convert.nl

This is the template for a Fortran namelist file called fort.4 which will be read by calc_etadot. It contains all the parameters calc_etadot needs.

&NAMGEN
  maxl = $maxl,
  maxb = $maxb,
  mlevel = $mlevel,
  mlevelist = "$mlevelist",
  mnauf = $mnauf,
  metapar = $metapar,
  rlo0 = $rlo0,
  rlo1 = $rlo1,
  rla0 = $rla0,
  rla1 = $rla1,
  momega = $momega,
  momegadiff = $momegadiff,
  mgauss = $mgauss,
  msmooth = $msmooth,
  meta = $meta,
  metadiff = $metadiff,
  mdpdeta = $mdpdeta
/

ecmwf_env.template

This template is used to create the ECMWF_ENV file in the application modes gateway and remote. It contains the user credentials and gateway server settings for the file transfers.

ECUID $user_name
ECGID $user_group
GATEWAY $gateway_name
DESTINATION $destination_name

compilejob.template

This template is used to create the job script file called compilejob.ksh during the installation process for the application modes remote and gateway.

At the beginning some directives for the batch system are set. On the ecgate server the SBATCH comments are the directives for the SLURM workload manager. A description of the single lines can be found at SLURM directives. For the high performance computers cca and ccb the PBS comments are necessary and can be view at PBS directives.

The software environment requirements mentioned in :ref:`ref-requirements` are prepared by loading the corresponding modules depending in the HOST. It should not be changed without testing.

?

Afterwards the installation steps as such are done. Including the generation of the root directory, putting files in place, compiling the Fortran program and sending a log file via email.

#!/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 $${HOST} in
  *ecg*)
  module unload grib_api
  module unload eccodes
  module unload python
  module unload emos
  module load python3
  module load eccodes/2.12.0
  module load emos/455-r64
  export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
  export MAKEFILE=$makefile
  ;;
  *cca*)
  module unload python
  module switch PrgEnv-cray PrgEnv-intel
  module load python3
  module load eccodes/2.12.0
  module load emos
  echo $${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

job.temp

This template is used to create the actual job script file called job.ksh for the execution of flex_extract in the application modes remote and gateway.

At the beginning some directives for the batch system are set. On the ecgate server the SBATCH comments are the directives for the SLURM workload manager. A description of the single lines can be found at SLURM directives. For the high performance computers cca and ccb the PBS comments are necessary and can be view at PBS directives.

The software environment requirements mentioned in :ref:`ref-requirements` are prepared by loading the corresponding modules depending in the HOST. It should not be changed without testing.

?

Afterwards the run directory and the CONTROL file are created and flex_extract is executed. In the end a log file is send via email.

#!/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/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 np
##PBS -S /usr/bin/ksh
## -o /scratch/ms/at/km4a/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=7.1
case $${HOST} in
  *ecg*)
  module unload grib_api
  module unload eccodes
  module unload python
  module unload emos
  module load python3
  module load eccodes/2.12.0
  module load emos/455-r64
  export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
  ;;
  *cca*)
  module unload python
  module switch PrgEnv-cray PrgEnv-intel
  module load python3
  module load eccodes/2.12.0
  module load emos
  export SCRATCH=$${TMPDIR}
  export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
  ;;
esac
cd $${SCRATCH}
mkdir -p python$$$$
cd python$$$$
export CONTROL=CONTROL
cat >$${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

job.template

This template is used to create the template for the execution job script job.temp for flex_extract in the installation process. A description of the file can be found under job.temp. A couple of parameters are set in this process, such as the user credentials and the flex_extract version number.

#!/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 $$$${HOST} in
  *ecg*)
  module unload grib_api
  module unload eccodes
  module unload python
  module unload emos
  module load python3
  module load eccodes/2.12.0
  module load emos/455-r64
  export PATH=$$$${PATH}:$fp_root_path
  ;;
  *cca*)
  module unload python
  module switch PrgEnv-cray PrgEnv-intel
  module load python3
  module load eccodes/2.12.0
  module load emos
  export SCRATCH=$$$${TMPDIR}
  export PATH=$$$${PATH}:$fp_root_path
  ;;
esac
cd $$$${SCRATCH}
mkdir -p python$$$$$$$$
cd python$$$$$$$$
export CONTROL=CONTROL
cat >$$$${CONTROL}<<EOF
$$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

.. toctree::
    :hidden:
    :maxdepth: 2