Port to S4

Externals.cfg

@@ -8,7 +8,7 @@ protocol = git
 required = True
 
 [gfs-utils]
-hash = 3a609ea
+hash = 7bf599f
 local_path = sorc/gfs_utils.fd
 repo_url = https://github.com/NOAA-EMC/gfs-utils
 protocol = git

README.md

@@ -7,13 +7,14 @@ The global-workflow depends on the following prerequisities to be available on t
 * workflow manager - ROCOTO (https://github.com/christopherwharrop/rocoto)
 * modules - NCEPLIBS (various), esmf v8.0.0bs48, hdf5, intel/ips v18, impi v18, wgrib2, netcdf v4.7.0, hpss, gempak (see module files under /modulefiles for additional details)
 
-The global-workflow current supports the following machines:
+The global-workflow current supports the following tier-1 machines:
 
-* WCOSS-Dell
-* WCOSS-Cray
 * Hera
 * Orion
 
+Additionally, the following tier-2 machine is supported:
+* S4 (Note that S2S+ experiments are not fully supported)
+
 Quick-start instructions are below. Full instructions are available in the [wiki](https://github.com/NOAA-EMC/global-workflow/wiki/Run-Global-Workflow)
 
 ## Build global-workflow:

env/S4.env

@@ -0,0 +1,294 @@
+#!/bin/bash -x
+
+if [ $# -ne 1 ]; then
+
+    echo "Must specify an input argument to set runtime environment variables!"
+    echo "argument can be any one of the following:"
+    echo "atmanalrun atmensanalrun"
+    echo "anal sfcanl fcst post vrfy metp"
+    echo "eobs eupd ecen efcs epos"
+    echo "postsnd awips gempak"
+    exit 1
+
+fi
+
+step=$1
+PARTITION_BATCH=${PARTITION_BATCH:-"s4"}
+
+if [[ ${PARTITION_BATCH} = "s4" ]]; then
+   export npe_node_max=32
+elif [[ ${PARTITION_BATCH} = "ivy" ]]; then
+   export npe_node_max=20
+fi
+export launcher="srun -l --export=ALL"
+
+# Configure MPI environment
+export OMP_STACKSIZE=2048000
+export NTHSTACK=1024000000
+
+ulimit -s unlimited
+ulimit -a
+
+export job=${PBS_JOBNAME:-${step}}
+export jobid=${job}.${PBS_JOBID:-$$}
+
+
+if [[ ${step} = "prep" || ${step} = "prepbufr" ]]; then
+
+    npe_node_prep=${npe_node_prep:-${npe_node_max}}
+    nth_max=$((npe_node_max / npe_node_prep))
+
+    export POE="NO"
+    export BACK="NO"
+    export sys_tp="S4"
+
+elif [[ ${step} = "waveinit" || ${step} = "waveprep" || ${step} = "wavepostsbs" || ${step} = "wavepostbndpnt" || ${step} = "wavepostbndpntbll" || ${step} = "wavepostpnt" ]]; then
+
+    export mpmd="--multi-prog"
+    export CFP_MP="YES"
+    if [[ ${step} = "waveprep" ]]; then export MP_PULSE=0 ; fi
+    export wavempexec=${launcher}
+    export wave_mpmd=${mpmd}
+
+elif [[ ${step} = "atmanalrun" ]]; then
+
+    export CFP_MP=${CFP_MP:-"YES"}
+    export USE_CFP=${USE_CFP:-"YES"}
+    export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
+
+    npe_node_atmanalrun=${npe_node_atmanalrun:-${npe_node_max}}
+    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:-0}"
+
+elif [[ ${step} = "atmensanalrun" ]]; then
+
+    export CFP_MP=${CFP_MP:-"YES"}
+    export USE_CFP=${USE_CFP:-"YES"}
+    export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
+
+    npe_node_atmensanalrun=${npe_node_atmensanalrun:-${npe_node_max}}
+    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:-0}"
+
+elif [[ ${step} = "aeroanlrun" ]]; then
+
+    export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
+
+    npe_node_aeroanlrun=${npe_node_aeroanlrun:-${npe_node_max}}
+    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:-0}"
+
+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 --multi-prog"
+
+    npe_node_anal=${npe_node_anal:-${npe_node_max}}
+    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=${launcher}
+
+    export NTHREADS_CALCINC=${nth_calcinc:-1}
+    [[ ${NTHREADS_CALCINC} -gt ${nth_max} ]] && export NTHREADS_CALCINC=${nth_max}
+    export APRUN_CALCINC=${launcher}
+
+    export NTHREADS_CYCLE=${nth_cycle:-12}
+    [[ ${NTHREADS_CYCLE} -gt ${npe_node_max} ]] && export NTHREADS_CYCLE=${npe_node_max}
+    npe_cycle=${ntiles:-6}
+    export APRUN_CYCLE="${launcher} -n ${npe_cycle:-0}"
+
+
+    export NTHREADS_GAUSFCANL=1
+    npe_gausfcanl=${npe_gausfcanl:-1}
+    export APRUN_GAUSFCANL="${launcher} -n ${npe_gausfcanl:-0}"
+
+elif [[ ${step} = "sfcanl" ]]; then
+    npe_node_sfcanl=${npe_node_sfcanl:-${npe_node_max}}
+    nth_max=$((npe_node_max / npe_node_sfcanl))
+
+    export NTHREADS_CYCLE=${nth_sfcanl:-14}
+    [[ ${NTHREADS_CYCLE} -gt ${npe_node_max} ]] && export NTHREADS_CYCLE=${npe_node_max}
