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Release netCDF memory-map pages after each frame #5463

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Release netCDF memory-map pages after each frame #5463

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48e0e7e
Release netCDF memory-map pages after each frame
erikfransson Aug 16, 2026
d1a5e45
Merge branch 'develop' into ncdf-release-mmap-pages
erikfransson Aug 22, 2026
ad24c04
Drop mmap page test and versionchanged directive
erikfransson Sep 5, 2026
5d9f6bd
Merge branch 'develop' into ncdf-release-mmap-pages
erikfransson Sep 5, 2026
c194a20
Add PR number to CHANGELOG entry
erikfransson Oct 2, 2026
c45c194
Merge branch 'develop' into ncdf-release-mmap-pages
orbeckst Nov 1, 2026
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2 changes: 1 addition & 1 deletion package/AUTHORS
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Original file line number Diff line number Diff line change
Expand Up @@ -287,7 +287,7 @@ Chronological list of authors
- Francesco Siciliani
- Akshit Boora
- Sumit Saraswat

- Erik Fransson

External code
-------------
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8 changes: 7 additions & 1 deletion package/CHANGELOG
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Expand Up @@ -14,11 +14,17 @@ The rules for this file:


-------------------------------------------------------------------------------
??/??/?? IAlibay, sumitsaraswat362
??/??/?? IAlibay, sumitsaraswat362, erikfransson

* 2.12.0

Fixes
* The NCDF reader now releases the pages of the memory map once a frame has
been read into the Timestep. Reading a netCDF trajectory with `mmap=True`
(the default for a file name) no longer grows the resident memory of the
process towards the size of the whole trajectory file. Requires a platform
that provides `MADV_DONTNEED`, i.e. not Windows (Discussion #4792,
PR #5463).
Comment on lines +26 to +27

@orbeckst orbeckst Nov 1, 2026

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Suggested change
that provides `MADV_DONTNEED`, i.e. not Windows (Discussion #4792,
PR #5463).
that provides `MADV_DONTNEED`, i.e. not Windows (#5541, PR #5463)

I raised a proper issue from the discussion #5541


Enhancements
* InterRDF and InterRDF_s now expose computed average box volume and densities
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5 changes: 5 additions & 0 deletions package/MDAnalysis/coordinates/TRJ.py
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Expand Up @@ -134,6 +134,7 @@
import warnings
import errno
import logging
import mmap
from math import isclose

import MDAnalysis
Expand Down Expand Up @@ -675,6 +676,10 @@ def _read_frame(self, frame):
self.convert_pos_from_native(ts.dimensions[:3])
ts.frame = frame # frame labels are 0-based
self._current_frame = frame
# the frame is now copied into ts, so its pages can be dropped again
mm = getattr(self.trjfile, "_mm", None)
if mm is not None and hasattr(mmap, "MADV_DONTNEED"):
mm.madvise(mmap.MADV_DONTNEED)
return ts

def _reopen(self):
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