Add placeholders for ecflow suite and job cards

build.sh

@@ -65,6 +65,7 @@ done
 case ${BUILD_TARGET} in
   ursa | hera | orion | hercules | wcoss2 | noaacloud | gaeac5 | gaeac6 )
     echo "Building obsForge on $BUILD_TARGET"
+    [[ -f $dir_root/versions/build.${BUILD_TARGET}.ver ]] && source $dir_root/versions/build.${BUILD_TARGET}.ver
     source $dir_root/ush/module-setup.sh
     module use $dir_root/modulefiles
     module load obsforge/$BUILD_TARGET.$COMPILER
@@ -81,11 +82,27 @@ esac
 
 CMAKE_OPTS+=" -DMACHINE=$BUILD_TARGET"
 
+# Default to skipping test-data downloads unless explicitly overridden.
+if [[ " ${CMAKE_OPTS} " != *" -DSKIP_DOWNLOAD_TEST_DATA="* ]]; then
+  CMAKE_OPTS+=" -DSKIP_DOWNLOAD_TEST_DATA=ON"
+fi
+
+# Default to disabling tests (including ioda tests) on wcoss2 unless explicitly overridden.
+if [[ $BUILD_TARGET == 'wcoss2' ]] && [[ " ${CMAKE_OPTS} " != *" -DBUILD_TESTING="* ]]; then
+  CMAKE_OPTS+=" -DBUILD_TESTING=OFF"
+fi
+
+# Default to C++17 (required by ioda code using std::exclusive_scan) unless overridden.
+if [[ " ${CMAKE_OPTS} " != *" -DCMAKE_CXX_STANDARD="* ]]; then
+  CMAKE_OPTS+=" -DCMAKE_CXX_STANDARD=17"
+fi
+
 # TODO: Remove LD_LIBRARY_PATH line as soon as permanent solution is available
 if [[ $BUILD_TARGET == 'wcoss2' ]]; then
-  export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/opt/cray/pe/mpich/8.1.29/ofi/intel/2022.1/lib"
+  mpich_ver_for_env="${cray_mpich_ver:-8.1.19}"
+  export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:/opt/cray/pe/mpich/${mpich_ver_for_env}/ofi/intel/2022.1/lib"
   export LMOD_MPI_NAME=cray-mpich
-  export LMOD_MPI_VERSION=8.1.29-xhbciau
+  export LMOD_MPI_VERSION="${mpich_ver_for_env}"
 fi
 
 BUILD_DIR=${BUILD_DIR:-$dir_root/build}

dev/jobs/JOBSFORGE_GLOBAL_MARINE_DUMP

@@ -6,6 +6,8 @@ source "${HOMEobsforge}/ush/jjob_header.sh"
 ##############################################
 # Set variables used in the script
 ##############################################
+PYTHONPATH="${HOMEobsforge}/ush/python${PYTHONPATH:+:${PYTHONPATH}}"
+export PYTHONPATH
 
