Merge branch 'develop' into feature/rm_sfcanl

RussTreadon-NOAA · May 9, 2022 · c4c860b · c4c860b
2 parents c9ac824 + 34294c1
commit c4c860b
Show file tree

Hide file tree

Showing 104 changed files with 710 additions and 475 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -82,7 +82,7 @@ project(GSI)
   option(BUILD_REG_TESTING "Build the Regression Testing Suite" ON)
   option(BUILD_UNIT_TESTING "Build the Unit Testing Suite" OFF)
   option(BUILD_GSDCLOUD_ARW "Build the GSD cloud analysis " OFF)
-  cmake_minimum_required(VERSION 2.8)
+  cmake_minimum_required(VERSION 3.16.1)
   set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
   set(CMAKE_LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}/lib")
   SET(LIBRARY_OUTPUT_PATH ${PROJECT_BINARY_DIR}/lib)
@@ -119,6 +119,9 @@ project(GSI)
   cmake_policy(SET CMP0009 NEW)
   cmake_policy(SET CMP0054 NEW)
   cmake_policy(SET CMP0074 NEW)
+  if(CMAKE_VERSION EQUAL 3.20.2)
+     cmake_policy(SET CMP0110 NEW)
+  endif()
   find_package(OpenMP)
   message("found openmp with flag ${OPENMP_Fortran_FLAGS}")
 

diff --git a/cmake/Modules/platforms/WCOSS2.cmake b/cmake/Modules/platforms/WCOSS2.cmake
@@ -0,0 +1,13 @@
+macro (setWCOSS2)
+  message("Setting flags and paths for WCOSS2")
+
+  option(FIND_HDF5 "Try to Find HDF5 libraries" OFF)
+  option(FIND_HDF5_HL "Try to Find HDF5 libraries" ON)
+  set(HDF5_USE_STATIC_LIBRARIES "ON" CACHE INTERNAL "HDF5_Static" )
+
+  set(HOST_FLAG "" CACHE INTERNAL "Host Flag")
+  set(MKL_FLAG "" CACHE INTERNAL "MKL flag" )
+  set(GSI_Intel_Platform_FLAGS "-DPOUND_FOR_STRINGIFY -fp-model strict -assume byterecl -convert big_endian -implicitnone -g -traceback -D_REAL8_ ${OpenMP_Fortran_FLAGS} ${MPI_Fortran_COMPILE_FLAGS} -O3" CACHE INTERNAL "")
+  set(ENKF_Platform_FLAGS "-O3 -fp-model strict -convert big_endian -assume byterecl -implicitnone -g -traceback -DGFS -D_REAL8_ ${OpenMP_Fortran_FLAGS} " CACHE INTERNAL "")
+  set(GSI_LDFLAGS "${OpenMP_Fortran_FLAGS}" CACHE INTERNAL "")
+endmacro()
diff --git a/cmake/Modules/setHOST.cmake b/cmake/Modules/setHOST.cmake
@@ -30,9 +30,9 @@ macro( setHOST )
   if( NOT HOST-WCOSS_C )# don't overwrite if we are on luna 
     string(REGEX MATCH "slogin" HOST-WCOSS_C ${HOSTNAME}  )
   endif()
-  string(REGEX MATCH "alogin01" HOST-Acorn ${HOSTNAME}  )
-  if( NOT HOST-Acorn )# don't overwrite if we are on node 1
-     string(REGEX MATCH "alogin02" HOST-Acorn ${HOSTNAME}  )
+  string(REGEX MATCH "clogin" HOST-WCOSS2 ${HOSTNAME}  )
+  if( NOT HOST-WCOSS2 )# don't overwrite if we are on Cactus
+     string(REGEX MATCH "dlogin" HOST-WCOSS2 ${HOSTNAME}  )
   endif()
   string(REGEX MATCH "discover" HOST-Discover ${HOSTNAME} )
   string(REGEX MATCH "cheyenne" HOST-Cheyenne ${HOSTNAME}  )
@@ -90,11 +90,11 @@ macro( setHOST )
     set(host "Discover"  )
     setDiscover()
     set( HOST-Discover "TRUE"  )
-  elseif( HOST-Acorn )
-    set( host "Acorn"  )
+  elseif( HOST-WCOSS2 )
+    set( host "WCOSS2"  )
     option(BUILD_CORELIBS "Build the Core libraries " OFF)
-    setAcorn()
-    set( HOST-Acorn "TRUE"  )
+    setWCOSS2()
+    set( HOST-WCOSS2 "TRUE"  )
   else(  )
     set( host "GENERIC" )
     option(BUILD_CORELIBS "Build the Core libraries " ON)

