update explanation

Author: hschellman

_extras/short_submission.md

@@ -2,58 +2,91 @@
 title: Short submission with your own code
 ---
 
-## this collects the sequence of steps for a batch submission with local code which produces both an artroot and root file
+## this collects the sequence of steps for a batch submission with local code which produces both an artroot and root file.
+
+It splits out different functions so you need to examine/adapt all of the support scripts which can be found [here](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/files/usefulcode.tar). 
+
+This sequence assumes you are in your top level mrb directory.
 
 ### in your top level mrb directory
 
+
 For example `/exp/dune/app/users/$USER/myworkarea`
 
 need to have a name for it as you will be making a tarball
 
 ~~~
 export DIRECTORY=myworkarea
 ~~~
+{: ..language-bash}
 
 ### copy these scripts into that top level directory
 
 You can access a tarball with them all [here](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/files/usefulcode.tar). 
 
-Download that tarball into the top level directory for your build and `tar xBf usefulcode.tar` to get the code.
+Download that tarball into the top level directory for your build and
+
+~~~
+tar xBf usefulcode.tar
+~~~
+{: ..language-bash}
+
+ to get the code.
 
-Here are links to each of the scripts. 
+### here are the scripts.. 
 
-[setup-grid](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/setup-grid) (should not need to modify)
+#### utilities you need
 
-[maketar.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/maketar.sh) 
+- [setup-grid](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/setup-grid) (should not need to modify)
+This replaces `setup` in your local_build directory.
+
+- [maketar.sh $DIRECTORY](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/maketar.sh) 
 (should not need to modify)
+This takes the contents of `$DIRECTORY` and makes a tarball in `/exp/data/users/$USER/`
+
+- [makerdcs.sh $DIRECTORY](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/makerdcs.sh) (should not need to modify)
+This takes the tarball and copies it to /cvmfs/ where grid jobs can find it.  It places the location in the file `$DIRECTORY/cvmfs.location` so you can find it. 
+
+#### setup scripts
+
+- [setup_before_submit.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/setup_before_submit.sh) (customize versions for your code)
+You need to modify this to reflect the code version you are setting up. Normally only need to run/modify this once/session.
+
+
+- [job_config.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/job_config.sh)  (you modify this to reflect your workflow.  Sets things like $FCL_FILE). This sets up essential job parameters.  You need to understand and modify these appropriately for your purpose. 
 
-[makerdcs.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/makerdcs.sh) (should not need to modify)
+#### Script to test and submit jobs
 
-[job_config.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/job_config.sh)  (you modify this to choose things like MQL query, number of events..)
+- [test_workflow.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/test_workflow.sh) (script to do interactive tests of your jobscript)
 
-[setup_before_submit.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/setup_before_submit.sh) (customize versions for your code)
+- [submit_workflow.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/submit_workflow.sh) (writes output to scratch. Modify running time and memory)
 
-[submit_workflow.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/submit_workflow.sh) (modify running time and memory)
+- [submit_workflow_rucio.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/submit_workflow_rucio.sh) (writes output to rucio. Modify running time and memory)
 
-[test_workflow.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/test_workflow.sh) (script to do interactive tests of your jobscript)
 
+#### scripts that run on the remote machine
 
 [extractor_new.py](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/extractor_new.py) (this makes metadata for your files)
 
 [submit_local_code.jobscript.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/submit_local_code.jobscript.sh) (may need to modify if expert)
 
 
 
-### modify two scripts (should not need to change the others)
+## How to run these scripts
 
-edit `setup_before_submit.sh` if you change code versions and `job_config.sh` if you change more temporary things like fcl files . 
+### modify two-three scripts (should not need to change the others)
+
+edit 
+
+- `setup_before_submit.sh` if you change code versions and 
+- `job_config.sh` if you change more temporary things like fcl files. 
 
 - choose your code version (code version has to match your build)
 - *make certain the fcl file is either in the fcl path or in `$DIRECTORY`*
 - add a string `APP_TAG` that will go in your filename
 - add a description in `DESCRIPTION`
 
-Then run it to set things up
+Then run those scripts to set things up
 
 ~~~
 source setup_before_submit.sh # sets up larsoft
@@ -67,20 +100,42 @@ If you have changed any scripts or code, you must redo this.
 ./maketar.sh $DIRECTORY
 ./makercds.sh $DIRECTORY
 ~~~
+{: ..language-bash}
 
-will take a while, produce a tarball on `/exp/dune/data/users` and put the cvmfs location in cvmfs.location in `$DIRECTORY`
+will take a while, produce a tarball on `/exp/dune/data/users/$USER/` and put the cvmfs location in cvmfs.location in `$DIRECTORY`
 
 Then edit `job_config.sh` to reflect the # of events you want and other run-time parameters.
 
+### Test your jobscript interactively
+
+[test_workflow.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/test_workflow.sh)
+
+results will show up in the 'tmp' area on your local machine. 
+
+
 ### Submit the job
 
 [submit_workflow.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/submit_workflow.sh)
 
+This one writes to `/pnfs/dune/scratch`
+
 ~~~
 ./submit_workflow.sh
 ~~~
+{: ..language-bash}
+
+[submit_workflow_rucio.sh](https://github.com/hschellman/computing-basics-batch-devel/blob/gh-pages/_includes/submit_workflow_rucio.sh)
+
+This one writes to a rucio location specified by `$NAMESPACE`
+
+~~~
+./submit_workflow_rucio.sh
+~~~
+{: ..language-bash}
+
+### after submission
 
-should get a workflow number back
+You should get a workflow number back
 
 go to [justin](https://dunejustin.fnal.gov/dashboard/?method=list-workflows)