feature/mpi_abort: Merge branch 'develop' into feature/mpi_abort

Issues #140.

.gitignore

@@ -0,0 +1,11 @@
+build/
+install/
+exec/
+
+*.[ao]
+*.mod
+*.so
+*.exe
+*.x
+
+*.swp

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "cmake"]
-	path = cmake
+	path = CMakeModules
 	url = https://github.com/NOAA-EMC/CMakeModules
 	branch = develop

CMakeLists.txt

@@ -6,7 +6,7 @@ project(
   ufs_util
   VERSION ${pVersion}
   LANGUAGES C Fortran)
-list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules/")
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/CMakeModules/Modules")
 
 if(NOT CMAKE_BUILD_TYPE MATCHES "^(Debug|Release|RelWithDebInfo|MinSizeRel)$")
   message(STATUS "Setting build type to 'Release' as none was specified.")
@@ -17,96 +17,52 @@ if(NOT CMAKE_BUILD_TYPE MATCHES "^(Debug|Release|RelWithDebInfo|MinSizeRel)$")
                                                "MinSizeRel" "RelWithDebInfo")
 endif()
 
-if(NOT CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel|GNU|Clang|AppleClang)$")
-  message(WARNING "Compiler not officially supported: ${CMAKE_Fortran_COMPILER_ID}")
+if(NOT CMAKE_C_COMPILER_ID MATCHES "^(Intel|GNU|Clang|AppleClang)$")
+  message(WARNING "Compiler not officially supported: ${CMAKE_C_COMPILER_ID}")
 endif()
 
-if(NOT CMAKE_C_COMPILER_ID MATCHES "^(Intel|GNU)$")
-  message(WARNING "Compiler not officially supported: ${CMAKE_C_COMPILER_ID}")
+if(NOT CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel|GNU)$")
+  message(WARNING "Compiler not officially supported: ${CMAKE_Fortran_COMPILER_ID}")
 endif()
 
 if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$")
-  set(CMAKE_Fortran_FLAGS "-g -traceback")
+  set(CMAKE_Fortran_FLAGS "${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")
-elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU|Clang|AppleClang)$")
-  set(CMAKE_Fortran_FLAGS "-g -fbacktrace")
+elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU)$")
+  set(CMAKE_Fortran_FLAGS "${CMAKE_Fortran_FLAGS} -g -fbacktrace")
   set(CMAKE_Fortran_FLAGS_RELEASE "-O3")
   set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -ggdb -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -fbounds-check")
 endif()
 
 if(CMAKE_C_COMPILER_ID MATCHES "^(Intel)$")
-  set(CMAKE_C_FLAGS "-g -traceback")
+  set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -traceback")
   set(CMAKE_C_FLAGS_RELEASE "-O2")
   set(CMAKE_C_FLAGS_DEBUG "-O0")
-elseif(CMAKE_C_COMPILER_ID MATCHES "^(GNU|Clang|AppleClang)$")
-  set(CMAKE_C_FLAGS " ")
-  set(CMAKE_C_FLAGS_RELEASE " ")
-  set(CMAKE_C_FLAGS_DEBUG " ")
 endif()
 
-find_package(PNG REQUIRED)
-find_package(ZLIB REQUIRED)
-find_package(Jasper REQUIRED)
 find_package(NetCDF REQUIRED C Fortran)
-find_package(MPI REQUIRED )
+find_package(MPI REQUIRED)
 find_package(ESMF MODULE REQUIRED)
-find_package(WGRIB2 REQUIRED)
 
 option(OPENMP "use OpenMP threading" ON)
 if(OPENMP)
   find_package(OpenMP REQUIRED COMPONENTS Fortran)
 endif()
 
-set(CMAKE_FIND_PACKAGE_PREFER_CONFIG true)
-
-if(NOT TARGET gfsio_4)
-  find_package(gfsio REQUIRED)
-endif()
-
-if(NOT TARGET sfcio_4)
-  find_package(sfcio REQUIRED)
-endif()
-
-if(NOT TARGET w3nco_d)
-  find_package(w3nco REQUIRED)
-endif()
-
-if(NOT TARGET landsfcutil_d)
-  find_package(landsfcutil REQUIRED)
-endif()
-
-if(NOT TARGET bacio_4)
-  find_package(bacio REQUIRED)
-endif()
-
-if(NOT TARGET nemsio)
-  find_package(nemsio REQUIRED)
-endif()
-
-if(NOT TARGET nemsiogfs)
-  find_package(nemsiogfs REQUIRED)
-endif()
-
-if(NOT TARGET sigio_4)
-  find_package(sigio REQUIRED)
-endif()
-
-if(NOT TARGET sp_d)
-  find_package(sp REQUIRED)
-endif()
-
-if(NOT TARGET ip_d)
-  find_package(ip REQUIRED)
-endif()
-
-if(NOT TARGET w3emc_d)
-  find_package(w3emc REQUIRED)
-endif()
-
-if(NOT TARGET g2_d)
-  find_package(g2 REQUIRED)
-endif()
+find_package(gfsio REQUIRED)
+find_package(sfcio REQUIRED)
+find_package(w3nco REQUIRED)
+find_package(landsfcutil REQUIRED)
+find_package(bacio REQUIRED)
+find_package(nemsio REQUIRED)
+find_package(nemsiogfs REQUIRED)
+find_package(sigio REQUIRED)
+find_package(sp REQUIRED)
+find_package(ip REQUIRED)
+find_package(w3emc REQUIRED)
+find_package(g2 REQUIRED)
+find_package(wgrib2 REQUIRED)
 
