feature/gdas_init.v16 This commit references ufs-community#102.

Merge branch 'develop' into feature/gdas_init.v16

.gitmodules

@@ -0,0 +1,4 @@
+[submodule "cmake"]
+	path = cmake
+	url = https://github.com/NOAA-EMC/CMakeModules
+	branch = release/public-v1

CMakeLists.txt

@@ -0,0 +1,117 @@
+cmake_minimum_required(VERSION 3.15)
+
+file(STRINGS "VERSION" pVersion)
+
+project(
+  ufs_util
+  VERSION ${pVersion}
+  LANGUAGES C Fortran)
+list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake/Modules/")
+
+if(NOT CMAKE_BUILD_TYPE MATCHES "^(Debug|Release|RelWithDebInfo|MinSizeRel)$")
+  message(STATUS "Setting build type to 'Release' as none was specified.")
+  set(CMAKE_BUILD_TYPE
+      "Release"
+      CACHE STRING "Choose the type of build." FORCE)
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release"
+                                               "MinSizeRel" "RelWithDebInfo")
+endif()
+
+if(NOT CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel|GNU|Clang|AppleClang)$")
+  message(WARNING "Compiler not officially supported: ${CMAKE_Fortran_COMPILER_ID}")
+endif()
+
+if(NOT CMAKE_C_COMPILER_ID MATCHES "^(Intel|GNU)$")
+  message(WARNING "Compiler not officially supported: ${CMAKE_C_COMPILER_ID}")
+endif()
+
+if(CMAKE_Fortran_COMPILER_ID MATCHES "^(Intel)$")
+  set(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)$")
+  set(CMAKE_Fortran_FLAGS "-g -fbacktrace")
+  set(CMAKE_Fortran_FLAGS_RELEASE "-O3")
+  set(CMAKE_Fortran_FLAGS_DEBUG "-O0 -ggdb -fno-unsafe-math-optimizations -frounding-math -fsignaling-nans -ffpe-trap=invalid,zero,overflow -fbounds-check")
+endif()
+
+if(CMAKE_C_COMPILER_ID MATCHES "^(Intel)$")
+  set(CMAKE_C_FLAGS "-g -traceback")
+  set(CMAKE_C_FLAGS_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(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()
+
+# EMC requires executables in ./exec
+set(exec_dir bin)
+if(EMC_EXEC_DIR)
+  set(exec_dir exec)
+endif()
+
+add_subdirectory(sorc)

build_all.sh

@@ -0,0 +1,32 @@
+#! /usr/bin/env bash
+set -eux
+
+target=${target:-"NULL"}
+
+if [[ $target == "linux.gnu" || $target == "linux.intel" ]]; then
+ unset -f module
+else
+ source ./sorc/machine-setup.sh > /dev/null 2>&1
+fi
+
+export MOD_PATH
+source ./modulefiles/build.$target             > /dev/null 2>&1
+
+#
+# --- 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
+fi
+
+make -j 8 VERBOSE=1
+make install
+
+exit

driver_scripts/driver_grid.cray.sh

@@ -49,8 +49,8 @@
 #
 #-----------------------------------------------------------------------
 
-. $MODULESHOME/init/sh
-module load PrgEnv-intel cfp-intel-sandybridge/1.1.0
+source ../sorc/machine-setup.sh > /dev/null 2>&1
+source ../modulefiles/build.$target
 module list
 
 #-----------------------------------------------------------------------

driver_scripts/driver_grid.dell.sh

@@ -51,13 +51,8 @@
 #
 #-----------------------------------------------------------------------
 
-module purge
-module load EnvVars/1.0.2
-module load lsf/10.1
-module load ips/18.0.1.163
-module load impi/18.0.1
-module load NetCDF/4.5.0
-module load HDF5-serial/1.10.1
+source ../sorc/machine-setup.sh > /dev/null 2>&1
+source ../modulefiles/build.$target
 module list
 
 #-----------------------------------------------------------------------

driver_scripts/driver_grid.hera.sh

@@ -51,12 +51,8 @@
 
 set -x
 
-. /apps/lmod/lmod/init/sh
-module purge
-module load intel/18.0.5.274
-module load impi/2018.0.4
-module load hdf5/1.10.5
-module load netcdf/4.7.0
+source ../sorc/machine-setup.sh > /dev/null 2>&1
+source ../modulefiles/build.$target
 module list
 
