), type, recvBuffer.data(),
+                  recvCounts.data(), recvDisp.data(), type, comm);
+  MPI_Type_free(&type);
+
+  std::vector<std::vector<T>> incoming(size);
+  for (int r = 0; r < size; ++r) {
+    incoming[r].assign(recvBuffer.begin() + recvDisp[r], recvBuffer.begin() + recvDisp[r + 1]);
+  }
+  return incoming;
+}
+
+/**
+ * Calls f(block, begin, count) for the parts of the items [first, last) of the concatenated
+ * blocks, where begin is relative to the block.
+ */
+template <typename Block, typename F>
+void forBlockRanges(const std::vector<Block>& blocks, std::uint64_t first, std::uint64_t last,
+                    F&& f) {
+  std::uint64_t blockStart = 0;
+  for (const auto& block : blocks) {
+    const std::uint64_t blockEnd = blockStart + block.count;
+    const std::uint64_t begin = std::max(first, blockStart);
+    const std::uint64_t end = std::min(last, blockEnd);
+    if (begin < end) {
+      f(block, begin - blockStart, end - begin);
+    }
+    blockStart = blockEnd;
+  }
+}
+
+std::uint64_t hashFace(const std::array<std::uint64_t, 3>& face);
+
+// items are read in pieces of at most this many
+constexpr std::uint64_t Piece = std::uint64_t{1} << 20;
+
+} // namespace distributed
+
+/**
+ * Reads a binary MSH 4.1 file with all ranks: rank 0 only locates the data, every rank reads a
+ * share of the nodes, cells and boundary faces, and the parts are sent to the ranks which own
+ * them in the chunk distribution of getChunksize. The boundary conditions are matched in a
+ * distributed table of the boundary faces; only faces whose vertices all lie on the surface mesh
+ * are looked up.
+ */
+template <std::size_t OrderP> class DistributedGMSHReader {
+  public:
+  constexpr static std::size_t Order = OrderP;
+  constexpr static std::size_t Dim = 3;
+  constexpr static bool SupportsIdentify = true;
+  constexpr static std::size_t NodesPerCell = nodeCount(Dim, Order);
+  constexpr static std::size_t NodesPerFacet = nodeCount(Dim - 1, Order);
+  constexpr static std::size_t Facet2Nodes[Dim + 1][Dim] = {
+      {1, 0, 2}, {0, 1, 3}, {1, 2, 3}, {2, 0, 3}};
+  constexpr static long BoundaryConditionOffset = 100;
+
+  explicit DistributedGMSHReader(MPI_Comm comm = MPI_COMM_WORLD) : comm(comm) {
+    MPI_Comm_rank(comm, &rank);
+    MPI_Comm_size(comm, &size);
+  }
+
+  void open(const char* meshFile) {
+    readIndex(meshFile);
+    distributed::RawMshFile file(meshFile, index);
+    readNodes(file);
+    readCells(file);
+    matchBoundaryConditions(file);
+    identifyPeriodicNodes();
+  }
+
+  [[nodiscard]] std::size_t nVertices() const { return index.numNodes; }
+  [[nodiscard]] std::size_t nElements() const { return numCells; }
+
+  // Each read function hands over one part of the local mesh and releases it, so it can be called
+  // only once.
+
+  void readVertices(double* vertices) { handOver(geometry, vertices); }
+  void readElements(std::size_t* elements) { handOver(connectivity, elements); }
+  void readGroups(int* groupsOut) { handOver(groups, groupsOut); }
+  void readBoundaries(int* boundariesOut) { handOver(boundaries, boundariesOut); }
+  [[nodiscard]] bool hasIdentify() const { return hasIdentify_; }
+  void readIdentify(std::size_t* vertices) { handOver(identify, vertices); }
+
+  private:
+  struct NodeRecord {
+    std::uint64_t index;
+    double x[3];
+  };
+  struct FaceRecord {
+    std::array<std::uint64_t, 3> vertices;
+    std::int64_t bc;
+  };
+  struct FaceQuery {
+    std::array<std::uint64_t, 3> vertices;
+    std::uint64_t localFace;
+  };
+  struct FaceReply {
+    std::uint64_t localFace;
+    std::int64_t bc;
+  };
+  struct Identification {
+    std::uint64_t vertex;
+    std::uint64_t representative;
+  };
+  constexpr static std::int64_t NoMatch = -1;
+
+  template <typename T, typename U> static void handOver(std::vector<T>& values, U* out) {
+    std::copy(values.begin(), values.end(), out);
+    std::vector<T>().swap(values);
+  }
+
+  [[nodiscard]] std::uint64_t localFirstVertex() const {
+    return getChunksum(index.numNodes, rank, size);
+  }
+  [[nodiscard]] std::uint64_t localVertexCount() const {
+    return getChunksize(index.numNodes, rank, size);
+  }
+  [[nodiscard]] int vertexOwner(std::uint64_t vertex) const {
+    return getChunkOwner(index.numNodes, vertex, size);
+  }
+
+  [[nodiscard]] std::uint64_t nodeIndex(std::uint64_t tag) const {
+    if (tag < index.firstNodeTag || tag - index.firstNodeTag >= index.numNodes) {
+      logError() << "Unknown node tag" << tag;
+    }
+    return tag - index.firstNodeTag;
+  }
+
+  template <typename T> void broadcastVector(std::vector<T>& values) {
+    std::uint64_t count = values.size();
+    MPI_Bcast(&count, 1, MPI_UINT64_T, 0, comm);
+    values.resize(count);
+    MPI_Bcast(values.data(), static_cast<int>(count * sizeof(T)), MPI_BYTE, 0, comm);
+  }
+
+  void readIndex(const char* meshFile) {
+    if (rank == 0) {
+      Msh4Indexer indexer(GMSHSimplexType<Dim, Order>::type, GMSHSimplexType<Dim - 1, Order>::type);
+      if (!indexer.parseFile(meshFile)) {
+        logError() << meshFile << std::endl << indexer.getErrorMessage();
+      }
+      index = indexer.getIndex();
+    }
+    std::array<std::uint64_t, 5> scalars{index.dataSize, index.swapBytes ? 1U : 0U,
+                                         index.firstNodeTag, index.numNodes,
+                                         index.periodic.empty() ? 0U : 1U};
+    MPI_Bcast(scalars.data(), scalars.size(), MPI_UINT64_T, 0, comm);
