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fix(slurm): request minimal /scratch allocation
From SciComp: > Slurm users: By default, Slurm jobs receive no /scratch allocation. If > your job runs entirely in memory and shared filesystems, this may be > fine. However, many applications implicitly use temporary scratch space. > If you encounter ENOSPC errors, you will need to request disk > explicitly, for example: > > ``` > #SBATCH --gres=disk:1G > ``` At least `module switch coatjava` has triggered 'no space left on device' errors, so let's request a bit of space. 32 MB should be way more than needed, but is also still very minimal, hopefully.
1 parent ebbe108 commit cbf7d97

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bin/qtl-histogram

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@@ -8,6 +8,7 @@ source $(dirname $0)/../libexec/environ.sh
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# constants ############################################################
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# slurm settings
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SLURM_MEMORY=2000 # must be more than max heap size in $TIMELINE_JAVA_OPTS
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SLURM_DISK=32M
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SLURM_TIME=10:00:00
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SLURM_LOG=/farm_out/%u/%x-%A_%a
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########################################################################
@@ -489,6 +490,7 @@ for key in ${jobkeys[@]}; do
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#SBATCH --account=clas12
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#SBATCH --mem-per-cpu=$SLURM_MEMORY
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#SBATCH --gres=disk:$SLURM_DISK
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#SBATCH --time=$SLURM_TIME
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#SBATCH --array=1-$(cat $joblist | wc -l)

bin/qtl-reheat

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@@ -6,6 +6,7 @@ source $(dirname $0)/../libexec/environ.sh
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# constants ############################################################
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# slurm settings
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SLURM_MEMORY=2000 # must be more than max heap size `java` calls
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SLURM_DISK=32M
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SLURM_TIME=12:00:00
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SLURM_LOG=/farm_out/%u/%x-%A_%a
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# reheating methods: name -> description
@@ -189,6 +190,7 @@ cat > $slurmScript << EOF
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#SBATCH --partition=production
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#SBATCH --account=clas12
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#SBATCH --mem-per-cpu=$SLURM_MEMORY
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#SBATCH --gres=disk:$SLURM_DISK
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#SBATCH --time=$SLURM_TIME
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#SBATCH --array=1-$(cat $jobList | wc -l)
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#SBATCH --ntasks=1

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