add files for public distribution
based on internal repository 0a462b6 2017-11-22 14:41:39 +0100
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178
bin/pmsco.sge.template
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178
bin/pmsco.sge.template
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#!/bin/bash
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#
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# SGE script template for MSC calculations
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#
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# This script uses the tight integration of openmpi-1.4.5-gcc-4.6.3 in SGE
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# using the parallel environment (PE) "orte".
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# This script must be used only with qsub command - do NOT run it as a stand-alone
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# shell script because it will start all processes on the local node.
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#
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# PhD arguments
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# copy this template to a new file, and set the arguments
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#
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# PHD_WORK_DIR
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# path to be used as working directory.
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# contains the SGE script derived from this template.
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# receives output and temporary files.
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#
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# PHD_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 $PHD_WORK_DIR.
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#
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# PHD_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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# PHD_SCAN_FILES
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# list of scan files.
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#
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# PHD_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 $PHD_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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# PHD_JOBNAME (required)
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# the job name is the base name for output files.
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#
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# PHD_NODES (required)
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# number of computing nodes (processes) to allocate for the job.
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#
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# PHD_WALLTIME_HR (required)
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# wall time limit (hours)
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#
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# PHD_WALLTIME_MIN (required)
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# wall time limit (minutes)
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#
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# PHD_MODE (optional)
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# calculation mode: single, swarm, grid, gradient
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#
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# PHD_CODE (optional)
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# calculation code: edac, msc, test
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#
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# PHD_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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# PHD_PROJECT_ARGS (optional)
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# extra arguments that are parsed by the project module.
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#
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PHD_WORK_DIR="_PHD_WORK_DIR"
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PHD_JOBNAME="_PHD_JOBNAME"
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PHD_NODES=_PHD_NODES
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PHD_WALLTIME_HR=_PHD_WALLTIME_HR
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PHD_WALLTIME_MIN=_PHD_WALLTIME_MIN
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PHD_PROJECT_FILE="_PHD_PROJECT_FILE"
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PHD_MODE="_PHD_MODE"
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PHD_CODE="_PHD_CODE"
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PHD_SOURCE_DIR="_PHD_SOURCE_DIR"
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PHD_SCAN_FILES="_PHD_SCAN_FILES"
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PHD_OUT="_PHD_JOBNAME"
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PHD_LOGLEVEL="_PHD_LOGLEVEL"
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PHD_PROJECT_ARGS="_PHD_PROJECT_ARGS"
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# Define your job name, parallel environment with the number of slots, and run time:
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#$ -cwd
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#$ -N _PHD_JOBNAME.job
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#$ -pe orte _PHD_NODES
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#$ -l ram=2G
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#$ -l s_rt=_PHD_WALLTIME_HR:_PHD_WALLTIME_MIN:00
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#$ -l h_rt=_PHD_WALLTIME_HR:_PHD_WALLTIME_MIN:30
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#$ -V
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###################################################
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# Fix the SGE environment-handling bug (bash):
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source /usr/share/Modules/init/sh
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export -n -f module
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# Load the environment modules for this job (the order may be important):
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module load python/python-2.7.5
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module load gcc/gcc-4.6.3
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module load mpi/openmpi-1.4.5-gcc-4.6.3
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module load blas/blas-20110419-gcc-4.6.3
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module load lapack/lapack-3.4.2-gcc-4.6.3
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export LD_LIBRARY_PATH=$PHD_SOURCE_DIR/lib/:$LD_LIBRARY_PATH
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###################################################
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# Set the environment variables:
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MPIEXEC=$OPENMPI/bin/mpiexec
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# OPENMPI is set by the mpi/openmpi-* module.
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export OMP_NUM_THREADS=1
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export OMPI_MCA_btl='openib,sm,self'
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# export OMPI_MCA_orte_process_binding=core
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##############
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# BEGIN DEBUG
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# Print the SGE environment on master host:
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echo "================================================================"
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echo "=== SGE job JOB_NAME=$JOB_NAME JOB_ID=$JOB_ID"
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echo "================================================================"
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echo DATE=`date`
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echo HOSTNAME=`hostname`
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echo PWD=`pwd`
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echo "NSLOTS=$NSLOTS"
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echo "PE_HOSTFILE=$PE_HOSTFILE"
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cat $PE_HOSTFILE
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echo "================================================================"
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echo "Running environment:"
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env
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echo "================================================================"
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echo "Loaded environment modules:"
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module list 2>&1
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echo
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# END DEBUG
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##############
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##############
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# Setup
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cd "$PHD_SOURCE_DIR"
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python -m compileall .
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cd "$PHD_WORK_DIR"
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ulimit -c 0
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###################################################
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# The command to run with mpiexec:
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CMD="python $PHD_PROJECT_FILE"
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ARGS="$PHD_PROJECT_ARGS"
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if [ -n "$PHD_SCAN_FILES" ]; then
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ARGS="-s $PHD_SCAN_FILES -- $ARGS"
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fi
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if [ -n "$PHD_CODE" ]; then
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ARGS="-c $PHD_CODE $ARGS"
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fi
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if [ -n "$PHD_MODE" ]; then
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ARGS="-m $PHD_MODE $ARGS"
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fi
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if [ -n "$PHD_OUT" ]; then
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ARGS="-o $PHD_OUT $ARGS"
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fi
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if [ "$PHD_WALLTIME_HR" -ge 1 ]
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then
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ARGS="-t $PHD_WALLTIME_HR $ARGS"
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else
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ARGS="-t 0.5 $ARGS"
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fi
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if [ -n "$PHD_LOGLEVEL" ]; then
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ARGS="--log-level $PHD_LOGLEVEL --log-file $PHD_JOBNAME.log $ARGS"
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fi
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# The MPI command to run:
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MPICMD="$MPIEXEC --prefix $OPENMPI -x PATH -x LD_LIBRARY_PATH -x OMP_NUM_THREADS -x OMPI_MCA_btl -np $NSLOTS $CMD $ARGS"
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echo "Command to run:"
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echo "$MPICMD"
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echo
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exec $MPICMD
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exit 0
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