Merge branch 'working' into develop

CMakeLists.txt

@@ -0,0 +1,65 @@
+cmake_minimum_required(VERSION 2.6)
+project(ufs_util)
+set(VERSION v1.1.1)
+enable_language (Fortran)
+if (NOT CMAKE_BUILD_TYPE)
+    set (CMAKE_BUILD_TYPE RELEASE CACHE STRING
+        "Choose the type of build, options are: PRODUCTION Debug Release."
+        FORCE)
+endif()
+if(CMAKE_CXX_COMPILER_ID STREQUAL "Intel")
+  message("setting intel true")
+  set(IntelComp true )
+elseif(CMAKE_CXX_COMPILER_ID MATCHES "GNU*")
+  set(GNUComp true )
+elseif(CMAKE_CXX_COMPILER_ID MATCHES "pgc*")
+  set(PGIComp true )
+endif()
+MESSAGE(${CMAKE_CURRENT_SOURCE_DIR})
+STRING(COMPARE EQUAL ${CMAKE_BUILD_TYPE} "RelWithDebInfo" BUILD_RELEASE)
+if(NOT BUILD_RELEASE )
+  STRING(COMPARE EQUAL ${CMAKE_BUILD_TYPE} "RELEASE" BUILD_RELEASE)
+endif()
+STRING(COMPARE EQUAL ${CMAKE_BUILD_TYPE} "PRODUCTION" BUILD_PRODUCTION)
+STRING(COMPARE EQUAL ${CMAKE_BUILD_TYPE} "DEGUG" BUILD_DEBUG)
+set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}/cmake/Modules/")
+
+if(POLICY CMP0054)
+    cmake_policy(SET CMP0054 NEW)
+endif()
+if(POLICY CMP0012)
+    cmake_policy(SET CMP0012 NEW)
+endif()
+find_package( NetCDF )
+find_package( OpenMP )
+message("openmp flags is ${OpenMP_Fortran_FLAGS}")
+find_package( MPI )
+find_package( LAPACK )
+find_package( LANDSFCUTIL )
+find_package( Jasper )
+find_package( PNG )
+find_package( SFCIO )
+find_package( ZLIB )
+find_package( W3NCO )
+#find_package( G2 )
+find_package( BACIO )
+find_package( NEMSIO )
+#find_package( NEMSIOGFS )
+find_package( SIGIO )
+#find_package( IP )
+find_package( SP )
+find_package( HDF5 COMPONENTS C HL Fortran_HL )
+find_package( ESMF )
+
+add_subdirectory(sorc/chgres_cube.fd)
+#add_subdirectory(sorc/emcsfc_ice_blend.fd)
+#add_subdirectory(sorc/emcsfc_snow2mdl.fd)
+#add_subdirectory(sorc/fre-nctools.fd)
+#add_subdirectory(sorc/global_chgres.fd)
+#add_subdirectory(sorc/global_cycle.fd)
+#add_subdirectory(sorc/nemsio_chgdate.fd)
+#add_subdirectory(sorc/nemsio_get.fd)
+#add_subdirectory(sorc/nemsio_read.fd)
+#add_subdirectory(sorc/nst_tf_chg.fd)
+#add_subdirectory(sorc/orog.fd)
+#add_subdirectory(sorc/sfc_climo_gen.fd)

modulefiles/chgres_cube.hera

@@ -4,20 +4,26 @@
 
 module load intel/18.0.5.274
 module load impi/2018.0.4
+#module use -a $MOD_PATH
+module use -a /contrib/da/spack/share/spack/modules/linux-centos7-skylake_avx512
+module load cmake/3.15.3-intel-19.0.4.243
+module load w3nco/v2.0.6-intel-19.0.4.243-impi
+module load nemsio/v2.2.3-intel-19.0.4.243-impi 
+module load nemsiogfs/v2.2.1-intel-19.0.4.243-impi
+module load ip/v3.0.0-intel-19.0.4.243
+module load g2/v3.1.0-intel-19.0.4.243
+module load landsfcutil/v2.1.0-intel-19.0.4.243
+module load bacio/v2.1.0-intel-19.0.4.243
+module load sp/v2.0.2-intel-19.0.4.243
+module load sfcio//v1.1.0-intel-19.0.4.243
+module load sigio/v2.1.0-intel-19.0.4.243-impi
+module load esmf/8.0.0b-intel-19.0.4.243-impi 
 
