public distro 2.1.0
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136
bin/pmsco.ra-git.template
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136
bin/pmsco.ra-git.template
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#!/bin/bash
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#
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# Slurm script template for PMSCO calculations on the Ra cluster
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# based on run_mpi_HPL_nodes-2.sl by V. Markushin 2016-03-01
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#
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# this version checks out the source code from a git repository
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# to a temporary location and compiles the code.
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# this is to minimize conflicts between different jobs
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# but requires that each job has its own git commit.
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#
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# Use:
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# - enter the appropriate parameters and save as a new file.
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# - call the sbatch command to pass the job script.
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# request a specific number of nodes and tasks.
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# example:
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# sbatch --nodes=2 --ntasks-per-node=24 --time=02:00:00 run_pmsco.sl
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# the qpmsco script does all this for you.
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#
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# PMSCO arguments
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# copy this template to a new file, and set the arguments
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#
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# PMSCO_WORK_DIR
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# path to be used as working directory.
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# contains the script derived from this template
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# and a copy of the pmsco code in the 'pmsco' directory.
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# receives output and temporary files.
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#
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# PMSCO_PROJECT_FILE
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# python module that declares the project and starts the calculation.
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# must include the file path relative to $PMSCO_WORK_DIR.
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#
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# PMSCO_OUT
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# name of output file. should not include a path.
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#
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# all paths are relative to $PMSCO_WORK_DIR or (better) absolute.
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#
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#
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# Further arguments
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#
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# PMSCO_JOBNAME (required)
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# the job name is the base name for output files.
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#
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# PMSCO_WALLTIME_HR (integer, required)
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# wall time limit in hours. must be integer, minimum 1.
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# this value is passed to PMSCO.
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# it should specify the same amount of wall time as requested from the scheduler.
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#
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# PMSCO_PROJECT_ARGS (optional)
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# extra arguments that are parsed by the project module.
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#
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#SBATCH --job-name="_PMSCO_JOBNAME"
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#SBATCH --output="_PMSCO_JOBNAME.o.%j"
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#SBATCH --error="_PMSCO_JOBNAME.e.%j"
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PMSCO_WORK_DIR="_PMSCO_WORK_DIR"
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PMSCO_JOBNAME="_PMSCO_JOBNAME"
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PMSCO_WALLTIME_HR=_PMSCO_WALLTIME_HR
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PMSCO_PROJECT_FILE="_PMSCO_PROJECT_FILE"
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PMSCO_OUT="_PMSCO_JOBNAME"
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PMSCO_PROJECT_ARGS="_PMSCO_PROJECT_ARGS"
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module load psi-python36/4.4.0
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module load gcc/4.8.5
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module load openmpi/3.1.3
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source activate pmsco3
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echo '================================================================================'
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echo "=== Running $0 at the following time and place:"
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date
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/bin/hostname
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cd $PMSCO_WORK_DIR
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pwd
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ls -lA
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#the intel compiler is currently not compatible with mpi4py. -mm 170131
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#echo
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#echo '================================================================================'
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#echo "=== Setting the environment to use Intel Cluster Studio XE 2016 Update 2 intel/16.2:"
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#cmd="source /opt/psi/Programming/intel/16.2/bin/compilervars.sh intel64"
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#echo $cmd
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#$cmd
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echo
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echo '================================================================================'
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echo "=== The environment is set as following:"
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env
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echo
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echo '================================================================================'
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echo "BEGIN test"
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which mpirun
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cmd="mpirun /bin/hostname"
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echo $cmd
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$cmd
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echo "END test"
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echo
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echo '================================================================================'
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echo "BEGIN mpirun pmsco"
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echo
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cd "$PMSCO_WORK_DIR"
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cd pmsco
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echo "code revision"
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git log --pretty=tformat:'%h %ai %d' -1
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make -C pmsco all
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python -m compileall pmsco
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python -m compileall projects
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echo
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cd "$PMSCO_WORK_DIR"
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PMSCO_CMD="python pmsco/pmsco $PMSCO_PROJECT_FILE"
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PMSCO_ARGS="$PMSCO_PROJECT_ARGS"
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if [ -n "$PMSCO_SCAN_FILES" ]; then
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PMSCO_ARGS="-s $PMSCO_SCAN_FILES $PMSCO_ARGS"
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fi
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if [ -n "$PMSCO_OUT" ]; then
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PMSCO_ARGS="-o $PMSCO_OUT $PMSCO_ARGS"
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fi
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if [ "$PMSCO_WALLTIME_HR" -ge 1 ]; then
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PMSCO_ARGS="-t $PMSCO_WALLTIME_HR $PMSCO_ARGS"
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fi
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if [ -n "$PMSCO_LOGLEVEL" ]; then
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PMSCO_ARGS="--log-level $PMSCO_LOGLEVEL --log-file $PMSCO_JOBNAME.log $PMSCO_ARGS"
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fi
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# Do no use the OpenMPI specific options, like "-x LD_LIBRARY_PATH", with the Intel mpirun.