+    index.dataSize = scalars[0];
+    index.swapBytes = scalars[1] != 0;
+    index.firstNodeTag = scalars[2];
+    index.numNodes = scalars[3];
+    hasIdentify_ = scalars[4] != 0;
+    broadcastVector(index.nodeBlocks);
+    broadcastVector(index.cellBlocks);
+    broadcastVector(index.facetBlocks);
+    numCells = 0;
+    for (const auto& block : index.cellBlocks) {
+      numCells += block.count;
+    }
+  }
+
+  void readNodes(distributed::RawMshFile& file) {
+    const std::uint64_t first = getChunksum(index.numNodes, rank, size);
+    const std::uint64_t last = first + getChunksize(index.numNodes, rank, size);
+
+    std::vector<std::vector<NodeRecord>> outgoing(size);
+    std::vector<std::uint64_t> tags;
+    std::vector<double> coordinates;
+    distributed::forBlockRanges(
+        index.nodeBlocks, first, last,
+        [&](const Msh4NodeBlock& block, std::uint64_t begin, std::uint64_t count) {
+          for (std::uint64_t done = 0; done < count; done += distributed::Piece) {
+            const auto n = std::min(distributed::Piece, count - done);
+            tags.resize(n);
+            coordinates.resize(n * block.valuesPerNode);
+            file.readSizes(block.tagsOffset + (begin + done) * index.dataSize, n, tags.data());
+            file.readDoubles(block.coordinatesOffset +
+                                 (begin + done) * block.valuesPerNode * sizeof(double),
+                             coordinates.size(), coordinates.data());
+            for (std::uint64_t i = 0; i < n; ++i) {
+              const auto vertex = nodeIndex(tags[i]);
+              const double* x = &coordinates[i * block.valuesPerNode];
+              outgoing[vertexOwner(vertex)].push_back({vertex, {x[0], x[1], x[2]}});
+            }
+          }
+        });
+
+    const auto incoming = distributed::exchange(outgoing, comm);
+    std::vector<std::vector<NodeRecord>>().swap(outgoing);
+
+    const auto localFirst = localFirstVertex();
+    geometry.assign(localVertexCount() * Dim, 0.0);
+    std::vector<bool> defined(localVertexCount(), false);
+    std::uint64_t numDefined = 0;
+    for (const auto& records : incoming) {
+      for (const auto& record : records) {
+        const auto local = record.index - localFirst;
+        if (defined[local]) {
+          logError() << "Duplicate node tag" << record.index + index.firstNodeTag;
+        }
+        defined[local] = true;
+        ++numDefined;
+        std::copy_n(record.x, Dim, &geometry[local * Dim]);
+      }
+    }
+    if (numDefined != localVertexCount()) {
+      logError() << "Missing nodes: the node tags are not unique";
+    }
+  }
+
+  void readCells(distributed::RawMshFile& file) {
+    const std::uint64_t first = getChunksum(numCells, rank, size);
+    const std::uint64_t count = getChunksize(numCells, rank, size);
+    connectivity.resize(count * NodesPerCell);
+    groups.resize(count);
+
+    constexpr std::uint64_t ValuesPerCell = 1 + NodesPerCell;
+    std::vector<std::uint64_t> values;
+    std::uint64_t cell = 0;
+    distributed::forBlockRanges(
+        index.cellBlocks, first, first + count,
+        [&](const Msh4ElementBlock& block, std::uint64_t begin, std::uint64_t blockCount) {
+          for (std::uint64_t done = 0; done < blockCount; done += distributed::Piece) {
+            const auto n = std::min(distributed::Piece, blockCount - done);
+            values.resize(n * ValuesPerCell);
+            file.readSizes(block.offset + (begin + done) * ValuesPerCell * index.dataSize,
+                           values.size(), values.data());
+            for (std::uint64_t e = 0; e < n; ++e, ++cell) {
+              for (std::size_t k = 0; k < NodesPerCell; ++k) {
+                connectivity[cell * NodesPerCell + k] =
+                    nodeIndex(values[e * ValuesPerCell + 1 + k]);
+              }
+              groups[cell] = static_cast<int>(block.physical);
+            }
+          }
+        });
+  }
+
+  void matchBoundaryConditions(distributed::RawMshFile& file) {
+    std::uint64_t numFacets = 0;
+    for (const auto& block : index.facetBlocks) {
+      numFacets += block.count;
+    }
+    const std::uint64_t first = getChunksum(numFacets, rank, size);
+    const std::uint64_t last = first + getChunksize(numFacets, rank, size);
+
+    // the boundary faces go to the ranks given by their hash; their vertices are marked in a bit
+    // set of all vertices, which all ranks share
+    std::vector<std::vector<FaceRecord>> outgoingFaces(size);
+    std::vector<std::uint64_t> onBoundary((index.numNodes + 63) / 64, 0);
+    constexpr std::uint64_t ValuesPerFacet = 1 + NodesPerFacet;
+    std::vector<std::uint64_t> values;
+    distributed::forBlockRanges(
+        index.facetBlocks, first, last,
+        [&](const Msh4ElementBlock& block, std::uint64_t begin, std::uint64_t count) {
+          for (std::uint64_t done = 0; done < count; done += distributed::Piece) {
+            const auto n = std::min(distributed::Piece, count - done);
+            values.resize(n * ValuesPerFacet);
+            file.readSizes(block.offset + (begin + done) * ValuesPerFacet * index.dataSize,
+                           values.size(), values.data());
+            for (std::uint64_t e = 0; e < n; ++e) {
+              std::array<std::uint64_t, 3> face{};
+              for (std::size_t k = 0; k < Dim; ++k) {
+                face[k] = nodeIndex(values[e * ValuesPerFacet + 1 + k]);
+                onBoundary[face[k] / 64] |= std::uint64_t{1} << (face[k] % 64);
