Merge branch '5.2-branch'

ECCC-ASTD-MRD · Aug 28, 2023 · a620567 · a620567
2 parents 1d711f7 + 3bb69b5
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diff --git a/.eccc_setup_gnu b/.eccc_setup_gnu
@@ -10,16 +10,16 @@
 DOMAIN=`hostname -d`
 
 if [[ ${DOMAIN} = "collab.science.gc.ca" ]]; then
-    . r.load.dot rpn/code-tools/ENV/cdt-1.6.3/SCIENCE/gpscc2/gnu-9.3.0
+    . r.load.dot rpn/code-tools/ENV/cdt-1.6.4/SCIENCE/gpscc2/gnu-9.3.0
 elif  [[ -z "${DOMAIN}" || ${DOMAIN} = "science.gc.ca" ]]; then
-    . r.load.dot rpn/code-tools/ENV/cdt-1.6.3/SCIENCE/gnu-9.3.0
+    . r.load.dot rpn/code-tools/ENV/cdt-1.6.4/SCIENCE/gnu-9.3.0
 else
-    . r.load.dot rpn/code-tools/ENV/cdt-1.6.3/ECCC/gnu-9.3.0
+    . r.load.dot rpn/code-tools/ENV/cdt-1.6.4/ECCC/gnu-9.3.0
 fi
 
 # Load latest version of RPN-SI libraries
-. r.load.dot rpn/libs/20230516
-. r.load.dot rpn/utils/20230414
+. r.load.dot rpn/libs/20230531
+. r.load.dot rpn/utils/20230531
 
 # We need a more recent version of cmake than the one available by default
 . ssmuse-sh -d main/opt/cmake/cmake-3.21.1

diff --git a/.eccc_setup_intel b/.eccc_setup_intel
@@ -10,16 +10,16 @@
 DOMAIN=`hostname -d`
 
 if [[ ${DOMAIN} = "collab.science.gc.ca" ]]; then
-    . r.load.dot rpn/code-tools/ENV/cdt-1.6.3/SCIENCE/gpscc2/inteloneapi-2022.1.2
+    . r.load.dot rpn/code-tools/ENV/cdt-1.6.4/SCIENCE/gpscc2/inteloneapi-2022.1.2
 elif  [[ -z "${DOMAIN}" || ${DOMAIN} = "science.gc.ca" ]]; then
-    . r.load.dot rpn/code-tools/ENV/cdt-1.6.3/SCIENCE/inteloneapi-2022.1.2
+    . r.load.dot rpn/code-tools/ENV/cdt-1.6.4/SCIENCE/inteloneapi-2022.1.2
 else
-    . r.load.dot rpn/code-tools/ENV/cdt-1.6.3/ECCC/inteloneapi-2022.1.2
+    . r.load.dot rpn/code-tools/ENV/cdt-1.6.4/ECCC/inteloneapi-2022.1.2
 fi
 
 # Load latest version of RPN-SI libraries and utilities
-. r.load.dot rpn/libs/20230516
-. r.load.dot rpn/utils/20230414
+. r.load.dot rpn/libs/20230531
+. r.load.dot rpn/utils/20230531
 
 # Load Intel FFTW if on rhel
 if  [[ ${ORDENV_DIST} = "rhel" ]]; then

diff --git a/.gitmodules b/.gitmodules
@@ -1,7 +1,7 @@
 [submodule "cmake_rpn"]
 	path = cmake_rpn
 	url = ../cmake_rpn.git
-	branch = dev
+	branch = master
 [submodule "src/rpn-si/vgrid"]
 	path = src/rpn-si/vgrid
 	url = ../vgrid.git

diff --git a/MANIFEST b/MANIFEST
@@ -1,5 +1,5 @@
 NAME       : gem
-VERSION    : 5.2.0-rc1
+VERSION    : 5.2.0-rc3
 BUILD      : RelWithDebInfo
 DESCRIPTION: ECCC-MRD Global Environmental Multi-scale model - GEM
 SUMMARY    : The Global Environmental Multiscale Model (GEM) is an integrated forecasting and data assimilation system developed by the Atmospheric Numerical Prediction Research Section, Meteorological Research Division, of Environment and Climate Change Canada.
@@ -15,5 +15,5 @@ tdpack >= 1.6.2
 vgrid >= 6.9.2
 rpncomm >= 4.6.3
 modelutils = 1.7.0-rc1
-rpnphy = 6.2.0-rc1
-gemdyn = 5.2.0-rc1
+rpnphy = 6.2.0-rc3
+gemdyn = 5.2.0-rc2
diff --git a/Makefile b/Makefile
@@ -10,7 +10,11 @@ MAKEFLAGS += --no-print-directory
 cmake:
 	( cd build-${GEM_ARCH} && cd `/bin/pwd` && cmake ${gem_DIR} )
 
