Merge branch 'master' into feature/bug_fixes

samsrabin · Aug 8, 2020 · bb79a7f · bb79a7f
2 parents bfa92e3 + 2fa1125
commit bb79a7f
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diff --git a/.github/workflows/extbuild.yml b/.github/workflows/extbuild.yml
@@ -0,0 +1,110 @@
+# This is a basic workflow to help you get started with Actions
+name: extbuild
+# Controls when the action will run. Triggers the workflow on push or pull request
+# events but only for the master branch
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # Build the ESMF library, if the cache contains a previous build it will be used instead
+  build-cdeps:
+    runs-on: ubuntu-latest
+    env:
+      CC: mpicc
+      FC: mpifort
+      CXX: mpicxx
+      CPPFLAGS: "-I/usr/include -I/usr/local/include"
+    steps:
+      - uses: actions/checkout@v2
+      - id: cache-esmf
+        uses: actions/cache@v2
+        with:
+          path: ~/ESMF
+          key: ${{ runner.os }}-ESMF
+      - id: load-env
+        run: sudo apt-get install gfortran wget openmpi-bin netcdf-bin libopenmpi-dev
+
+      - id: build-ESMF
+        if: steps.cache-esmf.outputs.cache-hit != 'true'
+        run: |
+          wget https://github.com/esmf-org/esmf/archive/ESMF_8_1_0_beta_snapshot_25.tar.gz
+          tar -xzvf ESMF_8_1_0_beta_snapshot_25.tar.gz
+          pushd esmf-ESMF_8_1_0_beta_snapshot_25
+          export ESMF_DIR=`pwd`
+          export ESMF_COMM=openmpi
+          export ESMF_YAMLCPP="internal"
+          export ESMF_INSTALL_PREFIX=$HOME/ESMF
+          export ESMF_BOPT=g
+          make
+          make install
+          popd
+      - id: cache-pnetcdf
+        uses: actions/cache@v2
+        with:
+          path: ~/pnetcdf
+          key: ${{ runner.os }}-pnetcdf
+      - name: pnetcdf build
+        if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
+        run: |
+          wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz
+          tar -xzvf pnetcdf-1.12.1.tar.gz
+          ls -l
+          pushd pnetcdf-1.12.1
+          ./configure --prefix=$HOME/pnetcdf --enable-shared --disable-cxx
+          make
+          make install
+          popd
+      - name: Cache netcdf-fortran
+        id: cache-netcdf-fortran
+        uses: actions/cache@v2
+        with:
+          path: ~/netcdf-fortran
+          key: ${{ runner.os }}-netcdf-fortran
+      - name: netcdf fortran build
+        if: steps.cache-netcdf-fortran.outputs.cache-hit != 'true'
+        run: |
+          sudo apt-get install libnetcdf-dev
+          wget https://github.com/Unidata/netcdf-fortran/archive/v4.5.2.tar.gz
+          tar -xzvf v4.5.2.tar.gz
+          ls -l
+          pushd netcdf-fortran-4.5.2
+          ./configure --prefix=$HOME/netcdf-fortran
+          make
+          make install
+
+      - name: Cache PIO
+        id: cache-PIO
+        uses: actions/cache@v2
+        with:
+          path: ~/pio
+          key: ${{ runner.os }}-pio
+          restore-keys: |
+            ${{ runner.os }}-netcdf-fortran
+            ${{ runner.os }}-pnetcdf
+      - name: Build PIO
+        if: steps.cache-PIO.outputs.cache-hit != 'true'
+        run: |
+          wget https://github.com/NCAR/ParallelIO/releases/download/pio_2_5_1/pio-2.5.1.tar.gz
+          tar -xzvf pio-2.5.1.tar.gz
+          mkdir build-pio
+          pushd build-pio
+          cmake -Wno-dev -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/usr/include -DCMAKE_PREFIX_PATH=/usr -DCMAKE_INSTALL_PREFIX=$HOME/pio -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off -DNetCDF_Fortran_PATH=$HOME/netcdf-fortran -DPnetCDF_PATH=$HOME/pnetcdf ../pio-2.5.1
+          make VERBOSE=1
+          make install
+          popd
+
+      - name: Build CDEPS
+        run: |
+          export ESMFMKFILE=$HOME/ESMF/lib/libg/Linux.gfortran.64.openmpi.default/esmf.mk
+          export PIO=$HOME/pio
+          git submodule init
+          git submodule update
+          mkdir build-cdeps
+          pushd build-cdeps
+          cmake -DCMAKE_BUILD_TYPE=DEBUG -DCMAKE_Fortran_FLAGS="-g -Wall -ffree-form -ffree-line-length-none" ../
+          make VERBOSE=1
+          popd
diff --git a/.gitmodules b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "fox"]
+	path = fox
+	url = https://github.com/ESMCI/fox.git
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -4,14 +4,19 @@ project(NUOPC_DATA_MODELS LANGUAGES Fortran VERSION 0.1)
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake)
 include(ExternalProject)
 find_package(ESMF REQUIRED)
+if (DEFINED PIO)
+  set(PIO_PATH ${PIO})
+else()
+  set(PIO_PATH $ENV{PIO})
+endif()
+find_package(PIO REQUIRED COMPONENT C Fortran PATH ${PIO_PATH})
 
