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Address shellcheck warnings in env files #1136

Merged
merged 12 commits into from
Nov 29, 2022
Merged

Address shellcheck warnings in env files #1136

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fd648d2
Remove outdated and unneeded gfs.ver from env folder
KateFriedman-NOAA Nov 16, 2022
2b140aa
Merge branch 'NOAA-EMC:develop' into feature/shellcheck
KateFriedman-NOAA Nov 17, 2022
bcfed57
Merge branch 'NOAA-EMC:develop' into feature/shellcheck
KateFriedman-NOAA Nov 17, 2022
046f4ba
Merge branch 'NOAA-EMC:develop' into feature/shellcheck
KateFriedman-NOAA Nov 18, 2022
0033786
Update env files for shellcheck SC2250
KateFriedman-NOAA Nov 18, 2022
5dc099d
Update env files for shellcheck SC2086
KateFriedman-NOAA Nov 18, 2022
9dd25de
Update env files for shellcheck SC2292
KateFriedman-NOAA Nov 18, 2022
2ae6b6b
Update env files for shellcheck SC2166 and more SC2292
KateFriedman-NOAA Nov 18, 2022
6cd424d
Update env files for shellcheck SC2004
KateFriedman-NOAA Nov 18, 2022
5ebd819
Update WCOSS2 env file for SC2034
KateFriedman-NOAA Nov 18, 2022
4a65ac4
Merge branch 'NOAA-EMC:develop' into feature/shellcheck
KateFriedman-NOAA Nov 28, 2022
213f36b
Merge branch 'NOAA-EMC:develop' into feature/shellcheck
KateFriedman-NOAA Nov 29, 2022
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246 changes: 123 additions & 123 deletions env/HERA.env
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
#! /usr/bin/env bash

if [ $# -ne 1 ]; then
if [[ $# -ne 1 ]]; then

echo "Must specify an input argument to set runtime environment variables!"
echo "argument can be any one of the following:"
Expand Down Expand Up @@ -33,260 +33,260 @@ export NTHSTACK=1024000000
ulimit -s unlimited
ulimit -a

export job=${PBS_JOBNAME:-$step}
export job=${PBS_JOBNAME:-${step}}
export jobid=${job}.${PBS_JOBID:-$$}


if [ $step = "prep" -o $step = "prepbufr" ]; then
if [[ "${step}" = "prep" ]] || [[ "${step}" = "prepbufr" ]]; then

nth_max=$(($npe_node_max / $npe_node_prep))
nth_max=$((npe_node_max / npe_node_prep))

export POE="NO"
export BACK="NO"
export sys_tp="HERA"
export launcher_PREP="srun"

elif [ $step = "waveinit" -o $step = "waveprep" -o $step = "wavepostsbs" -o $step = "wavepostbndpnt" -o $step = "wavepostbndpntbll" -o $step = "wavepostpnt" ]; then
elif [[ "${step}" = "waveinit" ]] || [[ "${step}" = "waveprep" ]] || [[ "${step}" = "wavepostsbs" ]] || [[ "${step}" = "wavepostbndpnt" ]] || [[ "${step}" = "wavepostbndpntbll" ]] || [[ "${step}" = "wavepostpnt" ]]; then

export CFP_MP="YES"
if [ $step = "waveprep" ]; then export MP_PULSE=0 ; fi
if [[ "${step}" = "waveprep" ]]; then export MP_PULSE=0 ; fi
export wavempexec=${launcher}
export wave_mpmd=${mpmd_opt}

elif [ $step = "atmanalrun" ]; then
elif [[ "${step}" = "atmanalrun" ]]; then

export CFP_MP=${CFP_MP:-"YES"}
export USE_CFP=${USE_CFP:-"YES"}
export APRUNCFP="$launcher -n \$ncmd ${mpmd_opt}"
export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

nth_max=$(($npe_node_max / $npe_node_atmanalrun))
nth_max=$((npe_node_max / npe_node_atmanalrun))

