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- universe = vanilla
- # resource requirements for each job
- request_cpus = 1
- request_memory = 3G
- request_disk = 4G
- # be nice and only use free resources
- nice_user = true
- # tell condor that a job is self contained and the executable
- # is enough to bootstrap the computation on the execute node
- should_transfer_files = yes
- # explicitly do not transfer anything back
- # we are using datalad for everything that matters
- transfer_output_files = ""
- # the actual job script, nothing condor-specific in it
- executable = $ENV(PWD)/code/participant_job
- # the job expects these environment variables for labeling and synchronization
- # - JOBID: subject AND process specific ID to make a branch name from
- # (must be unique across all (even multiple) submissions)
- # including the cluster ID will enable sorting multiple computing attempts
- # - DSLOCKFILE: lock (must be accessible from all compute jobs) to synchronize
- # write access to the output dataset
- # - DATALAD_GET_SUBDATASET__SOURCE__CANDIDATE__...:
- # (additional) locations for datalad to locate relevant subdatasets, in case
- # a configured URL is outdated
- # - GIT_AUTHOR_...: Identity information used to save dataset changes in compute
- # jobs
- environment = "\
- JOBID=$(subject).$(Cluster) \
- DSLOCKFILE=$ENV(PWD)/.condor_datalad_lock \
- GIT_AUTHOR_NAME='Felix Hoffstaedter' \
- GIT_AUTHOR_EMAIL='f.hoffstaedter@fz-juelich.de' \
- "
- # place the job logs into PWD/logs, using the same name as for the result branches
- # (JOBID)
- log = $ENV(PWD)/logs/$(subject)_$(Cluster).log
- output = $ENV(PWD)/logs/$(subject)_$(Cluster).out
- error = $ENV(PWD)/logs/$(subject)_$(Cluster).err
- # essential args for "participant_job"
- # 1: where to clone the analysis dataset
- # 2: location to push the result git branch to. The "ria+" prefix is stripped.
- # 3: ID of the subject to process
- arguments = "\
- ria+file:///data/project/cat_preprocessed/inputstore#b4fd561e-f414-4427-96ca-6a9717047537 \
- /data/project/infrasound/dataladstore/b4f/d561e-f414-4427-96ca-6a9717047537 \
- $(subject) \
- "
- queue
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