-module use -a $MOD_PATH
-module load w3nco/2.0.6
-module load nemsio/2.2.3
-module load bacio/2.0.2
-module load sp/2.0.2
-module load sfcio/1.1.0
-module load sigio/2.1.0
+#export NCEPLIBS=/scratch1/NCEPDEV/global/gwv/l819/lib
+#module use -a $NCEPLIBS/modulefiles
+#module load esmflocal/8_0_48b.netcdf47
 
-export NCEPLIBS=/scratch1/NCEPDEV/global/gwv/l819/lib
-module use -a $NCEPLIBS/modulefiles
-module load esmflocal/8_0_48b.netcdf47
-
-export FCOMP=mpiifort
-export FFLAGS="-O3 -fp-model precise -g -traceback -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
+#export FCOMP=mpiifort
+#export FFLAGS="-O3 -fp-model precise -g -traceback -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
 # for debugging
 #export FFLAGS="-O0 -g -traceback -r8 -i4 -qopenmp -convert big_endian -check bounds -warn unused -assume byterecl"

modulefiles/chgres_cube.theia

@@ -0,0 +1,23 @@
+#%Module#####################################################
+## chgres build module for Theia
+#############################################################
+
+module load intel/15.1.133
+module load impi/5.1.1.109
+module load netcdf/4.3.0
+
+module use /scratch4/NCEPDEV/nems/noscrub/emc.nemspara/soft/modulefiles
+module load esmf/8.0.0bs20
+
+module use -a /scratch3/NCEPDEV/nwprod/lib/modulefiles
+module load w3nco
+module load nemsio/v2.2.3
+module load bacio/v2.0.1
+module load sp/v2.0.2
+module load sfcio/v1.0.0
+module load sigio/v2.0.1
+
+export FCOMP=mpiifort
+export FFLAGS="-O3 -fp-model precise -g -traceback -r8 -i4 -qopenmp -convert big_endian -assume byterecl"
+# for debugging
+#export FFLAGS="-O0 -g -traceback -r8 -i4 -qopenmp -convert big_endian -check bounds -warn unused -assume byterecl"

modulefiles/fv3gfs/fre-nctools.theia

@@ -0,0 +1,7 @@
+#%Module#####################################################
+## Module file for fre-nctools
+#############################################################
+module load intel/14.0.2
+module load impi/4.1.3.048
+module load netcdf/4.3.0
+module load hdf5/1.8.14

modulefiles/fv3gfs/global_chgres.theia

@@ -0,0 +1,31 @@
+#%Module#####################################################
+## global_chgres component - theia
+#############################################################
+
+# Loading Intel Compiler Suite
+module load intel/14.0.2
+module load impi/5.1.2.150
+
+# Loding nceplibs modules
+module use -a $MOD_PATH
+module load sigio/v2.0.1
+module load w3nco/v2.0.6
+module load w3emc/v2.2.0
+module load sp/v2.0.2
+module load bacio/v2.0.2
+module load nemsio/v2.2.3
+module load nemsiogfs/v2.0.1
+export NEMSIOGFS_INC=/scratch4/NCEPDEV/global/save/glopara/svn/nceplibs/branches/nemsiogfsv2.0.1/include/nemsiogfs
+export NEMSIOGFS_LIB=/scratch4/NCEPDEV/global/save/glopara/svn/nceplibs/branches/nemsiogfsv2.0.1/libnemsiogfs.a
+
+module load ip/v3.0.0
+module load sfcio/v1.0.0
+module load gfsio/v1.1.0
+module load landsfcutil/v2.1.0
+module load netcdf/4.3.0
+module load hdf5/1.8.14
+
+export NETCDF_INCLUDE="-I${NETCDF}/include"
+export NETCDF_LDFLAGS_F="-L${NETCDF}/lib -lnetcdf -lnetcdff -L${HDF5}/lib -lhdf5 -lhdf5_fortran"
+
+set FCMP ifort