export NTHREADS_ATMANAL=${nth_atmanalrun:-$nth_max}
[[ $NTHREADS_ATMANAL -gt $nth_max ]] && export NTHREADS_ATMANAL=$nth_max
export APRUN_ATMANAL="$launcher -n $npe_atmanalrun"
export NTHREADS_ATMANAL=${nth_atmanalrun:-${nth_max}}
[[ ${NTHREADS_ATMANAL} -gt ${nth_max} ]] && export NTHREADS_ATMANAL=${nth_max}
export APRUN_ATMANAL="${launcher} -n ${npe_atmanalrun}"

elif [ $step = "atmensanalrun" ]; then
elif [[ "${step}" = "atmensanalrun" ]]; then

export CFP_MP=${CFP_MP:-"YES"}
export USE_CFP=${USE_CFP:-"YES"}
export APRUNCFP="$launcher -n \$ncmd ${mpmd_opt}"
export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

nth_max=$(($npe_node_max / $npe_node_atmensanalrun))
nth_max=$((npe_node_max / npe_node_atmensanalrun))

export NTHREADS_ATMENSANAL=${nth_atmensanalrun:-$nth_max}
[[ $NTHREADS_ATMENSANAL -gt $nth_max ]] && export NTHREADS_ATMENSANAL=$nth_max
export APRUN_ATMENSANAL="$launcher -n $npe_atmensanalrun"
export NTHREADS_ATMENSANAL=${nth_atmensanalrun:-${nth_max}}
[[ ${NTHREADS_ATMENSANAL} -gt ${nth_max} ]] && export NTHREADS_ATMENSANAL=${nth_max}
export APRUN_ATMENSANAL="${launcher} -n ${npe_atmensanalrun}"

elif [ $step = "aeroanlrun" ]; then
elif [[ "${step}" = "aeroanlrun" ]]; then

export APRUNCFP="$launcher -n \$ncmd ${mpmd_opt}"
export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

nth_max=$(($npe_node_max / $npe_node_aeroanlrun))
nth_max=$((npe_node_max / npe_node_aeroanlrun))

export NTHREADS_AEROANL=${nth_aeroanlrun:-$nth_max}
[[ $NTHREADS_AEROANL -gt $nth_max ]] && export NTHREADS_AEROANL=$nth_max
export APRUN_AEROANL="$launcher -n $npe_aeroanlrun"
export NTHREADS_AEROANL=${nth_aeroanlrun:-${nth_max}}
[[ ${NTHREADS_AEROANL} -gt ${nth_max} ]] && export NTHREADS_AEROANL=${nth_max}
export APRUN_AEROANL="${launcher} -n ${npe_aeroanlrun}"

elif [ $step = "anal" -o $step = "analcalc" ]; then
elif [[ "${step}" = "anal" ]] || [[ "${step}" = "analcalc" ]]; then

export MKL_NUM_THREADS=4
export MKL_CBWR=AUTO

export CFP_MP=${CFP_MP:-"YES"}
export USE_CFP=${USE_CFP:-"YES"}
export APRUNCFP="$launcher -n \$ncmd ${mpmd_opt}"
export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

nth_max=$(($npe_node_max / $npe_node_anal))
nth_max=$((npe_node_max / npe_node_anal))

export NTHREADS_GSI=${nth_anal:-$nth_max}
[[ $NTHREADS_GSI -gt $nth_max ]] && export NTHREADS_GSI=$nth_max
export APRUN_GSI="$launcher -n ${npe_gsi:-$npe_anal}"
export NTHREADS_GSI=${nth_anal:-${nth_max}}
[[ ${NTHREADS_GSI} -gt ${nth_max} ]] && export NTHREADS_GSI=${nth_max}
export APRUN_GSI="${launcher} -n ${npe_gsi:-${npe_anal}}"

export NTHREADS_CALCINC=${nth_calcinc:-1}
[[ $NTHREADS_CALCINC -gt $nth_max ]] && export NTHREADS_CALCINC=$nth_max
export APRUN_CALCINC="$launcher \$ncmd"
[[ ${NTHREADS_CALCINC} -gt ${nth_max} ]] && export NTHREADS_CALCINC=${nth_max}
export APRUN_CALCINC="${launcher} \$ncmd"

