GitHub Issue NOAA-EMC/GSI#44. netCDF interface with V16 updates for H…

…WRF.
lbi2018 · Jul 31, 2020 · 2fb4b6b · 2fb4b6b
1 parent 13366a1
commit 2fb4b6b
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Showing 37 changed files with 295 additions and 65 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -114,7 +114,7 @@ project(GSI)
   setHOST()
 
   if(FIND_HDF5_HL)
-    find_package(HDF5 COMPONENTS C HL Fortran_HL )
+    find_package(HDF5 COMPONENTS C HL)
   elseif(FIND_HDF5)
     find_package(HDF5)
   endif()

diff --git a/cmake/Modules/setIntelFlags.cmake b/cmake/Modules/setIntelFlags.cmake
@@ -64,7 +64,7 @@ function(set_GSI_ENKF_Intel)
 endfunction(set_GSI_ENKF_Intel)
 
 function (set_GSI_ENKF_Debug_Intel)
-    set(GSI_Fortran_FLAGS "-DPOUND_FOR_STRINGIFY -O0 -fp-model source -convert big_endian -assume byterecl -implicitnone -mcmodel medium -shared-intel -g -traceback -debug -ftrapuv -check all,noarg_temp_created -fp-stack-check -fstack-protector -warn all,nointerfaces -convert big_endian -implicitnone -D_REAL8_ ${OpenMP_Fortran_FLAGS} ${MPI_Fortran_COMPILE_FLAGS} ${GSDCLOUDOPT}" CACHE INTERNAL "")
+    set(GSI_Fortran_FLAGS "-DPOUND_FOR_STRINGIFY -O0 -fp-model source -convert big_endian -assume byterecl -implicitnone -g -traceback -debug -ftrapuv -check all,noarg_temp_created -fp-stack-check -fstack-protector -warn all,nointerfaces -convert big_endian -implicitnone -D_REAL8_ ${OpenMP_Fortran_FLAGS} ${MPI_Fortran_COMPILE_FLAGS} ${GSDCLOUDOPT}" CACHE INTERNAL "")
     set(ENKF_Fortran_FLAGS "-O0 ${HOST_FLAG} -warn all -implicitnone -traceback -g -debug all -check all,noarg_temp_created -fp-model strict -convert big_endian -assume byterecl -D_REAL8_  ${OpenMP_Fortran_FLAGS} ${GSDCLOUDOPT}" CACHE INTERNAL "")
     set(GSDCLOUD_Fortran_FLAGS "-DPOUND_FOR_STRINGIFY -O3 -convert big_endian" CACHE INTERNAL "")
     #Common debug flags

diff --git a/modulefiles/modulefile.ProdGSI.jet b/modulefiles/modulefile.ProdGSI.jet
@@ -11,21 +11,19 @@
 #module-whatis " GDAS_ENKF whatis description"
 #
 #
-module load newdefaults
-module load intel/2016.2.181 
-module load impi/5.1.1.109
+
+module load intel/18.0.5.274
+module load impi
 #
-module load szip/2.1   
+module load szip/2.1
 module load hdf5/1.8.9
-module load netcdf4/4.2.1.1  
 
-export COREPATH=/lfs3/projects/hfv3gfs/nwprod/lib
-export COREPATH=/mnt/lfs3/projects/hfv3gfs/gwv/ljtjet/lib
+export COREPATH=/lfs4/HFIP/hfv3gfs/gwv/l0530/lib
 export NCEPLIBS=$COREPATH
 module use $NCEPLIBS/modulefiles
 
-export FFLAGS="-openmp"
-export LDFLAGS="-openmp"
+export FFLAGS="-qopenmp"
+export LDFLAGS="-qopenmp"
 module load bacio-intel-sandybridge/2.0.2
 module load crtm-intel-sandybridge/2.2.5
 module load bufr-intel-sandybridge/11.1.0
@@ -35,10 +33,7 @@ module load w3emc-intel-sandybridge/2.2.0
 module load w3nco-intel-sandybridge/2.0.6
 module load sigio-intel-sandybridge/2.0.1
 module load sfcio-intel-sandybridge/1.0.0
+module load ip-intel-sandybridge/3.0.0
 
