Merge pull request ESMCI#1715 from NCAR/ejh_ncint

Getting CMake build to understand netCDF integration

.github/workflows/cmake_ncint.yml

@@ -0,0 +1,58 @@
+# This is the GitHub workflow file to build and test the PIO library with CMake, and netCDF integration.
+
+# Ed Hartnett 8/19/20
+
+  name: cmake_ncint
+
+on:
+  push:
+    branches: [ master ]
+  pull_request:
+    branches: [ master ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    env:
+      CC: mpicc
+      FC: mpifort
+      CPPFLAGS: "-I/usr/include -I/usr/local/include -I/home/runner/pnetcdf/include"
+      LDFLAGS: "-L/home/runner/pnetcdf/lib"
+      LD_LIBRARY_PATH: "/home/runner/pnetcdf/lib"
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Installs
+      run: |
+        sudo apt-get install netcdf-bin libnetcdf-dev doxygen graphviz wget gfortran libjpeg-dev libz-dev openmpi-bin libopenmpi-dev 
+
+    - name: cache-pnetcdf
+      id: cache-pnetcdf
+      uses: actions/cache@v2
+      with:
+        path: ~/pnetcdf
+        key: pnetcdf-${{ runner.os }}-1.12.1
+
+    - name: build-pnetcdf
+      if: steps.cache-pnetcdf.outputs.cache-hit != 'true'
+      run: |
+        set -x
+        wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz &> /dev/null
+        tar -xzvf pnetcdf-1.12.1.tar.gz
+        pushd pnetcdf-1.12.1
+        ./configure --prefix=/home/runner/pnetcdf --enable-shared --disable-cxx
+        make
+        sudo make install
+        popd
+
+    - name: cmake build
+      run: |
+        set -x
+        mkdir build
+        cd build
+        cmake -Wno-dev -DPIO_ENABLE_NETCDF_INTEGRATION=On -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/usr/include -DPnetCDF_PATH='/home/runner/pnetcdf' -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off ..
+        make VERBOSE=1
+        make tests VERBOSE=1
+        ctest -VV

CMakeLists.txt

@@ -77,6 +77,7 @@ option (PIO_ENABLE_LOGGING   "Enable debug logging (large output possible)" OFF)
 option (PIO_ENABLE_DOC       "Enable building PIO documentation"            ON)
 option (PIO_ENABLE_COVERAGE  "Enable code coverage"                         OFF)
 option (PIO_ENABLE_EXAMPLES  "Enable PIO examples"                          ON)
+option (PIO_ENABLE_NETCDF_INTEGRATION  "Enable netCDF integration"          OFF)
 option (PIO_INTERNAL_DOC     "Enable PIO developer documentation"           OFF)
 option (PIO_TEST_BIG_ENDIAN  "Enable test to see if machine is big endian"  ON)
 option (PIO_USE_MPIIO        "Enable support for MPI-IO auto detect"        ON)
@@ -106,6 +107,13 @@ else()
   set(ENABLE_LOGGING 0)
 endif()
 
+# Set a variable that appears in the config.h.in file.
+if(PIO_ENABLE_NETCDF_INTEGRATION)
+  set(NETCDF_INTEGRATION 1)
+else()
+  set(NETCDF_INTEGRATION 0)
+endif()
+
 if(PIO_USE_MPISERIAL)
   set(USE_MPI_SERIAL 1)
 else()
@@ -205,13 +213,6 @@ endif ()
 set (CMAKE_Fortran_COMPILER_DIRECTIVE "CPR${CMAKE_Fortran_COMPILER_NAME}"
   CACHE STRING "Fortran compiler name preprocessor directive")
 
-# configure a header file to pass some of the CMake settings
-# to the source code
-configure_file (
-  "${PROJECT_SOURCE_DIR}/cmake_config.h.in"
-  "${PROJECT_BINARY_DIR}/config.h"
-  )
-
 #==============================================================================
 #  SET CODE COVERAGE COMPILER FLAGS
 #==============================================================================
@@ -418,3 +419,12 @@ configure_file(
   ${CMAKE_CURRENT_SOURCE_DIR}/src/clib/pio_meta.h.in
   ${CMAKE_CURRENT_BINARY_DIR}/src/clib/pio_meta.h @ONLY)
 
