Merge branch 'develop' into bugfix/gcc_mpi

Fixes ufs-community#471

.github/workflows/debug-docs-test_coverage.yml

@@ -97,19 +97,13 @@ jobs:
         export CC=mpicc
         export CXX=mpicxx
         export FC=mpifort
-        # Findwgrib2 in module form does not search <libname>-version
-        # as NCEPLIBS installs it
         export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/jasper/lib;~/jasper/lib64"
-        export wgrib2_ROOT=`find ~/nceplibs -type d -maxdepth 1 -iname "wgrib2*"`
         cmake .. -DCMAKE_PREFIX_PATH='~/jasper;~/nceplibs' -DCMAKE_BUILD_TYPE=Debug -DENABLE_DOCS=On -DCMAKE_Fortran_FLAGS="-g -fprofile-arcs -ftest-coverage -O0"
         make -j2
 
     - name: test
       run: |
-        cd ufs_utils/build/tests
-        wget -i ./chgres_cube/data/files.txt -P ./chgres_cube/data
-        wget -i ./sfc_climo_gen/data/files.txt -P ./sfc_climo_gen/data
-        cd ../
+        cd ufs_utils/build
         export LSAN_OPTIONS=suppressions=LSanSuppress.supp
         ctest --rerun-failed --output-on-failure
         export PATH="/home/runner/.local/bin:$PATH"

.github/workflows/intel.yml

@@ -56,8 +56,8 @@ jobs:
         export CC=mpiicc
         export CPPFLAGS=-I${HOME}/netcdf/include
         export LDFLAGS=-L${HOME}/netcdf/lib
-        wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-4.7.4.tar.gz &> /dev/null
-        tar -xzf netcdf-c-4.7.4.tar.gz
+        wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v4.7.4.tar.gz &> /dev/null
+        tar -xzf v4.7.4.tar.gz
         pushd netcdf-c-4.7.4
         ./configure --prefix=${HOME}/netcdf --disable-dap --disable-utilities --disable-shared
         make -j2
@@ -160,17 +160,11 @@ jobs:
         export ESMFMKFILE=~/esmf/lib/esmf.mk
         cd ufs_utils
         mkdir build && cd build
-        # Findwgrib2 in module form does not search <libname>-version
-        # as NCEPLIBS installs it
         export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/jasper/lib;~/jasper/lib64"
-        export wgrib2_ROOT=`find ~/nceplibs -type d -maxdepth 1 -iname "wgrib2*"`
         cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_PREFIX_PATH='~;~/jasper;~/nceplibs;~/netcdf'
         make -j2
     
     - name: test
       run: |
-        cd ufs_utils/build/tests
-        wget -i ./chgres_cube/data/files.txt -P ./chgres_cube/data
-        wget -i ./sfc_climo_gen/data/files.txt -P ./sfc_climo_gen/data
-        cd ../
+        cd ufs_utils/build
         ctest --rerun-failed --output-on-failure

.github/workflows/linux-mac-nceplibs-mpi.yml

@@ -94,8 +94,8 @@ jobs:
         export CC=mpicc
         export CPPFLAGS=-I${HOME}/netcdf/include
         export LDFLAGS=-L${HOME}/netcdf/lib
-        wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-${{ matrix.netcdf_version }}.tar.gz &> /dev/null
-        tar -xzf netcdf-c-${{ matrix.netcdf_version }}.tar.gz
+        wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v${{ matrix.netcdf_version }}.tar.gz &> /dev/null
+        tar -xzf v${{ matrix.netcdf_version }}.tar.gz
         cd netcdf-c-${{ matrix.netcdf_version }}
         ./configure --prefix=${HOME}/netcdf --disable-dap --disable-utilities --disable-shared
         make -j2
@@ -214,20 +214,14 @@ jobs:
         export CC=mpicc
         export CXX=mpicxx
         export FC=mpifort
-        # Findwgrib2 in module form does not search <libname>-version
-        # as NCEPLIBS installs it
         export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/jasper/lib;~/jasper/lib64"
         export DYLD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/jasper/lib;~/jasper/lib64"
-        export wgrib2_ROOT=`find ~/nceplibs -type d -maxdepth 1 -iname "wgrib2*"`
         cmake .. -DCMAKE_PREFIX_PATH='~/jasper;~/nceplibs;~/netcdf'
         make -j2
 
