ecearth3/runtime/classic/platform/csc-puhti-intel-intelmpi.cfg.tmpl

# Platform dependent configuration functions for the 'rhino' machine
# (KNMI, NL)

function configure()
{
    # This function should configure all settings/modules needed to 
    # later prepare the EC-Earth run directory and set variables used 
    # in the run script

    module purge 
    module load intel/18.0.5
    module load intel-mpi/18.0.5
    module load intel-mkl/2018.0.5
    module load hdf/4.2.13
    module load hdf5/1.10.4-mpi
    module load netcdf/4.7.0
    module load netcdf-fortran/4.4.4
    module load grib-api/1.24.0
    module load cdo
    # Configure paths for building/running EC-Earth
    export ecearth_src_dir=[[[PLT:ACTIVE:ECEARTH_SRC_DIR]]]
    export run_dir=[[[PLT:ACTIVE:RUN_DIR]]]
    export ini_data_dir=[[[PLT:ACTIVE:INI_DATA_DIR]]]

    # File for standard output.
    # NOTE: This will be modified for restart jobs!
    stdout_file=${start_dir}/out/$(basename ${SLURM_JOB_NAME}).out

    # Resubmit this job for automatic restarts? [true/false]
    # Also, add options for the resubmit command here.
    resubmit_job=[[[PLT:ACTIVE:RESUBMIT_JOB]]]
    resubmit_opt="[[[PLT:ACTIVE:RESUBMIT_OPT]]]"

    # Configure grib api paths
    export GRIB_DEFINITION_PATH=[[[PLT:ACTIVE:ECEARTH_SRC_DIR]]]/util/grib_table_126:[[[PLT:ACTIVE:GRIBAPI_BASE_DIR]]]/[[[PLT:ACTIVE:GRIBAPI_DEFINITION_SUBDIR]]]
    export GRIB_SAMPLES_PATH=[[[PLT:ACTIVE:GRIBAPI_BASE_DIR]]]/[[[PLT:ACTIVE:GRIBAPI_SAMPLES_SUBDIR]]]
    export GRIB_BIN_PATH=[[[PLT:ACTIVE:GRIBAPI_BASE_DIR]]]/[[[PLT:ACTIVE:GRIBAPI_BIN_SUBDIR]]]

    # Configure GRIBEX paths
    export LOCAL_DEFINITION_TEMPLATES=[[[PLT:ACTIVE:GRIBEX_DEFINITION_PATH]]]
    #export ECMWF_LOCAL_TABLE_PATH=[[[PLT:ACTIVE:GRIBEX_DEFINITION_PATH]]]

    # Configure number of processors per node
    proc_per_node=[[[PLT:ACTIVE:PROC_PER_NODE]]]

    # Configure and load modules
    pre_load_modules_cmd="[[[PLT:ACTIVE:PRE_LOAD_MODULES_CMD]]]"
    module_list="[[[PLT:ACTIVE:MODULE_LIST]]]"

    if [ -n "${module_list}" ]
    then
        set +u
        if [ -n "${pre_load_modules_cmd}" ]
        then
            ${pre_load_modules_cmd}
        fi
        for m in "${module_list}"
        do
            eval $(/usr/bin/modulecmd sh add $m)
        done
        set -u
    fi

    # Add directories to the shared library search path
    if [ -n "[[[PLT:ACTIVE:ADD_TO_LD_LIBRARY_PATH]]]" ]
    then
        export LD_LIBRARY_PATH=${LD_LIBRARY_PATH:+${LD_LIBRARY_PATH}:}"[[[PLT:ACTIVE:ADD_TO_LD_LIBRARY_PATH]]]"
    fi
    echo $LD_LIBRARY_PATH
    ulimit -s unlimited
    ulimit -n 2048
    ulimit -c unlimited
    #ulimit -a
}

function launch_atos()
{
    # version using srun
    # banner launch
    cmd="srun --kill-on-bad-exit=1"

