created server specific templates for slurm job scripts (Reading vs Bologna)!...

created server specific templates for slurm job scripts (Reading vs Bologna)! Use static link file name in Python.

Source/Python/_config.py

@@ -87,9 +87,9 @@ FILE_MARS_REQUESTS = 'mars_requests.csv'
 FORTRAN_EXECUTABLE = 'calc_etadot'
 TEMPFILE_USER_ENVVARS = 'ECMWF_ENV.template'
 FILE_USER_ENVVARS = 'ECMWF_ENV'
-TEMPFILE_INSTALL_COMPILEJOB = 'installscript.template.bologna'
+TEMPFILE_INSTALL_COMPILEJOB = 'installscript.template'
 FILE_INSTALL_COMPILEJOB = 'compilejob.ksh'
-TEMPFILE_INSTALL_JOB = 'jobscript.template.bologna'
+TEMPFILE_INSTALL_JOB = 'jobscript.template'
 TEMPFILE_JOB = 'submitscript.template'
 FILE_JOB_OD = 'job.ksh'
 FILE_JOB_OP = 'jopoper.ksh'

Templates/installscript.template

-#!/bin/ksh
-
-# ON ECGB:
-# start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE  on gateway server
-# start with sbatch NAME_OF_THIS_FILE directly on machine
-
-#SBATCH --workdir=/scratch/ms/$usergroup/$username
-#SBATCH --qos=normal
-#SBATCH --job-name=flex_ecmwf
-#SBATCH --output=flex_ecmwf.%j.out
-#SBATCH --error=flex_ecmwf.%j.out
-#SBATCH --mail-type=FAIL
-#SBATCH --time=12:00:00
-
-## CRAY specific batch requests
-##PBS -N flex_ecmwf
-##PBS -q ns
-##PBS -S /usr/bin/ksh
-##PBS -o /scratch/ms/$usergroup/$username/flex_ecmwf.$${Jobname}.$${Job_ID}.out
-# job output is in .ecaccess_DO_NOT_REMOVE
-##PBS -j oe
-##PBS -V
-##PBS -l EC_threads_per_task=1
-##PBS -l EC_memory_per_task=3200MB
-
-set -x
-export VERSION=$version_number
-case $${HOST} in
-  *ecg*)
-  module unload grib_api
-  module unload emos
-  module load python3
-  module load eccodes
-  module load emos/455-r64
-  export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
-  export MAKEFILE=$makefile
-  ;;
-  *cca*)
-  module switch PrgEnv-cray PrgEnv-intel
-  module load python3
-  module load eccodes
-  module load emos/455-r64
-  echo $${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}/$${USER}
-  export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
-  export MAKEFILE=$makefile
-  ;;
-esac
-
-mkdir -p $${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$${VERSION}.tar
-cd Source/Fortran
-\rm *.o *.mod $fortran_program 
-make -f $${MAKEFILE} >flexcompile 2>flexcompile
-
-ls -l $fortran_program >>flexcompile
-if [ $$? -eq 0 ]; then
-  echo 'SUCCESS!' >>flexcompile
-  mail -s flexcompile.$${HOST}.$$$$ $${USER} <flexcompile
-else
-  echo Environment: >>flexcompile
-  env >> flexcompile
-  mail -s "ERROR! flexcompile.$${HOST}.$$$$" $${USER} <flexcompile
-fi