     - name: test
       run: |
-        cd ufs_utils/build/tests
-        wget -i ./chgres_cube/data/files.txt -P ./chgres_cube/data
-        wget -i ./sfc_climo_gen/data/files.txt -P ./sfc_climo_gen/data
-        cd ../
+        cd ufs_utils/build
         # Oversubscribe for OpenMPI to run more processes than CPUs
         export OMPI_MCA_rmaps_base_oversubscribe=1
         ctest --rerun-failed --output-on-failure

.github/workflows/netcdf-versions.yml

@@ -47,8 +47,8 @@ jobs:
         export CC=mpicc
         export CPPFLAGS=-I${HOME}/netcdf/include
         export LDFLAGS=-L${HOME}/netcdf/lib
-        wget https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-c-${{ matrix.netcdf_version }}.tar.gz &> /dev/null
-        tar -xzf netcdf-c-${{ matrix.netcdf_version }}.tar.gz
+        wget https://github.com/Unidata/netcdf-c/archive/refs/tags/v${{ matrix.netcdf_version }}.tar.gz &> /dev/null
+        tar -xzf v${{ matrix.netcdf_version }}.tar.gz
         cd netcdf-c-${{ matrix.netcdf_version }}
         ./configure --prefix=${HOME}/netcdf --disable-dap --disable-utilities --disable-shared
         make -j2
@@ -148,18 +148,12 @@ jobs:
         export CC=mpicc
         export CXX=mpicxx
         export FC=mpifort
-        # Findwgrib2 in module form does not search <libname>-version
-        # as NCEPLIBS installs it
         export LD_LIBRARY_PATH="${LD_LIBRARY_PATH}:~/jasper/lib;~/jasper/lib64"
-        export wgrib2_ROOT=`find ~/nceplibs -type d -maxdepth 1 -iname "wgrib2*"`
         cmake .. -DCMAKE_PREFIX_PATH='~/jasper;~/nceplibs;~/netcdf' -DCMAKE_BUILD_TYPE=Debug 
         make -j2
 
     - name: test
       run: |
-        cd ufs_utils/build/tests
-        wget -i ./chgres_cube/data/files.txt -P ./chgres_cube/data
-        wget -i ./sfc_climo_gen/data/files.txt -P ./sfc_climo_gen/data
-        cd ../
+        cd ufs_utils/build
         export LSAN_OPTIONS=suppressions=LSanSuppress.supp
         ctest --rerun-failed --output-on-failure

CMakeLists.txt

@@ -23,15 +23,19 @@ if(NOT CMAKE_BUILD_TYPE MATCHES "^(Debug|Release|RelWithDebInfo|MinSizeRel)$")
       CACHE STRING "Choose the type of build." FORCE)
   set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
                                                "MinSizeRel" "RelWithDebInfo")
-  message(STATUS "Set BUILD_TESTING to YES and build unit testing package under tests")
-  set(BUILD_TESTING "YES")
 endif()
 
 # Set compiler flags.
 if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -traceback")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -fp-model precise")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -check -check noarg_temp_created -check nopointer -fp-stack-check -fstack-protector-all -fpe0 -debug -ftrapuv")
+  if(APPLE)
+    # The linker on macOS does not include `common symbols` by default.
+    # Passing the -c flag includes them and fixes an error with undefined symbols.
+    set(CMAKE_Fortran_ARCHIVE_FINISH "<CMAKE_RANLIB> -c <TARGET>")
+    set(CMAKE_C_ARCHIVE_FINISH "<CMAKE_RANLIB> -c <TARGET>")
+  endif()
 elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$")
   set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -fbacktrace")
   if(${CMAKE_Fortran_COMPILER_VERSION} VERSION_GREATER_EQUAL 10)
@@ -63,8 +67,7 @@ find_package(nemsio 2.5.0 REQUIRED)
 find_package(sigio 2.3.0 REQUIRED)
 find_package(sp 2.3.3 REQUIRED)
 find_package(ip 3.3.3 REQUIRED)
-find_package(g2 3.4.0 REQUIRED)
-find_package(wgrib2 2.0.8 REQUIRED)
+find_package(g2 3.4.3 REQUIRED)
 find_package(sigio 2.3.0 REQUIRED)
 
