50 lines
1.9 KiB
Text
50 lines
1.9 KiB
Text
universe = vanilla
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# resource requirements for each job
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request_cpus = 1
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request_memory = 3000M
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request_disk = 100G
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# be nice and only use free resources
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# nice_user = true
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# tell condor that a job is self contained and the executable
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# is enough to bootstrap the computation on the execute node
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should_transfer_files = yes
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# explicitly do not transfer anything back
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# we are using datalad for everything that matters
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transfer_output_files = ""
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# the actual job script, nothing condor-specific in it
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executable = $ENV(PWD)/code/results.merger
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# the job expects these environment variables for labeling and synchronization
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# - JOBID: subject AND process specific ID to make a branch name from
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# (must be unique across all (even multiple) submissions)
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# including the cluster ID will enable sorting multiple computing attempts
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# - DSLOCKFILE: lock (must be accessible from all compute jobs) to synchronize
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# write access to the output dataset
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# - DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__...:
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# (additional) locations for datalad to locate relevant subdatasets, in case
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# a configured URL is outdated
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# - GIT_AUTHOR_...: Identity information used to save dataset changes in compute
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# jobs
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environment = "\
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JOBID=$(subject)_$(Cluster) \
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DSLOCKFILE=$ENV(PWD)/.condor_datalad_lock \
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GIT_AUTHOR_NAME='Felix Hoffstaedter' \
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GIT_AUTHOR_EMAIL='f.hoffstaedter@fz-juelich.de' \
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REPRONIM_USE_DUCT=1 \
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PATH=~/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin \
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"
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# place the job logs into PWD/logs, using the same name as for the result branches
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# (JOBID)
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log = $ENV(PWD)/logs/postpro_$(Cluster).log
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output = $ENV(PWD)/logs/postpro_$(Cluster).out
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error = $ENV(PWD)/logs/postpro_$(Cluster).err
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# essential args for "results.merger"
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# 1: where to clone the analysis dataset
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arguments = "\
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ria+file:///data/project/QC_workflow/TMP/RIA_QCworkflow#aae8905a-985f-46fb-91f5-35c772654ddd \
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"
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queue
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