 #-----------------------------------------------------------------------

driver_scripts/driver_grid.jet.sh

@@ -52,13 +52,8 @@
 
 set -x
 
-. /apps/lmod/lmod/init/sh
-module purge
-module load intel/18.0.5.274
-module load impi/2018.4.274
-module load szip
-module load hdf5
-module load netcdf/4.2.1.1
+source ../sorc/machine-setup.sh > /dev/null 2>&1
+source ../modulefiles/build.$target
 module list
 
 #-----------------------------------------------------------------------
@@ -92,8 +87,8 @@ fi
 #-----------------------------------------------------------------------
 
 export home_dir=$SLURM_SUBMIT_DIR/..
-export TMPDIR=/mnt/lfs3/projects/emcda/$LOGNAME/stmp/fv3_grid.$gtype
-export out_dir=/mnt/lfs3/projects/emcda/$LOGNAME/stmp/C${res}
+export TMPDIR=/lfs4/HFIP/emcda/$LOGNAME/stmp/fv3_grid.$gtype
+export out_dir=/lfs4/HFIP/emcda/$LOGNAME/stmp/C${res}
 
 #-----------------------------------------------------------------------
 # Should not need to change anything below here.

sorc/link_fixdirs.sh → fix/link_fixdirs.sh

@@ -42,9 +42,8 @@ elif [ $machine = "dell" ]; then
 elif [ $machine = "hera" ]; then
     FIX_DIR="/scratch1/NCEPDEV/global/glopara/fix"
 elif [ $machine = "jet" ]; then
-    FIX_DIR="/lfs3/projects/hfv3gfs/glopara/git/fv3gfs/fix"
+    FIX_DIR="/lfs4/HFIP/hfv3gfs/glopara/git/fv3gfs/fix"
 fi
-cd ${pwd}/../fix                ||exit 8
 for dir in fix_am fix_fv3 fix_orog fix_fv3_gmted2010 fix_sfc_climo; do
     [[ -d $dir ]] && rm -rf $dir
     $LINK $FIX_DIR/$dir  .

modulefiles/fv3gfs/global_chgres.hera → modulefiles/build.hera

@@ -1,24 +1,28 @@
 #%Module#####################################################
-## global_chgres component - hera
+## Build and run module for Hera
 #############################################################
 
-# Loading Intel Compiler Suite
+module load hpss
+module load cmake/3.16.1
 module load intel/18.0.5.274
 module load impi/2018.0.4
 
-# Loding nceplibs modules
-module use -a $MOD_PATH
-module load sigio/2.1.0
+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 sp/2.0.2
-module load bacio/2.0.2
 module load nemsio/2.2.3
-module load nemsiogfs/2.2.0
+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 load netcdf_parallel/4.7.4
+module load esmf/8.0.0_ParallelNetCDF
 
-set FCMP ifort
+export WGRIB2_ROOT="/scratch1/NCEPDEV/da/George.Gayno/noscrub/wgrib2"

modulefiles/build.jet

@@ -0,0 +1,30 @@
+#%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
+
+# 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

@@ -0,0 +1,31 @@
+#############################################################
+## Build module for Orion
+#############################################################
+
+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 sp/2.1.0
+module load sfcio/1.2.0
+module load sigio/2.2.0
+module load gfsio/1.2.0
+module load w3emc/2.5.0
+module load ip/3.1.0
+module load nemsiogfs/2.3.0
+module load landsfcutil/2.2.0
+
+# George V's version.
+module use -a /apps/contrib/NCEPLIBS/lib/modulefiles
+module load g2-intel-sandybridge/2.5.0
+
+export Jasper_ROOT="/apps/jasper-1.900.1"
+
+module load netcdf/4.7.2-parallel
+module load esmf/8.0.0_ParallelNetCDF
+
+export WGRIB2_ROOT="/work/noaa/da/ggayno/save/wgrib2"

modulefiles/build.wcoss_cray

@@ -0,0 +1,40 @@
+#%Module#####################################################
+## Build and run module for WCOSS-Cray
+#############################################################
+
+module load prod_util/1.1.0
+module load hpss/4.1.0.3
+module load xt-lsfhpc/9.1.3
+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 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
+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 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