source: CONFIG_DEVT/IPSLCM6.5_work_ENSEMBLES/oasis3-mct/examples/spoc/spoc_regridding/run_regrid.sh @ 5725

#!/bin/ksh
#set -x

host=`uname -n`
user=`whoami`

## - Define paths
srcdir=`pwd`
datadir=$srcdir/data_oasis
casename=`basename $srcdir`

## - Define case
if [ $# -eq 0 ] ; then
   echo "By default, i.e. without arguments, the source grid is bggd,"
   echo "the target grid is nogt and the remapping is 1st order conservative;"
   echo "2 nodes, 1 MPI task per node and 1 OpenMP thread per MPI task are used for the run."
   SRC_GRID=bggd
   TGT_GRID=nogt
   remap=conserv1st
   n_p_t=2_1_1
   nnode=2
   mpiprocs=1
   threads=1 
elif [ $# -ne 4 ] ; then
   echo "If you don't want to run the default case without arguments, "
   echo "you must run the script with 4 arguments i.e. './run_testinterp.sh src tgt remap nnodes_nprocs_nthreads'"
   echo "where 'src' is the source grid, 'tgt' the target grid and 'remap' the remapping,"
   echo "'nnodes' the total number of nodes for the run, 'nprocs' the number of MPI tasks per node"
   echo "and 'nthreads' the number of OpenMP threads per MPI task"
   exit
else
   SRC_GRID=$1
   TGT_GRID=$2
   remap=$3
   n_p_t=$4
   nnode=`echo $n_p_t | awk -F _ '{print $1}'`
   mpiprocs=`echo $n_p_t | awk -F _ '{print $2}'`
   threads=`echo $n_p_t | awk -F _ '{print $3}'`
fi
##
## User's choice of computing architecture
arch=pgi20.4_openmpi_openmp_linux  # nemo_lenovo_intel_impi_openmp, kraken_intel_impi_openmp,
              # training_computer, gfortran_openmpi_openmp_linux, belenos, mac
              # pgi_openmpi_openmp_linux, 
              # pgi20.4_openmpi_openmp_linux (not work with 4.0)
              # gnu1020_openmpi_openmp_linux (not work with 4.0)
##
######################################################################
## - Verification source grid type and remapping
#
## - Source grid : bggd, ssea or icos
## bggd is an atmosphere structured (LR) grid
## ssea is an atmosphere gaussian reduced grid (D) : no 2nd order conservative remapping
## icos is an atmosphere unstructured grid (U) : no bilinear, no bicubic nor 2nd order conservative remapping
##
## - Target grid : nogt
## nogt is an ocean structured (LR) grid
##
## - Remapping : distwgt (nearest-neighbour), bili (bilinear), bicu (bicubic), conserv1st or conserv2nd (1st or 2nd order conservative remapping)
##
## Configuration files 'namcouple' are given in /data_oasis3
## Warning: If you add any extra lines in one of the namcouple given as examples you will have to
## change the definition of SRC_GRID_TYPE, SRC_GRID_PERIOD and SRC_GRID_OVERLAP in this script (see below lines 140-142)
##
## - Verification source grid type and remapping
if [ ${SRC_GRID} == "ssea" ]; then
        if [ ${remap} == "conserv2nd" ]; then
                echo "Impossible to perform conserv2nd remapping from gaussian reduced grid ssea"
                exit
        fi
fi
if [ ${SRC_GRID} == "icos" ]; then
        if [ ${remap} == "conserv2nd" ] || [ ${remap} == "bicu" ] || [ ${remap} == "bili" ]; then
                echo "Impossible to perform ${remap} remapping from unstructured grid icos"
                exit
        fi
fi
##
rundir=$srcdir/${casename}_${SRC_GRID}_${TGT_GRID}_${remap}_${nnode}_${mpiprocs}_${threads}
##
######################################################################
##
## - Name of the executables
exe1=model1
exe2=model2
##
## - Define number of processes to run each executable
(( nproc = $nnode * $mpiprocs ))
(( nproc_exe2 = $nproc / 2 ))
(( nproc_exe1 = $nproc - $nproc_exe2 ))

echo ''
echo '**************************************************************************************************************'
echo '*** '$casename' : '$run
echo ''
echo "Running test_interpolation on $nnode nodes with $mpiprocs MPI tasks per node and $threads threads per MPI task"
echo '**************************************************************************************************************'
echo 'Source grid :' $SRC_GRID
echo 'Target grid :' $TGT_GRID
echo 'Rundir       :' $rundir
echo 'Architecture :' $arch
echo 'Host         : '$host
echo 'User         : '$user
echo 'Grids        : '$SRC_GRID'-->'$TGT_GRID
echo 'Remap        : '$remap
echo ''
echo $exe1' runs on '$nproc_exe1 'processes'
echo $exe2' runs on '$nproc_exe2 'processes'
echo ''
echo ''

