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IGV: pull up computation of jvm heap memory into OOD job script #77

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IGV: pull up computation of jvm heap memory into OOD job script #77

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11 changes: 10 additions & 1 deletion roles/ood_igv/files/script.sh.erb
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Original file line number Diff line number Diff line change
Expand Up @@ -28,10 +28,19 @@ cd "${HOME}"
# Start Integrative Genomics Viewer
#

# Determine memory for JVM in IGV
default_jvm_other_mb=512 # default to 0.5 GB
total_available_mb=$(($SLURM_MEM_PER_CPU * $SLURM_CPUS_PER_NODE))
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I don't see these two variables set in a job.

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didn't know this only set in a sbatch job, which is the way we start IGV job.
So I see it now.

if [ $total_available_mb -le $((default_jvm_other_mb * 10)) ]; then
heap_available_mb=$((9 * $total_available_mb / 10)) # total < 5G --> heap = 90% of total
else
heap_available_mb=$((total_available_mb - default_jvm_other_mb)) # otherwise heap = total - 512
fi

# Load the required environment
module load <%= context.version %>
# Launch IGV
module list
set -x
igvtools_gui.command &
igv.sh
igv.sh -Xmx${heap_available_mb}m