From 82ea3bc689ccb8889e27311fd8208890f597e2e7 Mon Sep 17 00:00:00 2001 From: Wirawan Purwanto Date: Wed, 24 May 2017 14:37:32 -0400 Subject: [PATCH] * Archived: SGE version of pwscf-5.3 script. --- turing/calculations/sge/pwscf-5.3 | 262 ++++++++++++++++++++++++++++++ 1 file changed, 262 insertions(+) create mode 100755 turing/calculations/sge/pwscf-5.3 diff --git a/turing/calculations/sge/pwscf-5.3 b/turing/calculations/sge/pwscf-5.3 new file mode 100755 index 0000000..39e7deb --- /dev/null +++ b/turing/calculations/sge/pwscf-5.3 @@ -0,0 +1,262 @@ +#!/bin/bash +# +# Submit job for Quantum Espresso PWSCF program +# Created: 20160708 +# Wirawan Purwanto +# + +if [ -n "$PWRUN_DEBUG_SCRIPT" ]; then + Debug=$PWRUN_DEBUG_SCRIPT +fi + +: ${PWRUN_TRACE_SCRIPT:=0} +if [ "$PWRUN_TRACE_SCRIPT" = 1 ]; then + set -x + export +fi + +set -e +shopt -s extglob + +# Default settings -- be careful changing these. +: ${PWRUN_COMPUTE_HOST:=batch} +: ${PWRUN_BATCHSYS_JOBNAME:=pwscf-5.3} +QE_ROOT=/cm/shared/apps/qe/5.3-gcc +: ${Debug:=} +# Some cluster defaults (may change over time) +# Reference: /etc/profile.d/modules.sh +MODULESHOME_DEFAULT=/cm/local/apps/environment-modules/3.2.10/Modules/3.2.10 +MODULEPATH_DEFAULT=/cm/local/modulefiles:/cm/shared/modulefiles:/cm/shared/compilers + +# RestoreModuleEnv restores module environment at batch-job runtime to be +# exactly the same as the environment at the time of job submission. +# It requires the following variables to be set: +# - MODULESHOME (optional; default provided above) +# - MODULEPATH +# - LOADEDMODULES + +RestoreModuleEnv () { + local LOADEDMODULES_SAVE + # : ${MODULESHOME:=$MODULESHOME_DEFAULT} + # : ${MODULEPATH:=$MODULEPATH_DEFAULT} + MODULESHOME=$MODULESHOME_DEFAULT + MODULEPATH=$MODULEPATH_DEFAULT + export MODULESHOME + export MODULEPATH + if [[ ":${MODULEPATH}:" != *":${MODULEPATH_DEFAULT}:"* ]]; then + MODULEPATH=${MODULEPATH}:${MODULEPATH_DEFAULT} + fi + + LOADEDMODULES_SAVE=$LOADEDMODULES + unset LOADEDMODULES + + source "$MODULESHOME/init/bash" + + if [ -n "$LOADEDMODULES_SAVE" ]; then + module load ${LOADEDMODULES_SAVE//:/" "} + fi + + if [ -n "$Debug" -o -n "$DEBUG_MODULES" ]; then + echo "Loaded modules after module restore: $LOADEDMODULES" + module list + fi +} + +InitModuleEnv () { + # Only do the initialization part of the module so "module" command + # is available for the script + local LOADEDMODULES_SAVE + : ${MODULESHOME:=$MODULESHOME_DEFAULT} + : ${MODULEPATH:=$MODULEPATH_DEFAULT} + export MODULESHOME + export MODULEPATH + + source "$MODULESHOME/init/bash" +} + +module_loaded () { + # Usage: module_loaded + # Returns code zero if the said module has been loaded, or nonzero if not. + case ":$LOADEDMODULES:" in + (*:$MOD:*) + return 0 + ;; + (*) + return 1 + ;; + esac +} + + +function path_search() +# Usage: path_search file path:path:path:... [testop] +{ + local IFS=: + local p d + local testop="${3:-"-f"}" + if [[ "$1" == /* ]]; then + if test $testop "$1"; then + echo "$1" + return 0 + else + return 1 + fi + fi + for d in $2; do + p=$d/$1 + if test $testop "$p"; then + echo "$p" + return 