## - Copy everything needed into rundir
\rm -fr $rundir/*
mkdir -p $rundir

ln -sf $datadir/grids.nc  $rundir/grids.nc
ln -sf $datadir/masks.nc  $rundir/masks.nc
ln -sf $datadir/areas.nc  $rundir/areas.nc
ln -sf $srcdir/$exe1 $rundir/.
ln -sf $srcdir/$exe2 $rundir/.
cp -f $datadir/namcouple_${SRC_GRID}_${TGT_GRID}_${remap} $rundir/namcouple

## - Grid source characteristics 
# These are read in the namcouple file. If you decide to use another namcouple than the ones coming from /data_oasis3
# you may have to change the 3 lines below
SRC_GRID_TYPE=`sed -n 20p $rundir/namcouple | tr -s ' ' | cut -d" " -f2` # source grid type
SRC_GRID_PERIOD=`sed -n 17p $rundir/namcouple | tr -s ' ' | cut -d" " -f1` # "P" for periodic, "R" for non-periodic
SRC_GRID_OVERLAP=`sed -n 17p $rundir/namcouple | tr -s ' ' | cut -d" " -f2` # Number of overlapping grid points for periodic grids

echo "SRC_GRID_TYPE : $SRC_GRID_TYPE"
echo "SRC_GRID_PERIOD : $SRC_GRID_PERIOD"
echo "SRC_GRID_OVERLAP : $SRC_GRID_OVERLAP"

## - Create name_grids.dat, that will be read by the models, from namcouple informations
cat <<EOF >> $rundir/name_grids.dat
\$grid_source_characteristics
cl_grd_src='$SRC_GRID'
cl_remap='$remap'
cl_type_src='$SRC_GRID_TYPE'
cl_period_src='$SRC_GRID_PERIOD'
il_overlap_src=$SRC_GRID_OVERLAP
\$end
\$grid_target_characteristics
cl_grd_tgt='$TGT_GRID'
\$end
EOF
#
cd $rundir

######################################################################
## - Creation of configuration scripts

###---------------------------------------------------------------------
### NEMO_LENOVO_INTEL_IMPI_OPENMP
###---------------------------------------------------------------------
if [ ${arch} == nemo_lenovo_intel_impi_openmp ]; then

  cat <<EOF > $rundir/run_$casename.$arch
#!/bin/bash -l
#SBATCH --partition prod
#SBATCH --job-name ${n_p_t}
#SBATCH --time=00:02:00
#SBATCH --output=$rundir/$casename.o
#SBATCH --error=$rundir/$casename.e
# Number of nodes
#SBATCH --nodes=$nnode
# Number of MPI tasks per node
#SBATCH --ntasks-per-node=$mpiprocs
# Number of OpenMP threads per MPI task
##SBATCH --cpus-per-task=24
cd $rundir

export KMP_STACKSIZE=1GB
export I_MPI_PIN_DOMAIN=omp
#export I_MPI_PIN_DOMAIN=socket
export I_MPI_WAIT_MODE=enable
export KMP_AFFINITY=verbose,granularity=fine,compact
export OASIS_OMP_NUM_THREADS=$threads

time mpirun -np $nproc_exe1 ./$exe1 : -np $nproc_exe2 ./$exe2 
EOF

###---------------------------------------------------------------------
### KRAKEN_INTEL_IMPI_OPENMP 
###---------------------------------------------------------------------
elif [ ${arch} == kraken_intel_impi_openmp ]; then

  timreq=00:30:00

  cat <<EOF > $rundir/run_$casename.$arch
#!/bin/bash -l
#Partition
#SBATCH --partition prod
# Nom du job
#SBATCH --job-name ${n_p_t}
# Time limit for the job
#SBATCH --time=$timreq
#SBATCH --output=$rundir/$casename.o
#SBATCH --error=$rundir/$casename.e
# Number of nodes
#SBATCH --nodes=$nnode
# Number of MPI tasks per node
#SBATCH --ntasks-per-node=$mpiprocs
# Number of OpenMP threads per MPI task
#SBATCH --cpus-per-task=36

cd $rundir
module purge
module load compiler/intel/18.0.1.163
module load mpi/intelmpi/2018.1.163
module load lib/netcdf-fortran/4.4.4_impi
module load lib/netcdf-c/4.6.1_impi

export KMP_STACKSIZE=1GB
export I_MPI_PIN_DOMAIN=omp
export I_MPI_WAIT_MODE=enable
(( map = $threads - 1 ))
affin="verbose,granularity=fine,proclist=[0"
for place in \$(seq \$map); do
  affin=\${affin}",\${place}"
  echo \$place
done
echo affin1 \$affin
affin=\${affin}"],explicit"
export KMP_AFFINITY=\$affin
echo KMP_AFFINITY \$KMP_AFFINITY
export OASIS_OMP_NUM_THREADS=$threads
export OMP_NUM_THREADS=$threads

