add files for public distribution

based on internal repository 0a462b6 2017-11-22 14:41:39 +0100
2017-11-22 14:55:20 +01:00
parent 96d206fc7b
commit bbd16d0f94
102 changed files with 230209 additions and 0 deletions
--- a/bin/qpmsco.sge
+++ b/bin/qpmsco.sge
@ -0,0 +1,128 @@
+#!/bin/sh
+#
+# submission script for PMSCO calculations on Merlin cluster
+#
+
+if [ $# -lt 1 ]; then
+  echo "Usage: $0 [NOSUB] JOBNAME NODES WALLTIME:HOURS PROJECT MODE [LOG_LEVEL]"
+  echo ""
+  echo "       NOSUB (optional): do not submit the script to the queue. default: submit."
+  echo "       WALLTIME:HOURS (integer): sets the wall time limits."
+  echo "          soft limit = HOURS:00:00"
+  echo "          hard limit = HOURS:00:30"
+  echo "          for short.q: HOURS = 0 (-> MINUTES=30)"
+  echo "          for all.q:   HOURS <= 24"
+  echo "          for long.q:  HOURS <= 96"
+  echo "       PROJECT: python module (file path) that declares the project and starts the calculation."
+  echo "       MODE: PMSCO calculation mode (single|swarm|gradient|grid)."
+  echo "       LOG_LEVEL (optional): one of DEBUG, INFO, WARNING, ERROR if log files should be produced."
+  echo ""
+  echo "the job script complete with the program code and input/output data is generated in ~/jobs/\$JOBNAME"
+  exit 1
+fi
+
+# location of the pmsco package is derived from the path of this script
+SCRIPTDIR="$(dirname $(readlink -f $0))"
+SOURCEDIR="$SCRIPTDIR/.."
+PHD_SOURCE_DIR="$SOURCEDIR"
+
+PHD_CODE="edac"
+
+# read arguments
+if [ "$1" == "NOSUB" ]; then
+  NOSUB="true"
+  shift
+else
+  NOSUB="false"
+fi
+
+PHD_JOBNAME=$1
+shift
+
+PHD_NODES=$1
+shift
+
+PHD_WALLTIME_HR=$1
+PHD_WALLTIME_MIN=0
+shift
+
+PHD_PROJECT_FILE="$(readlink -f $1)"
+PHD_PROJECT_ARGS=""
+shift
+
+PHD_MODE="$1"
+shift
+
+PHD_LOGLEVEL=""
+if [ "$1" == "DEBUG" ] || [ "$1" == "INFO" ] || [ "$1" == "WARNING" ] || [ "$1" == "ERROR" ]; then
+  PHD_LOGLEVEL="$1"
+  shift
+fi
+
+# ignore remaining arguments
+PHD_SCAN_FILES=""
+
+# select allowed queues
+QUEUE=short.q,all.q,long.q
+
+# for short queue (limit 30 minutes)
+if [ "$PHD_WALLTIME_HR" -lt 1 ]; then
+    PHD_WALLTIME_HR=0
+    PHD_WALLTIME_MIN=30
+fi
+
+# set up working directory
+cd ~
+if [ ! -d "jobs" ]; then
+    mkdir jobs
+fi
+cd jobs
+if [ ! -d "$PHD_JOBNAME" ]; then
+    mkdir "$PHD_JOBNAME"
+fi
+cd "$PHD_JOBNAME"
+WORKDIR="$(pwd)"
+PHD_WORK_DIR="$WORKDIR"
+
+# provide revision information, requires git repository
+cd "$SOURCEDIR"
+PHD_REV=$(git log --pretty=format:"Data revision %h, %ad" --date=iso -1)
+if [ $? -ne 0 ]; then
+   PHD_REV="Data revision unknown, "$(date +"%F %T %z")
+fi
+cd "$WORKDIR"
+echo "$PHD_REV" > revision.txt
+
+# generate job script from template
+sed -e "s:_PHD_WORK_DIR:$PHD_WORK_DIR:g" \
+    -e "s:_PHD_JOBNAME:$PHD_JOBNAME:g" \
+    -e "s:_PHD_NODES:$PHD_NODES:g" \
+    -e "s:_PHD_WALLTIME_HR:$PHD_WALLTIME_HR:g" \
+    -e "s:_PHD_WALLTIME_MIN:$PHD_WALLTIME_MIN:g" \
+    -e "s:_PHD_PROJECT_FILE:$PHD_PROJECT_FILE:g" \
+    -e "s:_PHD_PROJECT_ARGS:$PHD_PROJECT_ARGS:g" \
+    -e "s:_PHD_CODE:$PHD_CODE:g" \
+    -e "s:_PHD_MODE:$PHD_MODE:g" \
+    -e "s:_PHD_SOURCE_DIR:$PHD_SOURCE_DIR:g" \
+    -e "s:_PHD_SCAN_FILES:$PHD_SCAN_FILES:g" \
+    -e "s:_PHD_LOGLEVEL:$PHD_LOGLEVEL:g" \
+    "$SCRIPTDIR/pmsco.sge.template" > $PHD_JOBNAME.job
+
+chmod u+x "$PHD_JOBNAME.job"
+
+if [ "$NOSUB" != "true" ]; then
+
+# suppress bash error [stackoverflow.com/questions/10496758]
+unset module
+
+# submit the job script
+# EMAIL must be defined in the environment
+if [ -n "$EMAIL" ]; then
+  qsub -q $QUEUE -m ae -M $EMAIL $PHD_JOBNAME.job
+else
+  qsub -q $QUEUE $PHD_JOBNAME.job
+fi
+
+fi
+
+exit 0