Nemo example runscript

date set -vx cd ${HOME}/modipsl/config/ORCA2_LIM/EXP00 export LD_LIBRARY_PATH="/usr/local/Cluster-Apps/ofed/1.2.5/lib:/usr/local/Cluster-Apps/ofed/1.2.5/lib64:/usr/loca l/Cluster-Apps/torque/2.1.7//lib/:/usr/local/Cluster-Apps/maui/3.2.6p19//lib/:/usr/local/Cluster-Apps/pgi/6.2.5/l inux86-64/6.2/libso:/usr/local/Cluster-Apps/ofed/1.2.5/mpi/pgi/mvapich-0.9.9/lib:/usr/local/Cluster-Apps/ofed/1.2 .5/mpi/pgi/mvapich-0.9.9/lib/shared:/usr/local/netcdf/3.6.2/pgi-251/lib" export DUMP2HOLD="/exports/gpfsbig/work/bristol/${USER}/" R_FORCING="${HOME}/NEMO_forcing" R_EXPER=${PWD} R_EXEDIR=${HOME}/modipsl R_TMP="$DUMP2HOLD/NEMO/$$/" R_SORTIE_OCE=${R_TMP}/output/
 * 1) SX6NEC   CEA ##
 * 2) PBS -N EXP.1
 * 3) PBS -o output_EXP.1
 * 4) PBS -j oe
 * 5) PBS -S /usr/bin/ksh
 * 6) PBS -l mem=3.6gb
 * 7) PBS -l cput=1:01:00
 * 8) PBS -q long_ib
 * 9) PBS -l cpunum_prc=4
 * 10) PBS -q parallel
 * 11)      Script to run a short experiment when installing the
 * 12)      ORCA2_LIM configuration
 * 13)            Rachid Benshila, OPA System Team
 * 14) -- print echo of commands before and after shell interpretation
 * 1)      Script to run a short experiment when installing the
 * 2)      ORCA2_LIM configuration
 * 3)            Rachid Benshila, OPA System Team
 * 4) -- print echo of commands before and after shell interpretation
 * 1) -- print echo of commands before and after shell interpretation
 * 1) -- print echo of commands before and after shell interpretation
 * 1) -- print echo of commands before and after shell interpretation
 * 1) -- print echo of commands before and after shell interpretation
 * 1) Beginning of user modification
 * 1) Beginning of user modification
 * 1) -- define some directories :
 * 1) - Input file storing
 * 1) - Launching run repository
 * 1) - modipsl repository
 * 1) - execution repository
 * 1) - output files storing

NB_PROC=1
 * 1) -- define processus number : to change when running in mpp


 * 1) End of user modification
 * 1) End of user modification

Rapatrie { [ -f $1/$2 ] || ( cp ${R_FORCING}/$2 $1 ; cd $1; tar xvf $2 ;) }
 * 1) -- define a fonction to get the input tarfile

[ -d ${R_TMP} ] || mkdir -p ${R_TMP} cd ${R_TMP}

cp ${R_EXEDIR}/bin/opa opa.xx chmod 777 opa.xx
 * 1) -- get the executable

cp ${R_EXPER}/namelist_ice namelist_ice cp ${R_EXPER}/namelist namelist
 * 1) --  Copy ancillary files
 * 2) - Namelist for ocean and ice
 * 1) - Namelist for ocean and ice

cp ${R_EXPER}/1_namelist_ice 1_namelist_ice cp ${R_EXPER}/1_namelist 1_namelist cp ${R_EXPER}/AGRIF_FixedGrids.in AGRIF_FixedGrids.in
 * 1) - Namelist for ocean and ice (agrif fine grid)

Rapatrie ${R_TMP} ORCA2_LIM_nemo_v2.tar
 * 1) - Files for the configuration and ocean dynamics

ls -alF

export F_PROGINF=yes export F_ERRCNT=5

set
 * 1) - To be use for a mpp run
 * 2) mpirun -np ${NB_PROC} ./opa.xx

echo $HOSTNAME ldd opa.xx ls /usr/local/netcdf/3.6.2/pgi-251/lib/libnetcdff.so.4

./opa.xx

ls -alF
 * 1) -- Save output files
 * 1) - to copy on a storage machine
 * 2) DPUT=putfer
 * 3) [ -d ${R_SORTIE_OCE} ] || mkdir -p ${R_SORTIE_OCE}
 * 4) - Save ocean output files
 * 5) $DPUT *ocean.output ${R_SORTIE_OCE}/.
 * 6) $DPUT *solver.stat ${R_SORTIE_OCE}/.
 * 7) [ -f *mpp.output* ] && $DPUT *mpp.output* ${R_SORTIE_OCE}/.
 * 8) for file_netcdf in *_grid_*.nc
 * do
 * 1) $DPUT ${file_netcdf} ${R_SORTIE_OCE}/${file_netcdf}
 * 2) done
 * 3) - Save ice output files
 * 4) for file_netcdf in *icemod*
 * do
 * 1) $DPUT ${file_netcdf} ${R_SORTIE_OCE}/${file_netcdf}
 * 2) done
 * 3) $DPUT ice.evolu ${R_SORTIE_OCE}/ice.evolu
 * 4) - Save restart files
 * 5) for restart in *restart*
 * do
 * 1) $DPUT ${restart} ${R_SORTIE_OCE}/${restart}
 * 2) done
 * 3) - Save ftrace file
 * 4) [ -f ftrace.out* ] && $DPUT ftrace.out* ${R_SORTIE_OCE}/.
 * 1) done
 * 2) - Save ftrace file
 * 3) [ -f ftrace.out* ] && $DPUT ftrace.out* ${R_SORTIE_OCE}/.
 * 1) [ -f ftrace.out* ] && $DPUT ftrace.out* ${R_SORTIE_OCE}/.