 # EMC requires executables in ./exec
@@ -87,6 +90,6 @@ add_subdirectory(sorc)
 # Run unit tests.
 include(CTest)
 if(BUILD_TESTING)
+  message(STATUS "Set BUILD_TESTING to YES and build unit testing package under tests")
   add_subdirectory(tests)
 endif()
-

README.md

@@ -40,7 +40,6 @@ This package uses the [hpc-stack](https://github.com/NOAA-EMC/hpc-stack) for the
  - [NCEPLIBS-sp](https://github.com/NOAA-EMC/NCEPLIBS-sp)
  - [NCEPLIBS-ip](https://github.com/NOAA-EMC/NCEPLIBS-ip)
  - [NCEPLIBS-g2](https://github.com/NOAA-EMC/NCEPLIBS-g2)
- - [NCEPLIBS-wgrib2](https://github.com/NOAA-EMC/NCEPLIBS-wgrib2)
 
 And for the following third party libraries:
 

build_all.sh

@@ -26,8 +26,18 @@ else
  set -x
 fi
 
-CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON"
-#CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON -DENABLE_DOCS=ON"
+# The unit test data download is part of the build system. Not all machines can
+# access the EMC ftp site, so turn off the build (-DBUILD_TESTING=OFF) of the units tests accordingly.
+# Those with access to the EMC ftp site are: Orion, Hera, WCOSS-Cray, WCOSS-Dell.
+
+if [[ "$target" == "hera" || "$target" == "orion" || "$target" == "wcoss_cray" || "$target" == "wcoss_dell_p3" ]]; then
+  CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON -DBUILD_TESTING=OFF"
+   #CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON -DBUILD_TESTING=ON"
+   #CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON -DENABLE_DOCS=ON -DBUILD_TESTING=ON"
+else
+  CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON -DBUILD_TESTING=OFF"
+   #CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON -DENABLE_DOCS=ON -DBUILD_TESTING=OFF"
+fi
 
 rm -fr ./build
 mkdir ./build && cd ./build
@@ -37,4 +47,7 @@ cmake .. ${CMAKE_FLAGS}
 make -j 8 VERBOSE=1
 make install
 
+#make test
+#ctest -I 4,5
+
 exit

modulefiles/build.cheyenne.intel

@@ -20,7 +20,6 @@ module load w3nco/2.4.1
 module load sigio/2.3.2
 
 module load sfcio/1.4.1
-module load wgrib2/2.0.8
 module load netcdf/4.7.4
 
 setenv ESMFMKFILE /glade/p/ral/jntp/GMTB/tools/NCEPLIBS-ufs-v2.0.0/intel-19.1.1/mpt-2.19/lib64/esmf.mk

modulefiles/build.hera.gnu.lua

@@ -28,7 +28,7 @@ load(pathJoin("esmf", esmf_ver))
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
 
-g2_ver=os.getenv("g2_ver") or "3.4.1"
+g2_ver=os.getenv("g2_ver") or "3.4.3"
 load(pathJoin("g2", g2_ver))
 
 ip_ver=os.getenv("ip_ver") or "3.3.3"
@@ -49,9 +49,6 @@ load(pathJoin("sfcio", sfcio_ver))
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-wgrib2_ver=os.getenv("wgrib2_ver") or "2.0.8"
-load(pathJoin("wgrib2", wgrib2_ver))
-
 nccmp_ver=os.getenv("nccmp_ver") or "1.8.7.0"
 load(pathJoin("nccmp", nccmp_ver))
 

modulefiles/build.hera.intel.lua

@@ -22,7 +22,7 @@ load(pathJoin("hpc-impi", impi_ver))
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
 
-g2_ver=os.getenv("g2_ver") or "3.4.1"
+g2_ver=os.getenv("g2_ver") or "3.4.3"
 load(pathJoin("g2", g2_ver))
 
 ip_ver=os.getenv("ip_ver") or "3.3.3"
@@ -43,9 +43,6 @@ load(pathJoin("sfcio", sfcio_ver))
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-wgrib2_ver=os.getenv("wgrib2_ver") or "2.0.8"
-load(pathJoin("wgrib2", wgrib2_ver))
-
 zlib_ver=os.getenv("zlib_ver") or "1.2.11"
 load(pathJoin("zlib", zlib_ver))
 

modulefiles/build.jet.intel.lua

@@ -52,12 +52,9 @@ load(pathJoin("sfcio", sfcio_ver))
 nemsio_ver=os.getenv("nemsio_ver") or "2.5.2"
 load(pathJoin("nemsio", nemsio_ver))
 