export NTHREADS_CYCLE=${nth_cycle:-12}
[[ $NTHREADS_CYCLE -gt $npe_node_max ]] && export NTHREADS_CYCLE=$npe_node_max
[[ ${NTHREADS_CYCLE} -gt ${npe_node_max} ]] && export NTHREADS_CYCLE=${npe_node_max}
npe_cycle=${ntiles:-6}
export APRUN_CYCLE="$launcher -n $npe_cycle"
export APRUN_CYCLE="${launcher} -n ${npe_cycle}"


export NTHREADS_GAUSFCANL=1
npe_gausfcanl=${npe_gausfcanl:-1}
export APRUN_GAUSFCANL="$launcher -n $npe_gausfcanl"
export APRUN_GAUSFCANL="${launcher} -n ${npe_gausfcanl}"

elif [ $step = "sfcanl" ]; then
nth_max=$(($npe_node_max / $npe_node_sfcanl))
elif [[ "${step}" = "sfcanl" ]]; then
nth_max=$((npe_node_max / npe_node_sfcanl))

export NTHREADS_CYCLE=${nth_sfcanl:-14}
[[ $NTHREADS_CYCLE -gt $npe_node_max ]] && export NTHREADS_CYCLE=$npe_node_max
[[ ${NTHREADS_CYCLE} -gt ${npe_node_max} ]] && export NTHREADS_CYCLE=${npe_node_max}
npe_sfcanl=${ntiles:-6}
export APRUN_CYCLE="$launcher -n $npe_sfcanl"
export APRUN_CYCLE="${launcher} -n ${npe_sfcanl}"

elif [ $step = "gldas" ]; then
elif [[ "${step}" = "gldas" ]]; then

export USE_CFP="NO"
export CFP_MP="YES"

nth_max=$(($npe_node_max / $npe_node_gldas))
nth_max=$((npe_node_max / npe_node_gldas))

export NTHREADS_GLDAS=${nth_gldas:-$nth_max}
[[ $NTHREADS_GLDAS -gt $nth_max ]] && export NTHREADS_GLDAS=$nth_max
export APRUN_GLDAS="$launcher -n $npe_gldas"
export NTHREADS_GLDAS=${nth_gldas:-${nth_max}}
[[ ${NTHREADS_GLDAS} -gt ${nth_max} ]] && export NTHREADS_GLDAS=${nth_max}
export APRUN_GLDAS="${launcher} -n ${npe_gldas}"

export NTHREADS_GAUSSIAN=${nth_gaussian:-1}
[[ $NTHREADS_GAUSSIAN -gt $nth_max ]] && export NTHREADS_GAUSSIAN=$nth_max
export APRUN_GAUSSIAN="$launcher -n $npe_gaussian"
[[ ${NTHREADS_GAUSSIAN} -gt ${nth_max} ]] && export NTHREADS_GAUSSIAN=${nth_max}
export APRUN_GAUSSIAN="${launcher} -n ${npe_gaussian}"

# Must run data processing with exactly the number of tasks as time
# periods being processed.

npe_gldas_data_proc=$(($gldas_spinup_hours + 12))
export APRUN_GLDAS_DATA_PROC="$launcher -n $npe_gldas_data_proc ${mpmd_opt}"
npe_gldas_data_proc=$((gldas_spinup_hours + 12))
export APRUN_GLDAS_DATA_PROC="${launcher} -n ${npe_gldas_data_proc} ${mpmd_opt}"

elif [ $step = "eobs" ]; then
elif [[ "${step}" = "eobs" ]]; then

export MKL_NUM_THREADS=4
export MKL_CBWR=AUTO

nth_max=$(($npe_node_max / $npe_node_eobs))
nth_max=$((npe_node_max / npe_node_eobs))

export NTHREADS_GSI=${nth_eobs:-$nth_max}
[[ $NTHREADS_GSI -gt $nth_max ]] && export NTHREADS_GSI=$nth_max
export APRUN_GSI="$launcher -n ${npe_gsi:-$npe_eobs}"
export NTHREADS_GSI=${nth_eobs:-${nth_max}}
[[ ${NTHREADS_GSI} -gt ${nth_max} ]] && export NTHREADS_GSI=${nth_max}
export APRUN_GSI="${launcher} -n ${npe_gsi:-${npe_eobs}}"

