add files for public distribution
based on internal repository 0a462b6 2017-11-22 14:41:39 +0100
This commit is contained in:
145
bin/qpmsco.ra.sh
Executable file
145
bin/qpmsco.ra.sh
Executable file
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#!/bin/sh
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#
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# submission script for PMSCO calculations on the Ra cluster
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if [ $# -lt 1 ]; then
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echo "Usage: $0 [NOSUB] JOBNAME NODES TASKS_PER_NODE WALLTIME:HOURS PROJECT MODE [ARGS [ARGS [...]]]"
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echo ""
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echo " NOSUB (optional): do not submit the script to the queue. default: submit."
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echo " JOBNAME (text): name of job. use only alphanumeric characters, no spaces."
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echo " NODES (integer): number of computing nodes. (1 node = 24 or 32 processors)."
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echo " do not specify more than 2."
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echo " TASKS_PER_NODE (integer): 1...24, or 32."
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echo " 24 or 32 for full-node allocation."
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echo " 1...23 for shared node allocation."
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echo " WALLTIME:HOURS (integer): requested wall time."
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echo " 1...24 for day partition"
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echo " 24...192 for week partition"
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echo " 1...192 for shared partition"
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echo " PROJECT: python module (file path) that declares the project and starts the calculation."
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echo " MODE: PMSCO calculation mode (single|swarm|gradient|grid)."
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echo " ARGS (optional): any number of further PMSCO or project arguments (except mode and time)."
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echo ""
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echo "the job script complete with the program code and input/output data is generated in ~/jobs/\$JOBNAME"
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exit 1
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fi
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# location of the pmsco package is derived from the path of this script
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SCRIPTDIR="$(dirname $(readlink -f $0))"
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SOURCEDIR="$SCRIPTDIR/.."
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PMSCO_SOURCE_DIR="$SOURCEDIR"
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# read arguments
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if [ "$1" == "NOSUB" ]; then
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NOSUB="true"
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shift
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else
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NOSUB="false"
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fi
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PMSCO_JOBNAME=$1
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shift
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PMSCO_NODES=$1
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PMSCO_TASKS_PER_NODE=$2
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PMSCO_TASKS=$(expr $PMSCO_NODES \* $PMSCO_TASKS_PER_NODE)
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shift 2
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PMSCO_WALLTIME_HR=$1
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PMSCO_WALLTIME_MIN=$(expr $PMSCO_WALLTIME_HR \* 60)
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shift
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# select partition
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if [ $PMSCO_WALLTIME_HR -ge 25 ]; then
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PMSCO_PARTITION="week"
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else
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PMSCO_PARTITION="day"
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fi
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if [ $PMSCO_TASKS_PER_NODE -lt 24 ]; then
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PMSCO_PARTITION="shared"
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fi
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PMSCO_PROJECT_FILE="$(readlink -f $1)"
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shift
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PMSCO_MODE="$1"
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shift
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PMSCO_PROJECT_ARGS="$*"
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# use defaults, override explicitly in PMSCO_PROJECT_ARGS if necessary
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PMSCO_SCAN_FILES=""
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PMSCO_LOGLEVEL=""
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PMSCO_CODE=""
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# set up working directory
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cd ~
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if [ ! -d "jobs" ]; then
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mkdir jobs
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fi
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cd jobs
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if [ ! -d "$PMSCO_JOBNAME" ]; then
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mkdir "$PMSCO_JOBNAME"
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fi
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cd "$PMSCO_JOBNAME"
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WORKDIR="$(pwd)"
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PMSCO_WORK_DIR="$WORKDIR"
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# provide revision information, requires git repository
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cd "$SOURCEDIR"
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PMSCO_REV=$(git log --pretty=format:"Data revision %h, %ai" -1)
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if [ $? -ne 0 ]; then
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PMSCO_REV="Data revision unknown, "$(date +"%F %T %z")
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fi
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cd "$WORKDIR"
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echo "$PMSCO_REV" > revision.txt
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# generate job script from template
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sed -e "s:_PMSCO_WORK_DIR:$PMSCO_WORK_DIR:g" \
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-e "s:_PMSCO_JOBNAME:$PMSCO_JOBNAME:g" \
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-e "s:_PMSCO_NODES:$PMSCO_NODES:g" \
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-e "s:_PMSCO_WALLTIME_HR:$PMSCO_WALLTIME_HR:g" \
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-e "s:_PMSCO_PROJECT_FILE:$PMSCO_PROJECT_FILE:g" \
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-e "s:_PMSCO_PROJECT_ARGS:$PMSCO_PROJECT_ARGS:g" \
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-e "s:_PMSCO_CODE:$PMSCO_CODE:g" \
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-e "s:_PMSCO_MODE:$PMSCO_MODE:g" \
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-e "s:_PMSCO_SOURCE_DIR:$PMSCO_SOURCE_DIR:g" \
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-e "s:_PMSCO_SCAN_FILES:$PMSCO_SCAN_FILES:g" \
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-e "s:_PMSCO_LOGLEVEL:$PMSCO_LOGLEVEL:g" \
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"$SCRIPTDIR/pmsco.ra.template" > $PMSCO_JOBNAME.job
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chmod u+x "$PMSCO_JOBNAME.job"
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# request nodes and tasks
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#
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# The option --ntasks-per-node is meant to be used with the --nodes option.
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# (For the --ntasks option, the default is one task per node, use the --cpus-per-task option to change this default.)
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#
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# sbatch options
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# --cores-per-socket=16
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# 32 cores per node
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# --partition=[shared|day|week]
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# --time=8-00:00:00
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# override default time limit (2 days in long queue)
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# time formats: "minutes", "minutes:seconds", "hours:minutes:seconds", "days-hours", "days-hours:minutes", "days-hours:minutes:seconds"
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# --mail-type=ALL
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# --test-only
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# check script but do not submit
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#
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SLURM_ARGS="--nodes=$PMSCO_NODES --ntasks-per-node=$PMSCO_TASKS_PER_NODE"
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if [ $PMSCO_TASKS_PER_NODE -gt 24 ]; then
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SLURM_ARGS="--cores-per-socket=16 $SLURM_ARGS"
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fi
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SLURM_ARGS="--partition=$PMSCO_PARTITION $SLURM_ARGS"
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SLURM_ARGS="--time=$PMSCO_WALLTIME_HR:00:00 $SLURM_ARGS"
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CMD="sbatch $SLURM_ARGS $PMSCO_JOBNAME.job"
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echo $CMD
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if [ "$NOSUB" != "true" ]; then
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$CMD
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fi
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exit 0
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