 if (DEFINED CIMEROOT)
   message("Using CIME in ${CIMEROOT} with compiler ${COMPILER}")
   include(${CASEROOT}/Macros.cmake)
   if (${PIO_VERSION} LESS 2)
     message( FATAL_ERROR "Version 2 of the PIO library required")
   endif()
-  set(FOX ${LIBROOT})
   set(CMAKE_Fortran_FLAGS "${FFLAGS} -I${LIBROOT}/include -I${LIBROOT}/finclude -I${LIBROOT}/nuopc/esmf/${NINST_VALUE}/include")
 else ()
   set(BLD_STANDALONE TRUE)
@@ -23,10 +28,10 @@ endif()
 if(BLD_STANDALONE)
   add_subdirectory(share)
   list(APPEND EXTRA_LIBS cdeps_share)
-  list(APPEND EXTRA_INCLUDES "${PIO_INCDIR}" "${CMAKE_BINARY_DIR}/share" )
+  list(APPEND EXTRA_INCLUDES "${CMAKE_BINARY_DIR}/share" )
 endif()
 
-
+add_subdirectory(fox)
 add_subdirectory(streams)
 add_subdirectory(dshr)
 

diff --git a/cime_config/buildlib b/cime_config/buildlib
@@ -22,7 +22,6 @@ logger = logging.getLogger(__name__)
 def buildlib(bldroot, libroot, case, compname=None):
     if bldroot.endswith("obj") and not compname:
         compname = os.path.basename(os.path.abspath(os.path.join(bldroot,os.pardir)))
-    print "HERE compname is {} libroot={} bldroot={}".format(compname, libroot, bldroot)
 
     if case.get_value("DEBUG"):
         strdebug = "debug"
@@ -58,6 +57,8 @@ def buildlib(bldroot, libroot, case, compname=None):
         cmake_flags += " -DCMAKE_INSTALL_PREFIX={} ".format(libroot)
         cmake_flags += " -DLIBROOT={} ".format(libroot) + srcpath
         cmake_flags += " -DMPILIB={} ".format(mpilib)
+        cmake_flags += " -DPIO_C_LIBRARY={path}/lib -DPIO_C_INCLUDE_DIR={path}/include ".format(path=os.path.join(case.get_value("EXEROOT"),sharedpath))
+        cmake_flags += " -DPIO_Fortran_LIBRARY={path}/lib -DPIO_Fortran_INCLUDE_DIR={path}/include ".format(path=os.path.join(case.get_value("EXEROOT"),sharedpath))
 
         logger.info("cmake_flags {}".format(cmake_flags))
         s,o,e = run_cmd("cmake {} ".format(cmake_flags), from_dir=bldroot, verbose=True)

