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Merge pull request #5625 from bernt-matthias/topic/memperslot

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added GALAXY_MEMORY_MB_PER_SLOT variable
This commit is contained in:
John Chilton
2018-03-20 09:34:59 -04:00
committed by GitHub
parent 11b32f38f4 b92a5e1b47
commit 5f23f5da72
3 changed files with 34 additions and 2 deletions
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doc/source/admin/cluster.md
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@@ -195,7 +195,7 @@ Most options available to `qsub(1b)` and `pbs_submit(3b)` are supported. Except
```
The value of *ppn=* is used by PBS to define the environment variable $PBS_NCPUS which in turn is used by galaxy for [GALAXY_SLOTS](https://galaxyproject.org/admin/config/galaxy_slots/).
The value of *ppn=* is used by PBS to define the environment variable `$PBS_NCPUS` which in turn is used by galaxy for [GALAXY_SLOTS](https://galaxyproject.org/admin/config/galaxy_slots/).
### Condor
@@ -355,6 +355,30 @@ It is also a good idea to make sure that only trusted users, e.g. root, have wri
Some maintenance and support of this code will be provided via the usual [Support](https://galaxyproject.org/support/) channels, but improvements and fixes would be greatly welcomed, as this is a complex feature which is not used by the Galaxy Development Team.
## Special environment variables for job resources
Galaxy *tries* to define special environment variables for each job that contain
the information on the number of available slots and the amount of available
memory:
* `GALAXY_SLOTS`: number of available slots
* `GALAXY_MEMORY_MB`: total amount of available memory in MB
* `GALAXY_MEMORY_MB_PER_SLOT`: amount of memory that is available for each slot in MB
More precisely Galaxy inserts bash code in the job submit script that
tries to determine these values. This bash code is defined here:
* lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh
* lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
If this code is unable to determine the variables, then they will not be set.
Therefore in the tool XML files the variables should be used with a default,
e.g. `\${GALAXY_SLOTS:-1}` (see also https://planemo.readthedocs.io/en/latest/writing_advanced.html#cluster-usage).
In particular `GALAXY_MEMORY_MB` and `GALAXY_MEMORY_MB_PER_SLOT` are currently
defined only for a few cluster types. Contributions are very welcome, e.g. let
the Galaxy developers know how to modify that file to support your cluster.
## Contributors
* **Oleksandr Moskalenko**, debugged a number of problems related to running jobs as the real user and using DRMAA with TORQUE.
lib/galaxy/jobs/runners/util/job_script/MEMORY_STATEMENT.sh
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@@ -1,4 +1,11 @@
if [ -n "$SLURM_JOB_ID" ]; then
GALAXY_MEMORY_MB=`scontrol -do show job "$SLURM_JOB_ID" | sed 's/.*\( \|^\)Mem=\([0-9][0-9]*\)\( \|$\).*/\2/p;d'` 2>memory_statement.log
fi
if [ -z "$GALAXY_MEMORY_MB_PER_SLOT" -a -n "$GALAXY_MEMORY_MB" ]; then
GALAXY_MEMORY_MB_PER_SLOT=$(($GALAXY_MEMORY_MB / $GALAXY_SLOTS))
elif [ -z "$GALAXY_MEMORY_MB" -a -n "$GALAXY_MEMORY_MB_PER_SLOT" ]; then
GALAXY_MEMORY_MB=$(($GALAXY_MEMORY_MB_PER_SLOT * $GALAXY_SLOTS))
fi
[ "${GALAXY_MEMORY_MB--1}" -gt 0 ] 2>>memory_statement.log && export GALAXY_MEMORY_MB || unset GALAXY_MEMORY_MB
[ "${GALAXY_MEMORY_MB_PER_SLOT--1}" -gt 0 ] 2>>memory_statement.log && export GALAXY_MEMORY_MB_PER_SLOT || unset GALAXY_MEMORY_MB_PER_SLOT
lib/galaxy/tools/xsd/galaxy.xsd
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@@ -2656,7 +2656,8 @@ be escaped with a backslash (``\``) when appearing in ``command`` or ``configfil
Name | Description
---- | -----------
``\${GALAXY_SLOTS:-4}`` | Number of cores/threads allocated by the job runner or resource manager to the tool for the given job (here 4 is the default number of threads to use if running via custom runner that does not configure GALAXY_SLOTS or in an older Galaxy runtime).
``\$GALAXY_MEMORY_MB`` | Amount of memory in megabytes (1024^2 bytes) allocated by the administrator (via the resource manager) to the tool for the given job. If unset, tools should not attempt to limit memory usage.
``\$GALAXY_MEMORY_MB`` | Total amount of memory in megabytes (1024^2 bytes) allocated by the administrator (via the resource manager) to the tool for the given job. If unset, tools should not attempt to limit memory usage.
``\$GALAXY_MEMORY_MB_PER_SLOT`` | Amount of memory per slot in megabytes (1024^2 bytes) allocated by the administrator (via the resource manager) to the tool for the given job. If unset, tools should not attempt to limit memory usage.
See the [Planemo docs](https://planemo.readthedocs.io/en/latest/writing_advanced.html#cluster-usage)
on the topic of ``GALAXY_SLOTS`` for more information and examples.