 
 ##############################################

ecf/defs/obsforge_v1.def

@@ -0,0 +1,124 @@
+suite obsforge_v1
+  family primary
+    edit PACKAGEHOME '/lfs/h2/emc/da/noscrub/cory.r.martin/obsforge/git/release/obsforge.v1.0.0'
+    edit OUTPUTDIR '/lfs/h2/emc/ptmp/cory.r.martin/obsforge/output'
+    edit obsforge_ver 'v1.0.0'
+    edit QUEUE 'dev'
+    edit QUEUE_ARCH 'dev_transfer'
+    edit PROJENVIR 'DEV'
+    edit MACHINE_SITE 'development'
+    edit ENVIR 'para'
+    edit EXPDIR '%PACKAGEHOME%/parm/config/obsforge'
+    edit DATAROOT '/lfs/h2/emc/ptmp/cory.r.martin/obsforge/dataroot'
+    edit DBNLOGDIR '/lfs/h2/emc/ptmp/cory.r.martin/obsforge/com/dbnlog'
+    edit ECF_INCLUDE '/lfs/h2/emc/da/noscrub/cory.r.martin/obsforge/git/release/obsforge.v1.0.0/ecf/include'
+    family 00
+      edit CYC '00'
+      family obsforge
+        family gfs
+          edit ECF_FILES '%PACKAGEHOME%/ecf/gfs'
+          edit JTYP 'gfs'
+          family marine
+            task jobsforge_gfs_marine_dump
+              trigger :TIME >= 0237 and :TIME <= 0837
+            task jobsforge_gfs_marine_bufr_dump
+              trigger :TIME >= 0256 and :TIME <= 0837
+              # trigger: /prod/primary/00/obsproc/v1.2/gfs/atmos/prep/jobsproc_gfs_atmos_dump == complete
+          endfamily # marine
+        endfamily # gfs
+        family gdas
+          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts/gdas'
+          edit JTYP 'gdas'
+          family marine
+            task jobsforge_gdas_marine_dump
+              trigger :TIME >= 0540 and :TIME <= 1140
+            task jobsforge_gdas_marine_bufr_dump
+              trigger :TIME >= 0559 and :TIME <= 1140
+              # trigger: /prod/primary/00/obsproc/v1.2/gdas/atmos/prep/jobsproc_gdas_atmos_dump == complete
+          endfamily # marine
+        endfamily # gdas
+      endfamily # obsforge
+    endfamily # 00
+    family 06
+      edit CYC '06'
+      family obsforge
+        family gfs
+          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts/gfs'
+          edit JTYP 'gfs'
+          family marine
+            task jobsforge_gfs_marine_dump
+              trigger :TIME >= 0837 and :TIME <= 1437
+            task jobsforge_gfs_marine_bufr_dump
+              trigger :TIME >= 0856 and :TIME <= 1437
+              # trigger: /prod/primary/06/obsproc/v1.2/gfs/atmos/prep/jobsproc_gfs_atmos_dump == complete
+          endfamily # marine
+        endfamily # gfs
+        family gdas
+          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts/gdas'
+          edit JTYP 'gdas'
+          family marine
+            task jobsforge_gdas_marine_dump
+              trigger :TIME >= 1140 and :TIME <= 1740
+            task jobsforge_gdas_marine_bufr_dump
+              trigger :TIME >= 1159 and :TIME <= 1740
+              # trigger: /prod/primary/06/obsproc/v1.2/gdas/atmos/prep/jobsproc_gdas_atmos_dump == complete
+          endfamily # marine
+        endfamily # gdas
+      endfamily # obsforge
+    endfamily # 06
+    family 12
+      edit CYC '12'
+      family obsforge
+        family gfs
+          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts/gfs'
+          edit JTYP 'gfs'
+          family marine
+            task jobsforge_gfs_marine_dump
+              trigger :TIME >= 1437 and :TIME <= 2037
+            task jobsforge_gfs_marine_bufr_dump
+              trigger :TIME >= 1456 and :TIME <= 2037
+              # trigger: /prod/primary/12/obsproc/v1.2/gfs/atmos/prep/jobsproc_gfs_atmos_dump == complete
+          endfamily # marine
+        endfamily # gfs
+        family gdas
+          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts/gdas'
+          edit JTYP 'gdas'
+          family marine
+            task jobsforge_gdas_marine_dump
+              trigger :TIME >= 1740 and :TIME <= 2340
+            task jobsforge_gdas_marine_bufr_dump
+              trigger :TIME >= 1759 and :TIME <= 2340
+              # trigger: /prod/primary/12/obsproc/v1.2/gdas/atmos/prep/jobsproc_gdas_atmos_dump == complete
+          endfamily # marine
+        endfamily # gdas
+      endfamily # obsforge
+    endfamily # 12
+    family 18
+      edit CYC '18'
+      family obsforge
+        family gfs
+          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts/gfs'
+          edit JTYP 'gfs'
+          family marine
+            task jobsforge_gfs_marine_dump
+              trigger :TIME >= 2037 and :TIME <= 0237
+            task jobsforge_gfs_marine_bufr_dump
+              trigger :TIME >= 2056 and :TIME <= 0237
+              # trigger: /prod/primary/18/obsproc/v1.2/gfs/atmos/prep/jobsproc_gfs_atmos_dump == complete
+          endfamily # marine
+        endfamily # gfs
+        family gdas
+          edit ECF_FILES '%PACKAGEHOME%/ecf/scripts/gdas'
+          edit JTYP 'gdas'
+          family marine
+            task jobsforge_gdas_marine_dump
+              trigger :TIME >= 2340 and :TIME <= 0540
+            task jobsforge_gdas_marine_bufr_dump
+              trigger :TIME >= 2359 and :TIME <= 0540
+              # trigger: /prod/primary/18/obsproc/v1.2/gdas/atmos/prep/jobsproc_gdas_atmos_dump == complete
+          endfamily # marine
+        endfamily # gdas
+      endfamily # obsforge
+    endfamily # 18
+  endfamily # primary
+endsuite