diff --git a/cmake/Modules/setIntelFlags.cmake b/cmake/Modules/setIntelFlags.cmake
@@ -19,12 +19,12 @@ function(set_LIBRARY_UTIL_Intel)
     set (W3NCO_4_Fortran_FLAGS " -O3 -auto -assume nocc_omp -i${intsize}     -convert big_endian -assume byterecl -fp-model strict ${OpenMP_Fortran_FLAGS} " CACHE INTERNAL "" )
     set (W3NCO_C_FLAGS "-O0 -DUNDERSCORE -DLINUX -D__linux__ " CACHE INTERNAL "" )
     set (NDATE_Fortran_FLAGS "${HOST_FLAG} -fp-model source -ftz -assume byterecl -convert big_endian -heap-arrays  -DCOMMCODE -DLINUX -DUPPLITTLEENDIAN -O3 -Wl,-noinhibit-exec" CACHE INTERNAL "" )
-    set(NCDIAG_Fortran_FLAGS "-free -assume byterecl -convert big_endian" CACHE INTERNAL "" )
-    set(FV3GFS_NCIO_Fortran_FLAGS "-free" CACHE INTERNAL "" )
-    set(UTIL_Fortran_FLAGS "-O3 ${HOST_FLAG} -warn all -implicitnone -traceback -fp-model strict -convert big_endian -DWRF -D_REAL8_ ${OpenMP_Fortran_FLAGS}" CACHE INTERNAL "")
-    set(UTIL_COM_Fortran_FLAGS "-O3 -fp-model source -convert big_endian -assume byterecl -implicitnone" CACHE INTERNAL "")
+    set(NCDIAG_Fortran_FLAGS "-free -assume byterecl -convert big_endian -g -traceback" CACHE INTERNAL "" )
+    set(FV3GFS_NCIO_Fortran_FLAGS "-free -g -traceback" CACHE INTERNAL "" )
+    set(UTIL_Fortran_FLAGS "-O3 ${HOST_FLAG} -implicitnone -g -traceback -fp-model strict -convert big_endian -DWRF -D_REAL8_ ${OpenMP_Fortran_FLAGS}" CACHE INTERNAL "")
+    set(UTIL_COM_Fortran_FLAGS "-O3 -fp-model source -convert big_endian -assume byterecl -implicitnone -g -traceback" CACHE INTERNAL "")
 #    set(COV_CALC_FLAGS "-O3 ${HOST_FLAG} -warn all -implicitnone -traceback -fp-model strict -convert little_endian -D_REAL8_ -openmp -fpp -auto" CACHE INTERNAL "" )
-   set(COV_CALC_FLAGS "-O3 ${HOST_FLAG} -warn all -implicitnone -traceback -fp-model strict -convert little_endian ${OpenMP_Fortran_FLAGS}" CACHE INTERNAL "")
+   set(COV_CALC_FLAGS "-O3 ${HOST_FLAG} -implicitnone -g -traceback -fp-model strict -convert little_endian ${OpenMP_Fortran_FLAGS}" CACHE INTERNAL "")
 #   set(COV_CALC_FLAGS ${GSI_Intel_Platform_FLAGS} CACHE INTERNAL "Full GSI Fortran FLAGS" )
 endfunction(set_LIBRARY_UTIL_Intel)
 

diff --git a/cmake/Modules/setPlatformVariables.cmake b/cmake/Modules/setPlatformVariables.cmake
@@ -8,5 +8,5 @@ include(${CMAKE_CURRENT_LIST_DIR}/platforms/Gaea.cmake)
 include(${CMAKE_CURRENT_LIST_DIR}/platforms/Cheyenne.cmake)
 include(${CMAKE_CURRENT_LIST_DIR}/platforms/Discover.cmake)
 include(${CMAKE_CURRENT_LIST_DIR}/platforms/WCOSS-D.cmake)
-include(${CMAKE_CURRENT_LIST_DIR}/platforms/Acorn.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/platforms/WCOSS2.cmake)
 include(${CMAKE_CURRENT_LIST_DIR}/platforms/Generic.cmake)
diff --git a/fix b/fix
diff --git a/jobs/JGDAS_ATMOS_ANALYSIS_DIAG b/jobs/JGDAS_ATMOS_ANALYSIS_DIAG
@@ -1,4 +1,4 @@
-#!/bin/ksh
+#!/bin/bash
 set -x
 