-# Outside CMC: COMPILER_SUITE must be specified for Intel
+# Using static Intel libraries
+cmake-static:
+	( cd build-${GEM_ARCH} && cd `/bin/pwd` && cmake -DSTATIC_INTEL=ON ${gem_DIR} )
+
+# Outside CMC: COMPILER_SUITE may need to be specified for Intel
 cmake-intel:
 	( cd build-${GEM_ARCH} && cd `/bin/pwd` && cmake -DCOMPILER_SUITE=intel ${gem_DIR} )
 

diff --git a/README-install.md b/README-install.md
@@ -17,7 +17,7 @@ Before the first build:
 . ./.initial_setup
 
 # building and installing GEM
-# please see other options with cado -h
+# please see other options with cado -h or by using tab completion
 cado cmake
 cado -j work
 
@@ -39,7 +39,7 @@ To compile and run GEM, you will need:
 - OpenMP support (optional)
 - (BLAS,LAPACK) or equivalent mathematical/scientific library (ie: MKL), with development package,
 - fftw3 library (with development package),
-- basic Unix utilities such as cmake (version 3.16 minimum), bash, sed, etc.
+- basic Unix utilities such as cmake (version 3.20 minimum), bash, sed, etc.
 
 ```
 # clone everything, including libraries and tools included as git submodules
@@ -67,8 +67,6 @@ mkdir -p build
 cd build
 # default compiler is gnu
 cmake ..
-# or, for Intel:
-cmake .. -DCOMPILER_SUITE=intel
 # Create an execution environment for GEM
 make -j work
 
@@ -100,7 +98,7 @@ voir -iment RUNMOD/output/cfg0000/ ...
 fststat -fst RUNMOD/output/cfg0000/ ...
 ```
 
-[SPI](https://github.com/ECCC-ASTD-MRD/SPI) can be used to view the output
+[SPI](https://github.com/ECCC-ASTD-MRD/SPI-Bundle) can be used to view the output
 files.
 
 2D fields can also be displayed with
@@ -117,7 +115,7 @@ To compile and run GEM, you will need:
 - OpenMP support (optional)
 - (BLAS,LAPACK) or equivalent mathematical/scientific library (ie: MKL), with development package,
 - fftw3 library (with development package),
-- basic Unix utilities such as cmake (version 3.16 minimum), bash, sed, etc.
+- basic Unix utilities such as cmake (version 3.20 minimum), bash, sed, etc.
 
 ## Data for examples
 
@@ -133,7 +131,7 @@ link:
 - By default GEM is configured to use gfortran and gcc compilers, and OpenMPI
 - Changes to the C and Fortran flags can be done in the  **CMakeLists.txt**
   file, under the section **# Adding specific flags for GEM**.
-- You can also check  the C and Fortran flags in **cmake_rpn/ec_compiler_presets/default/Linux-x86_64/gnu.cmake**
+- You can also check  the C and Fortran flags in **cmake_rpn/modules/ec_compiler_presets/default/Linux-x86_64/gnu.cmake**
 - Make sure the compilers and libraries paths are set in the appropriate
   environment variables (PATH and LD_LIBRARY_PATH).  Here are some examples
   of commands, which you will need to adapt for your setup:
@@ -156,13 +154,13 @@ link:
 
 - Changes to the C and Fortran flags can be done in the  **CMakeLists.txt**
   file, under the section **# Adding specific flags for GEM**.
-- You can also check  the C and Fortran flags in **cmake_rpn/ec_compiler_presets/default/Linux-x86_64/intel.cmake**
+- You can also check  the C and Fortran flags in **cmake_rpn/modules/ec_compiler_presets/default/Linux-x86_64/intel.cmake**
 - You may need to modify ```-march``` to generate code that can run on your
   system
 - Make sure the compilers and libraries are in the appropriate
   environment variables (```PATH``` and ```LD_LIBRARY_PATH```)
-- As gnu is the default compiler suite, use the following command to compile
-  with Intel: ```cmake .. -DCOMPILER_SUITE=intel```
+- As gnu is the default compiler suite, you may have to use the following
+  command to compile with Intel: ```cmake .. -DCOMPILER_SUITE=intel```
 
 ## Compiling and installing GEM
 
@@ -181,12 +179,12 @@ command line.
 This release has been tested with GNU and Intel compilers on Linux x86_64.
 Other compilers have also been used in the past, but have not been tested
 with the current release.  You will likely have to modify the *.cmake files
-in the **cmake_rpn/ec_compiler_presets/default/** folder.
+in the **cmake_rpn/modules/ec_compiler_presets/default/** folder.
 