Templates/installscript.template

+installscript.template.bologna
\ No newline at end of file

Templates/installscript.template.bologna

+#!/bin/ksh
+
+# ON ECS or HPC servers:
+# start with ecaccess-job-submit -queueName <QUEUENAME> <NAME_OF_THIS_FILE>  on gateway server
+# start with srun <NAME_OF_THIS_FILE> directly on machine
+
+#SBATCH --chdir=$$SCRATCH
+#SBATCH --qos=el
+#SBATCH --job-name=flex_extract
+#SBATCH --output=flex_extract.%j.out
+#SBATCH --error=flex_error.%j.out
+#SBATCH --mail-type=FAIL
+#SBATCH --mail-user=$username
+
+## CRAY specific batch requests
+##PBS -N flex_ecmwf
+##PBS -q ns
+##PBS -S /usr/bin/ksh
+##PBS -o $$SCRATCH/flex_extract.$${Jobname}.$${Job_ID}.out
+# job output is in .ecaccess_DO_NOT_REMOVE
+##PBS -j oe
+##PBS -V
+##PBS -l EC_threads_per_task=1
+##PBS -l EC_memory_per_task=3200MB
+
+set -x
+export VERSION=$version_number
+case $${EC_CLUSTER} in
+  *ecs*)
+#  module switch prgenv/gnu
+  module load ecmwf-toolbox
+  module load python3
+  module load ecaccess
+  export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
+  export MAKEFILE=$makefile
+  ;;
+  *hpc*)
+#  module switch PrgEnv-cray PrgEnv-intel
+  module load python3
+  module load ecmwf-toolbox
+  module load ecaccess
+  echo $${GROUP}
+  echo $${HOME}
+  echo $${HOME} | awk -F / '{print $1, $2, $3, $4}'
+  export GROUP=`echo $${HOME} | awk -F / '{print $4}'`
+  export SCRATCH=$${SCRATCH}
+  export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
+  export MAKEFILE=$makefile
+  ;;
+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
+cd Source/Fortran
+\rm *.o *.mod $fortran_program 
+make -f $${MAKEFILE} >flexcompile 2>flexcompile
+
+ls -l $fortran_program >>flexcompile
+if [ $$? -eq 0 ]; then
+  echo 'SUCCESS!' >>flexcompile
+  mail -s flexcompile.$${HOST}.$$$$ $${USER} <flexcompile
+else
+  echo Environment: >>flexcompile
+  env >> flexcompile
+  mail -s "ERROR! flexcompile.$${HOST}.$$$$" $${USER} <flexcompile
+fi

Templates/installscript.template.reading

+#!/bin/ksh
+
+# ON ECGB:
+# start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE  on gateway server
+# start with sbatch NAME_OF_THIS_FILE directly on machine
+
+#SBATCH --workdir=/scratch/ms/$usergroup/$username
+#SBATCH --qos=normal
+#SBATCH --job-name=flex_ecmwf
+#SBATCH --output=flex_ecmwf.%j.out
+#SBATCH --error=flex_ecmwf.%j.out
+#SBATCH --mail-type=FAIL
+#SBATCH --time=12:00:00
+
+## CRAY specific batch requests
+##PBS -N flex_ecmwf
+##PBS -q ns
+##PBS -S /usr/bin/ksh
+##PBS -o /scratch/ms/$usergroup/$username/flex_ecmwf.$${Jobname}.$${Job_ID}.out
+# job output is in .ecaccess_DO_NOT_REMOVE
+##PBS -j oe
+##PBS -V
+##PBS -l EC_threads_per_task=1
+##PBS -l EC_memory_per_task=3200MB
+
+set -x
+export VERSION=$version_number
+case $${HOST} in
+  *ecg*)
+  module unload grib_api
+  module unload emos
+  module load python3
+  module load eccodes
+  module load emos/455-r64
+  export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
+  export MAKEFILE=$makefile
+  ;;
+  *cca*)
+  module switch PrgEnv-cray PrgEnv-intel
+  module load python3
+  module load eccodes
+  module load emos/455-r64
+  echo $${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}/$${USER}
+  export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
+  export MAKEFILE=$makefile
+  ;;
+esac
+
+mkdir -p $${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$${VERSION}.tar
+cd Source/Fortran
+\rm *.o *.mod $fortran_program 
+make -f $${MAKEFILE} >flexcompile 2>flexcompile
+
+ls -l $fortran_program >>flexcompile
+if [ $$? -eq 0 ]; then
+  echo 'SUCCESS!' >>flexcompile
+  mail -s flexcompile.$${HOST}.$$$$ $${USER} <flexcompile
+else
+  echo Environment: >>flexcompile
+  env >> flexcompile
+  mail -s "ERROR! flexcompile.$${HOST}.$$$$" $${USER} <flexcompile
+fi