 export RUN_ENVIR=${RUN_ENVIR:-"nco"}
@@ -59,9 +59,6 @@ export pgmerr=errfile
 export CDATE=${CDATE:-${PDY}${cyc}}
 export CDUMP=${CDUMP:-${RUN:-"gfs"}}
 export COMPONENT=${COMPONENT:-atmos}
-if [ $RUN_ENVIR = "nco" ]; then
-    export ROTDIR=${COMROOT:?}/$NET/$envir
-fi
 export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"} 
 
 
@@ -84,12 +81,12 @@ export ASUFFIX=${ASUFFIX:-$SUFFIX}
 if [ $RUN_ENVIR = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
     export COMIN=${COMIN:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
     export COMOUT=${COMOUT:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
-    export COMIN_OBS=${COMIN_OBS:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
-    export COMIN_GES_OBS=${COMIN_GES_OBS:-$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT}
+    export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$GDUMP.$gPDY/$gcyc/$COMPONENT}
 else
     export COMOUT="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
-    export COMIN_OBS="$DMPDIR/$CDATE/$CDUMP"
-    export COMIN_GES_OBS="$DMPDIR/$GDATE/$GDUMP"
+    export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
+    export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
 fi
 mkdir -m 775 -p $COMOUT
 # COMIN_GES and COMIN_GES_ENS are used in script
@@ -116,8 +113,7 @@ fi
 ###############################################################
 # Run relevant script
 env
-msg="HAS BEGUN on `hostname`"
-postmsg "$jlogfile" "$msg"
+echo "HAS BEGUN on $(hostname)"
 $LOGSCRIPT
 
 
@@ -138,8 +134,7 @@ if [ -e "$pgmout" ] ; then
 fi
 
 
-msg="ENDED NORMALLY."
-postmsg "$jlogfile" "$msg"
+echo "ENDED NORMALLY."
 
 
 ##########################################

diff --git a/jobs/JGDAS_ATMOS_CHGRES_FORENKF b/jobs/JGDAS_ATMOS_CHGRES_FORENKF
@@ -1,4 +1,4 @@
-#!/bin/ksh
+#!/bin/bash
 set -x
 
 export RUN_ENVIR=${RUN_ENVIR:-"nco"}
@@ -59,9 +59,6 @@ export pgmerr=errfile
 export CDATE=${CDATE:-${PDY}${cyc}}
 export CDUMP=${CDUMP:-${RUN:-"gfs"}}
 export COMPONENT=${COMPONENT:-atmos}
-if [ $RUN_ENVIR = "nco" ]; then
-    export ROTDIR=${COMROOT:?}/$NET/$envir
-fi
 export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"}
 
 
@@ -85,13 +82,13 @@ if [ $RUN_ENVIR = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
     export COMIN=${COMIN:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
     export COMOUT=${COMOUT:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
     export COMOUT_ENS=${COMOUT_ENS:-$ROTDIR/enkfgdas.$PDY/$cyc/$COMPONENT}
-    export COMIN_OBS=${COMIN_OBS:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
-    export COMIN_GES_OBS=${COMIN_GES_OBS:-$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT}
+    export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$GDUMP.$gPDY/$gcyc/$COMPONENT}
 else
     export COMOUT="$ROTDIR/$CDUMP.$PDY/$cyc/$COMPONENT"
     export COMOUT_ENS="$ROTDIR/enkfgdas.$PDY/$cyc/$COMPONENT"
-    export COMIN_OBS="$DMPDIR/$CDATE/$CDUMP"
-    export COMIN_GES_OBS="$DMPDIR/$GDATE/$GDUMP"
+    export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
+    export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
 fi
 mkdir -m 775 -p $COMOUT
 # COMIN_GES and COMIN_GES_ENS are used in script
@@ -101,8 +98,7 @@ export COMIN_GES_ENS="$ROTDIR/enkfgdas.$gPDY/$gcyc/$COMPONENT"
 ###############################################################
 # Run relevant script
 env
-msg="HAS BEGUN on `hostname`"
-postmsg "$jlogfile" "$msg"
+echo "HAS BEGUN on $(hostname)"
 $LOGSCRIPT
 
 
@@ -123,8 +119,7 @@ if [ -e "$pgmout" ] ; then
 fi
 
 
-msg="ENDED NORMALLY."
-postmsg "$jlogfile" "$msg"
+echo "ENDED NORMALLY."
 