diff --git a/cmake/FindPIO.cmake b/cmake/FindPIO.cmake
@@ -0,0 +1,103 @@
+# - Try to find PIO
+#
+# This can be controled by setting PIO_PATH or PIO_<lang>_PATH Cmake variables,
+# where <lang> is the COMPONENT language one needs.
+#
+# Once done, this will define:
+#
+#  PIO_<lang>_FOUND   (BOOL) - system has PIO
+#  PIO_<lang>_IS_SHARED (BOOL) - whether the library is shared/dynamic
+#  PIO_<lang>_INCLUDE_DIR (PATH) - Location of the header files and modules
+#  PIO_<lang>_LIBRARY     (File) - Path to the <lang> library files
+#  PIO_<lang>_LIBRARIES   (List) - link these to use PIO
+#
+# Available COMPONENTS are: C Fortran
+# If no components are specified only C is assumed
+include (LibFind)
+include (LibCheck)
+
+# Define PIO C Component
+define_package_component(PIO DEFAULT
+                         COMPONENT C
+                         INCLUDE_NAMES pio.h
+                         LIBRARY_NAMES pioc)
+
+# Define PIO Fortran Component
+define_package_component(PIO
+                         COMPONENT Fortran
+                         INCLUDE_NAMES pio.mod pio.inc
+                         LIBRARY_NAMES piof)
+
+# Search for list of valid components requested
+find_valid_components(PIO)
+
+#==============================================================================
+# SEARCH FOR VALIDATED COMPONENTS
+foreach (pcomp IN LISTS PIO_FIND_VALID_COMPONENTS)
+
+    # If not found already, search...
+    if (NOT PIO_${pcomp}_FOUND)
+
+        # Manually add the MPI include and library dirs to search paths
+        # and search for the package component
+        if (MPI_${pcomp}_FOUND)
+            initialize_paths (PIO_${pcomp}_PATHS
+                              INCLUDE_DIRECTORIES ${MPI_${pcomp}_INCLUDE_PATH}
+                              LIBRARIES ${MPI_${pcomp}_LIBRARIES})
+            find_package_component(PIO COMPONENT ${pcomp}
+                                   PATHS ${PIO_${pcomp}_PATHS})
+        else ()
+            find_package_component(PIO COMPONENT ${pcomp} HINT PIO_${pcomp}_PATH=${PIO_PATH})
+        endif ()
+
+        # Continue only if component found
+        if (PIO_${pcomp}_FOUND)
+
+            # Checks
+            if (pcomp STREQUAL C)
+
+                # Check version
+                check_version (PIO
+                               NAME "pio_meta.h"
+                               HINTS ${PIO_C_INCLUDE_DIRS}
+                               MACRO_REGEX "PIO_VERSION_")
+
+            endif ()
+
+            # Dependencies
+            if (pcomp STREQUAL C AND NOT PIO_C_IS_SHARED)
+
+                # DEPENDENCY: PnetCDF (if PnetCDF enabled)
+                check_macro (PIO_HAS_PNETCDF
+                             NAME TryPIO_PNETCDF.c
+                             HINTS ${CMAKE_MODULE_PATH}
+                             DEFINITIONS -I${PIO_C_INCLUDE_DIR}
+                             COMMENT "whether PIO has PnetCDF support")
+                if (PIO_HAS_PNETCDF)
+                    find_package (PnetCDF COMPONENTS C)
+                endif ()
+
+
+            elseif (pcomp STREQUAL Fortran AND NOT PIO_Fortran_IS_SHARED)
+
+                # DEPENDENCY: PIO
+                set (orig_comp ${pcomp})
+                set (orig_comps ${PIO_FIND_VALID_COMPONENTS})
+                find_package (PIO COMPONENTS C)
+                set (PIO_FIND_VALID_COMPONENTS ${orig_comps})
+                set (pcomp ${orig_comp})
+                if (PIO_C_FOUND)
+                    list (APPEND PIO_Fortran_INCLUDE_DIRS ${PIO_C_INCLUDE_DIRS})
+                    list (APPEND PIO_Fortran_LIBRARIES ${PIO_C_LIBRARIES})
+                endif ()
+
+            endif ()
+
+        endif ()
+
+    endif ()
+
+endforeach ()
+message("PIO_C_FOUND ${PIO_C_FOUND}")
+message("PIO_Fortran_FOUND ${PIO_Fortran_FOUND}")
+message("PIO_Fortran_INCLUDE_DIR ${PIO_Fortran_INCLUDE_DIR}")
diff --git a/cmake/LibCheck.cmake b/cmake/LibCheck.cmake
@@ -0,0 +1,104 @@
+include (CMakeParseArguments)
+include (CheckFunctionExists)