ecf/include/envir-p1.h

@@ -0,0 +1,17 @@
+# envir-p1.h
+export job=${job:-$PBS_JOBNAME}
+export jobid=${jobid:-$job.$PBS_JOBID}
+
+if [[ "$envir" == prod && "$SENDDBN" == YES ]]; then
+    export eval=%EVAL:NO%
+    if [ $eval == YES ]; then export SIPHONROOT=${UTILROOT}/para_dbn
+    else export SIPHONROOT=/lfs/h1/ops/prod/dbnet_siphon
+    fi
+    if [ "$PARATEST" == YES ]; then export SIPHONROOT=${UTILROOT}/fakedbn; export NODBNFCHK=YES; fi
+else
+    export SIPHONROOT=${UTILROOT}/fakedbn
+fi
+
+export DBNROOT=$SIPHONROOT
+
+if [[ ! " prod para test " =~ " ${envir} " && " ops.prod ops.para " =~ " $(whoami) " ]]; then err_exit "ENVIR must be prod, para, or test [envir-p1.h]"; fi

ecf/include/head.h

@@ -0,0 +1,99 @@
+date
+hostname
+set -xe  # print commands as they are executed and enable signal trapping
+
+export PS4='+ $SECONDS + '
+
+# Variables needed for communication with ecFlow
+export ECF_NAME=%ECF_NAME%
+export ECF_HOST=%ECF_LOGHOST%
+export ECF_PORT=%ECF_PORT%
+export ECF_PASS=%ECF_PASS%
+export ECF_TRYNO=%ECF_TRYNO%
+export ECF_RID=${ECF_RID:-${PBS_JOBID:-$(hostname -s).$$}}
+export ECF_JOB=%ECF_JOB%
+export ECF_JOBOUT=%ECF_JOBOUT%
+export ecflow_ver=%ecflow_ver%
+
+if [ -d /apps/ops/prod ]; then # On WCOSS2
+  set +x
+  echo "Running 'module reset'"
+  module reset
+  set -x
+fi
+
+modelhome=%PACKAGEHOME:%
+eval "export HOME${model:?'model undefined'}=$modelhome"
+eval "versionfile=\$HOME${model}/versions/run.ver"
+if [ -f "$versionfile" ]; then . $versionfile ; fi
+modelver=$(echo ${modelhome} | perl -pe "s:.*?/${model}\.(v[\d\.a-z]+).*:\1:")
+eval "export ${model}_ver=$modelver"
+
+export envir=%ENVIR%
+export MACHINE_SITE=%MACHINE_SITE%
+export RUN_ENVIR=${RUN_ENVIR:-nco}
+export SENDECF=${SENDECF:-YES}
+export SENDCOM=${SENDCOM:-YES}
+if [ -n "%PDY:%" ]; then export PDY=${PDY:-%PDY:%}; fi
+if [ -n "%PARATEST:%" ]; then export PARATEST=${PARATEST:-%PARATEST:%}; fi
+if [ -n "%COMPATH:%" ]; then export COMPATH=${COMPATH:-%COMPATH:%}; fi
+if [ -n "%MAILTO:%" ]; then export MAILTO=${MAILTO:-%MAILTO:%}; fi
+if [ -n "%DBNLOGDIR:%" ]; then export DBNLOG=YES; fi
+export KEEPDATA=${KEEPDATA:-%KEEPDATA:NO%}
+export SENDDBN=${SENDDBN:-%SENDDBN:YES%}
+export SENDDBN_NTC=${SENDDBN_NTC:-%SENDDBN_NTC:YES%}
+
+if [ -d /apps/ops/prod ]; then # On WCOSS2
+  set +x
+  if [ $(whoami) == ops.para ]; then
+    module use -a /apps/ops/para/nco/modulefiles/core
+  fi
+  echo "Running module load ecflow/$ecflow_ver"
+  module load ecflow/$ecflow_ver
+  echo "ecflow module location: $(module display ecflow |& head -2 | tail -1 | sed 's/:$//')"
+  set -x
+  . ${ECF_ROOT}/versions/run.ver
+  set +x
+  module load prod_util/${prod_util_ver}
+  module load prod_envir/${prod_envir_ver}
+  echo "Listing modules from head.h:"
+  module list
+  set -x
+  if [[ ! " ops.prod ops.para " =~ " $(whoami) " ]]; then
+    echo "Allow over-riding defaults for developers"
+    if [ -n "%COMROOT:%" ]; then export COMROOT="%COMROOT:%"; fi
+    if [ -n "%DATAROOT:%" ]; then export DATAROOT="%DATAROOT:%"; fi
+    if [ -n "%DCOMROOT:%" ]; then export DCOMROOT="%DCOMROOT:%"; fi
+  fi
+fi
+
+timeout 300 ecflow_client --init=${ECF_RID}
+
+if [[ " ops.prod ops.para " =~ " $(whoami) " ]]; then
+  POST_OUT=${POST_OUT:-/lfs/h1/ops/%ENVIR%/tmp/posts/ecflow_post_in.${ECF_RID}}
+  echo 'export ECF_NAME=${ECF_NAME}' > $POST_OUT
+  echo 'export ECF_HOST=${ECF_HOST}' >> $POST_OUT
+  echo 'export ECF_PORT=${ECF_PORT}' >> $POST_OUT
+  echo 'export ECF_PASS=${ECF_PASS}' >> $POST_OUT
+  echo 'export ECF_TRYNO=${ECF_TRYNO}' >> $POST_OUT
+  echo 'export ECF_RID=${ECF_RID}' >> $POST_OUT
+fi
+
+# Define error handler
+ERROR() {
+  set +ex
+  if [ "$1" -eq 0 ]; then
+     msg="Killed by signal (likely via qdel)"
+  else
+     msg="Killed by signal $1"
+  fi
+  ecflow_client --abort="$msg"
+  echo $msg
+  if [[ " ops.prod ops.para " =~ " $(whoami) " ]]; then
+    echo "# Trap Caught" >>$POST_OUT
+  fi
+  trap $1; exit $1
+}
+# Trap all error and exit signals
+trap 'ERROR $?' ERR EXIT
+