Templates/jobscript.template

-#!/bin/ksh
-
-# ON ECGB:
-# start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE  on gateway server
-# start with sbatch NAME_OF_THIS_FILE directly on machine
-
-#SBATCH --workdir=/scratch/ms/$usergroup/$username
-#SBATCH --qos=normal
-#SBATCH --job-name=flex_ecmwf
-#SBATCH --output=flex_ecmwf.%j.out
-#SBATCH --error=flex_ecmwf.%j.out
-#SBATCH --mail-type=FAIL
-#SBATCH --time=12:00:00
-
-## CRAY specific batch requests
-##PBS -N flex_ecmwf
-##PBS -q np
-##PBS -S /usr/bin/ksh
-## -o /scratch/ms/$usergroup/$username/flex_ecmwf.$$$${PBS_JOBID}.out
-## job output is in .ecaccess_DO_NOT_REMOVE
-##PBS -j oe
-##PBS -V
-##PBS -l EC_threads_per_task=24
-##PBS -l EC_memory_per_task=32000MB
-
-set -x
-export VERSION=$version_number
-case $$$${HOST} in
-  *ecg*)
-  module unload grib_api
-  module unload emos
-  module load python3
-  module load eccodes
-  module load emos/455-r64
-  export PATH=$$$${PATH}:$fp_root_path
-  ;;
-  *cca*)
-  module switch PrgEnv-cray PrgEnv-intel
-  module load python3
-  module load eccodes
-  module load emos/455-r64
-  export SCRATCH=$$$${TMPDIR}
-  export PATH=$$$${PATH}:$fp_root_path
-  ;;
-esac
-
-cd $$$${SCRATCH}
-mkdir -p extract$$$$$$$$
-cd extract$$$$$$$$
-
-export CONTROL=CONTROL
-
-cat >$$$${CONTROL}<<EOF
-$$control_content
-EOF
-
-
-submit.py --controlfile=$$$${CONTROL} --inputdir=./work --outputdir=./work 1> prot 2>&1
-
-if [ $? -eq 0 ] ; then
-  l=0
-  for muser in `grep -i MAILOPS $$$${CONTROL}`; do
-      if [ $$$${l} -gt 0 ] ; then 
-         mail -s flex.$$$${HOST}.$$$$$$$$ $$$${muser} <prot
-      fi
-      l=$(($$$${l}+1))
-  done
-else
-  l=0
-  for muser in `grep -i MAILFAIL $$$${CONTROL}`; do
-      if [ $$$${l} -gt 0 ] ; then 
-         mail -s "ERROR! flex.$$$${HOST}.$$$$$$$$" $$$${muser} <prot
-      fi
-      l=$(($$$${l}+1))
-  done
-fi
-

Templates/jobscript.template

+jobscript.template.reading
\ No newline at end of file

Templates/jobscript.template.bologna

+#!/bin/ksh
+
+# ON ECS or HPC:
+# start with ecaccess-job-submit -queueName <QUEUE_NAME> <NAME_OF_THIS_FILE>  on gateway server
+# start with srun <NAME_OF_THIS_FILE> directly on machine
+
+#SBATCH --chdir=$$$$SCRATCH
+#SBATCH --qos=el
+#SBATCH --job-name=flex_extract
+#SBATCH --output=flex_extract.%j.out
+#SBATCH --error=flex_error.%j.out
+#SBATCH --mail-type=FAIL
+#SBATCH --mail-user=$username
+#SBATCH --time=24:00:00
+
+## CRAY specific batch requests
+##PBS -N flex_extract
+##PBS -q np
+##PBS -S /usr/bin/ksh
+## -o $$$${SCRATCH}/flex_ecmwf.$$$${PBS_JOBID}.out
+## job output is in .ecaccess_DO_NOT_REMOVE
+##PBS -j oe
+##PBS -V
+##PBS -l EC_threads_per_task=24
+##PBS -l EC_memory_per_task=32000MB
+
+set -x
+export VERSION=$version_number
+case $$$${EC_CLUSTER} in
+  *ecs*)
+  module load python3
+  module load ecmwf-toolbox
+  module load ecaccess
+  export PATH=$$$${PATH}:$fp_root_path
+  ;;
+  *hpc*)
+#  module switch PrgEnv-cray PrgEnv-intel
+  module load python3
+  module load ecmwf-toolbox
+  module load ecaccess
+  export SCRATCH=$$$${TMPDIR}
+  export PATH=$$$${PATH}:$fp_root_path
+  ;;
+esac
+
+cd $$$${SCRATCH}
+mkdir -p extract$$$$$$$$
+cd extract$$$$$$$$
+
+export CONTROL=CONTROL
+
+cat >$$$${CONTROL}<<EOF
+$$control_content
+EOF
+
+
+submit.py --controlfile=$$$${CONTROL} --inputdir=./work --outputdir=./work 1> prot 2>&1
+
+if [ $? -eq 0 ] ; then
+  l=0
+  for muser in `grep -i MAILOPS $$$${CONTROL}`; do
+      if [ $$$${l} -gt 0 ] ; then 
+         mail -s flex.$$$${HOST}.$$$$$$$$ $$$${muser} <prot
+      fi
+      l=$(($$$${l}+1))
+  done
+else
+  l=0
+  for muser in `grep -i MAILFAIL $$$${CONTROL}`; do
+      if [ $$$${l} -gt 0 ] ; then 
+         mail -s "ERROR! flex.$$$${HOST}.$$$$$$$$" $$$${muser} <prot
+      fi
+      l=$(($$$${l}+1))
+  done
+fi
+