-g2_ver=os.getenv("g2_ver") or "3.4.1"
+g2_ver=os.getenv("g2_ver") or "3.4.3"
 load(pathJoin("g2", g2_ver))
 
-wgrib2_ver=os.getenv("wgrib2_ver") or "2.0.8"
-load(pathJoin("wgrib2", wgrib2_ver))
-
 prod_util_ver=os.getenv("prod_util_ver") or "1.2.2"
 load(pathJoin("prod_util", prod_util_ver))
 

modulefiles/build.odin.intel

@@ -25,13 +25,10 @@ module load sigio
 module load sfcio
 module load nemsio
 module load g2
-module load wgrib2
 
 #module load esmf/8.0.0
 #setenv ESMFMKFILE /oldscratch/ywang/external/NCEPLIBS_SRW/lib64/esmf.mk
 setenv ESMFMKFILE /oldscratch/ywang/external/NCEPLIBS_SRWv2.0/lib64/esmf.mk
 
 setenv CMAKE_Fortran_COMPILER ftn
 setenv CMAKE_C_COMPILER cc
-
-#setenv WGRIB2_ROOT /oldscratch/ywang/external/NCEPLIBS_SRWv2.0/wgrib2-2.0.8

modulefiles/build.orion.intel.lua

@@ -19,7 +19,7 @@ load(pathJoin("hpc-impi", impi_ver))
 bacio_ver=os.getenv("bacio_ver") or "2.4.1"
 load(pathJoin("bacio", bacio_ver))
 
-g2_ver=os.getenv("g2_ver") or "3.4.1"
+g2_ver=os.getenv("g2_ver") or "3.4.3"
 load(pathJoin("g2", g2_ver))
 
 ip_ver=os.getenv("ip_ver") or "3.3.3"
@@ -40,9 +40,6 @@ load(pathJoin("sfcio", sfcio_ver))
 sigio_ver=os.getenv("sigio_ver") or "2.3.2"
 load(pathJoin("sigio", sigio_ver))
 
-wgrib2_ver=os.getenv("wgrib2_ver") or "2.0.8"
-load(pathJoin("wgrib2", wgrib2_ver))
-
 zlib_ver=os.getenv("zlib_ver") or "1.2.11"
 load(pathJoin("zlib", zlib_ver))
 

modulefiles/build.s4.intel

@@ -16,7 +16,6 @@ module load sp/2.3.3
 module load w3nco/2.4.1
 module load sfcio/1.4.1
 module load sigio/2.3.2
-module load wgrib2/2.0.8
 
 module load jasper/2.0.22
 module load zlib/1.2.11

modulefiles/build.stampede.intel

@@ -32,7 +32,6 @@ module load sigio
 module load sfcio
 module load nemsio
 module load g2
-module load wgrib2
 
 #setenv ESMFMKFILE /work/00315/tg455890/stampede2/regional_fv3/NCEPLIBS_SRWv2.0/lib64/esmf.mk
 

modulefiles/build.wcoss_cray.intel

@@ -18,20 +18,22 @@ module load cray-hdf5/1.8.14
 
 module use /usrx/local/nceplibs/NCEPLIBS/cmake/install/NCEPLIBS-v1.3.0/modules
 module load bacio/2.4.1
-module load g2/3.4.1
 module load ip/3.3.3
 module load nemsio/2.5.2
 module load sp/2.3.3
 module load w3nco/2.4.1
 module load sfcio/1.4.1
 module load sigio/2.3.2
-module load wgrib2/2.0.8
 
 setenv ZLIB_ROOT /usrx/local/prod/zlib/1.2.7/intel/haswell
 setenv PNG_ROOT /usrx/local/prod/png/1.2.49/intel/haswell
 setenv Jasper_ROOT /usrx/local/prod/jasper/1.900.1/intel/haswell
 
+module use /usrx/local/nceplibs/NCEPLIBS/cmake/install/NCEPLIBS-v1.4.0/modules
+module load g2/3.4.5
+
 module load esmf/820
+
 setenv NETCDF /opt/cray/netcdf/4.3.3.1/INTEL/14.0
 module rm gcc
 module load gcc/6.3.0