Merge remote-tracking branch 'remotes/origin/release/hafs_v2' into su…

…pport/HAFS

.github/workflows/gcc.yml

@@ -62,6 +62,7 @@ jobs:
           spack add [email protected]
           spack concretize
           spack install -v --fail-fast --dirty
+          spack clean --all
 
   build:
     needs: setup

.github/workflows/intel.yml

@@ -9,7 +9,7 @@ defaults:
 
 # Set I_MPI_CC/F90 so Intel MPI wrapper uses icc/ifort instead of gcc/gfortran
 env:
-  cache_key: intel2  # The number (#) following the cache_key "intel" is to flush Action cache.
+  cache_key: intel3  # The number (#) following the cache_key "intel" is to flush Action cache.
   CC: icc
   FC: ifort
   CXX: icpc
@@ -33,7 +33,7 @@ env:
 
 jobs:
   setup:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
       - name: checkout-upp  # This is for getting spack.yaml
@@ -45,7 +45,7 @@ jobs:
       # Cache spack, compiler and dependencies
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack
@@ -59,14 +59,13 @@ jobs:
           sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS.PUB
           echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
           sudo apt-get update
-          sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic
+          sudo apt-get install intel-oneapi-dev-utilities intel-oneapi-mpi-devel intel-oneapi-openmp intel-oneapi-compiler-fortran-2023.2.1 intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.2.1
           echo "source /opt/intel/oneapi/setvars.sh" >> ~/.bash_profile
 
       # Install dependencies using Spack
       - name: install-dependencies-with-spack
         if: steps.cache-env.outputs.cache-hit != 'true'
         run: |
-          sudo mv /usr/local/ /usr_local_mv
           git clone -c feature.manyFiles=true https://github.com/NOAA-EMC/spack.git
           source spack/share/spack/setup-env.sh
           spack env create upp-env UPP/ci/spack.yaml
@@ -77,10 +76,11 @@ jobs:
           spack add intel-oneapi-mpi
           spack concretize
           spack install --dirty -v --fail-fast
+          spack clean --all
 
   build:
     needs: setup
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
       - name: checkout-upp
@@ -94,7 +94,7 @@ jobs:
 
       - name: cache-env
         id: cache-env
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: |
             spack

.gitmodules

@@ -2,3 +2,7 @@
   path = sorc/ncep_post.fd/post_gtg.fd
   url = https://github.com/NCAR/UPP_GTG
   update = none
+[submodule "sorc/libIFI.fd"]
+  path = sorc/libIFI.fd
+  url = https://github.com/NCAR/UPP_IFI
+  update = none

.readthedocs.yml

@@ -4,6 +4,10 @@
 
 # Required
 version: 2
+build: 
+  os: ubuntu-20.04
+  tools: 
+    python: "3.9"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -17,8 +21,7 @@ sphinx:
 formats: all
 
 # Optionally set the version of Python and requirements required to build your docs
-#python:
+python:
 #  version: 3.7
-#  install:
-
-#    - requirements: docs/requirements.txt
+  install:
+    - requirements: docs/requirements.txt

CMakeLists.txt

@@ -7,14 +7,16 @@ file(STRINGS "VERSION" pVersion LIMIT_COUNT 1)
 project(
   upp
   VERSION ${pVersion}
-  LANGUAGES Fortran)
+  LANGUAGES Fortran C CXX)
 
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
 
 # Handle user options.
 option(OPENMP "use OpenMP threading" ON)
 option(BUILD_POSTEXEC "Build NCEPpost executable" ON)
 option(BUILD_WITH_WRFIO "Build NCEPpost with WRF-IO library" OFF)
+option(BUILD_WITH_IFI "Build NCEPpost with In-Flight Icing (IFI) library if present" OFF)
+option(REQUIRE_IFI "Abort if libIFI is not found ; enables BUILD_WITH_IFI=ON" OFF)
 option(BUILD_WITH_GTG   "Build NCEPpost with NCAR/GTG" OFF)
 option(ENABLE_DOCS "Enable generation of doxygen-based documentation." OFF)
 
@@ -52,6 +54,35 @@ if(BUILD_WITH_GTG)
   find_package(ip REQUIRED)
 endif()
 