+# configure a header file to pass some of the CMake settings
+# to the source code
+configure_file (
+  "${PROJECT_SOURCE_DIR}/cmake_config.h.in"
+  "${PROJECT_BINARY_DIR}/config.h"
+  )
+
+
+

cmake_config.h.in

@@ -30,11 +30,16 @@
 
 #define USE_VARD @USE_VARD@
 
-#define HAVE_PAR_FILTERS @HAVE_PAR_FILTERS@
-
+/* Does netCDF and HDF5 support parallel I/O filters? */
 #cmakedefine HAVE_PAR_FILTERS
+
+/* Was PIO built with netCDF integration? */
 #cmakedefine NETCDF_INTEGRATION
+
+/* Does PIO support netCDF/HDF5 files? */
 #cmakedefine _NETCDF4
+
+/* Does PIO support using pnetcdf for I/O? */
 #cmakedefine _PNETCDF
 
 #endif /* _PIO_CONFIG_ */

src/clib/CMakeLists.txt

@@ -6,10 +6,15 @@ project (PIOC C)
 #  DEFINE THE TARGET
 #==============================================================================
 
-add_library (pioc topology.c pio_file.c pioc_support.c pio_lists.c
+set (src topology.c pio_file.c pioc_support.c pio_lists.c
   pioc.c pioc_sc.c pio_spmd.c pio_rearrange.c pio_nc4.c bget.c
   pio_nc.c pio_put_nc.c pio_get_nc.c pio_getput_int.c pio_msg.c
   pio_darray.c pio_darray_int.c pio_get_vard.c pio_put_vard.c pio_error.c)
+if (NETCDF_INTEGRATION)
+  set (src ${src} ../ncint/nc_get_vard.c ../ncint/ncintdispatch.c ../ncint/ncint_pio.c ../ncint/nc_put_vard.c)
+endif ()
+
+add_library (pioc ${src})
 
 # set up include-directories
 include_directories(
@@ -21,6 +26,10 @@ include_directories(
 target_include_directories (pioc
   PUBLIC ${CMAKE_CURRENT_SOURCE_DIR})
 
+# Include the ncint source directory
+target_include_directories (pioc
+  PUBLIC ${CMAKE_CURRENT_SOURCE_DIR}/../ncint)
+
 # System and compiler CPP directives
 target_compile_definitions (pioc
   PUBLIC ${CMAKE_SYSTEM_DIRECTIVE})

src/flib/CMakeLists.txt

@@ -31,6 +31,11 @@ set (PIO_Fortran_MODS ${CMAKE_CURRENT_BINARY_DIR}/pio.mod
   ${CMAKE_CURRENT_BINARY_DIR}/pionfatt_mod.mod
   ${CMAKE_CURRENT_BINARY_DIR}/pionfput_mod.mod)
 
+if (NETCDF_INTEGRATION)
+  set (PIO_Fortran_SRCS ${PIO_Fortran_SRCS} ncint_mod.F90)
+  set (PIO_Fortran_MODS ${PIO_Fortran_MODS} ${CMAKE_CURRENT_BINARY_DIR}/ncint_mod.mod)
+endif ()
+
 add_library (piof ${PIO_Fortran_SRCS} ${PIO_GenF90_SRCS})
 if (NOT PIO_ENABLE_FORTRAN)
   set_target_properties(piof PROPERTIES EXCLUDE_FROM_ALL TRUE)

tests/CMakeLists.txt

@@ -26,3 +26,7 @@ if (PIO_ENABLE_FORTRAN)
     message (STATUS "Cannot build performance test without gptl timing library")
   endif ()
 endif()
+
+if (NETCDF_INTEGRATION)
+  add_subdirectory(ncint)
+endif ()

tests/ncint/CMakeLists.txt

@@ -0,0 +1,31 @@
+# This is part of the PIO library.
+#
+# This is the cmake file to build the test directory for netCDF integration.
+#
+# Ed Hartnett 8/19/20
+
+include (LibMPI)
+
+include_directories("${CMAKE_SOURCE_DIR}/tests/ncint")
+include_directories("${CMAKE_BINARY_DIR}")
+
+set (my_tests tst_async_multi tst_ncint_async_perf
+  tst_ncint_perf tst_pio_async tst_pio_udf)
+
+# Test Timeout in seconds.
+if (PIO_VALGRIND_CHECK)
+  set (DEFAULT_TEST_TIMEOUT 480)
+else ()
+  set (DEFAULT_TEST_TIMEOUT 240)
+endif ()
+
+FOREACH(tst ${my_tests})
+  add_executable (${tst} EXCLUDE_FROM_ALL ${tst}.c)
+  add_dependencies (tests ${tst})
+  target_link_libraries (${tst} pioc)
+  add_mpi_test(${tst}
+    EXECUTABLE ${CMAKE_CURRENT_BINARY_DIR}/${tst}
+    NUMPROCS 4
+    TIMEOUT ${DEFAULT_TEST_TIMEOUT})
+ENDFOREACH()
+