+    npe_sfcanl=${ntiles:-6}
+    export APRUN_CYCLE="${launcher} -n ${npe_sfcanl:-0}"
+
+elif [[ ${step} = "gldas" ]]; then
+
+    npe_node_gldas=${npe_node_gldas:-${npe_node_max}}
+    nth_max=$((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 ${npe_gldas:-0}"
+
+    export NTHREADS_GAUSSIAN=${nth_gaussian:-1}
+    [[ ${NTHREADS_GAUSSIAN} -gt ${nth_max} ]] && export NTHREADS_GAUSSIAN=${nth_max}
+    export APRUN_GAUSSIAN="${launcher} -n ${npe_gaussian:-0}"
+
+# Must run data processing with exactly the number of tasks as time
+# periods being processed.
+
+    gldas_spinup_hours=${gldas_spinup_hours:-0}
+    npe_gldas_data_proc=$((gldas_spinup_hours + 12))
+    export APRUN_GLDAS_DATA_PROC="${launcher} -n ${npe_gldas_data_proc} --multi-prog"
+
+elif [[ ${step} = "eobs" ]]; then
+
+    export MKL_NUM_THREADS=4
+    export MKL_CBWR=AUTO
+
+    export CFP_MP=${CFP_MP:-"YES"}
+    export USE_CFP=${USE_CFP:-"YES"}
+    export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
+
+    npe_node_eobs=${npe_node_eobs:-${npe_node_max}}
+    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}
+
+elif [[ ${step} = "eupd" ]]; then
+
+    export CFP_MP=${CFP_MP:-"YES"}
+    export USE_CFP=${USE_CFP:-"YES"}
+    export APRUNCFP="${launcher} -n \$ncmd --multi-prog"
+
+    npe_node_eupd=${npe_node_eupd:-${npe_node_max}}
+    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}
+
+elif [[ ${step} = "fcst" ]]; then
+
+    #PEs and PEs/node can differ for GFS and GDAS forecasts if threading differs
+    if [[ ${CDUMP:-gdas} == "gfs" ]]; then
+        npe_fcst=${npe_fcst_gfs:-0}
+        npe_node_fcst=${npe_node_fcst_gfs:-${npe_node_max}}
+        nth_fv3=${nth_fv3_gfs:-1}
+    fi
+
+    npe_node_fcst=${npe_node_fcst:-${npe_node_max}}
+    nth_max=$((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 ${npe_fcst:-0}"
+
+    export NTHREADS_REGRID_NEMSIO=${nth_regrid_nemsio:-1}
+    [[ ${NTHREADS_REGRID_NEMSIO} -gt ${nth_max} ]] && export NTHREADS_REGRID_NEMSIO=${nth_max}
+    export APRUN_REGRID_NEMSIO=${launcher}
+
+    export NTHREADS_REMAP=${nth_remap:-2}
+    [[ ${NTHREADS_REMAP} -gt ${nth_max} ]] && export NTHREADS_REMAP=${nth_max}
+    export APRUN_REMAP=${launcher}
+    export I_MPI_DAPL_UD="enable"
+
+elif [[ ${step} = "efcs" ]]; then
+
+    npe_node_efcs=${npe_node_efcs:-${npe_node_max}}
+    nth_max=$((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 ${npe_efcs:-0}"
+
+    export NTHREADS_REGRID_NEMSIO=${nth_regrid_nemsio:-1}
+    [[ ${NTHREADS_REGRID_NEMSIO} -gt ${nth_max} ]] && export NTHREADS_REGRID_NEMSIO=${nth_max}
+    export APRUN_REGRID_NEMSIO="${launcher} ${LEVS:-128}"
+
+elif [[ ${step} = "post" ]]; then
+
+    npe_node_post=${npe_node_post:-npe_node_max}
+    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=${launcher}
+
+    export NTHREADS_DWN=${nth_dwn:-1}
+    [[ ${NTHREADS_DWN} -gt ${nth_max} ]] && export NTHREADS_DWN=${nth_max}
+    export APRUN_DWN=${launcher}
+
+elif [[ ${step} = "ecen" ]]; then
+
+    npe_node_ecen=${npe_node_ecen:-${npe_node_max}}
+    nth_max=$((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=${launcher}
+
+    export NTHREADS_CHGRES=${nth_chgres:-12}
+    [[ ${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}
+
+elif [[ ${step} = "esfc" ]]; then
+
+    npe_node_esfc=${npe_node_esfc:-${npe_node_max}}
+    nth_max=$((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 ${npe_esfc:-0}"
+
+    export NTHREADS_CYCLE=${nth_cycle:-14}
+    [[ ${NTHREADS_CYCLE} -gt ${npe_node_max} ]] && export NTHREADS_CYCLE=${npe_node_max}
+    export APRUN_CYCLE="${launcher} -n ${npe_esfc:-0}"
+
+elif [[ ${step} = "epos" ]]; then
+
+    npe_node_epos=${npe_node_epos:-${npe_node_max}}
+    nth_max=$((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}
+
+elif [[ ${step} = "init" ]]; then
+
+    export APRUN=${launcher}
+
+elif [[ ${step} = "postsnd" ]]; then
+
+    npe_node_postsnd=${npe_node_postsnd:-${npe_node_max}}
+    nth_max=$((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=${launcher}
+
+    export NTHREADS_POSTSNDCFP=${nth_postsndcfp:-1}
+    [[ ${NTHREADS_POSTSNDCFP} -gt ${nth_max} ]] && export NTHREADS_POSTSNDCFP=${nth_max}
+    export APRUN_POSTSNDCFP=${launcher}
+
+elif [[ ${step} = "awips" ]]; then
+
+     echo "WARNING: ${step} is not enabled on S4!"
+
+elif [[ ${step} = "gempak" ]]; then
+
+     echo "WARNING: ${step} is not enabled on S4!"
+fi