export CFP_MP=${CFP_MP:-"YES"}
export USE_CFP=${USE_CFP:-"YES"}
export APRUNCFP="$launcher -n \$ncmd ${mpmd_opt}"
export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

elif [ $step = "eupd" ]; then
elif [[ "${step}" = "eupd" ]]; then

nth_max=$(($npe_node_max / $npe_node_eupd))
nth_max=$((npe_node_max / npe_node_eupd))

export NTHREADS_ENKF=${nth_eupd:-$nth_max}
[[ $NTHREADS_ENKF -gt $nth_max ]] && export NTHREADS_ENKF=$nth_max
export APRUN_ENKF="$launcher -n ${npe_enkf:-$npe_eupd}"
export NTHREADS_ENKF=${nth_eupd:-${nth_max}}
[[ ${NTHREADS_ENKF} -gt ${nth_max} ]] && export NTHREADS_ENKF=${nth_max}
export APRUN_ENKF="${launcher} -n ${npe_enkf:-${npe_eupd}}"

export CFP_MP=${CFP_MP:-"YES"}
export USE_CFP=${USE_CFP:-"YES"}
export APRUNCFP="$launcher -n \$ncmd ${mpmd_opt}"
export APRUNCFP="${launcher} -n \$ncmd ${mpmd_opt}"

elif [ $step = "fcst" ]; then
elif [[ "${step}" = "fcst" ]]; then

#PEs and PEs/node can differ for GFS and GDAS forecasts if threading differs
if [[ $CDUMP == "gfs" ]]; then
npe_fcst=$npe_fcst_gfs
npe_node_fcst=$npe_node_fcst_gfs
nth_fv3=$nth_fv3_gfs
if [[ ${CDUMP} == "gfs" ]]; then
npe_fcst=${npe_fcst_gfs}
npe_node_fcst=${npe_node_fcst_gfs}
nth_fv3=${nth_fv3_gfs}
fi

nth_max=$(($npe_node_max / $npe_node_fcst))
nth_max=$((npe_node_max / npe_node_fcst))

export NTHREADS_FV3=${nth_fv3:-$nth_max}
[[ $NTHREADS_FV3 -gt $nth_max ]] && export NTHREADS_FV3=$nth_max
export cores_per_node=$npe_node_max
export APRUN_FV3="$launcher -n $npe_fcst"
export NTHREADS_FV3=${nth_fv3:-${nth_max}}
[[ ${NTHREADS_FV3} -gt ${nth_max} ]] && export NTHREADS_FV3=${nth_max}
export cores_per_node=${npe_node_max}
export APRUN_FV3="${launcher} -n ${npe_fcst}"

export NTHREADS_REGRID_NEMSIO=${nth_regrid_nemsio:-1}
[[ $NTHREADS_REGRID_NEMSIO -gt $nth_max ]] && export NTHREADS_REGRID_NEMSIO=$nth_max
export APRUN_REGRID_NEMSIO="$launcher -n ${LEVS}"
[[ ${NTHREADS_REGRID_NEMSIO} -gt ${nth_max} ]] && export NTHREADS_REGRID_NEMSIO=${nth_max}
export APRUN_REGRID_NEMSIO="${launcher} -n ${LEVS}"

export NTHREADS_REMAP=${nth_remap:-2}
[[ $NTHREADS_REMAP -gt $nth_max ]] && export NTHREADS_REMAP=$nth_max
export APRUN_REMAP="$launcher -n ${npe_remap:-$npe_fcst}"
[[ ${NTHREADS_REMAP} -gt ${nth_max} ]] && export NTHREADS_REMAP=${nth_max}
export APRUN_REMAP="${launcher} -n ${npe_remap:-${npe_fcst}}"
export I_MPI_DAPL_UD="enable"

elif [ $step = "efcs" ]; then
elif [[ "${step}" = "efcs" ]]; then

nth_max=$(($npe_node_max / $npe_node_efcs))
nth_max=$((npe_node_max / npe_node_efcs))

export NTHREADS_FV3=${nth_efcs:-$nth_max}
[[ $NTHREADS_FV3 -gt $nth_max ]] && export NTHREADS_FV3=$nth_max
export cores_per_node=$npe_node_max
export APRUN_FV3="$launcher -n $npe_efcs"
export NTHREADS_FV3=${nth_efcs:-${nth_max}}
[[ ${NTHREADS_FV3} -gt ${nth_max} ]] && export NTHREADS_FV3=${nth_max}
export cores_per_node=${npe_node_max}
export APRUN_FV3="${launcher} -n ${npe_efcs}"