 
 ##########################################

diff --git a/jobs/JGDAS_ENKF_DIAG b/jobs/JGDAS_ENKF_DIAG
@@ -1,4 +1,4 @@
-#!/bin/ksh
+#!/bin/bash
 set -x
 
 export RUN_ENVIR=${RUN_ENVIR:-"nco"}
@@ -58,9 +58,6 @@ export pgmerr=errfile
 export CDATE=${CDATE:-${PDY}${cyc}}
 export CDUMP=${CDUMP:-${RUN:-"gdas"}}
 export COMPONENT=${COMPONENT:-atmos}
-if [ $RUN_ENVIR = "nco" ]; then
-    export ROTDIR=${COMROOT:?}/$NET/$envir
-fi
 
 
 ##############################################
@@ -82,11 +79,11 @@ export GSUFFIX="${GSUFFIX:-".ensmean${SUFFIX}"}"
 export ASUFFIX="${ASUFFIX:-"${SUFFIX}"}"
 
 if [ $RUN_ENVIR = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
-    export COMIN_OBS=${COMIN_OBS:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
-    export COMIN_GES_OBS=${COMIN_GES_OBS:-$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT}
+    export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$GDUMP.$gPDY/$gcyc/$COMPONENT}
 else
-    export COMIN_OBS="$DMPDIR/$CDATE/$CDUMP"
-    export COMIN_GES_OBS="$DMPDIR/$GDATE/$GDUMP"
+    export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
+    export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
 fi
 
 # COMIN_GES, COMIN_ANL COMIN_GES_ENS, and COMOUT  are used in script
@@ -105,15 +102,13 @@ fi
 
 
 # Link observational data
-export PREPQC="$COMIN_ANL/${OPREFIX}prepbufr"
+export PREPQC="$COMIN_OBS/${OPREFIX}prepbufr"
 if [ ! -f $PREPQC ]; then
-    echo "WARNING: PREPBUFR FILE $PREPQC MISSING"
-    msg="WARNING : Global PREPBUFR file is missing"
-    postmsg "$jlogfile" "$msg"
+    echo "WARNING: Global PREPBUFR FILE $PREPQC MISSING"
 fi
-export PREPQCPF="$COMIN_ANL/${OPREFIX}prepbufr.acft_profiles"
+export PREPQCPF="$COMIN_OBS/${OPREFIX}prepbufr.acft_profiles"
 export TCVITL="$COMIN_ANL/${OPREFIX}syndata.tcvitals.tm00"
-[[ $DONST = "YES" ]] && export NSSTBF="$COMIN_ANL/${OPREFIX}nsstbufr"
+[[ $DONST = "YES" ]] && export NSSTBF="$COMIN_OBS/${OPREFIX}nsstbufr"
 
 # Guess Bias correction coefficients related to control
 export GBIAS=${COMIN_GES_CTL}/${GPREFIX}abias
@@ -153,8 +148,7 @@ done
 ###############################################################
 # Run relevant script
 env
-msg="HAS BEGUN on `hostname`"
-postmsg "$jlogfile" "$msg"
+echo "HAS BEGUN on $(hostname)"
 $LOGSCRIPT
 
 
@@ -175,8 +169,7 @@ if [ -e "$pgmout" ] ; then
 fi
 
 
-msg="ENDED NORMALLY."
-postmsg "$jlogfile" "$msg"
+echo "ENDED NORMALLY."
 
