50 lines
2.1 KiB
Text
50 lines
2.1 KiB
Text
universe = vanilla
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# resource requirements for each job
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request_cpus = 2
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request_memory = 20G
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request_disk = 250G
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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 = $ENV(PWD)/code/participant_job
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# the job expects these environment variables for labeling and synchronization
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# - JOBID: subject AND process specific ID to make a branch name from
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# (must be unique across all (even multiple) submissions)
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# including the cluster ID will enable sorting multiple computing attempts
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# - DSLOCKFILE: lock (must be accessible from all compute jobs) to synchronize
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# write access to the output dataset
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# - DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__...:
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# (additional) locations for datalad to locate relevant subdatasets, in case
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# a configured URL is outdated (optional)
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# - GIT_AUTHOR_...: Identity information used to save dataset changes in compute
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# jobs
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environment = "\
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JOBID=$(subject).$(Cluster) \
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DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__100origin=ria+file:///data/project/fMRIPrep_CamCAN/TMP/RIA#{id} \
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DSLOCKFILE=$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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"
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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 = $ENV(PWD)/logs/$(subject)_$(Cluster).log
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output = $ENV(PWD)/logs/$(subject)_$(Cluster).out
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error = $ENV(PWD)/logs/$(subject)_$(Cluster).err
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# essential args for 'participant_job'
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# 1: where to clone the analysis dataset
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# 2: location to push the result git branch to. The 'ria+' prefix is stripped.
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# 3: ID of the subject to process
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arguments = "\
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ria+file:///data/project/fMRIPrep_CamCAN/TMP/RIA/inputstore#832192b7-0fcb-40eb-8532-ef9eb998d33d \
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file:///data/project/fMRIPrep_CamCAN/TMP/RIA/832/192b7-0fcb-40eb-8532-ef9eb998d33d \
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$(subject) \
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"
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queue
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