+              }
+              std::sort(face.begin(), face.end());
+              outgoingFaces[distributed::hashFace(face) % size].push_back({face, block.physical});
+            }
+          }
+        });
+
+    std::vector<FaceRecord> faceTable;
+    for (const auto& faces : distributed::exchange(outgoingFaces, comm)) {
+      faceTable.insert(faceTable.end(), faces.begin(), faces.end());
+    }
+    std::vector<std::vector<FaceRecord>>().swap(outgoingFaces);
+    const auto byVertices = [](const FaceRecord& a, const FaceRecord& b) {
+      return a.vertices < b.vertices;
+    };
+    std::sort(faceTable.begin(), faceTable.end(), byVertices);
+
+    MPI_Allreduce(MPI_IN_PLACE, onBoundary.data(), static_cast<int>(onBoundary.size()),
+                  MPI_UINT64_T, MPI_BOR, comm);
+    const auto vertexOnBoundary = [&](std::uint64_t vertex) {
+      return ((onBoundary[vertex / 64] >> (vertex % 64)) & 1) != 0;
+    };
+
+    const std::uint64_t numLocalCells = groups.size();
+    // only faces with all vertices on the surface mesh can be part of it
+    std::vector<std::vector<FaceQuery>> queries(size);
+    for (std::uint64_t cell = 0; cell < numLocalCells; ++cell) {
+      std::array<bool, Dim + 1> flagged{};
+      std::size_t numFlagged = 0;
+      for (std::size_t k = 0; k < Dim + 1; ++k) {
+        flagged[k] = vertexOnBoundary(connectivity[cell * NodesPerCell + k]);
+        numFlagged += flagged[k] ? 1 : 0;
+      }
+      if (numFlagged < Dim) {
+        continue;
+      }
+      for (std::size_t localFace = 0; localFace < Dim + 1; ++localFace) {
+        std::array<std::uint64_t, 3> face{};
+        bool candidate = true;
+        for (std::size_t k = 0; k < Dim; ++k) {
+          candidate = candidate && flagged[Facet2Nodes[localFace][k]];
+          face[k] = connectivity[cell * NodesPerCell + Facet2Nodes[localFace][k]];
+        }
+        if (candidate) {
+          std::sort(face.begin(), face.end());
+          queries[distributed::hashFace(face) % size].push_back(
+              {face, cell * (Dim + 1) + localFace});
+        }
+      }
+    }
+
+    const auto received = distributed::exchange(queries, comm);
+    std::vector<std::vector<FaceQuery>>().swap(queries);
+    std::vector<std::vector<FaceReply>> replies(size);
+    for (int r = 0; r < size; ++r) {
+      for (const auto& query : received[r]) {
+        const FaceRecord key{query.vertices, 0};
+        const auto [lower, upper] =
+            std::equal_range(faceTable.begin(), faceTable.end(), key, byVertices);
+        if (upper - lower > 1) {
+          logError() << "A face of an element exists multiple times in the surface mesh.";
+        }
+        replies[r].push_back({query.localFace, lower != upper ? lower->bc : NoMatch});
+      }
+    }
+
+    boundaries.assign(numLocalCells * (Dim + 1), 0);
+    for (const auto& answersFrom : distributed::exchange(replies, comm)) {
+      for (const auto& reply : answersFrom) {
+        if (reply.bc != NoMatch) {
+          const auto bc =
+              reply.bc >= BoundaryConditionOffset ? reply.bc - BoundaryConditionOffset : reply.bc;
+          boundaries[reply.localFace] = static_cast<int>(bc);
+        }
+      }
+    }
+  }
+
+  void identifyPeriodicNodes() {
+    if (!hasIdentify_) {
+      return;
+    }
+    // rank 0 joins the periodic nodes into classes, represented by their smallest vertex
+    std::vector<std::vector<Identification>> outgoing(size);
+    if (rank == 0) {
+      std::unordered_map<std::uint64_t, std::uint64_t> parent;
+      const auto find = [&](std::uint64_t vertex) {
+        auto it = parent.try_emplace(vertex, vertex).first;
+        while (it->second != it->first) {
+          const auto next = parent.find(it->second);
+          it->second = next->second;
+          it = next;
+        }
+        return it->first;
+      };
+      for (const auto& [nodeTag, masterTag] : index.periodic) {
+        const auto a = find(nodeIndex(nodeTag));
+        const auto b = find(nodeIndex(masterTag));
+        parent[std::max(a, b)] = std::min(a, b);
+      }
+      std::vector<std::uint64_t> vertices;
+      vertices.reserve(parent.size());
+      for (const auto& entry : parent) {
+        vertices.push_back(entry.first);
+      }
+      for (const auto vertex : vertices) {
+        outgoing[vertexOwner(vertex)].push_back({vertex, find(vertex)});
+      }
+    }
+
+    const auto localFirst = localFirstVertex();
+    identify.resize(localVertexCount());
+    std::iota(identify.begin(), identify.end(), localFirst);
+    for (const auto& identifications : distributed::exchange(outgoing, comm)) {
+      for (const auto& identification : identifications) {
+        identify[identification.vertex - localFirst] = identification.representative;
+      }
+    }
+  }
+
+  MPI_Comm comm;
+  int rank = 0;
+  int size = 1;
+  Msh4Index index;
+  std::uint64_t numCells = 0;
+  bool hasIdentify_ = false;
+  std::vector<double> geometry;
+  std::vector<std::size_t> connectivity;
+  std::vector<int> groups;
+  std::vector<int> boundaries;
+  std::vector<std::size_t> identify;
+};
+
+} // namespace puml
+
+#endif // PUMGEN_SRC_MESHREADER_DISTRIBUTEDGMSHREADER_H_
diff --git a/src/meshreader/GMSH4Parser.h b/src/meshreader/GMSH4Parser.h
index 77f8c5b..bc7794c 100644
--- a/src/meshreader/GMSH4Parser.h
+++ b/src/meshreader/GMSH4Parser.h
@@ -21,12 +21,13 @@ class GMSH4Parser : public GMSHParser {
   public:
   using GMSHParser::GMSHParser;
 