jobs/JGDAS_ENKF_DIAG

@@ -56,6 +56,8 @@ export pgmerr=errfile
 export CDATE=${CDATE:-${PDY}${cyc}}
 export CDUMP=${CDUMP:-${RUN:-"gdas"}}
 export COMPONENT=${COMPONENT:-atmos}
+export MAKE_NSSTBUFR=${MAKE_NSSTBUFR:-"NO"}
+export MAKE_ACFTBUFR=${MAKE_ACFTBUFR:-"NO"}
 
 
 ##############################################
@@ -104,9 +106,20 @@ export PREPQC="$COMIN_OBS/${OPREFIX}prepbufr"
 if [ ! -f $PREPQC ]; then
     echo "WARNING: Global PREPBUFR FILE $PREPQC MISSING"
 fi
-export PREPQCPF="$COMIN_OBS/${OPREFIX}prepbufr.acft_profiles"
 export TCVITL="$COMIN_ANL/${OPREFIX}syndata.tcvitals.tm00"
-[[ $DONST = "YES" ]] && export NSSTBF="$COMIN_OBS/${OPREFIX}nsstbufr"
+if [[ $DONST = "YES" ]]; then
+   if [[ $MAKE_NSSTBUFR == "YES" ]]; then
+      export NSSTBF="${COMOUT}/${OPREFIX}nsstbufr"
+   else
+      export NSSTBF="${COMIN_OBS}/${OPREFIX}nsstbufr"
+   fi
+fi
+
+if [[ $MAKE_ACFTBUFR == "YES" ]]; then
+   export PREPQCPF="${COMOUT}/${OPREFIX}prepbufr.acft_profiles"
+else
+   export PREPQCPF="${COMIN_OBS}/${OPREFIX}prepbufr.acft_profiles"
+fi
 
 # Guess Bias correction coefficients related to control
 export GBIAS=${COMIN_GES_CTL}/${GPREFIX}abias

jobs/JGDAS_ENKF_SELECT_OBS

@@ -56,6 +56,8 @@ export pgmerr=errfile
 export CDATE=${CDATE:-${PDY}${cyc}}
 export CDUMP=${CDUMP:-${RUN:-"gdas"}}
 export COMPONENT=${COMPONENT:-atmos}
+export MAKE_NSSTBUFR=${MAKE_NSSTBUFR:-"NO"}
+export MAKE_ACFTBUFR=${MAKE_ACFTBUFR:-"NO"}
 
 
 ##############################################
@@ -107,9 +109,20 @@ export PREPQC="$COMIN_OBS/${OPREFIX}prepbufr"
 if [ ! -f $PREPQC ]; then
     echo "WARNING: Global PREPBUFR FILE $PREPQC MISSING"
 fi
-export PREPQCPF="$COMIN_OBS/${OPREFIX}prepbufr.acft_profiles"
 export TCVITL="$COMIN_ANL/${OPREFIX}syndata.tcvitals.tm00"
-[[ $DONST = "YES" ]] && export NSSTBF="$COMIN_OBS/${OPREFIX}nsstbufr"
+if [[ $DONST = "YES" ]]; then
+   if [[ $MAKE_NSSTBUFR == "YES" ]]; then
+      export NSSTBF="${COMOUT}/${OPREFIX}nsstbufr"
+   else
+      export NSSTBF="${COMIN_OBS}/${OPREFIX}nsstbufr"
+   fi
+fi
+
+if [[ $MAKE_ACFTBUFR == "YES" ]]; then
+   export PREPQCPF="${COMOUT}/${OPREFIX}prepbufr.acft_profiles"
+else
+   export PREPQCPF="${COMIN_OBS}/${OPREFIX}prepbufr.acft_profiles"
+fi
 
 # Guess Bias correction coefficients related to control
 export GBIAS=${COMIN_GES_CTL}/${GPREFIX}abias