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ssadedin
Support for generic job submission options
Some executors (eg: Slurm) don't have support for options to allow an arbitrary command line parameter to be added to the job submission. It would be good to support this with one general config option rather than a specific one for each executor.
See discussion on google group.
Tested it with slurm 16.05.5 and am getting an error:
Test mode: Abort due to Test Mode!
Branch aFile would execute: touch aFile.test_module
using Slurm Job [Command Id: null ] with config [max_per_command_threads:16, executor:slurm, walltime:00:01:00, procs:1, queue:ikmb_a, memory:1, custom_submit_options:--qos=ikmb_a, name:test]
--> looks OK!
Execute mode:
ERROR: stage test_module failed: Job runner bpipe.executor.SlurmCommandExecutor failed to return a job id for job 2 (test_module) despite reporting success exit code for command:
bash /ifs/data/nfs_share/ikmb_repository/software/bpipe/devel/bin/../bin/bpipe-slurm.sh start
Raw output was:[ ]
less .bpipe/commandtmp/2/job.slurm
#!/bin/bash #SBATCH --job-name=test_module
#SBATCH --mem=1024 #SBATCH --time=00:01:00 #SBATCH --ntasks=1 #SBATCH --nodes=1 #SBATCH -p ikmb_a
set -o errexit
(touch aFile.test_module) > .bpipe/commandtmp/2/2.out 2> .bpipe/commandtmp/2/2.err
Maybe to clarify - the Bpipe test mode shows that the optional parameter "--qos=ikmb_a" is seen by the tool, but the slurm submit script does not include this option. Somewhere between reading all parameters and writing the execution script, the new option is lost.
Can you look in the bpipe log file (.bpipe/bpipe.log) and search for the sbatch command? hopefully it should be logged in there and we can see exactly what is being used.
Also, could you just confirm - you're building from the branch I created, not master, correct?
Hi,
so I redid the whole thing and arrived add an compilation error:
git clone https://github.com/ssadedin/bpipe.git devel
git fetch
git checkout -b custom_submit_opts origin/custom_submit_opts Branch custom_submit_opts set up to track remote branch custom_submit_opts from origin. Switched to a new branch 'custom_submit_opts'
git branch
- custom_submit_opts master
/gradlew dist
================================================================================ No Gridgain library found. Gridgain support disabled in this build.
:compileJava UP-TO-DATE :compileGroovy startup failed: /ifs/data/nfs_share/ikmb_repository/software/bpipe/devel/src/main/groovy/bpipe/CommandManager.groovy: 327: unexpected token: << @ line 327, column 1. <<<<<<< HEAD ^
1 error
:compileGroovy FAILED
Sorry about that ... don't quite know how it happened but hopefully fixed now. Can you try again?
Hi, anything else that needs testing here? Or will this be merged into master now? /M
Should be merged in now.
On Mar 20, 2017 8:05 PM, "marchoeppner" [email protected] wrote:
Hi, anything else that needs testing here? Or will this be merged into master now? /M
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