    # Binding IntelMPI
    MAP_CPU="0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35"
    INTELMPI_BINDING="-env I_MPI_PIN_PROCESSOR_LIST \${MAP_CPU}"
    I_IMPI_BINDING="-env I_MPI_PERHOST \${mpiprocs} \${INTELMPI_BINDING}"

time mpirun -np $nproc_exe1 ./$exe1 : -np $nproc_exe2 ./$exe2 
EOF

elif [ $arch == belenos ] ; then
  cat <<EOF > $rundir/run_$casename.$arch
#!/bin/bash
#SBATCH --exclusive
#SBATCH --partition=normal256
#SBATCH --job-name ${remap}_${nthreads}
#SBATCH --time=02:00:00
#SBATCH -o $rundir/$casename.o
#SBATCH -e $rundir/$casename.e
#SBATCH -N $nnode
#SBATCH --ntasks-per-node=$mpiprocs
#
ulimit -s unlimited
cd $rundir
#
module load intelmpi/2018.5.274
module load intel/2018.5.274
module load netcdf-fortran/4.5.2_V2
#
export KMP_STACKSIZE=1GB
export I_MPI_WAIT_MODE=enable
export KMP_AFFINITY=verbose,granularity=fine,compact
export OASIS_OMP_NUM_THREADS=$threads
export OMP_NUM_THREADS=$threads
#
time mpirun -np ${nproc_exe1} ./$exe1 : -np ${nproc_exe2} ./$exe2
#
EOF

fi 

######################################################################
### - Execute the model

if [ ${arch} == training_computer ]; then
    export OASIS_OMP_NUM_THREADS=$threads
    MPIRUN=/usr/local/intel/impi/2018.1.163/bin64/mpirun
    echo 'Executing the model using '$MPIRUN
    $MPIRUN -np $nproc_exe1 ./$exe1 : -np $nproc_exe2 ./$exe2 > runjob.err
elif [ ${arch} == gfortran_openmpi_openmp_linux ]; then
    export OASIS_OMP_NUM_THREADS=$threads
    MPIRUN=/usr/lib64/openmpi/bin/mpirun
    echo 'Executing the model using '$MPIRUN
    $MPIRUN -np $nproc_exe1 ./$exe1 : -np $nproc_exe2 ./$exe2 > runjob.err
elif [ $arch == pgi_openmpi_openmp_linux ]; then
    MPIRUN=/usr/local/pgi/linux86-64/18.7/mpi/openmpi-2.1.2/bin/mpirun
    echo 'Executing the model using '$MPIRUN
    $MPIRUN -np $nproc_exe1 ./$exe1 : -np $nproc_exe2 ./$exe2 > runjob.err
elif [ ${arch} == gnu1020_openmpi_openmp_linux ]; then
    export OASIS_OMP_NUM_THREADS=$threads
    MPIRUN=/usr/local/openmpi/4.1.0_gcc1020/bin/mpirun
    echo 'Executing the model using '$MPIRUN
    $MPIRUN -oversubscribe -np $nproc_exe1 ./$exe1 : -np $nproc_exe2 ./$exe2 > runjob.err
elif [ $arch == pgi20.4_openmpi_openmp_linux ]; then
    MPIRUN=/usr/local/pgi/linux86-64/20.4/mpi/openmpi-3.1.3/bin/mpirun
    echo 'Executing the model using '$MPIRUN
    $MPIRUN -oversubscribe -np $nproc_exe1 ./$exe1 : -np $nproc_exe2 ./$exe2 > runjob.err
elif [ $arch == nemo_lenovo_intel_impi_openmp ]; then
    echo 'Submitting the job to queue using sbatch'
    sbatch $rundir/run_$casename.$arch
    squeue -u $USER
elif [ $arch == kraken_intel_impi_openmp ]; then
    echo 'Submitting the job to queue using sbatch'
    sbatch $rundir/run_$casename.$arch
    squeue -u $USER
elif [ $arch == belenos ]; then
    echo 'Submitting the job to queue using sbatch'
    sbatch $rundir/run_$casename.$arch
    squeue -u $user
elif [ ${arch} == mac ]; then
    echo 'Executing the model using mpirun'
    mpirun --oversubscribe -np $nproc_exe1 ./$exe1 : -np $nproc_exe2 ./$exe2
fi

echo $casename 'is executed or submitted to queue.'
echo 'Results are found in rundir : '$rundir 

######################################################################