 
 ##########################################

diff --git a/jobs/JGDAS_ENKF_ECEN b/jobs/JGDAS_ENKF_ECEN
@@ -1,4 +1,4 @@
-#!/bin/ksh
+#!/bin/bash
 set -x
 
 export RUN_ENVIR=${RUN_ENVIR:-"nco"}
@@ -58,9 +58,6 @@ export pgmerr=errfile
 export CDATE=${CDATE:-${PDY}${cyc}}
 export CDUMP=${CDUMP:-${RUN:-"gdas"}}
 export COMPONENT=${COMPONENT:-atmos}
-if [ $RUN_ENVIR = "nco" ]; then
-    export ROTDIR=${COMROOT:?}/$NET/$envir
-fi
 
 
 ##############################################
@@ -90,11 +87,11 @@ export GSUFFIX=${GSUFFIX:-$SUFFIX}
 export ASUFFIX=${ASUFFIX:-$SUFFIX}
 
 if [ $RUN_ENVIR = "nco" -o ${ROTDIR_DUMP:-NO} = "YES" ]; then
-    export COMIN_OBS=${COMIN_OBS:-$ROTDIR/$RUN.$PDY/$cyc/$COMPONENT}
-    export COMIN_GES_OBS=${COMIN_GES_OBS:-$ROTDIR/$GDUMP.$gPDY/$gcyc/$COMPONENT}
+    export COMIN_OBS=${COMIN_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$RUN.$PDY/$cyc/$COMPONENT}
+    export COMIN_GES_OBS=${COMIN_GES_OBS:-$(compath.py ${envir}/obsproc/${obsproc_ver})/$GDUMP.$gPDY/$gcyc/$COMPONENT}
 else
-    export COMIN_OBS="$DMPDIR/$CDATE/$CDUMP"
-    export COMIN_GES_OBS="$DMPDIR/$GDATE/$GDUMP"
+    export COMIN_OBS="$DMPDIR/$CDUMP.$PDY/$cyc"
+    export COMIN_GES_OBS="$DMPDIR/$GDUMP.$gPDY/$gcyc"
 fi
 
 # COMIN, COMIN_ENS and COMIN_GES_ENS are used in script
@@ -107,8 +104,7 @@ export COMIN_GES_ENS="$ROTDIR/enkf$CDUMP.$gPDY/$gcyc/$COMPONENT"
 ###############################################################
 # Run relevant script
 env
-msg="HAS BEGUN on `hostname`"
-postmsg "$jlogfile" "$msg"
+echo "HAS BEGUN on $(hostname)"
 $LOGSCRIPT
 
 
@@ -129,8 +125,7 @@ if [ -e "$pgmout" ] ; then
 fi
 
 
-msg="ENDED NORMALLY."
-postmsg "$jlogfile" "$msg"
+echo "ENDED NORMALLY."
 
 
 ##########################################

diff --git a/jobs/JGDAS_ENKF_FCST b/jobs/JGDAS_ENKF_FCST
@@ -1,4 +1,4 @@
-#!/bin/ksh
+#!/bin/bash
 set -x
 
 export RUN_ENVIR=${RUN_ENVIR:-"nco"}
@@ -58,9 +58,6 @@ export pgmerr=errfile
 export CDATE=${CDATE:-${PDY}${cyc}}
 export CDUMP=${CDUMP:-${RUN:-"gdas"}}
 export COMPONENT=${COMPONENT:-atmos}
-if [ $RUN_ENVIR = "nco" ]; then
-    export ROTDIR=${COMROOT:?}/$NET/$envir
-fi
 
 
 ##############################################
@@ -80,15 +77,14 @@ export FHMAX=$FHMAX_ENKF
 
 
 # Get ENSBEG/ENSEND from ENSGRP and NMEM_EFCSGRP
-export ENSEND=$((NMEM_EFCSGRP * ENSGRP))
+export ENSEND=$((NMEM_EFCSGRP * 10#${ENSGRP}))
 export ENSBEG=$((ENSEND - NMEM_EFCSGRP + 1))
 
 
 ###############################################################
 # Run relevant script
 env
-msg="HAS BEGUN on `hostname`"
-postmsg "$jlogfile" "$msg"
+echo "HAS BEGUN on $(hostname)"
 $LOGSCRIPT
 
 
@@ -131,8 +127,7 @@ if [ -e "$pgmout" ] ; then
 fi
 
 
-msg="ENDED NORMALLY."
-postmsg "$jlogfile" "$msg"
+echo "ENDED NORMALLY."
 
 
 ##########################################