-  private:
+  protected:
   void parse_() override;
   void parseEntities();
-  void parseNodes();
-  void parseElements();
-  void parsePeriodic();
+  // overridden by readers which only locate the data of these sections
+  virtual void parseNodes();
+  virtual void parseElements();
+  virtual void parsePeriodic();
 
   /**
    * Starts the data of a section; in binary files, the data begins after the line break.
diff --git a/src/meshreader/Msh4Index.cpp b/src/meshreader/Msh4Index.cpp
new file mode 100644
index 0000000..a73b71c
--- /dev/null
+++ b/src/meshreader/Msh4Index.cpp
@@ -0,0 +1,139 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#include "Msh4Index.h"
+
+#include <cstdio>
+#include <string>
+
+namespace puml {
+
+void Msh4Indexer::skipData(std::size_t bytes) {
+  if (!input->seek(input->offset() + bytes)) {
+    failFile("Unexpected end of file in binary data");
+  }
+}
+
+void Msh4Indexer::parseNodes() {
+  if (!binary) {
+    failFile("Only binary MSH 4.1 files can be read in parallel");
+  }
+  beginSectionData();
+  const std::size_t numBlocks = readSize();
+  const std::size_t numVertices = readSize();
+  const std::size_t minNodeTag = readSize();
+  const std::size_t maxNodeTag = readSize();
+  if (numVertices > 0 &&
+      (minNodeTag == 0 || maxNodeTag < minNodeTag || maxNodeTag - minNodeTag + 1 != numVertices)) {
+    char buf[192];
+    snprintf(buf, sizeof(buf),
+             "Non-contiguous node tags are not supported (%zu nodes with tags from %zu to %zu)",
+             numVertices, minNodeTag, maxNodeTag);
+    fail(buf);
+  }
+  hasNodes = true;
+  firstNodeTag = minNodeTag;
+  numNodes = numVertices;
+  index.dataSize = dataSize;
+  index.swapBytes = swapBytes;
+  index.firstNodeTag = minNodeTag;
+  index.numNodes = numVertices;
+
+  std::size_t numInBlocks = 0;
+  for (std::size_t blockIdx = 0; blockIdx < numBlocks; ++blockIdx) {
+    const long dim = readInt();
+    readInt(); // entity tag
+    const long parametric = readInt();
+    const std::size_t count = readSize();
+    Msh4NodeBlock block{};
+    block.count = count;
+    block.valuesPerNode = 3 + (parametric != 0 ? static_cast<std::uint64_t>(dim) : 0);
+    block.tagsOffset = input->offset();
+    block.coordinatesOffset = block.tagsOffset + count * dataSize;
+    skipData(count * dataSize + count * block.valuesPerNode * sizeof(double));
+    if (count > 0) {
+      index.nodeBlocks.push_back(block);
+    }
+    numInBlocks += count;
+  }
+  if (numInBlocks != numVertices) {
+    failFile("The node blocks contain " + std::to_string(numInBlocks) + " nodes instead of " +
+             std::to_string(numVertices));
+  }
+  expectToken("$EndNodes");
+}
+
+void Msh4Indexer::parseElements() {
+  if (!hasNodes) {
+    fail("Expected $Nodes before $Elements");
+  }
+  beginSectionData();
+  const std::size_t numBlocks = readSize();
+  readSize(); // number of elements
+  readSize(); // minimal element tag
+  readSize(); // maximal element tag
+
+  for (std::size_t blockIdx = 0; blockIdx < numBlocks; ++blockIdx) {
+    const long dim = readInt();
+    const long entityTag = readInt();
+    const auto typeOffset = position();
+    const long type = readInt();
+    if (type < 1 || type > static_cast<long>(NumTypes) || NumNodes[type - 1] == 0) {
+      failAt(typeOffset, "Unknown element type " + std::to_string(type));
+    }
+    const std::size_t count = readSize();
+    const Msh4ElementBlock block{count, input->offset(),
+                                 count > 0 ? physicalTag(dim, entityTag) : 0};
+    skipData(count * (1 + NumNodes[type - 1]) * dataSize);
+    if (count > 0 && type == cellType) {
+      index.cellBlocks.push_back(block);
+    } else if (count > 0 && type == facetType) {
+      index.facetBlocks.push_back(block);
+    }
+  }
+  expectToken("$EndElements");
+}
+
+void Msh4Indexer::parsePeriodic() {
+  if (!hasNodes) {
+    fail("Expected $Nodes before $Periodic");
+  }
+  beginSectionData();
+  const std::size_t numPeriodic = readSize();
+  for (std::size_t blockIdx = 0; blockIdx < numPeriodic; ++blockIdx) {
+    readInt(); // entity dimension
+    readInt(); // entity tag
+    readInt(); // master entity tag
+    const std::size_t numAffine = readSize();
+    for (std::size_t i = 0; i < numAffine; ++i) {
+      readDouble();
+    }
+    const std::size_t numIdentified = readSize();
+    for (std::size_t i = 0; i < numIdentified; ++i) {
+      const auto nodeOffset = position();
+      const std::size_t node = readSize();
+      nodeIndex(node, nodeOffset);
+      const auto masterOffset = position();
+      const std::size_t master = readSize();
+      nodeIndex(master, masterOffset);
+      index.periodic.emplace_back(node, master);
+    }
+  }
+  expectToken("$EndPeriodic");
+}
+
+bool isBinaryMsh4(const std::string& fileName) {
+  try {
+    MshInput input(fileName);
+    if (input.readToken() != "$MeshFormat") {
+      return false;
+    }
+    const auto version = input.readReal();
+    const auto fileType = input.readInteger<long>();
+    return version && fileType && *version >= 4.1 && *version < 5.0 && *fileType == 1;
+  } catch (const std::exception&) {
+    return false;
+  }
+}
+
+} // namespace puml
diff --git a/src/meshreader/Msh4Index.h b/src/meshreader/Msh4Index.h
new file mode 100644
index 0000000..3d24d18
--- /dev/null
+++ b/src/meshreader/Msh4Index.h
@@ -0,0 +1,82 @@
+// SPDX-FileCopyrightText: 2026 SeisSol Group
+//
+// SPDX-License-Identifier: BSD-3-Clause
+#ifndef PUMGEN_SRC_MESHREADER_MSH4INDEX_H_
+#define PUMGEN_SRC_MESHREADER_MSH4INDEX_H_
+
+#include <cstdint>
+#include <string>
+#include <utility>
+#include <vector>
+
+#include "GMSH4Parser.h"
+
+namespace puml {
+
+/**
+ * A block of nodes in a binary MSH 4.1 file: first the tags, then the coordinates.
+ */
+struct Msh4NodeBlock {
+  std::uint64_t count;
+  std::uint64_t tagsOffset;
+  std::uint64_t coordinatesOffset;
+  // three coordinates and the parametric coordinates, if any
+  std::uint64_t valuesPerNode;
+};
+
+/**
+ * A block of elements of one type in a binary MSH 4.1 file: per element its tag and its nodes.
+ */
+struct Msh4ElementBlock {
+  std::uint64_t count;
+  std::uint64_t offset;
+  std::int64_t physical;
+};
+
+/**
+ * Where the data of a binary MSH 4.1 file lies.
+ */
+struct Msh4Index {
+  std::uint64_t dataSize = 8;
+  bool swapBytes = false;
+  // the node tags form the contiguous range [firstNodeTag, firstNodeTag + numNodes)
+  std::uint64_t firstNodeTag = 0;
+  std::uint64_t numNodes = 0;
+  std::vector<Msh4NodeBlock> nodeBlocks;
+  std::vector<Msh4ElementBlock> cellBlocks;
+  std::vector<Msh4ElementBlock> facetBlocks;
+  // pairs of node tags (node, master) from $Periodic
+  std::vector<std::pair<std::uint64_t, std::uint64_t>> periodic;
+};
+
+/**
+ * Reads the structure of a binary MSH 4.1 file (entities, block headers, periodic nodes) and
+ * skips the node and element data, recording where they lie.
+ */
+class Msh4Indexer : public GMSH4Parser {
+  public:
+  Msh4Indexer(long cellType, long facetType)
+      : GMSH4Parser(nullptr), cellType(cellType), facetType(facetType) {}
+
+  [[nodiscard]] const Msh4Index& getIndex() const { return index; }
+
+  private:
+  void parseNodes() override;
+  void parseElements() override;
+  void parsePeriodic() override;
+
+  void skipData(std::size_t bytes);
+
+  long cellType;
+  long facetType;
+  Msh4Index index;
+};
+
+/**
+ * Whether the file is a binary MSH 4.1 file; only reads its header.
+ */
+bool isBinaryMsh4(const std::string& fileName);
+
+} // namespace puml
+
+#endif // PUMGEN_SRC_MESHREADER_MSH4INDEX_H_
diff --git a/src/meshreader/MshInput.cpp b/src/meshreader/MshInput.cpp
index aeee650..10683f2 100644
--- a/src/meshreader/MshInput.cpp
+++ b/src/meshreader/MshInput.cpp
@@ -77,6 +77,25 @@ bool MshInput::readRaw(void* data, std::size_t bytes) {
   return true;
 }
 