export NTHREADS_REGRID_NEMSIO=${nth_regrid_nemsio:-1}
[[ $NTHREADS_REGRID_NEMSIO -gt $nth_max ]] && export NTHREADS_REGRID_NEMSIO=$nth_max
export APRUN_REGRID_NEMSIO="$launcher -n ${LEVS}"
[[ ${NTHREADS_REGRID_NEMSIO} -gt ${nth_max} ]] && export NTHREADS_REGRID_NEMSIO=${nth_max}
export APRUN_REGRID_NEMSIO="${launcher} -n ${LEVS}"

elif [ $step = "post" ]; then
elif [[ "${step}" = "post" ]]; then

nth_max=$(($npe_node_max / $npe_node_post))
nth_max=$((npe_node_max / npe_node_post))

export NTHREADS_NP=${nth_np:-1}
[[ $NTHREADS_NP -gt $nth_max ]] && export NTHREADS_NP=$nth_max
export APRUN_NP="$launcher -n ${npe_post}"
[[ ${NTHREADS_NP} -gt ${nth_max} ]] && export NTHREADS_NP=${nth_max}
export APRUN_NP="${launcher} -n ${npe_post}"

export NTHREADS_DWN=${nth_dwn:-1}
[[ $NTHREADS_DWN -gt $nth_max ]] && export NTHREADS_DWN=$nth_max
export APRUN_DWN="$launcher -n ${npe_dwn}"
[[ ${NTHREADS_DWN} -gt ${nth_max} ]] && export NTHREADS_DWN=${nth_max}
export APRUN_DWN="${launcher} -n ${npe_dwn}"

elif [ $step = "ecen" ]; then
elif [[ "${step}" = "ecen" ]]; then

nth_max=$(($npe_node_max / $npe_node_ecen))
nth_max=$((npe_node_max / npe_node_ecen))

export NTHREADS_ECEN=${nth_ecen:-$nth_max}
[[ $NTHREADS_ECEN -gt $nth_max ]] && export NTHREADS_ECEN=$nth_max
export APRUN_ECEN="$launcher -n ${npe_ecen}"
export NTHREADS_ECEN=${nth_ecen:-${nth_max}}
[[ ${NTHREADS_ECEN} -gt ${nth_max} ]] && export NTHREADS_ECEN=${nth_max}
export APRUN_ECEN="${launcher} -n ${npe_ecen}"

export NTHREADS_CHGRES=${nth_chgres:-12}
[[ $NTHREADS_CHGRES -gt $npe_node_max ]] && export NTHREADS_CHGRES=$npe_node_max
[[ ${NTHREADS_CHGRES} -gt ${npe_node_max} ]] && export NTHREADS_CHGRES=${npe_node_max}
export APRUN_CHGRES="time"

export NTHREADS_CALCINC=${nth_calcinc:-1}
[[ $NTHREADS_CALCINC -gt $nth_max ]] && export NTHREADS_CALCINC=$nth_max
export APRUN_CALCINC="$launcher -n ${npe_ecen}"
[[ ${NTHREADS_CALCINC} -gt ${nth_max} ]] && export NTHREADS_CALCINC=${nth_max}
export APRUN_CALCINC="${launcher} -n ${npe_ecen}"

elif [ $step = "esfc" ]; then
elif [[ "${step}" = "esfc" ]]; then

nth_max=$(($npe_node_max / $npe_node_esfc))
nth_max=$((npe_node_max / npe_node_esfc))

export NTHREADS_ESFC=${nth_esfc:-$nth_max}
[[ $NTHREADS_ESFC -gt $nth_max ]] && export NTHREADS_ESFC=$nth_max
export APRUN_ESFC="$launcher -n $npe_esfc"
export NTHREADS_ESFC=${nth_esfc:-${nth_max}}
[[ ${NTHREADS_ESFC} -gt ${nth_max} ]] && export NTHREADS_ESFC=${nth_max}
export APRUN_ESFC="${launcher} -n ${npe_esfc}"

