* pwscf: Initial version of self-submitting script to launch pwscf

calculation (version 5.3).

turing/calculations/pwscf-5.3

@@ -0,0 +1,257 @@
+#!/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
+# - LAODEDMODULES
+
+RestoreModuleEnv () {
+  local LOADEDMODULES_SAVE
+  : ${MODULESHOME:=$MODULESHOME_DEFAULT}
+  : ${MODULEPATH:=$MODULEPATH_DEFAULT}
+  export MODULESHOME
+  export MODULEPATH
+
+  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 "$MODULESHOME/init/bash"
+}
+
+module_loaded () {
+  # Usage: module_loaded  <module_pattern>
+  # Returns code zero if the said module has been loaded, or nonzero if not.
+  case ":$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 &
+	
+