* pwscf: Initial version of self-submitting script to launch pwscf
calculation (version 5.3).
This commit is contained in:
Wirawan Purwanto
257
turing/calculations/pwscf-5.3
Executable file
257
turing/calculations/pwscf-5.3
Executable file
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#!/bin/bash
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#
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# Submit job for Quantum Espresso PWSCF program
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# Created: 20160708
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# Wirawan Purwanto
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#
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if [ -n "$PWRUN_DEBUG_SCRIPT" ]; then
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Debug=$PWRUN_DEBUG_SCRIPT
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fi
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: ${PWRUN_TRACE_SCRIPT:=0}
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if [ "$PWRUN_TRACE_SCRIPT" = 1 ]; then
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set -x
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export
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fi
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set -e
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shopt -s extglob
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# Default settings -- be careful changing these.
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: ${PWRUN_COMPUTE_HOST:=batch}
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: ${PWRUN_BATCHSYS_JOBNAME:=pwscf-5.3}
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QE_ROOT=/cm/shared/apps/qe/5.3-gcc
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: ${Debug:=}
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# Some cluster defaults (may change over time)
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# Reference: /etc/profile.d/modules.sh
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MODULESHOME_DEFAULT=/cm/local/apps/environment-modules/3.2.10/Modules/3.2.10
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MODULEPATH_DEFAULT=/cm/local/modulefiles:/cm/shared/modulefiles:/cm/shared/compilers
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# RestoreModuleEnv restores module environment at batch-job runtime to be
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# exactly the same as the environment at the time of job submission.
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# It requires the following variables to be set:
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# - MODULESHOME (optional; default provided above)
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# - MODULEPATH
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# - LAODEDMODULES
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RestoreModuleEnv () {
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local LOADEDMODULES_SAVE
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: ${MODULESHOME:=$MODULESHOME_DEFAULT}
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: ${MODULEPATH:=$MODULEPATH_DEFAULT}
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export MODULESHOME
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export MODULEPATH
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LOADEDMODULES_SAVE=$LOADEDMODULES
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unset LOADEDMODULES
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source "$MODULESHOME/init/bash"
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if [ -n "$LOADEDMODULES_SAVE" ]; then
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module load ${LOADEDMODULES_SAVE//:/" "}
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fi
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if [ -n "$Debug" -o -n "$DEBUG_MODULES" ]; then
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echo "Loaded modules after module restore: $LOADEDMODULES"
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module list
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fi
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}
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InitModuleEnv () {
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# Only do the initialization part of the module so "module" command
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# is available for the script
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local LOADEDMODULES_SAVE
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: ${MODULESHOME:=$MODULESHOME_DEFAULT}
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: ${MODULEPATH:=$MODULEPATH_DEFAULT}
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export MODULESHOME
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export MODULEPATH
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source "$MODULESHOME/init/bash"
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}
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module_loaded () {
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# Usage: module_loaded <module_pattern>
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# Returns code zero if the said module has been loaded, or nonzero if not.
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case ":$LOADEDMODULES:" in
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(*:$MOD:*)
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return 0
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;;
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(*)
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return 1
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;;
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esac
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}
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function path_search()
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# Usage: path_search file path:path:path:... [testop]
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{
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local IFS=:
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local p d
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local testop="${3:-"-f"}"
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if [[ "$1" == /* ]]; then
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if test $testop "$1"; then
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echo "$1"
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return 0
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else
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return 1
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fi
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fi
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for d in $2; do
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p=$d/$1
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if test $testop "$p"; then
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echo "$p"
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return 0
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fi
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done
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return 1
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}
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Help () {
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echo "Usage: $MYSELF [number_of_processors] [inputfile] [outputfile]"
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echo
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echo "Example: $MYSELF 4 MgO.in MgO.out"
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}
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Preamble () {
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MYSELF_PATH=$(path_search "$0" "$PATH")
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MYSELF=$(basename "$MYSELF_PATH")
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if ((Debug >= 10)); then
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echo "Env-vars:"
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export
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fi
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}
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ParseArgs () {
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# FIXME: This is very primitive but accomodates what the original
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# qe-q-5.3 provides.