export NTHREADS_CYCLE=${nth_cycle:-14}
[[ $NTHREADS_CYCLE -gt $npe_node_max ]] && export NTHREADS_CYCLE=$npe_node_max
export APRUN_CYCLE="$launcher -n $npe_esfc"
[[ ${NTHREADS_CYCLE} -gt ${npe_node_max} ]] && export NTHREADS_CYCLE=${npe_node_max}
export APRUN_CYCLE="${launcher} -n ${npe_esfc}"

elif [ $step = "epos" ]; then
elif [[ "${step}" = "epos" ]]; then

nth_max=$(($npe_node_max / $npe_node_epos))
nth_max=$((npe_node_max / npe_node_epos))

export NTHREADS_EPOS=${nth_epos:-$nth_max}
[[ $NTHREADS_EPOS -gt $nth_max ]] && export NTHREADS_EPOS=$nth_max
export APRUN_EPOS="$launcher -n $npe_epos"
export NTHREADS_EPOS=${nth_epos:-${nth_max}}
[[ ${NTHREADS_EPOS} -gt ${nth_max} ]] && export NTHREADS_EPOS=${nth_max}
export APRUN_EPOS="${launcher} -n ${npe_epos}"

elif [ $step = "init" ]; then
elif [[ "${step}" = "init" ]]; then

export APRUN="$launcher -n ${npe_init}"
export APRUN="${launcher} -n ${npe_init}"

elif [ $step = "postsnd" ]; then
elif [[ "${step}" = "postsnd" ]]; then

nth_max=$(($npe_node_max / $npe_node_postsnd))
nth_max=$((npe_node_max / npe_node_postsnd))

export NTHREADS_POSTSND=${nth_postsnd:-1}
[[ $NTHREADS_POSTSND -gt $nth_max ]] && export NTHREADS_POSTSND=$nth_max
export APRUN_POSTSND="$launcher -n ${npe_postsnd}"
[[ ${NTHREADS_POSTSND} -gt ${nth_max} ]] && export NTHREADS_POSTSND=${nth_max}
export APRUN_POSTSND="${launcher} -n ${npe_postsnd}"

export NTHREADS_POSTSNDCFP=${nth_postsndcfp:-1}
[[ $NTHREADS_POSTSNDCFP -gt $nth_max ]] && export NTHREADS_POSTSNDCFP=$nth_max
export APRUN_POSTSNDCFP="$launcher -n ${npe_postsnd} ${mpmd_opt}"
[[ ${NTHREADS_POSTSNDCFP} -gt ${nth_max} ]] && export NTHREADS_POSTSNDCFP=${nth_max}
export APRUN_POSTSNDCFP="${launcher} -n ${npe_postsnd} ${mpmd_opt}"

elif [ $step = "awips" ]; then
elif [[ "${step}" = "awips" ]]; then

nth_max=$(($npe_node_max / $npe_node_awips))
nth_max=$((npe_node_max / npe_node_awips))

export NTHREADS_AWIPS=${nth_awips:-2}
[[ $NTHREADS_AWIPS -gt $nth_max ]] && export NTHREADS_AWIPS=$nth_max
export APRUN_AWIPSCFP="$launcher -n $npe_awips ${mpmd_opt}"
[[ ${NTHREADS_AWIPS} -gt ${nth_max} ]] && export NTHREADS_AWIPS=${nth_max}
export APRUN_AWIPSCFP="${launcher} -n ${npe_awips} ${mpmd_opt}"

elif [ $step = "gempak" ]; then
elif [[ "${step}" = "gempak" ]]; then

nth_max=$(($npe_node_max / $npe_node_gempak))
nth_max=$((npe_node_max / npe_node_gempak))

export NTHREADS_GEMPAK=${nth_gempak:-1}
[[ $NTHREADS_GEMPAK -gt ${nth_max} ]] && export NTHREADS_GEMPAK=${nth_max}
[[ ${NTHREADS_GEMPAK} -gt ${nth_max} ]] && export NTHREADS_GEMPAK=${nth_max}
export APRUN="${launcher} -n ${npe_gempak} ${mpmd_opt}"
fi
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