 If you get error messages (for example, compiler, OpenMP or MPI/OpenMPI not
 found), make sure that the ```PATH``` and ```LD_LIBRARY_PATH``` environment
 variables contain the appropriate paths.  You can also add
-```-DCMAKE_VERBOSE_MAKEFILE=ON``` to you **cmake** command line to generate
+```-DCMAKE_VERBOSE_MAKEFILE=ON``` to your **cmake** command line to generate
 verbose makefiles which will print the exact compiler command lines issued.
 
 If the compiler or compile options are not right:
@@ -199,7 +197,7 @@ If the compiler or compile options are not right:
 The installation process will create a directory named after the operating system
 on which the compilation was executed, and the compiler you used
 (work-[OS_NAME]-[COMPILER_NAME]). For example
-*work-Fedora-34-x86_64-gnu-11.2.1* would be created in the main directory,
+*work-FedoraLinux-37-x86_64-gnu-12.3.1* would be created in the main directory,
 and the following executables installed in the *bin* sub-folder: 
 
 - cclargs_lite
@@ -221,13 +219,23 @@ and the following executables installed in the *bin* sub-folder:
 - voir
 - yy2global
 
-A script named GEM-config is also installed. It displays a summary of the
+A script named gem-config is also installed. It displays a summary of the
 architecture, compiler, and flags used.
 
+## Structure of the working environment
+
+The following environment variables are created:
+- gem_DIR = directory where the git clone was created
+- GEM_WORK = work directory
+- GEM_ARCH = architecture, for example FedoraLinux-37-x86_64-gnu-12.3.1
+- ATM_MODEL_DFILES = gem database directory
+- COMPILER_SUITE = compiler suite, for example gnu
+- COMPILER_VERSION = compiler version, for example 12.3.1
+
 ## Running GEM
 
 Go to the working directory, named *work-[OS_NAME]-[COMPILER_NAME]*, for
-example *work-Fedora-34-x86_64-gnu-11.2.1*
+example *work-FedoraLinux-37-x86_64-gnu-12.3.1*
 
 ```
 cd work-[OS_NAME]-[COMPILER_NAME]
@@ -238,7 +246,7 @@ runprep.sh -dircfg configurations/GEM_cfgs_GY_FISL_P
 runmod.sh -dircfg configurations/GEM_cfgs_GY_FISL_P
 ```
 
-*runmod.sh*'s ```-ptopo``` argument can be used to specify the number of CPU to
+*runmod.sh* ```-ptopo``` argument can be used to specify the number of CPU to
 use.  For example,  ```-ptopo 2x2x1``` will use 4 cpus for a LAM, and
 8 cpus for global Yin-Yang.
 
