Support HTCondor in CLUSTER_SLOTS_STATEMENT.sh#405
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mvdbeek merged 3 commits intoJul 17, 2025
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HTCondor sets a couple of environment variables read by various frameworks to control the number of threads they are allowed to use. A list can be found on the HTCondor docs https://htcondor.readthedocs.io/en/24.0/admin-manual/configuration-macros.html#STARTER_NUM_THREADS_ENV_VARS. The list itself is configurable (it is an HTCondor configuration macro). Any of these variables can be used to set GALAXY_SLOTS. Set it using the variable ROOT_MAX_THREADS (designed to control the ROOT data analysis framework from CERN).
Contributor
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@bgruening, @mvdbeek does this make sense to you? |
Contributor
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This is what would happen if the PR was merged. galaxy@sn06:~$ cd /data/jwd06/pulsar_staging/86195857
galaxy@sn06:/data/jwd06/pulsar_staging/86195857$ cat external_id
"64664468"
galaxy@sn06:/data/jwd06/pulsar_staging/86195857$ condor_ssh_to_job 64664468
...
galaxy@vgcnbwc-worker-c8m40g1-0008:~/server$ docker ps
CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES
d8e9fadbcd3d quay.io/bgruening/anylabeling:0.4.30 "/bin/sh /data/jwd06…" 2 minutes ago Up 2 minutes 5900/tcp, 0.0.0.0:32862->5800/tcp, :::32862->5800/tcp 11e6c2910bf447f3b78a9aceff0c069f
...
galaxy@vgcnbwc-worker-c8m40g1-0008:~/server$ docker exec -it d8e9fadbcd3d /bin/bash
root@d8e9fadbcd3d:/data/jwd06/pulsar_staging/86195857/working# echo $GALAXY_SLOTS
4 |
mvdbeek
reviewed
Jul 16, 2025
…bmitted jobs At the moment, Pulsar is using ROOT_MAX_THREADS (designed to control the ROOT data analysis framework from CERN) to set GALAXY_SLOTS. Switch to PYTHON_CPU_COUNT (controls the amount of CPUs that Python sees).
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It should be good to merge now. |
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@mvdbeek is it realistic to get a new release, that Galaxy stable depends on? Or should we carry patches? |
mvdbeek
approved these changes
Jul 17, 2025
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We can do that, no problem |
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Can I ask you to also open the same PR on galaxy and drop the hardcoding of galaxy_slots ? dev would be fine since this works |
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HTCondor sets a couple of environment variables read by various frameworks to control the number of threads they are allowed to use. A list can be found in the HTCondor docs https://htcondor.readthedocs.io/en/24.0/admin-manual/configuration-macros.html#STARTER_NUM_THREADS_ENV_VARS. The list itself is configurable (it is an HTCondor configuration macro).
Any of these variables can be used to set GALAXY_SLOTS. Set it using the variable ROOT_MAX_THREADS (designed to control the ROOT data analysis framework from CERN).