0 + fi + done + return 1 +} + + +Help () { + echo "Usage: $MYSELF [number_of_processors] [inputfile] [outputfile]" + echo + echo "Example: $MYSELF 4 MgO.in MgO.out" +} + + +Preamble () { + MYSELF_PATH=$(path_search "$0" "$PATH") + MYSELF=$(basename "$MYSELF_PATH") + + if ((Debug >= 10)); then + echo "Env-vars:" + export + fi +} + + +ParseArgs () { +# FIXME: This is very primitive but accomodates what the original +# qe-q-5.3 provides. + + PWRUN_OUTPUT= + if [ $# -lt 2 ]; then + Help >&2 + exit 1 + fi + PWRUN_NUM_TASKS=$1 + PWRUN_INPUT=$2 + + if [ ! -f "$PWRUN_INPUT" ]; then + echo "Error: input file $PWRUN_INPUT cannot be found" >&2 + exit 2 + fi + + if [ -z "$3" ]; then + PWRUN_OUTPUT="${PWRUN_INPUT%.in}.out" + else + PWRUN_OUTPUT=$3 + fi + + if ((Debug > 0)); then + echo "PWRUN_INPUT=$PWRUN_INPUT" + echo "PWRUN_OUTPUT=$PWRUN_OUTPUT" + fi + + if [ $# -gt 3 ]; then + shift 3 + PWRUN_BATCHSYS_OPTS=( "$@" ) + if ((Debug > 0)); then + echo "Added extra flags to batch system: ${PWRUN_BATCHSYS_OPTS[*]}" + fi + fi +} + +SubmitBatchJob () { + export PWRUN_COMPUTE_HOST=computenode + local VARS + VARS=LOADEDMODULES,MODULESHOME,MODULEPATH + VARS=$VARS,PWRUN_COMPUTE_HOST,PWRUN_INPUT,PWRUN_OUTPUT,PWRUN_NUM_TASKS + VARS=$VARS,Debug,PWRUN_TRACE_SCRIPT + export ${VARS//,/" "} + if ((Debug > 0)); then + set -x + fi + qsub -cwd -S /bin/bash -v $VARS -pe qe "$PWRUN_NUM_TASKS" -j yes \ + "${PWRUN_BATCHSYS_OPTS[@]}" \ + "$MYSELF_PATH" +} + +RunBatchJob () { + RestoreModuleEnv + + # Provides some fallback modules if they are not loaded + if ! module_loaded "gcc/*"; then + if ((Debug > 0)); then + echo "Note: adding fallback module gcc/5.3.0" + fi + module load gcc/5.3.0 + fi + if ! module_loaded "openmpi/gcc/64/*"; then + if ((Debug > 0)); then + echo "Note: adding fallback module openmpi/gcc/64/1.10.2" + fi + module load openmpi/gcc/64/1.10.2 + fi + + # TEMPORARY FIX + export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/cm/shared/apps/fftw/fftw-3.3.4-shared/lib + + QE_PROG=$QE_ROOT/pw.x + + if ((Debug > 0)); then + echo "PWRUN_INPUT=$PWRUN_INPUT" + echo "PWRUN_OUTPUT=$PWRUN_OUTPUT" + + if ((Debug > 1)); then + echo "Loaded-modules::" + module list >&1 || true + echo "" + echo "LD_LIBRARY_PATH=$LD_LIBRARY_PATH" + echo "QE_PROG=$QE_PROG" + ldd $QE_PROG || true + fi + set -x + fi + + mpirun -np "$PWRUN_NUM_TASKS" "$QE_PROG" -i "$PWRUN_INPUT" > "$PWRUN_OUTPUT" + exit $? +} + + + +Main() { + Preamble + + case "$PWRUN_COMPUTE_HOST" in + (computenode) + RunBatchJob + ;; + + (batch) + ParseArgs "$@" + SubmitBatchJob + ;; + esac +} + +Main "$@" +exit $? + +eval `/cm/local/apps/environment-modules/3.2.10/bin/modulecmd bash load /cm/shared/modulefiles/gcc/5.3.0` +eval `/cm/local/apps/environment-modules/3.2.10/bin/modulecmd bash load /cm/shared/modulefiles/openmpi/gcc/64/1.10.2` + +name=`basename $0` + +if [ $# -ne 3 ]; then + echo "Usage: $name [number of processors {1 - 256}] [inputfile] [outputfile]" + echo + echo "Example: $name 4 data.in results.out" + exit -1 +fi + + +qrsh -V -cwd -N QE-SUB -pe qe $1 mpirun -np $1 /cm/shared/apps/qe/5.3-gcc/pw.x -i $2 > $3 & + +