update public distribution

based on internal repository c9a2ac8 2019-01-03 16:04:57 +0100
tagged rev-master-2.0.0

bin/pmsco.ra.template

@@ -120,7 +120,7 @@ python -m compileall projects
 cd "$PMSCO_WORK_DIR"
 echo
 
-PMSCO_CMD="python $PMSCO_PROJECT_FILE"
+PMSCO_CMD="python $PMSCO_SOURCE_DIR/pmsco $PMSCO_PROJECT_FILE"
 PMSCO_ARGS="$PMSCO_PROJECT_ARGS"
 if [ -n "$PMSCO_SCAN_FILES" ]; then
     PMSCO_ARGS="-s $PMSCO_SCAN_FILES $PMSCO_ARGS"

bin/qpmsco.ra.sh

@@ -3,9 +3,10 @@
 # submission script for PMSCO calculations on the Ra cluster
 
 if [ $# -lt 1 ]; then
-  echo "Usage: $0 [NOSUB] JOBNAME NODES TASKS_PER_NODE WALLTIME:HOURS PROJECT MODE [ARGS [ARGS [...]]]"
+  echo "Usage: $0 [NOSUB] DESTDIR JOBNAME NODES TASKS_PER_NODE WALLTIME:HOURS PROJECT MODE [ARGS [ARGS [...]]]"
   echo ""
   echo "       NOSUB (optional): do not submit the script to the queue. default: submit."
+  echo "       DESTDIR: destination directory. must exist. a sub-dir \$JOBNAME is created."
   echo "       JOBNAME (text): name of job. use only alphanumeric characters, no spaces."
   echo "       NODES (integer): number of computing nodes. (1 node = 24 or 32 processors)."
   echo "          do not specify more than 2."
@@ -20,7 +21,7 @@ if [ $# -lt 1 ]; then
   echo "       MODE: PMSCO calculation mode (single|swarm|gradient|grid)."
   echo "       ARGS (optional): any number of further PMSCO or project arguments (except mode and time)."
   echo ""
-  echo "the job script complete with the program code and input/output data is generated in ~/jobs/\$JOBNAME"
+  echo "the job script is written to \$DESTDIR/\$JOBNAME which is also the destination of calculation output."
   exit 1
 fi
 
@@ -37,6 +38,9 @@ else
   NOSUB="false"
 fi
 
+DEST_DIR="$1"
+shift
+
 PMSCO_JOBNAME=$1
 shift
 
@@ -73,11 +77,7 @@ PMSCO_LOGLEVEL=""
 PMSCO_CODE=""
 
 # set up working directory
-cd ~
-if [ ! -d "jobs" ]; then
-    mkdir jobs
-fi
-cd jobs
+cd "$DEST_DIR"
 if [ ! -d "$PMSCO_JOBNAME" ]; then
     mkdir "$PMSCO_JOBNAME"
 fi