modulefiles/fv3gfs/global_cycle.theia

@@ -0,0 +1,20 @@
+#%Module#####################################################
+## global_cycle component - theia
+#############################################################
+
+# Loading Intel Compiler Suite
+module load intel/16.1.150
+module load impi
+
+# Loding nceplibs modules
+module use -a /scratch3/NCEPDEV/nwprod/lib/modulefiles
+module load w3nco/v2.0.6
+module load sp/v2.0.2
+module load bacio/v2.0.1
+module load ip/v3.0.0
+module load netcdf/4.3.0
+module load hdf5/1.8.14
+export NETCDF_INCLUDE="-I${NETCDF}/include"
+export NETCDF_LDFLAGS_F="-L${NETCDF}/lib -lnetcdf -lnetcdff -L${HDF5}/lib -lhdf5 -lhdf5_fortran"
+
+export FCMP=mpiifort

modulefiles/fv3gfs/nst_tf_chg.theia

@@ -0,0 +1,21 @@
+#%Module#####################################################
+## gaussian_sfcanl build module for Theia
+#############################################################
+
+# Loading Intel Compiler Suite
+module load intel/15.1.133
+
+# Loding nceplibs modules
+module use -a /scratch3/NCEPDEV/nwprod/lib/modulefiles
+module load w3nco/v2.0.6
+module load bacio/v2.0.2
+module load nemsio/v2.2.3
+module load netcdf/4.3.0
+module load hdf5/1.8.14
+export NETCDF_INCLUDE="-I${NETCDF}/include"
+export NETCDF_LDFLAGS_F="-L${NETCDF}/lib -lnetcdf -lnetcdff -L${HDF5}/lib -lhdf5 -lhdf5_fortran"
+
+export FCOMP=ifort
+export FFLAGS="-O3 -fp-model precise -g -r8 -i4"
+# for debugging
+#export FFLAGS="-g -r8 -i4 -warn unused -check bounds"

modulefiles/fv3gfs/orog.theia

@@ -0,0 +1,16 @@
+#%Module#####################################################
+## Module file for orog
+#############################################################
+# Loading Intel Compiler Suite
+module unload intel
+module load intel/16.1.150
+
+module load netcdf/4.3.0
+
+# Loding nceplibs modules
+module use -a $MOD_PATH
+module load ip/v2.0.0
+module load sp/v2.0.2
+module load w3emc/v2.2.0
+module load w3nco/v2.0.6
+module load bacio/v2.0.2

modulefiles/module-setup.csh.inc

@@ -0,0 +1,89 @@
+set __ms_shell=csh
+
+eval "if ( -d / ) set __ms_shell=tcsh"
+
+if ( { test -d /lfs3 } ) then 
+    if ( ! { module help >& /dev/null } ) then
+            source /apps/lmod/lmod/init/$__ms_shell
+    endif
+    module purge
+else if ( { test -d /scratch3 } ) then
+    # We are on NOAA Theia
+    if ( ! { module help >& /dev/null } ) then
+        source /apps/lmod/lmod/init/$__ms_shell
+    endif
+    module purge
+else if ( { test -d /gpfs/hps -a -e /etc/SuSE-release } ) then
+    # We are on NOAA Luna or Surge
+    if ( ! { module help >& /dev/null } ) then
+	source /opt/modules/default/init/$__ms_shell
+    endif
+    module purge
+    module purge
+    unset _LMFILES_
+    unset LOADEDMODULES
+    module use /opt/modulefiles
+    module use /opt/cray/ari/modulefiles
+    module use /opt/cray/craype/default/alt-modulefiles
+    module use /opt/cray/alt-modulefiles
+    module use /gpfs/hps/nco/ops/nwprod/modulefiles
+    module use /gpfs/hps/nco/ops/nwprod/lib/modulefiles
+    module use /usrx/local/prod/modulefiles
+else if ( { test -d /dcom -a -d /hwrf } ) then
+    # We are on NOAA Tide or Gyre
+    if ( ! { module help >& /dev/null } ) then
+        source /usrx/local/Modules/default/init/$__ms_shell
+    endif
+    module purge
+else if ( { test -L /usrx && sh -c "readlink /usrx 2> /dev/null | grep dell" } ) then
+    # We are on WCOSS Mars or Venus
+    if ( ! { module help >& /dev/null } ) then
+        source /usrx/local/prod/lmod/lmod/init/$__ms_shell
+    endif
+    module purge
+else if ( { test -d /glade } ) then
+    # We are on NCAR Yellowstone
+    if ( ! { module help >& /dev/null } ) then
+        source /usr/share/Modules/init/$__ms_shell
+    endif
+    module purge
+else if ( { test -d /lustre -a -d /ncrc } ) then
+    # We are on GAEA. 
+    if ( ! { module help >& /dev/null } ) then
+        # We cannot simply load the module command.  The GAEA
+        # /etc/csh.login modifies a number of module-related variables
+        # before loading the module command.  Without those variables,
+        # the module command fails.  Hence we actually have to source
+        # /etc/csh.login here.
+        source /etc/csh.login
+        set __ms_source_etc_csh_login=yes
+    else
+        set __ms_source_etc_csh_login=no
+    endif
+    module purge
+    unsetenv _LMFILES_
+    unsetenv _LMFILES_000
+    unsetenv _LMFILES_001
+    unsetenv LOADEDMODULES
+    module load modules
+    if ( { test -d /opt/cray/ari/modulefiles } ) then
+        module use -a /opt/cray/ari/modulefiles
+    endif
+    if ( { test -d /opt/cray/pe/ari/modulefiles } ) then
+        module use -a /opt/cray/pe/ari/modulefiles
+    endif
+    if ( { test -d /opt/cray/pe/craype/default/modulefiles } ) then
+        module use -a /opt/cray/pe/craype/default/modulefiles
+    endif
+    setenv NCEPLIBS /lustre/f1/pdata/ncep_shared/NCEPLIBS/lib
+    if ( { test -d /lustre/f1/pdata/ncep_shared/NCEPLIBS/lib } ) then
+      module use $NCEPLIBS/modulefiles
+    endif
+    if ( "$__ms_source_etc_csh_login" == yes ) then
+      source /etc/csh.login
+      unset __ms_source_etc_csh_login
+    endif
+else
+    # Workaround for csh limitation.  Use sh to print to stderr.
+    sh -c 'echo WARNING: UNKNOWN PLATFORM 1>&2'
+endif