ecf/include/tail.h

@@ -0,0 +1,3 @@
+timeout 300 ecflow_client --complete  # Notify ecFlow of a normal end
+trap 0                    # Remove all traps
+exit 0                    # End the shell

ecf/scripts/gdas/jobsforge_gdas_marine_bufr_dump.ecf

@@ -0,0 +1,61 @@
+#PBS -S /bin/bash
+#PBS -N jobsforge_gfs_marine_bufr_dump_%CYC%
+#PBS -j oe
+#PBS -q %QUEUE%
+#PBS -A GFS-DEV 
+#PBS -l walltime=00:10:00
+#PBS -l select=1:mpiprocs=1:ompthreads=1:ncpus=1
+#PBS -l place=vscatter:exclhost
+#PBS -l debug=true
+
+model=obsforge
+%include <head.h>
+%include <envir-p1.h>
+
+set -x
+
+export RUN=%JTYP%
+
+############################################################
+# Load modules
+############################################################
+module load prod_util/${prod_util_ver}
+module load intel/${intel_ver}
+module load craype/${craype_ver}
+module load cray-mpich/${cray_mpich_ver}
+module load cray-pals/${cray_pals_ver}
+
+module load hdf5-D/${hdf5D_ver}
+module load pnetcdf/${pnetcdfD_ver}
+module load netcdf-D/${netcdfD_ver}
+module load boost/${boost_ver}
+module load eigen/${eigen_ver}
+module load eckit/${eckit_ver}
+module load fckit/${fckit_ver}
+module load udunits/${udunits_ver}
+module load python/${python_ver}
+module load ve/gcafs/${ve_obsforge_ver} # TODO: change later
+
+module list
+
+#############################################################
+# environment settings
+#############################################################
+export cyc=%CYC%
+export cycle=t%CYC%z
+
+############################################################
+# CALL executable job script here
+############################################################
+${HOMEobsforge}/jobs/JOBSFORGE_GDAS_MARINE_BUFR_DUMP
+
+if [ $? -ne 0 ]; then
+   ecflow_client --msg="***JOB ${ECF_NAME} ERROR RUNNING J-SCRIPT ***"
+   ecflow_client --abort
+   exit
+fi
+
+%include <tail.h>
+%manual
+
+%end