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PWRUN_OUTPUT=
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if [ $# -lt 2 ]; then
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Help >&2
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exit 1
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fi
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PWRUN_NUM_TASKS=$1
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PWRUN_INPUT=$2
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if [ ! -f "$PWRUN_INPUT" ]; then
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echo "Error: input file $PWRUN_INPUT cannot be found" >&2
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exit 2
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fi
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if [ -z "$3" ]; then
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PWRUN_OUTPUT="${PWRUN_INPUT%.in}.out"
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else
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PWRUN_OUTPUT=$3
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fi
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if ((Debug > 0)); then
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echo "PWRUN_INPUT=$PWRUN_INPUT"
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echo "PWRUN_OUTPUT=$PWRUN_OUTPUT"
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fi
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if [ $# -gt 3 ]; then
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shift 3
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PWRUN_BATCHSYS_OPTS=( "$@" )
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if ((Debug > 0)); then
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echo "Added extra flags to batch system: ${PWRUN_BATCHSYS_OPTS[*]}"
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fi
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fi
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}
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SubmitBatchJob () {
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export PWRUN_COMPUTE_HOST=computenode
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local VARS
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VARS=LOADEDMODULES,MODULESHOME,MODULEPATH
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VARS=$VARS,PWRUN_COMPUTE_HOST,PWRUN_INPUT,PWRUN_OUTPUT,PWRUN_NUM_TASKS
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VARS=$VARS,Debug,PWRUN_TRACE_SCRIPT
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export ${VARS//,/" "}
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if ((Debug > 0)); then
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set -x
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fi
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qsub -cwd -S /bin/bash -v $VARS -pe qe "$PWRUN_NUM_TASKS" -j yes \
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"${PWRUN_BATCHSYS_OPTS[@]}" \
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"$MYSELF_PATH"
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}
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RunBatchJob () {
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RestoreModuleEnv
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# Provides some fallback modules if they are not loaded
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if ! module_loaded "gcc/*"; then
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if ((Debug > 0)); then
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echo "Note: adding fallback module gcc/5.3.0"
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fi
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module load gcc/5.3.0
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fi
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if ! module_loaded "openmpi/gcc/64/*"; then
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if ((Debug > 0)); then
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echo "Note: adding fallback module openmpi/gcc/64/1.10.2"
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fi
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module load openmpi/gcc/64/1.10.2
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fi
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# TEMPORARY FIX
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export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/cm/shared/apps/fftw/fftw-3.3.4-shared/lib
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QE_PROG=$QE_ROOT/pw.x
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if ((Debug > 0)); then
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echo "PWRUN_INPUT=$PWRUN_INPUT"
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echo "PWRUN_OUTPUT=$PWRUN_OUTPUT"
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if ((Debug > 1)); then
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echo "Loaded-modules::"
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module list >&1 || true
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echo ""
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echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH"
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echo "QE_PROG=$QE_PROG"
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ldd $QE_PROG || true
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fi
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set -x
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fi
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mpirun -np "$PWRUN_NUM_TASKS" "$QE_PROG" -i "$PWRUN_INPUT" > "$PWRUN_OUTPUT"
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exit $?
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}
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Main() {
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Preamble
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case "$PWRUN_COMPUTE_HOST" in
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(computenode)
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RunBatchJob
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;;
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(batch)
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ParseArgs "$@"
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SubmitBatchJob
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;;
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esac
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}
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Main "$@"
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exit $?
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eval `/cm/local/apps/environment-modules/3.2.10/bin/modulecmd bash load /cm/shared/modulefiles/gcc/5.3.0`
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eval `/cm/local/apps/environment-modules/3.2.10/bin/modulecmd bash load /cm/shared/modulefiles/openmpi/gcc/64/1.10.2`
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name=`basename $0`
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if [ $# -ne 3 ]; then
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echo "Usage: $name [number of processors {1 - 256}] [inputfile] [outputfile]"
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echo
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echo "Example: $name 4 data.in results.out"
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exit -1
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fi
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qrsh -V -cwd -N QE-SUB -pe qe $1 mpirun -np $1 /cm/shared/apps/qe/5.3-gcc/pw.x -i $2 > $3 &
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