modulefiles/module_base.hera

@@ -2,10 +2,14 @@
 ##
 ##      FV3GFS prerequisites
 ##
-
+setenv CC icc
+setenv CXX icpc
+setenv FC ifort
+module use -a /contrib/da/spack/share/spack/modules/linux-centos7-skylake_avx512
 module load intel/18.0.5.274
 module load impi/2018.0.4
 module load hpss/hpss
-module load netcdf/4.7.0
+module load netcdf/4.6.2-intel-19.0.4.243-impi 
+module load netcdf-fortran/4.4.5-intel-19.0.4.243-impi
 module load nco/4.7.0
-module load hdf5/1.10.5
+module load hdf5/1.10.5-intel-19.0.4.243-impi

modulefiles/module_base.theia

@@ -0,0 +1,19 @@
+#%Module######################################################################
+##
+##      FV3GFS prerequisites
+##
+
+module load intel/16.1.150
+module load impi/5.1.2.150
+module load wgrib2
+module load hpss
+module load netcdf
+module load nco
+module load hdf5/1.8.14
+module load gempak/6.7.0
+
+module use /scratch3/NCEPDEV/nwprod/lib/modulefiles
+module load EnvVars/v1.0.2
+
+module use /scratch4/NCEPDEV/nems/noscrub/emc.nemspara/soft/modulefiles
+module load prod_util

modulefiles/module_nemsutil.theia

@@ -0,0 +1,15 @@
+#%Module#####################################################
+## Module file for nemsutil
+#############################################################
+
+# Loading Intel Compiler Suite
+module load intel/14.0.2
+module load impi/5.1.2.150
+
+# Loding nceplibs modules
+module use -a $MOD_PATH
+module load w3nco/v2.0.6
+module load bacio/v2.0.1
+module load nemsio/v2.2.1
+
+export FCMP=ifort

modulefiles/modulefile.global_emcsfc_ice_blend.theia

@@ -0,0 +1,17 @@
+#%Module#####################################################
+## emcsfc_ice_blend build module for Theia
+#############################################################
+
+module load intel/14.0.2
+export FCOMP=ifort
+export FFLAGS="-O0 -i4"
+
+# load ncep library modules
+
+module use -a /scratch3/NCEPDEV/nwprod/lib/modulefiles
+module load w3nco/v2.0.6
+module load bacio/v2.0.1
+module load jasper
+module load z
+module load png
+module load g2/v2.5.0