 # EMC requires executables in ./exec
 set(exec_dir bin)

build_all.sh

@@ -3,29 +3,35 @@ set -eux
 
 target=${target:-"NULL"}
 
-if [[ $target == "linux.gnu" || $target == "linux.intel" ]]; then
+if [[ "$target" == "linux.gnu" || "$target" == "linux.intel" ]]; then
  unset -f module
 else
+ set +x
  source ./sorc/machine-setup.sh > /dev/null 2>&1
+ set -x
 fi
 
 export MOD_PATH
+set +x
 source ./modulefiles/build.$target             > /dev/null 2>&1
+module list
+set -x
 
-#
 # --- Build all programs.
 #
 
 rm -fr ./build
 mkdir ./build
 cd ./build
 
-if [[ $target == "wcoss_cray" ]]; then
-  cmake .. -DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON
-else
-  cmake .. -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_C_COMPILER=icc -DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON
+CMAKE_FLAGS="-DCMAKE_INSTALL_PREFIX=../ -DEMC_EXEC_DIR=ON"
+
+if [[ "$target" != "wcoss_cray" ]]; then
+  CMAKE_FLAGS+=" -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_C_COMPILER=icc"
 fi
 
+cmake .. ${CMAKE_FLAGS}
+
 make -j 8 VERBOSE=1
 make install
 

modulefiles/build.hera

@@ -7,22 +7,23 @@ module load cmake/3.16.1
 module load intel/18.0.5.274
 module load impi/2018.0.4
 
-module use -a /scratch2/NCEPDEV/nwprod/NCEPLIBS/modulefiles
-module load prod_util/1.1.0
-module load w3nco/2.0.6
-module load w3emc/2.3.0
-module load nemsio/2.2.3
-module load bacio/2.0.2
-module load sp/2.0.2
-module load ip/3.0.1
-module load sfcio/1.1.0
-module load sigio/2.1.0
-module load gfsio/1.1.0
-module load nemsiogfs/2.2.0
-module load landsfcutil/2.1.0
-module load g2/2.5.0
+module use /scratch2/NCEPDEV/nwprod/NCEPLIBS/cmake/install/NCEPLIBS-v1.2.0/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 w3emc/2.7.3
+module load w3nco/2.4.1
+module load gfsio/1.4.1
+module load sfcio/1.4.1
+module load sigio/2.3.2
+module load nemsiogfs/2.5.3
+module load landsfcutil/2.4.1
+module load wgrib2/2.0.8
+
+module use /scratch1/NCEPDEV/nems/emc.nemspara/soft/modulefiles
+module load hdf5_parallel/1.10.6
 module load netcdf_parallel/4.7.4
 module load esmf/8.0.0_ParallelNetCDF
-
-export WGRIB2_ROOT="/scratch1/NCEPDEV/da/George.Gayno/noscrub/wgrib2"

modulefiles/build.jet

@@ -1,30 +1,34 @@
 #%Module#####################################################
 ## Build and run module for Jet
 #############################################################
-
-module use /lfs4/HFIP/hfv3gfs/nwprod/NCEPLIBS/modulefiles
 module load cmake/3.16.1
 module load intel/18.0.5.274
 module load impi/2018.4.274
 module load szip/2.1
-module load hdf5/1.10.4
-module load netcdf/4.6.1
-export NETCDF="/apps/netcdf/4.6.1/intel/18.0.5.274"
-module load w3nco/v2.0.6
-module load w3emc/v2.2.0
-module load sp/v2.0.2
-module load ip/v3.0.0
-module load bacio/v2.0.2
-module load sigio/v2.1.0
-module load sfcio/v1.0.0
-module load nemsio/v2.2.3
-module load nemsiogfs/v2.0.1
-module load gfsio/v1.1.0
-module load landsfcutil/v2.1.0
-module load g2/v3.1.0
+module load hdf5/1.10.5
+module load netcdf/4.7.0
+
+export CC=icc
+export FC=ifort
+export CXX=icpc
+
+export ESMFMKFILE=/lfs4/HFIP/hfv3gfs/software/NCEPLIBS-ufs-v2.0.0beta01/intel-18.0.5.274/impi-2018.4.274/lib64/esmf.mk
+export Jasper_ROOT=/lfs4/HFIP/hfv3gfs/software/NCEPLIBS-ufs-v2.0.0beta01/intel-18.0.5.274/impi-2018.4.274
+
+module use /lfs4/HFIP/hfv3gfs/software/NCEPLIBS-ufs-v2.0.0beta01/intel-18.0.5.274/impi-2018.4.274/modules
+module load w3nco/2.4.1
+module load w3emc/2.7.3
+module load sp/2.3.3
+module load ip/3.3.3
+module load bacio/2.4.1
+module load sigio/2.3.2
+module load sfcio/1.4.1
+module load nemsio/2.5.2
+module load nemsiogfs/2.5.3
+module load gfsio/1.4.1
+module load landsfcutil/2.4.1
+module load g2/3.4.1
+module load wgrib2/2.0.8
+
 
