158 lines
4.7 KiB
Bash
158 lines
4.7 KiB
Bash
#!/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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# 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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#
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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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# 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_SOURCE_DIR
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# path to the pmsco source directory
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# (the directory which contains the bin, lib, pmsco sub-directories)
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#
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# PMSCO_SCAN_FILES
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# list of scan files.
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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_MODE (optional)
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# calculation mode: single, swarm, grid, gradient
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#
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# PMSCO_CODE (optional)
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# calculation code: edac, msc, test
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#
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# PMSCO_LOGLEVEL (optional)
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# request log level: DEBUG, INFO, WARNING, ERROR
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# create a log file based on the job name.
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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_MODE="_PMSCO_MODE"
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PMSCO_CODE="_PMSCO_CODE"
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PMSCO_SOURCE_DIR="_PMSCO_SOURCE_DIR"
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PMSCO_SCAN_FILES="_PMSCO_SCAN_FILES"
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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-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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echo "=== Intel native mpirun will get the number of nodes and the machinefile from Slurm"
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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 "Intel native mpirun will get the number of nodes and the machinefile from Slurm"
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echo
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echo "code revision"
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cd "$PMSCO_SOURCE_DIR"
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git log --pretty=tformat:'%h %ai %d' -1
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python -m compileall pmsco
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python -m compileall projects
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cd "$PMSCO_WORK_DIR"
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echo
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PMSCO_CMD="python $PMSCO_SOURCE_DIR/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_CODE" ]; then
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PMSCO_ARGS="-c $PMSCO_CODE $PMSCO_ARGS"
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fi
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if [ -n "$PMSCO_MODE" ]; then
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PMSCO_ARGS="-m $PMSCO_MODE $PMSCO_ARGS"
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fi
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if [ -n "$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 $PMSCO_ARGS"
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fi
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which mpirun
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ls -l "$PMSCO_SOURCE_DIR"
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ls -l "$PMSCO_PROJECT_FILE"
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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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date
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ls -lAtr
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echo '================================================================================'
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exit 0
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