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cmd="mpirun $PMSCO_CMD $PMSCO_ARGS"
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echo $cmd
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$cmd
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echo "END mpirun pmsco"
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echo '================================================================================'
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cd "$PMSCO_WORK_DIR"
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rm -rf pmsco
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date
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ls -lAtr
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echo '================================================================================'
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exit 0
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@ -75,10 +75,10 @@ PMSCO_OUT="_PMSCO_JOBNAME"
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PMSCO_LOGLEVEL="_PMSCO_LOGLEVEL"
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PMSCO_PROJECT_ARGS="_PMSCO_PROJECT_ARGS"
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module load psi-python27/2.4.1
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module load psi-python36/4.4.0
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module load gcc/4.8.5
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module load openmpi/1.10.2
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source activate pmsco
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module load openmpi/3.1.3
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source activate pmsco3
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echo '================================================================================'
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echo "=== Running $0 at the following time and place:"
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145
bin/qpmsco.ra-git.sh
Executable file
145
bin/qpmsco.ra-git.sh
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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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#
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# this version clones the current git repository at HEAD to the work directory.
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# thus, version conflicts between jobs are avoided.
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#
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if [ $# -lt 1 ]; then
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echo "Usage: $0 [NOSUB] GIT_TAG DESTDIR JOBNAME NODES TASKS_PER_NODE WALLTIME:HOURS PROJECT [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 " GIT_TAG: git tag or branch name of the code. HEAD for current code."
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echo " DESTDIR: destination directory. must exist. a sub-dir \$JOBNAME is created."
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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 " ARGS (optional): any number of further PMSCO or project arguments (except time)."
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echo ""
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echo "the job script is written to \$DESTDIR/\$JOBNAME which is also the destination of calculation output."
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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 $0))"
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SOURCEDIR="$(readlink -f $SCRIPTDIR/..)"
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PMSCO_SOURCE_DIR="$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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if [ "$1" == "HEAD" ]; then
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BRANCH_ARG=""
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else
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BRANCH_ARG="-b $1"
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fi
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shift
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DEST_DIR="$1"
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shift
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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 $1)"
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shift
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PMSCO_PROJECT_ARGS="$*"
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# set up working directory
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cd "$DEST_DIR"
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if [ ! -d "$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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# copy code
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PMSCO_SOURCE_REPO="file://$PMSCO_SOURCE_DIR"
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echo "$PMSCO_SOURCE_REPO"
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cd "$PMSCO_WORK_DIR"
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git clone $BRANCH_ARG --single-branch --depth 1 $PMSCO_SOURCE_REPO pmsco || exit
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cd pmsco
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PMSCO_REV=$(git log --pretty=format:"%h, %ai" -1) || exit
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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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"$SCRIPTDIR/pmsco.ra-git.template" > $PMSCO_JOBNAME.job
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chmod u+x "$PMSCO_JOBNAME.job" || exit
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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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@ -1,6 +1,12 @@
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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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#
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# CAUTION: the job will execute the pmsco code which is present in the directory tree
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# of this script _at the time of job execution_, not submission!
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# before changing the code, make sure that all pending jobs have started execution,
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# otherwise you will experience version conflicts.
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# it's better to use the qpmsco.ra-git.sh script which clones the code.
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if [ $# -lt 1 ]; then
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echo "Usage: $0 [NOSUB] DESTDIR JOBNAME NODES TASKS_PER_NODE WALLTIME:HOURS PROJECT MODE [ARGS [ARGS [...]]]"
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@ -87,9 +93,9 @@ PMSCO_WORK_DIR="$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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PMSCO_REV=$(git log --pretty=format:"%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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PMSCO_REV="revision unknown, "$(date +"%F %T %z")
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fi
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cd "$WORKDIR"
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echo "$PMSCO_REV" > revision.txt
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@ -86,9 +86,9 @@ PHD_WORK_DIR="$WORKDIR"
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# provide revision information, requires git repository
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cd "$SOURCEDIR"
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PHD_REV=$(git log --pretty=format:"Data revision %h, %ad" --date=iso -1)
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PHD_REV=$(git log --pretty=format:"%h, %ad" --date=iso -1)
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if [ $? -ne 0 ]; then
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PHD_REV="Data revision unknown, "$(date +"%F %T %z")
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PHD_REV="revision unknown, "$(date +"%F %T %z")
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fi
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cd "$WORKDIR"
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echo "$PHD_REV" > revision.txt
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