-# Use DTCs version of esmf v8.  POC Dom H.
-module use -a /lfs4/HFIP/hfv3gfs/software/modulefiles/intel-18.0.5.274/impi-2018.4.274
-module load esmf/8.0.0
 
-export WGRIB2_ROOT="/lfs4/HFIP/hwrfv3/Jili.Dong/wgrib2-2.0.8/grib2/lib"

modulefiles/build.orion

@@ -6,23 +6,24 @@ module load cmake/3.15.4
 module load intel/2020
 module load impi/2020
 
-module use -a /apps/contrib/NCEPLIBS/orion/modulefiles
-module load w3nco/2.1.0
-module load nemsio/2.3.0
-module load bacio/2.2.0
-module load sfcio/1.2.0
-module load sigio/2.2.0
-module load gfsio/1.2.0
-module load w3emc/2.4.0
-module load ip/3.1.0
-module load nemsiogfs/2.3.0
-module load landsfcutil/2.2.0
-module load g2/3.1.1
-module load sp/2.0.3
+module use /apps/contrib/NCEPLIBS/orion/cmake/install/NCEPLIBS-v1.2.0/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 w3emc/2.7.3
+module load w3nco/2.4.1
+module load gfsio/1.4.1
+module load sfcio/1.4.1
+module load sigio/2.3.2
+module load nemsiogfs/2.5.3
+module load landsfcutil/2.4.1
+module load wgrib2/2.0.8
+
 export Jasper_ROOT="/apps/jasper-1.900.1"
 
 module use -a /apps/contrib/NCEPLIBS/lib/modulefiles
 module load netcdfp/4.7.4.release
 module load esmflocal/8_0_0.release
 
-export WGRIB2_ROOT="/work/noaa/da/ggayno/save/wgrib2"

modulefiles/build.wcoss_cray

@@ -9,32 +9,36 @@ module load cfp-intel-sandybridge/1.1.0
 module load cmake/3.16.2
 module load PrgEnv-intel/5.2.56
 module rm intel
-module load intel/16.3.210
+module load intel/18.1.163
 module load cray-mpich/7.2.0
 module load craype-haswell
 module load alps/5.2.4-2.0502.9822.32.1.ari
 module load cray-netcdf/4.3.3.1
 module load cray-hdf5/1.8.14
-module load w3nco-intel/2.0.6
-module load nemsio-intel/2.2.3
-module load bacio-intel/2.0.2
-module load sp-intel/2.0.2
-module load ip-intel/3.0.0
-module load sigio-intel/2.1.0
-module load sfcio-intel/1.0.0
-module load landsfcutil-intel/2.1.0
-module load gfsio-intel/1.1.0
-module load w3emc-intel/2.2.0
-module load nemsiogfs-intel/2.0.1
-module load g2-intel/2.5.0
+
+module use /usrx/local/nceplibs/NCEPLIBS/cmake/install/NCEPLIBS-v1.2.0/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 w3emc/2.7.3
+module load w3nco/2.4.1
+module load gfsio/1.4.1
+module load sfcio/1.4.1
+module load sigio/2.3.2
+module load nemsiogfs/2.5.3
+module load landsfcutil/2.4.1
+module load wgrib2/2.0.8
+
 export ZLIB_ROOT=/usrx/local/prod/zlib/1.2.7/intel/haswell
 export PNG_ROOT=/usrx/local/prod//png/1.2.49/intel/haswell
 export Jasper_ROOT=/usrx/local/prod/jasper/1.900.1/intel/haswell
 
 module use /gpfs/hps3/emc/nems/noscrub/emc.nemspara/soft/modulefiles
 module load esmf/8.0.0
+export ESMFMKFILE=/gpfs/hps3/emc/nems/noscrub/emc.nemspara/soft/esmf/8.0.0/lib/esmf.mk
 export NETCDF=/opt/cray/netcdf/4.3.3.1/INTEL/14.0
 module rm gcc
 module load gcc/6.3.0
 
-export WGRIB2_ROOT=/gpfs/hps3/emc/global/noscrub/George.Gayno/wgrib2