+bool MshInput::seek(std::size_t offset) {
+  if (offset >= bufferOffset && offset <= bufferOffset + end) {
+    begin = offset - bufferOffset;
+    return true;
+  }
+  if (std::fseek(file, 0, SEEK_END) != 0) {
+    return false;
+  }
+  const auto size = static_cast<std::size_t>(std::ftell(file));
+  if (offset > size || std::fseek(file, static_cast<long>(offset), SEEK_SET) != 0) {
+    return false;
+  }
+  bufferOffset = offset;
+  begin = end = 0;
+  buffer[0] = '\0';
+  eof = false;
+  return true;
+}
+
 bool MshInput::skipTo(std::string_view marker) {
   while (true) {
     const std::string_view data(buffer.data() + begin, end - begin);
diff --git a/src/meshreader/MshInput.h b/src/meshreader/MshInput.h
index f00e6eb..0cc77f5 100644
--- a/src/meshreader/MshInput.h
+++ b/src/meshreader/MshInput.h
@@ -127,6 +127,12 @@ class MshInput {
    */
   bool readRaw(void* data, std::size_t bytes);
 
+  /**
+   * Continues reading at the given file offset; returns false if the offset lies behind the end
+   * of the file.
+   */
+  bool seek(std::size_t offset);
+
   /**
    * Skips everything up to and including the next occurrence of the marker.
    */
diff --git a/src/pumgen.cpp b/src/pumgen.cpp
index cb83b58..89b0eec 100644
--- a/src/pumgen.cpp
+++ b/src/pumgen.cpp
@@ -44,6 +44,7 @@
 #ifdef USE_SIMMOD
 #include "input/SimModSuite.h"
 #endif // USE_SIMMOD
+#include "meshreader/DistributedGMSHReader.h"
 #include "meshreader/GMSH2Parser.h"
 #include "meshreader/GMSH4Parser.h"
 #include "meshreader/ParallelGMSHReader.h"
@@ -227,6 +228,8 @@ template <std::size_t Order>
 using SMF2 = SerialMeshFile<puml::ParallelGMSHReader<puml::GMSH2Parser, Order>>;
 template <std::size_t Order>
 using SMF4 = SerialMeshFile<puml::ParallelGMSHReader<puml::GMSH4Parser, Order>>;
+template <std::size_t Order>
+using SMF4Distributed = SerialMeshFile<puml::DistributedGMSHReader<Order>>;
 
