Changeset c5074d2 in flex_extract.git for templates

Timestamp:

Oct 9, 2018, 8:42:16 PM (6 years ago)

Author:

Anne Philipp <anne.philipp@…>

Branches:

master, ctbto, dev

Children:

aa275fc

Parents:

0a06607

Message:

added making of namelist file and jobscript via genshi templates

Location:

templates

Files:

• compilejob.temp (deleted)
• compilejob.template (modified) (4 diffs)
• convert.nl (added)
• job.template (moved) (moved from templates/job.temp.o) (5 diffs)

templates/compilejob.template

@@ -17 +17 @@
 ##PBS -q ns
 ##PBS -S /usr/bin/ksh
-##PBS -o /scratch/ms/$usergroup/$username/flex_ecmwf.$Jobname.$Job_ID.out
+##PBS -o /scratch/ms/$usergroup/$username/flex_ecmwf.$${Jobname}.$${Job_ID}.out
 # job output is in .ecaccess_DO_NOT_REMOVE
 ##PBS -j oe
@@ -26 +26 @@
 set -x
 export VERSION=$version_number
-case $HOST in
+case $${HOST} in
   *ecg*)
   module load python
@@ -41 +41 @@
   module load emos
   module load python
-  echo ${GROUP}
-  echo ${HOME}
-  echo $HOME | awk -F / '{print $1, $2, $3, $4}'
-  export GROUP=`echo $HOME | awk -F / '{print $4}'`
-  export SCRATCH=/scratch/ms/${GROUP}/${USER}
+  echo $${GROUP}
+  echo $${HOME}
+  echo $${HOME} | awk -F / '{print $1, $2, $3, $4}'
+  export GROUP=`echo $${HOME} | awk -F / '{print $4}'`
+  export SCRATCH=/scratch/ms/$${GROUP}/$${USER}
   export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
   export MAKEFILE=$makefile
@@ -51 +51 @@
 esac
 
-mkdir -p $FLEXPART_ROOT_SCRIPTS/flex_extract_v$VERSION
-cd $FLEXPART_ROOT_SCRIPTS/flex_extract_v$VERSION   # if FLEXPART_ROOT is not set this means cd to the home directory
-tar -xvf $HOME/flex_extract_v$VERSION.tar
+mkdir -p $${FLEXPART_ROOT_SCRIPTS}/flex_extract_v$${VERSION}
+cd $${FLEXPART_ROOT_SCRIPTS}/flex_extract_v$${VERSION}   # if FLEXPART_ROOT is not set this means cd to the home directory
+tar -xvf $${HOME}/flex_extract_v$${VERSION}.tar
 cd src
 \rm *.o *.mod $fortran_program 
-make -f $MAKEFILE >flexcompile 2>flexcompile
+make -f $${MAKEFILE} >flexcompile 2>flexcompile
 
 ls -l $fortran_program >>flexcompile
-if [ $? -eq 0 ]; then
+if [ $$? -eq 0 ]; then
   echo 'SUCCESS!' >>flexcompile
-  mail -s flexcompile.$HOST.$$ $USER <flexcompile
+  mail -s flexcompile.$${HOST}.$$$$ $${USER} <flexcompile
 else
   echo Environment: >>flexcompile
   env >> flexcompile
-  mail -s "ERROR! flexcompile.$HOST.$$" $USER <flexcompile
+  mail -s "ERROR! flexcompile.$${HOST}.$$$$" $${USER} <flexcompile
 fi

templates/job.template

@@ -5 +5 @@
 # start with sbatch NAME_OF_THIS_FILE directly on machine
 
-#SBATCH --workdir=/scratch/ms/spatlh00/lh0
+#SBATCH --workdir=/scratch/ms/$usergroup/$username
 #SBATCH --qos=normal
 #SBATCH --job-name=flex_ecmwf
@@ -17 +17 @@
 ##PBS -q np
 ##PBS -S /usr/bin/ksh
-## -o /scratch/ms/spatlh00/lh0/flex_ecmwf.$PBS_JOBID.out
+## -o /scratch/ms/$usergroup/$username/flex_ecmwf.$${PBS_JOBID}.out
 ## job output is in .ecaccess_DO_NOT_REMOVE
 ##PBS -j oe
@@ -25 +25 @@
 
 set -x
-export VERSION=7.1
-case $HOST in
+export VERSION=$version_number
+case $${HOST} in
   *ecg*)
   module load python
@@ -33 +33 @@
   module load grib_api/1.14.5
   module load emos/437-r64
-  export PATH=${PATH}:
+  export PATH=$${PATH}:$fp_root_path
   ;;
   *cca*)
@@ -40 +40 @@
   module load emos
   module load python
-  export SCRATCH=$TMPDIR
-  export PATH=${PATH}:
+  export SCRATCH=$${TMPDIR}
+  export PATH=$${PATH}:$fp_root_path
   ;;
 esac
 
-cd $SCRATCH
-mkdir -p python$$
-cd python$$
+cd $${SCRATCH}
+mkdir -p python$$$$
+cd python$$$$
 
 export CONTROL=CONTROL
 
-cat >$CONTROL<<EOF
+cat >$${CONTROL}<<EOF
 EOF
 
 
-submit.py --controlfile=$CONTROL --inputdir=./work --outputdir=./work 1> prot 2>&1
+submit.py --controlfile=$${CONTROL} --inputdir=./work --outputdir=./work 1> prot 2>&1
 
 if [ $? -eq 0 ] ; then
   l=0
-  for muser in `grep -i MAILOPS $CONTROL`; do
-      if [ $l -gt 0 ] ; then 
-         mail -s flex.${HOST}.$$ $muser <prot
+  for muser in `grep -i MAILOPS $${CONTROL}`; do
+      if [ $${l} -gt 0 ] ; then 
+         mail -s flex.$${HOST}.$$$$ $${muser} <prot
       fi
-      l=$(($l+1))
+      l=$(($${l}+1))
   done
 else
   l=0
-  for muser in `grep -i MAILFAIL $CONTROL`; do
-      if [ $l -gt 0 ] ; then 
-         mail -s "ERROR! flex.${HOST}.$$" $muser <prot
+  for muser in `grep -i MAILFAIL $${CONTROL}`; do
+      if [ $${l} -gt 0 ] ; then 
+         mail -s "ERROR! flex.$${HOST}.$$$$" $${muser} <prot
       fi
-      l=$(($l+1))
+      l=$(($${l}+1))
   done
 fi
+