-module use /home/George.Vandenberghe/t1/l1025/lib/modulefiles
-module load hdf5
-module load netcdf
 
-export NETCDF=${NETCDF4}
-export NETCDF_DIR=${NETCDF4}
+module load netcdfp/4.7.4
diff --git a/modulefiles/modulefile.ProdGSI.wcoss_c b/modulefiles/modulefile.ProdGSI.wcoss_c
@@ -40,16 +40,17 @@ module unload intel/15.0.3.187
 module load intel/18.1.163
 
 # Loading pe environment
+module load craype-sandybridge
 module load cray-mpich/7.2.0
-module load craype-haswell
 
 module use /usrx/local/dev/modulefiles
 module load cmake/3.6.2
 module unuse /usrx/local/dev/modulefiles
 
 # Loading netcdf modules
-module load cray-netcdf/4.3.2
-module load cray-hdf5/1.8.14
+module use /usrx/local/dev/modulefiles
+module load NetCDF-intel-sandybridge/4.7.4
+module load HDF5-parallel-intel-sandybridge/1.10.6
 
 # Loading nceplibs modules
 module use /gpfs/hps/nco/ops/nwprod/lib/modulefiles

diff --git a/regression/regression_var.sh b/regression/regression_var.sh
@@ -138,6 +138,8 @@ case $machine in
       export noscrub="/gpfs/hps3/emc/global/noscrub/$LOGNAME"
    elif [ -d /gpfs/hps3/emc/da/noscrub/$LOGNAME ]; then
       export noscrub="/gpfs/hps3/emc/da/noscrub/$LOGNAME"
+   elif [ -d /gpfs/hps3/emc/hwrf/noscrub/$LOGNAME ]; then
+       export noscrub="/gpfs/hps3/emc/hwrf/noscrub/$LOGNAME"
    fi
    if [[ "$cmaketest" = "false" ]]; then
      export basedir="/gpfs/hps3/emc/global/noscrub/$LOGNAME/svn/gsi"

diff --git a/src/enkf/CMakeLists.txt b/src/enkf/CMakeLists.txt
@@ -78,7 +78,7 @@ if(BUILD_ENKF)
   set(ENKFEXEC "${ENKF_BASE}${debug_suffix}${GSISUFFIX}" CACHE INTERNAL "ENKF Executable name")
   add_executable(${ENKFEXEC} enkf_main.f90)
   target_link_libraries(${ENKFEXEC} enkflib enkfdeplib ${GSILIB} ${GSISHAREDLIB} ${CORE_LIBRARIES}
-  ${MPI_Fortran_LIBRARIES} ${LAPACK_LIBRARIES} ${NETCDF_LIBRARIES_F90} ${NETCDF_LIBRARIES}  ${HDF5_Fortran_HL_LIBRARIES}
+  ${MPI_Fortran_LIBRARIES} ${LAPACK_LIBRARIES} ${NETCDF_LIBRARIES_F90} ${NETCDF_LIBRARIES}  ${HDF5_HL_LIBRARIES}
   ${EXTRA_LINKER_FLAGS} ${HDF5_LIBRARIES} ${CURL_LIBRARIES} ${GSI_LDFLAGS} ${CORE_BUILT} ${CORE_LIBRARIES} ${CORE_BUILT} ${NCDIAG_LIBRARIES} ${FV3GFS_NCIO_LIBRARIES})
   install(TARGETS ${ENKFEXEC} enkfdeplib enkflib 
         RUNTIME DESTINATION ${CMAKE_INSTALL_PREFIX}/bin

diff --git a/src/enkf/gridio_wrf.f90 b/src/enkf/gridio_wrf.f90
@@ -46,7 +46,8 @@ module gridio
   ! Define all public subroutines within this module
   private
   public :: readgriddata, readgriddata_pnc
-  public :: writegriddata, writegriddata_pnc, WRITEINCREMENT, WRITEINCREMENT_PNC
+  public :: writegriddata, writegriddata_pnc
+  public :: writeincrement, writeincrement_pnc
 