 int main(int argc, char* argv[]) {
   int rank = 0;
@@ -289,6 +292,11 @@ int main(int argc, char* argv[]) {
   args.addAdditionalOption("input", "Input file (mesh or model)");
   args.addAdditionalOption("output", "Output parallel unstructured mesh file", false);
   args.addOption("order", 'o', "Mesh order (default: 1)", utils::Args::Required, false);
+  const auto gmshReaders = std::vector<std::string>{"auto", "serial"};
+  args.addEnumOption("gmsh-reader", gmshReaders, 0,
+                     "Reader for msh4 meshes (default: auto, which reads binary MSH 4.1 files "
+                     "with all ranks; serial: rank 0 reads the file)",
+                     false);
   args.addOption("velocity-check", 0,
                  "Compare the cell sizes with the velocity-aware mesh size of the "
                  "VelocityAwareMeshing element of a mesh attributes file (XML)",
@@ -390,10 +398,21 @@ int main(int argc, char* argv[]) {
     logInfo() << "Using GMSH mesh format 2 (msh2) mesh";
     meshInput = puml::makePointer<MeshData, SMF2>(meshOrder, inputFile, faceOffset);
     break;
-  case 2:
-    logInfo() << "Using GMSH mesh format 4 (msh4) mesh";
-    meshInput = puml::makePointer<MeshData, SMF4>(meshOrder, inputFile, faceOffset);
+  case 2: {
+    int distributed = 0;
+    if (rank == 0) {
+      distributed = args.getArgument<int>("gmsh-reader", 0) == 0 && puml::isBinaryMsh4(inputFile);
+    }
+    MPI_Bcast(&distributed, 1, MPI_INT, 0, MPI_COMM_WORLD);
+    if (distributed != 0) {
+      logInfo() << "Using GMSH mesh format 4 (msh4) mesh, binary, read by all ranks";
+      meshInput = puml::makePointer<MeshData, SMF4Distributed>(meshOrder, inputFile, faceOffset);
+    } else {
+      logInfo() << "Using GMSH mesh format 4 (msh4) mesh";
+      meshInput = puml::makePointer<MeshData, SMF4>(meshOrder, inputFile, faceOffset);
+    }
     break;
+  }
   case 3:
 #ifdef USE_NETCDF
     logInfo() << "Using netCDF mesh";
diff --git a/tests/CMakeLists.txt b/tests/CMakeLists.txt
index 5e342e3..d353628 100644
--- a/tests/CMakeLists.txt
+++ b/tests/CMakeLists.txt
@@ -186,6 +186,26 @@ pumgen_add_test(msh4.periodic-binary.np2 RANKS 2 SOURCE msh4 INPUT periodic-bina
 pumgen_add_test(msh4.coarse-binary-truncated RANKS 1 SOURCE msh4
                 INPUT coarse-binary-truncated-v41.msh EXPECT_ERROR "Unexpected end of file")
 
