public distro 2.1.0

bin/pmsco.ra-git.template

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+#!/bin/bash
+#
+# Slurm script template for PMSCO calculations on the Ra cluster
+# based on run_mpi_HPL_nodes-2.sl by V. Markushin 2016-03-01
+#
+# this version checks out the source code from a git repository
+# to a temporary location and compiles the code.
+# this is to minimize conflicts between different jobs
+# but requires that each job has its own git commit.
+#
+# Use:
+# - enter the appropriate parameters and save as a new file.
+# - call the sbatch command to pass the job script.
+#   request a specific number of nodes and tasks.
+#   example:
+#   sbatch --nodes=2  --ntasks-per-node=24 --time=02:00:00 run_pmsco.sl
+# the qpmsco script does all this for you.
+#
+# PMSCO arguments
+# copy this template to a new file, and set the arguments
+#
+# PMSCO_WORK_DIR
+#   path to be used as working directory.
+#   contains the script derived from this template
+#   and a copy of the pmsco code in the 'pmsco' directory.
+#   receives output and temporary files.
+#
+# PMSCO_PROJECT_FILE
+#   python module that declares the project and starts the calculation.
+#   must include the file path relative to $PMSCO_WORK_DIR.
+#
+# PMSCO_OUT
+#   name of output file. should not include a path.
+#
+# all paths are relative to $PMSCO_WORK_DIR or (better) absolute.
+#
+#
+# Further arguments
+#
+# PMSCO_JOBNAME (required)
+#   the job name is the base name for output files.
+#
+# PMSCO_WALLTIME_HR (integer, required)
+#   wall time limit in hours. must be integer, minimum 1.
+#   this value is passed to PMSCO.
+#   it should specify the same amount of wall time as requested from the scheduler.
+#
+# PMSCO_PROJECT_ARGS (optional)
+#   extra arguments that are parsed by the project module.
+#
+#SBATCH --job-name="_PMSCO_JOBNAME"
+#SBATCH --output="_PMSCO_JOBNAME.o.%j"
+#SBATCH --error="_PMSCO_JOBNAME.e.%j"
+
+PMSCO_WORK_DIR="_PMSCO_WORK_DIR"
+PMSCO_JOBNAME="_PMSCO_JOBNAME"
+PMSCO_WALLTIME_HR=_PMSCO_WALLTIME_HR
+
+PMSCO_PROJECT_FILE="_PMSCO_PROJECT_FILE"
+PMSCO_OUT="_PMSCO_JOBNAME"
+PMSCO_PROJECT_ARGS="_PMSCO_PROJECT_ARGS"
+
+module load psi-python36/4.4.0
+module load gcc/4.8.5
+module load openmpi/3.1.3
+source activate pmsco3
+
+echo '================================================================================'
+echo "=== Running $0 at the following time and place:"
+date
+/bin/hostname
+cd $PMSCO_WORK_DIR
+pwd
+ls -lA
+#the intel compiler is currently not compatible with mpi4py. -mm 170131
+#echo
+#echo '================================================================================'
+#echo "=== Setting the environment to use Intel Cluster Studio XE 2016 Update 2 intel/16.2:"
+#cmd="source /opt/psi/Programming/intel/16.2/bin/compilervars.sh intel64"
+#echo $cmd
+#$cmd
+echo
+echo '================================================================================'
+echo "=== The environment is set as following:"
+env
+echo
+echo '================================================================================'
+echo "BEGIN test"
+which mpirun
+cmd="mpirun /bin/hostname"
+echo $cmd
+$cmd
+echo "END test"
+echo
+echo '================================================================================'
+echo "BEGIN mpirun pmsco"
+echo
+
+cd "$PMSCO_WORK_DIR"
+cd pmsco
+echo "code revision"
+git log --pretty=tformat:'%h %ai %d' -1
+make -C pmsco all
+python -m compileall pmsco
+python -m compileall projects
+echo
+
+cd "$PMSCO_WORK_DIR"
+PMSCO_CMD="python pmsco/pmsco $PMSCO_PROJECT_FILE"
+PMSCO_ARGS="$PMSCO_PROJECT_ARGS"
+if [ -n "$PMSCO_SCAN_FILES" ]; then
+    PMSCO_ARGS="-s $PMSCO_SCAN_FILES $PMSCO_ARGS"
+fi
+if [ -n "$PMSCO_OUT" ]; then
+    PMSCO_ARGS="-o $PMSCO_OUT $PMSCO_ARGS"
+fi
+if [ "$PMSCO_WALLTIME_HR" -ge 1 ]; then
+    PMSCO_ARGS="-t $PMSCO_WALLTIME_HR $PMSCO_ARGS"
+fi
+if [ -n "$PMSCO_LOGLEVEL" ]; then
+    PMSCO_ARGS="--log-level $PMSCO_LOGLEVEL --log-file $PMSCO_JOBNAME.log $PMSCO_ARGS"
+fi
+
+# Do no use the OpenMPI specific options, like "-x LD_LIBRARY_PATH", with the Intel mpirun.
+cmd="mpirun $PMSCO_CMD $PMSCO_ARGS"
+echo $cmd
+$cmd
+echo "END mpirun pmsco"
+echo '================================================================================'
+cd "$PMSCO_WORK_DIR"
+rm -rf pmsco
+date
+ls -lAtr
+echo '================================================================================'
+
+exit 0