@@ -291,7 +299,7 @@ various tasks on the output files:
   editfst -s <input FST> -d <output FST> -i <editfst.directives>
   ```
 
-[SPI](https://github.com/ECCC-ASTD-MRD/SPI) is a scientific and
+[SPI](https://github.com/ECCC-ASTD-MRD/SPI-Bundle) is a scientific and
 meteorological virtual globe offering processing, analysis and visualization
 capabilities, with a user interface similar to Google Earth and NASA World
 Wind, developed by Environment Canada.
@@ -306,8 +314,8 @@ Research Division, Environment and Climate Change Canada.
 The execution of all three components of GEM is configurable through the use
 of three configuration files called:
 - gem_settings.nml: file containing some namelists to configure the model execution
-- outcfg.out: file use to configure the model output
-- configexp.cfg: file use to configure the execution shell environment
+- outcfg.out: file used to configure the model output
+- configexp.cfg: file used to configure the execution shell environment
 
 Examples of these files can be found in the test cases in the configurations
 directory.

diff --git a/_cado b/_cado
@@ -5,8 +5,13 @@ cado_commands=(
     cmake-all
     cmake-debug
     cmake-debug-extra
+    cmake-mach
+    cmake-mach-static
+    cmake-all-mach
+    cmake-mach-debug
     build
     work
+    install
     package
     help
 )
@@ -21,6 +26,7 @@ favorite_makefile_targets=(
     rpnphy
     rmn
     modelutils
+    install
     # ...
 )
 

diff --git a/cado b/cado
@@ -34,9 +34,14 @@ this_project=GEM
         cmake_all_command='WITH_SYSTEM_RPN=FALSE cmake -S . -B ${build_dir} "$@"'
       cmake_debug_command='cmake -S . -B ${build_dir}  -DCMAKE_BUILD_TYPE=Debug" $@"'
 cmake_debug_extra_command='cmake -S . -B ${build_dir}  -DCMAKE_BUILD_TYPE=Debug" -DEXTRA_CHECKS_ON $@"'
+       cmake_mach_command='cmake -S . -B ${build_dir}  -DWITH_MACH=TRUE "$@"'
+cmake_mach_static_command='cmake -S . -B ${build_dir}  -DWITH_MACH=TRUE -DSTATIC_INTEL=ON "$@"'
+   cmake_all_mach_command='WITH_SYSTEM_RPN=FALSE cmake -S . -B ${build_dir}  -DWITH_MACH=TRUE "$@"'
+ cmake_mach_debug_command='cmake -S . -B ${build_dir}  -DWITH_MACH=TRUE -DCMAKE_BUILD_TYPE=Debug" $@"'
 
   build_command='cmake --build ${build_dir} -- "$@"'
    work_command='cmake --build ${build_dir} --target work -- "$@"'
+install_command='cmake --build ${build_dir} --target install -- "$@"'
 package_command='cmake --build ${build_dir} --target package -- "$@"'
   clean_command='cmake --build ${build_dir} --target clean -- "$@"'
 
@@ -105,6 +110,10 @@ COMMANDS:
     cmake-all: configure using sources of RPN libraries (WITH_SYSTEM_RPN is set to FALSE)
     cmake-debug: configure with debug flags (-DCMAKE_BUILD_TYPE=Debug)
     cmake-debug-extra:  configure with debug flags and extra compile-time checks (-DCMAKE_BUILD_TYPE=Debug -DEXTRA_CHECKS=ON)
+    cmake-mach: configure using installed RPN libraries (-DWITH_MACH=TRUE)
+    cmake-mach-static: configure using installed RPN libraries and static Intel libraries (-DSTATIC_INTEL=ON -DWITH_MACH=TRUE)
+    cmake-all-mach: configure using sources of RPN libraries (WITH_SYSTEM_RPN is set to FALSE -DWITH_MACH=TRUE)
+    cmake-mach-debug: configure with debug flags (-DCMAKE_BUILD_TYPE=Debug -DWITH_MACH=TRUE)
 
   building: (Additional arguments forwarded to make (like -j))
     build: Build entire project
@@ -155,8 +164,13 @@ case "${name}" in
             cmake-all) cmd=${cmake_all_command} ;;
           cmake-debug) cmd=${cmake_debug_command} ;;
     cmake-debug-extra) cmd=${cmake_debug_extra_command} ;;
+           cmake-mach) cmd=${cmake_mach_command} ;;
+    cmake-mach-static) cmd=${cmake_mach_static_command} ;;
+       cmake-all-mach) cmd=${cmake_all_mach_command} ;;
+     cmake-mach-debug) cmd=${cmake_mach_debug_command} ;;
                 build) cmd=${build_command} ;;
                  work) cmd=${work_command} ;;
+              install) cmd=${install_command} ;;
               package) cmd=${package_command} ;;
                 clean) cmd=${clean_command} ;;
           help|--help) print_cado_help ; exit 0 ;;

diff --git a/scripts/gem_nml_mkref b/scripts/gem_nml_mkref
@@ -3,7 +3,6 @@
 # @Author: S.Chamberland
 # @Date:   Feb 2016
 
-set -x
 DESC='Create a reference nml for gem'
 
 eval $(rpy.cclargparse \
@@ -33,6 +32,8 @@ EOF
    exit 1
 fi
 
+export gemdyn_version=${gemdyn_version:-${ATM_MODEL_VERSION}}
+export rpnphy_version=${rpnphy_version:-${ATM_MODEL_VERSION}}
 a=$(which gemdyn_nml_mkref)
 b=$(which rpnphy_nml_mkref)
 if [[ x"${a}" == x"" || x"${b}" == x"" ]] ; then
@@ -60,4 +61,3 @@ mv ${nmlfilename} ${myfile}
 cd ${here}
 rm -rf ${localtmp}
 exit 0
-set +x