+# binary MSH 4.1 files are read by all ranks unless --gmsh-reader=serial
+foreach(ranks 4 7)
+  pumgen_add_test(msh4.layered-binary.np${ranks} RANKS ${ranks} SOURCE msh4
+                  INPUT layered-binary-v41.msh REFERENCE layered.puml.h5 TOLERANCE 1e-12)
+endforeach()
+pumgen_add_test(msh4.layered-binary-serial.np3 RANKS 3 SOURCE msh4 INPUT layered-binary-v41.msh
+                REFERENCE layered.puml.h5 TOLERANCE 1e-12 ARGS --gmsh-reader=serial)
+pumgen_add_test(msh4.periodic-binary-serial.np2 RANKS 2 SOURCE msh4 INPUT periodic-binary-v41.msh
+                REFERENCE periodic.puml.h5 TOLERANCE 1e-12 IDENTIFY ARGS --gmsh-reader=serial)
+pumgen_add_test(msh4.periodic-binary.np3 RANKS 3 SOURCE msh4 INPUT periodic-binary-v41.msh
+                REFERENCE periodic.puml.h5 TOLERANCE 1e-12 IDENTIFY)
+pumgen_add_test(msh4.tiny-binary.np3 RANKS 3 SOURCE msh4 INPUT tiny-binary-v41.msh
+                REFERENCE tiny.puml.h5)
+pumgen_add_test(msh4.tiny-binary-duplicate RANKS 1 SOURCE msh4 INPUT tiny-binary-duplicate-v41.msh
+                EXPECT_ERROR "Duplicate node tag 2")
+pumgen_add_test(msh4.tiny-binary-badnode RANKS 1 SOURCE msh4 INPUT tiny-binary-badnode-v41.msh
+                EXPECT_ERROR "Unknown node tag 9")
+pumgen_add_test(msh4.tiny-binary-sparse RANKS 1 SOURCE msh4 INPUT tiny-binary-sparse-v41.msh
+                EXPECT_ERROR "Non-contiguous node tags are not supported")
+
 # a face of the surface mesh given twice
 pumgen_add_test(msh2.tiny-duplicateface RANKS 1 SOURCE msh2 INPUT tiny-duplicateface-v22.msh
                 EXPECT_ERROR "exists multiple times in the surface mesh")
diff --git a/tests/fixtures/generate.py b/tests/fixtures/generate.py
index c75b460..227fe8c 100644
--- a/tests/fixtures/generate.py
+++ b/tests/fixtures/generate.py
@@ -350,6 +350,19 @@ def generate_periodic():
 """
 
