I've written a CWL that I know works on the Arvados CWL runner on our SLURM cluster with Docker.
I'm trying to run it using the toil-cwl-runner on the same SLURM cluster using singularity 2.5.x.
I've created a virtualenv and ran
pip install toil[cwl] and it appears to have installed.
I'm trying to kick off a workflow using the following command lines on our SLURM cluster's login node, which is a two core VM with 8 GB of RAM
export TOIL_SLURM_ARGS='--partition allnodes' ; toil-cwl-runner --jobStore ~/tmp/toil-test --singularity --batchSystem Slurm dnaseq.cwl dnaseq-test.yml
Almost instantly, this warns me:
WARNING:toil.batchSystems.singleMachine:Limiting maxMemory to physically available memory (8201486336).
How do I change the maxMemory as this is way below what I need? The CWL requests more memory in many of the jobs, so this is coming from Toil, not CWL.