The compilation job script compilejob.ksh

The compile job is a Korn-shell script which will be created during the installation process for the application modes remote and gateway from a template called installscript.template in the template directory.

Flex_extract uses the Python package genshi to generate the Korn-shell script from the template files by substituting the individual parameters. These individual parameters are marked by a doubled $ sign in installscript.template.

The compilation script has a number of settings for the batch system which are fixed, and it differentiates between the ecgate and the cca/ccb server system to load the necessary modules for the environment when submitted to the batch queue.

The submission is done by the ECaccess tool from within flex_extract with the command ecaccess-job-submit.

What does the compilation script do?

  1. It sets the necessary batch-system parameters

  2. It prepares the job environment at the ECMWF servers by loading the necessary library modules

  3. It sets some environment variables for the single session

  4. It creates the flex_extract root directory in the $HOME path of the user

  5. It untars the tarball into the root directory.

  6. It compiles the Fortran program using makefile.

  7. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.

Example compilejob.ksh


# 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/at/km4a
#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/at/km4a/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=7.1
case ${HOST} in
  module unload grib_api
  module unload emos
  module load python3
  module load eccodes
  module load emos/455-r64
  export MAKEFILE=makefile_ecgate
  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 MAKEFILE=makefile_ecgate

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 calc_etadot
make -f ${MAKEFILE} >flexcompile 2>flexcompile

ls -l calc_etadot >>flexcompile
if [ $? -eq 0 ]; then
  echo 'SUCCESS!' >>flexcompile
  mail -s flexcompile.${HOST}.$$ ${USER} <flexcompile
  echo Environment: >>flexcompile
  env >> flexcompile
  mail -s "ERROR! flexcompile.${HOST}.$$" ${USER} <flexcompile