Templates/jobscript.template.reading

+#!/bin/ksh
+
+# ON ECGB:
+# start with ecaccess-job-submit -queueName ecgb NAME_OF_THIS_FILE  on gateway server
+# start with sbatch NAME_OF_THIS_FILE directly on machine
+
+#SBATCH --workdir=/scratch/ms/$usergroup/$username
+#SBATCH --qos=normal
+#SBATCH --job-name=flex_ecmwf
+#SBATCH --output=flex_ecmwf.%j.out
+#SBATCH --error=flex_ecmwf.%j.out
+#SBATCH --mail-type=FAIL
+#SBATCH --time=12:00:00
+
+## CRAY specific batch requests
+##PBS -N flex_ecmwf
+##PBS -q np
+##PBS -S /usr/bin/ksh
+## -o /scratch/ms/$usergroup/$username/flex_ecmwf.$$$${PBS_JOBID}.out
+## job output is in .ecaccess_DO_NOT_REMOVE
+##PBS -j oe
+##PBS -V
+##PBS -l EC_threads_per_task=24
+##PBS -l EC_memory_per_task=32000MB
+
+set -x
+export VERSION=$version_number
+case $$$${HOST} in
+  *ecg*)
+  module unload grib_api
+  module unload emos
+  module load python3
+  module load eccodes
+  module load emos/455-r64
+  export PATH=$$$${PATH}:$fp_root_path
+  ;;
+  *cca*)
+  module switch PrgEnv-cray PrgEnv-intel
+  module load python3
+  module load eccodes
+  module load emos/455-r64
+  export SCRATCH=$$$${TMPDIR}
+  export PATH=$$$${PATH}:$fp_root_path
+  ;;
+esac
+
+cd $$$${SCRATCH}
+mkdir -p extract$$$$$$$$
+cd extract$$$$$$$$
+
+export CONTROL=CONTROL
+
+cat >$$$${CONTROL}<<EOF
+$$control_content
+EOF
+
+
+submit.py --controlfile=$$$${CONTROL} --inputdir=./work --outputdir=./work 1> prot 2>&1
+
+if [ $? -eq 0 ] ; then
+  l=0
+  for muser in `grep -i MAILOPS $$$${CONTROL}`; do
+      if [ $$$${l} -gt 0 ] ; then 
+         mail -s flex.$$$${HOST}.$$$$$$$$ $$$${muser} <prot
+      fi
+      l=$(($$$${l}+1))
+  done
+else
+  l=0
+  for muser in `grep -i MAILFAIL $$$${CONTROL}`; do
+      if [ $$$${l} -gt 0 ] ; then 
+         mail -s "ERROR! flex.$$$${HOST}.$$$$$$$$" $$$${muser} <prot
+      fi
+      l=$(($$$${l}+1))
+  done
+fi
+