    export I_MPI_PMI_LIBRARY=/usr/lib64/libpmi.so
    export I_MPI_FAST_COLLECTIVES=1
    export I_MPI_EXTRA_FILESYSTEM=on
    export I_MPI_EXTRA_FILESYSTEM_LIST=lustre
    export OMP_PROC_BIND=true
    export KMP_AFFINITY=verbose,compact,granularity=fine
    export KMP_AFFINITY=compact,granularity=fine
    export PMI_TIME=10
    export MKL_NUM_THREADS=1
    export OMP_STACKSIZE=256m
    export MXM_LOG_LEVEL=ERROR
    export OMPI_MCA_hwloc_base_binding_policy=none
    CONF_FILE=$1
    NODESET=$2
    NBTASKS=$3
    BINDING=$4
    export OMP_NUM_THREADS=$5
    export TIME="launch timing : %e elapsed %U user %S system"
    NBNODES=`nodeset -c $NODESET`
    ls /usr/bin
    #/usr/bin/time 
    $cmd --nodes=$NBNODES --nodelist=$NODESET --ntasks=$NBTASKS --distribution=block --cpu_bind=$BINDING -l --multi-prog $CONF_FILE
}

function launch()
{
    # version using srun
    echo $#
    #cmd="srun "
    _task1=-1
    NBTASKS=0    
    rm -rf conf.txt
    while (( "$#" ))
    do
        nranks=$1
        executable=./$(basename $2)
        shift
        shift

        _task0=$((_task1+1))
        _task1=$((_task0+nranks-1))

        cmd="${_task0}-${_task1} ${executable}"

        NBTASKS=$((NBTASKS+nranks))
        
        while (( "$#" )) && [ "$1" != "--" ]
        do
            cmd+=" $1"
            shift
        done
        echo ${cmd} >>conf.txt
        shift || true
    done
    export CONF_FILE=conf.txt
    #cat $CONF_FILE
    export OMP_NUM_THREADS=1
    

    srun  --multi-prog $CONF_FILE
    
}


function finalise()
{
    # This function should execute of any post run functionality, e.g. 
    # platform dependent cleaning or a resubmit

    if ${resubmit_job} && [ $(date -d "${leg_end_date}" +%s) -lt $(date -d "${run_end_date}" +%s) ]
    then
        info "Resubmitting job for leg $((leg_number+1))"
	cd ${start_dir} 
	sbatch ${SLURM_JOB_NAME}        
        # # Need to go to start_dir to find the run script
        # cd ${start_dir}
        # # Submit command
        # # Note: This does not work if you specify a job name with sbatch -J jobname!
        # sbatch -N ${SLURM_JOB_NUM_NODES}                                                 \
        #        -n $((ifs_numproc + nem_numproc + tm5_numproc))                           \
        #        --exclusive                                                               \
        #        --ntasks-per-node=${proc_per_node}                                        \
        #        -o ${run_dir}/$(basename ${stdout_file}).$(printf %03d $((leg_number+1))) \
        #        -e ${run_dir}/$(basename ${stdout_file}).$(printf %03d $((leg_number+1))) \
        #        -d ${SLURM_JOB_ID}                                                        \
        #        ${resubmit_opt}                                                           \
        #        ./${SLURM_JOB_NAME}
    fi

}

function postprocess()
{
    # This function submits a script to postprocess the IFS output
    data_dir=`pwd`/$1
    script_file="$1/postprocess"
    cat >"${script_file}" <<EOF
#! /bin/bash
cd "${start_dir}/../../../postprocessing"
./postprocess_leg "${data_dir}" "${data_dir}/postprocessed"
EOF
    sbatch -N 1 --exclusive \
               -o ${data_dir}/$(basename ${stdout_file}).$(printf %03d $((leg_number+1))) \
               -e ${data_dir}/$(basename ${stdout_file}).$(printf %03d $((leg_number+1))) \
               "${script_file}"
}