 
+def tiny_binary(node_tags, element_nodes, node_header=(1, 4, 1, 4)):
+    """The single tetrahedron of TINY_V41 as binary MSH 4.1 file."""
+    data = b"$MeshFormat\n4.1 1 8\n" + struct.pack("<i", 1) + b"\n$EndMeshFormat\n"
+    data += b"$Entities\n" + struct.pack("<4Q", 0, 0, 0, 1)
+    data += struct.pack("<i6dQiQ", 1, 0, 0, 0, 1, 1, 1, 1, 7, 0) + b"\n$EndEntities\n"
+    data += b"$Nodes\n" + struct.pack("<4Q", *node_header) + struct.pack("<3iQ", 3, 1, 0, 4)
+    data += struct.pack("<4Q", *node_tags)
+    data += struct.pack("<12d", 0, 0, 0, 1, 0, 0, 0, 1, 0, 0, 0, 1) + b"\n$EndNodes\n"
+    data += b"$Elements\n" + struct.pack("<4Q", 1, 1, 1, 1) + struct.pack("<3iQ", 3, 1, 4, 1)
+    data += struct.pack("<5Q", 1, *element_nodes) + b"\n$EndElements\n"
+    return data
+
+
 def generate_tiny():
     variants = {
         "tiny-v41.msh": TINY_V41,
@@ -373,6 +386,15 @@ def generate_tiny():
     for name, content in variants.items():
         with open(name, "w") as out:
             out.write(content)
+    binary_variants = {
+        "tiny-binary-v41.msh": tiny_binary((1, 2, 3, 4), (1, 2, 3, 4)),
+        "tiny-binary-duplicate-v41.msh": tiny_binary((1, 2, 2, 4), (1, 2, 3, 4)),
+        "tiny-binary-badnode-v41.msh": tiny_binary((1, 2, 3, 4), (1, 2, 3, 9)),
+        "tiny-binary-sparse-v41.msh": tiny_binary((1, 2, 3, 5), (1, 2, 3, 5), (1, 4, 1, 5)),
+    }
+    for name, content in binary_variants.items():
+        with open(name, "wb") as out:
+            out.write(content)
     write_reference("tiny.puml.h5", "tiny-v41.msh")
 
 
diff --git a/tests/fixtures/tiny-binary-badnode-v41.msh b/tests/fixtures/tiny-binary-badnode-v41.msh
new file mode 100644
index 0000000000000000000000000000000000000000..826a331196424067d73ea42bd1127dbeb724a7e0
GIT binary patch
literal 482
zcmY%KO)buF%P-1JEa5WIGgL5Cu;5~3U|`@<am`CXk^^!}GD|X3i@AW3SOG{E2*79v
z4;%Tx9wLgMVS3n+l!ILWw^hY2KLuzxOd$(YAv&KKD2^@$<1<0^fYg8h%nS$*7YTDD
r`SM_oK%B4Qnv<HFnpcAG2+VQlG|VF)N21HY_~;(ugt`$Daxj|!9bqSX

literal 0
HcmV?d00001

diff --git a/tests/fixtures/tiny-binary-duplicate-v41.msh b/tests/fixtures/tiny-binary-duplicate-v41.msh
new file mode 100644
index 0000000000000000000000000000000000000000..9a0eeed91bd600ae155c6606f5e83026c52d2ced
GIT binary patch
literal 482
zcmY%KO)buF%P-1JEa5WIGgL5Cu;5~3U|`@<am`CXk^^!}GD|X3i@AW3SOG{E2*79v
z4;%Tx9wLgMVS3n+l!ILWw^hY2KLuzxOd$(YAv&KKD2^@$<1<0^z-X8mNOodj!W@Z3
w3M@oe9_$f_^Hp4PQgc)DN)R4_IS!qMc?9H0bU7Fw<`Ixu5P*3I5^^w`02~A-bpQYW

literal 0
HcmV?d00001

diff --git a/tests/fixtures/tiny-binary-sparse-v41.msh b/tests/fixtures/tiny-binary-sparse-v41.msh
new file mode 100644
index 0000000000000000000000000000000000000000..a4d961c8ca1ab902c54d864cd9bd007570db073b
GIT binary patch
literal 482
zcmY%KO)buF%P-1JEa5WIGgL5Cu;5~3U|`@<am`CXk^^!}GD|X3i@AW3SOG{E2*79v
z4;%Tx9wLgMVS3n+l!ILWw^hY2KLuzxOd$(YA&k!o<ue0mm>9YmCL}c=CQJ`h7zYJ&
sBo1i?!t!8`K%B4Qnv<HFnpcAG2+XnQG|VF)PoT@e__#a-2|1We03Qn{c>n+a

literal 0
HcmV?d00001

diff --git a/tests/fixtures/tiny-binary-v41.msh b/tests/fixtures/tiny-binary-v41.msh
new file mode 100644
index 0000000000000000000000000000000000000000..233943537770095f5d6124b481fa5dacf110699a
GIT binary patch
literal 482
zcmY%KO)buF%P-1JEa5WIGgL5Cu;5~3U|`@<am`CXk^^!}GD|X3i@AW3SOG{E2*79v
z4;%Tx9wLgMVS3n+l!ILWw^hY2KLuzxOd$(YAv&KKD2^@$<1<0^fYg8h%nS$*7YTDD
o`SM_oK%B4Qnv<HFnpcAG2+VQlG|VF)N21HY__#a-2|1We037otb^rhX

literal 0
HcmV?d00001