memory requests not being used in fh-cromwell.conf about diy-cromwell-server

[jayoung]

the wdl:

version 1.0

workflow hello_hostname_2 {
  call hostname2 {
  }
  output {
    File stdout = hostname2.out
  }
}

## Task Descriptions
task hostname2 {
  command {
    echo $(hostname)
  }
  runtime {
    memory: 2000
    cpu: 2
  }
  output {
    File out = stdout()
  }
}

[jayoung]

the options.json:

{   
    "write_to_cache": true,
    "read_from_cache": false
}

[jayoung]

resulting script.submit:

#!/bin/bash
set -e
source /app/lmod/lmod/init/bash
module use /app/modules/all
module purge

if [ ! -z '' ]; then

# Ensure singularity is loaded if it's installed as a module
module load Singularity/3.5.3
# Build the Docker image into a singularity image
DOCKER_NAME=$(sed -e 's/[^A-Za-z0-9._-]/_/g' <<< )
# The image will live together with all the other images to force caching of the .sif files themselves - note, always use docker hub tags!!!
IMAGE=$SINGULARITYCACHEDIR/$DOCKER_NAME.sif

echo $DOCKER_NAME
echo $IMAGE
echo $SINGULARITYCACHEDIR
echo $SCRATCHPATH

if [ ! -f $IMAGE ]; then  # If we already have the image, skip everything
    singularity pull $IMAGE docker://
fi   

# Submit the script to SLURM
sbatch \
  --partition=campus-new \
  -J cromwell_22741cd7_hostname2 \
  -D /fh/scratch/delete90/malik_h/jayoung/cromwell-executions/hello_hostname_2/22741cd7-4edb-414e-925c-17f76da9ebe2/call-hostname2 \
  -o /fh/scratch/delete90/malik_h/jayoung/cromwell-executions/hello_hostname_2/22741cd7-4edb-414e-925c-17f76da9ebe2/call-hostname2/execution/stdout \
  -e /fh/scratch/delete90/malik_h/jayoung/cromwell-executions/hello_hostname_2/22741cd7-4edb-414e-925c-17f76da9ebe2/call-hostname2/execution/stderr \
  --cpus-per-task=2   \
  --wrap "singularity exec --bind $SCRATCHPATH $IMAGE /bin/bash /fh/scratch/delete90/malik_h/jayoung/cromwell-executions/hello_hostname_2/22741cd7-4edb-414e-925c-17f76da9ebe2/call-hostname2/execution/script"

else
module load 

sbatch \
  --partition=campus-new \
  -J cromwell_22741cd7_hostname2 \
  -D /fh/scratch/delete90/malik_h/jayoung/cromwell-executions/hello_hostname_2/22741cd7-4edb-414e-925c-17f76da9ebe2/call-hostname2 \
  -o /fh/scratch/delete90/malik_h/jayoung/cromwell-executions/hello_hostname_2/22741cd7-4edb-414e-925c-17f76da9ebe2/call-hostname2/execution/stdout \
  -e /fh/scratch/delete90/malik_h/jayoung/cromwell-executions/hello_hostname_2/22741cd7-4edb-414e-925c-17f76da9ebe2/call-hostname2/execution/stderr \
  --cpus-per-task=2   \
  --wrap "/bin/bash /fh/scratch/delete90/malik_h/jayoung/cromwell-executions/hello_hostname_2/22741cd7-4edb-414e-925c-17f76da9ebe2/call-hostname2/execution/script"
fi

[jayoung]

never mind. Our slurm configuration doesn't pay attention to memory requests anyway - https://sciwiki.fredhutch.org/scicomputing/compute_jobs/#memory