+if(INTERNAL_IFI)
+  if(BUILD_WITH_IFI)
+    message(SEND_ERROR "Cannot use INTERNAL_IFI with either BUILD_WITH_IFI or REQUIRE_IFI.")
+  endif()
+  if(IFI_DIR)
+    message(SEND_ERROR "When INTERNAL_IFI is specified, do not set IFI_DIR.")
+  endif()
+  set(REQUIRE_IFI ON)
+  set(BUILD_WITH_IFI ON)
+  set(IFI_FOUND ON)
+  set(IFI_DIR ${CMAKE_INSTALL_DIR})
+  message(NOTICE "Building IFI inside the post.")
+else()
+  if(REQUIRE_IFI)
+    set(BUILD_WITH_IFI ON)
+  endif()
+
+  if(BUILD_WITH_IFI)
+    if(REQUIRE_IFI)
+      find_package(IFI REQUIRED)
+    else()
+      find_package(IFI)
+    endif()
+  endif()
+  if(IFI_FOUND)
+    message(NOTICE "Linking to IFI external to the post.")
+  endif()
+endif()
+
 if(BUILD_POSTEXEC)
   find_package(nemsio REQUIRED)
   find_package(sfcio REQUIRED)
@@ -61,6 +92,22 @@ if(BUILD_POSTEXEC)
   if(BUILD_WITH_WRFIO)
     find_package(wrf_io REQUIRED)
   endif()
+  if(IFI_FOUND)
+    if(CMAKE_Fortran_COMPILER_ID MATCHES "^Intel$")
+      set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -cxxlib")
+    elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^GNU$")
+      set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -lstdc++")
+    elseif(CMAKE_Fortran_COMPILER_ID MATCHES "^(GNU|AppleClang)$")
+      # This one is a wild guess. I haven't tried linking a Fortran
+      # executable with C++ libraries in clang.
+      set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -stdlib=libc++ -lc++abi")
+    endif()
+  endif()
+endif()
+
+if(IFI_FOUND OR INTERNAL_IFI)
+  message(NOTICE "Enabling USE_IFI in the post.")
+  add_definitions(-DUSE_IFI=1)
 endif()
 
 add_subdirectory(sorc)

README.md

@@ -63,16 +63,22 @@ Code Managers: Wen Meng, Huiya Chuang, Kate Fossell
 
 ## Prerequisites
 
-The UPP requires certain NCEPLIB packages to be installed via
-the HPC-Stack project.  
+The UPP requires certain NCEPLIBS packages to be installed via the 
+HPC-Stack project. For instructions on installing these packages as a 
+bundle via HPC-Stack, see: https://hpc-stack.readthedocs.io/en/latest/.
+Users may instead install packages via spack-stack. For instructions,
+see: https://spack-stack.readthedocs.io/en/latest/.
+The `UPP/modulefiles` directory indicates which package versions are 
+used and supported on Level 1 systems. 
+
+Required NCEPLIBS packages:
 
 - [NCEPLIBS-g2](https://github.com/NOAA-EMC/NCEPLIBS-g2)
 - [NCEPLIBS-g2tmpl](https://github.com/NOAA-EMC/NCEPLIBS-g2tmpl)
 - [NCEPLIBS-sp](https://github.com/NOAA-EMC/NCEPLIBS-sp)
 - [NCEPLIBS-ip](https://github.com/NOAA-EMC/NCEPLIBS-ip)
 - [NCEPLIBS-bacio](https://github.com/NOAA-EMC/NCEPLIBS-bacio)
 - [NCEPLIBS-w3emc](https://github.com/NOAA-EMC/NCEPLIBS-w3emc)
-- [NCEPLIBS-w3nco](https://github.com/NOAA-EMC/NCEPLIBS-w3nco)
 - [CRTM](https://github.com/noaa-emc/emc_crtm)
 
 Also required to build NCEPpost executable (cmake option
@@ -89,11 +95,13 @@ option BUILD_WITH_WRFIO).
 
 The following third-party libraries are required:
 
+- [netcdf](https://github.com/Unidata/netcdf)
 - [netcdf-c](https://github.com/Unidata/netcdf-c)
 - [netcdf-fortran](https://github.com/Unidata/netcdf-fortran)
 - [Jasper](https://github.com/jasper-software/jasper)
 - [libpng](http://www.libpng.org/pub/png/libpng.html)
-- [libz](https://zlib.net/)
+- [zlib](https://zlib.net/)
+- [hdf5](https://github.com/HDFGroup/hdf5)
 
 ## Building
 
@@ -128,3 +136,7 @@ Commerce. The Department of Commerce seal and logo, or the seal and
 logo of a DOC bureau, shall not be used in any manner to imply
 endorsement of any commercial product or activity by DOC or the United
 States Government.
+
+## UPP Terms of Use Notice
+
+The UPP Terms of Use Notice is available at: https://github.com/NOAA-EMC/UPP/wiki/UPP-Terms-of-Use-Notice