   !-------------------------------------------------------------------------
 
@@ -74,6 +75,7 @@ subroutine readgriddata(nanal1,nanal2,vars3d,vars2d,n3d,n2d,levels,ndim,ntimes,f
 
   end subroutine readgriddata
 
+
   !========================================================================
   ! readgriddata_arw.f90: read WRF-ARW state or control vector
   !-------------------------------------------------------------------------
@@ -730,7 +732,7 @@ subroutine writegriddata(nanal1,nanal2,vars3d,vars2d,n3d,n2d,levels,ndim,vargrid
 
     !----------------------------------------------------------------------
     if (nbackgrounds > 1) then
-       write(6,*)'gridio/writegriddata: writing multiple backgrounds not yet supported'
+       write(6,*)'gridio/writegriddata_wrf: writing multiple backgrounds not yet supported'
        call stop2(23)
     endif
 
@@ -1036,6 +1038,7 @@ subroutine writegriddata(nanal1,nanal2,vars3d,vars2d,n3d,n2d,levels,ndim,vargrid
 
   end subroutine writegriddata
 
+
   !======================================================================
   ! readwrfvar.f90: This subroutine reads a varname variable from WRF
   ! ARW or NMM netcdf file and returns the variable interpolated to 

diff --git a/src/gsi/CMakeLists.txt b/src/gsi/CMakeLists.txt
@@ -145,7 +145,7 @@ cmake_minimum_required(VERSION 2.8)
   endif()
 # Specify all the libraries to be linked into the executable
   target_link_libraries(${GSIEXEC} ${GSISHAREDLIB} ${GSILIB} ${GSISHAREDLIB} ${WRF_LIBRARIES} 
-         ${NETCDF_LIBRARIES_F90} ${NETCDF_LIBRARIES} ${HDF5_Fortran_HL_LIBRARIES} ${MPI_Fortran_LIBRARIES} 
+         ${NETCDF_LIBRARIES_F90} ${NETCDF_LIBRARIES} ${HDF5_HL_LIBRARIES} ${MPI_Fortran_LIBRARIES} 
          ${LAPACK_LIBRARIES} -L./ ${EXTRA_LINKER_FLAGS} ${HDF5_LIBRARIES} ${CURL_LIBRARIES} ${CORE_LIBRARIES} ${CORE_BUILT}
          ${GSI_LDFLAGS} ${NCDIAG_LIBRARIES} ${GSDCLOUD_LIBRARY} ${ZLIB_LIBRARIES} ${wrflib} ${EXTRA_LINKER_FLAGS} ${FV3GFS_NCIO_LIBRARIES})
   install(TARGETS ${GSIEXEC}

diff --git a/src/gsi/gesinfo.F90 b/src/gsi/gesinfo.F90
@@ -255,6 +255,9 @@ subroutine gesinfo
            jcap=gfshead%jcap, ntrac=gfshead%ntrac, idvc=gfshead%idvc, &
            idsl=gfshead%idsl,   ncldt=gfshead%ncldt, iret=iret2)
 
+        ! FV3GFS write component does not include JCAP, infer from DIMY-2
+        !if (gfshead%jcap<0) gfshead%jcap=gfshead%latb-2
+
         if ( iret2 /= 0 .or. TRIM(filetype) /= 'NEMSIO' ) then
            write(6,*)' GESINFO:  UNKNOWN FORMAT FOR GFSATM file = ', &
               trim(filename),' Status = ',iret2