+#==============================================================================
+#
+#  FUNCTIONS TO HELP WITH Check* MODULES
+#
+#==============================================================================
+
+#______________________________________________________________________________
+# - Basic function to check a property of a package using a try_compile step
+#
+# SYNTAX:  check_macro (<return_variable>
+#                          NAME <filename>
+#                          HINTS <path> <path> ...
+#                          DEFINITIONS <definition1> <definition> ...
+#                          COMMENT <string_comment>)
+#
+function (check_macro VARIABLE)
+
+    # Parse the input arguments
+    set (oneValueArgs COMMENT NAME)
+    set (multiValueArgs HINTS DEFINITIONS)
+    cmake_parse_arguments (${VARIABLE} "" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    # If the return variable is defined, already, don't continue
+    if (NOT DEFINED ${VARIABLE})
+
+        message (STATUS "Checking ${${VARIABLE}_COMMENT}")
+        find_file (${VARIABLE}_TRY_FILE
+                   NAMES ${${VARIABLE}_NAME}
+                   HINTS ${${VARIABLE}_HINTS})
+        if (${VARIABLE}_TRY_FILE)
+            try_compile (COMPILE_RESULT
+                         ${CMAKE_CURRENT_BINARY_DIR}/try${VARIABLE}
+                         SOURCES ${${VARIABLE}_TRY_FILE}
+                         COMPILE_DEFINITIONS ${${VARIABLE}_DEFINITIONS}
+                         OUTPUT_VARIABLE TryOUT)
+            if (COMPILE_RESULT)
+                message (STATUS "Checking ${${VARIABLE}_COMMENT} - yes")
+            else ()
+                message (STATUS "Checking ${${VARIABLE}_COMMENT} - no")
+            endif ()
+
+            set (${VARIABLE} ${COMPILE_RESULT}
+                 CACHE BOOL "${${VARIABLE}_COMMENT}")
+
+        else ()
+            message (STATUS "Checking ${${VARIABLE}_COMMENT} - failed")
+        endif ()
+
+        unset (${VARIABLE}_TRY_FILE CACHE)
+    endif ()
+
+endfunction ()
+
+#______________________________________________________________________________
+# - Basic function to check the version of a package using a try_run step
+#
+# SYNTAX:  check_version (<pkg>
+#                         NAME <try_version_file>
+#                         HINTS <path> <path> ...
+#                         DEFINITIONS <definition1> <definition> ...)
+#
+function (check_version PKG)
+
+    # Parse the input arguments
+    set (oneValueArgs NAME MACRO_REGEX)
+    set (multiValueArgs HINTS)
+    cmake_parse_arguments (${PKG} "" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    # If the return variable is defined, already, don't continue
+    if (NOT DEFINED ${PKG}_VERSION)
+
+        message (STATUS "Checking ${PKG} version")
+        find_file (${PKG}_VERSION_HEADER
+                   NAMES ${${PKG}_NAME}
+                   HINTS ${${PKG}_HINTS})
+        if (${PKG}_VERSION_HEADER)
+            set (def)
+            file (STRINGS ${${PKG}_VERSION_HEADER} deflines
+                  REGEX "^#define[ \\t]+${${PKG}_MACRO_REGEX}")
+            foreach (defline IN LISTS deflines)
+                string (REPLACE "\"" "" defline "${defline}")
+                string (REPLACE "." "" defline "${defline}")
+                string (REGEX REPLACE "[ \\t]+" ";" deflist "${defline}")
+                list (GET deflist 2 arg)
+                list (APPEND def ${arg})
+            endforeach ()
+            string (REPLACE ";" "." vers "${def}")
+            message (STATUS "Checking ${PKG} version - ${vers}")
+            set (${PKG}_VERSION ${vers}
+                 CACHE STRING "${PKG} version string")
+            if (${PKG}_VERSION VERSION_LESS ${PKG}_FIND_VERSION})
+                message (FATAL_ERROR "${PKG} version insufficient")
+            endif ()
+        else ()
+            message (STATUS "Checking ${PKG} version - failed")
+        endif ()
+
+        unset (${PKG}_VERSION_HEADER CACHE)
+
+    endif ()
+
+endfunction ()