merged master

.github/workflows/c-cpp.yml → .github/workflows/autotools.yml

@@ -1,4 +1,4 @@
-name: C/C++ CI
+name: autotools
 
 on:
   push:
@@ -31,18 +31,14 @@ jobs:
         tar -xzvf pnetcdf-1.11.0.tar.gz
         ls -l
         pushd pnetcdf-1.11.0
-        ./configure --prefix=/usr --enable-shared
+        ./configure --prefix=/usr --enable-shared --disable-cxx
         make
         sudo make install
         popd
 
     - name: autoreconf
       run: autoreconf -i
     - name: configure
-      run: ./configure
-    - name: make
-      run: make
+      run: ./configure --enable-fortran --enable-docs
     - name: make check
-      run: make check
-    - name: make distcheck
-      run: make distcheck
+      run: make -j check

.github/workflows/cmake.yml

@@ -0,0 +1,44 @@
+name: cmake
+
+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"
+
+    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: pnetcdf build
+      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=/usr --enable-shared --disable-cxx
+        make
+        sudo make install
+        popd
+
+    - name: cmake build
+      run: |
+        find /usr -name libnetcdf.so
+        mkdir build
+        cd build
+        cmake -Wno-dev -DNetCDF_C_LIBRARY=/usr/lib/x86_64-linux-gnu/libnetcdf.so -DNetCDF_C_INCLUDE_DIR=/usr/include -DCMAKE_PREFIX_PATH=/usr -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

.github/workflows/strict_autotools.yml

@@ -0,0 +1,47 @@
+name: strict_autotools
+
+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"
+
+    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: pnetcdf build
+      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=/usr --enable-shared --disable-cxx
+        make
+        sudo make install
+        popd
+
+    - name: autoreconf
+      run: autoreconf -i
+    - name: configure
+      run: |
+          export CFLAGS="-std=c99  -fsanitize=address -fno-omit-frame-pointer -Werror"
+          export FFLAGS="-fsanitize=address -fno-omit-frame-pointer -Werror"
+          export FCFLAGS="-fsanitize=address -fno-omit-frame-pointer -Werror"
+          ./configure
+    - name: make -j distcheck
+      run: |
+        export DISTCHECK_CONFIGURE_FLAGS="--enable-fortran"
+        make -j distcheck

.travis.yml

@@ -23,11 +23,10 @@ before_script:
   - export CC=mpicc
   - export FC=mpif90
   - export CPPFLAGS='-I/usr/include'
-  - wget https://parallel-netcdf.github.io/Release/pnetcdf-1.11.0.tar.gz 
-  - tar -xzvf pnetcdf-1.11.0.tar.gz
-  - ls -l
-  - pushd pnetcdf-1.11.0
-  - ./configure --prefix=/usr --enable-shared
+  - wget https://parallel-netcdf.github.io/Release/pnetcdf-1.12.1.tar.gz
+  - tar -xzvf pnetcdf-1.12.1.tar.gz
+  - pushd pnetcdf-1.12.1
+  - ./configure --prefix=/usr --enable-shared --disable-cxx 
   - make
   - sudo make install
   - popd
@@ -38,7 +37,7 @@ env:
     - CPPFLAGS='-I/usr/include'
     - CFLAGS='-std=c99'
     - LDFLAGS='-L/usr/lib'
-  
+
 script:
   - autoreconf -i
   - export CFLAGS='-std=c99  -fsanitize=address -fno-omit-frame-pointer -Werror'
@@ -54,4 +53,4 @@ script:
   - cmake -DPIO_HDF5_LOGGING=On -DPIO_USE_MALLOC=On -DPIO_ENABLE_LOGGING=On -DPIO_ENABLE_TIMING=Off ..
   - make VERBOSE=1
   - make tests VERBOSE=1
-  - make test VERBOSE=1
+  - ctest -VV

CMakeLists.txt

@@ -273,6 +273,28 @@ find_package (PnetCDF)
 
 SET(STATUS_PNETCDF PnetCDF_C_FOUND)
 
+###
+# Check to see if netcdf-4 capability is present in netcdf-c.
+###
+CHECK_C_SOURCE_COMPILES("
+#include <netcdf_meta.h>
+#if !NC_HAS_NC4
+      choke me
+#endif
+int main() {return 0;}" HAVE_NETCDF4)
+
+###
+# Check to see if netcdf-4 parallel I/O capability is present in
+# netcdf-c. (Really we should be checking NC_HAS_PARALLEL4, but that
+# was only recently introduced, so we will go with NC_HAS_PARALLEL.)
+###
+CHECK_C_SOURCE_COMPILES("
+#include <netcdf_meta.h>
+#if !NC_HAS_PARALLEL
+      choke me
+#endif
+int main() {return 0;}" HAVE_NETCDF_PAR)
+
 ###
 # Check to see if szip write capability is present in netcdf-c.
 ###
@@ -285,7 +307,7 @@ CHECK_C_SOURCE_COMPILES("
 int main() {return 0;}" HAVE_SZIP_WRITE)
 
 ###
-# Check to see if szip write capability is present in netcdf-c.
+# Check to see if parallel filters are supported by HDF5/netcdf-c.
 ###
 CHECK_C_SOURCE_COMPILES("
 #include <netcdf_meta.h>
@@ -327,12 +349,10 @@ SET(host_os "${osrel}")
 SET(abs_top_builddir "${CMAKE_CURRENT_BINARY_DIR}")
 SET(abs_top_srcdir "${CMAKE_CURRENT_SOURCE_DIR}")
 
-SET(CC_VERSION "${CMAKE_C_COMPILER}")
-
-# Build *FLAGS for libpio.settings.
-SET(CFLAGS "${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_${CMAKE_BUILD_TYPE}}")
-SET(CPPFLAGS "${CMAKE_CPP_FLAGS} ${CMAKE_CPP_FLAGS_${CMAKE_BUILD_TYPE}}")
-SET(LDFLAGS "${CMAKE_SHARED_LINKER_FLAGS} ${CMAKE_SHARED_LINKER_FLAGS_${CMAKE_BUILD_TYPE}}")
+SET(CC_VERSION "${CMAKE_C_COMPILER_ID} ${CMAKE_C_COMPILER_VERSION}")
+SET(FC_VERSION "${CMAKE_Fortran_COMPILER_ID} ${CMAKE_Fortran_COMPILER_VERSION}")
+# Build *FLAGS for libpio.settings.  (CFLAGS, CPPFLAGS, FFLAGS promoted from src)
+SET(LDFLAGS "${CMAKE_EXE_LINKER_FLAGS} ${CMAKE_EXE_LINKER_FLAGS_${CMAKE_BUILD_TYPE}}")
 
 is_disabled(BUILD_SHARED_LIBS enable_static)
 is_enabled(BUILD_SHARED_LIBS enable_shared)
@@ -341,6 +361,8 @@ is_enabled(USE_SZIP HAS_SZIP_WRITE)
 is_enabled(STATUS_PNETCDF HAS_PNETCDF)
 is_enabled(HAVE_H5Z_SZIP HAS_SZLIB)
 is_enabled(HDF5_HAS_PAR_FILTERS HAS_PAR_FILTERS)
+is_enabled(HAVE_NETCDF4 HAS_NETCDF4)
+is_enabled(HAVE_NETCDF_PAR HAS_NETCDF4_PAR)
 
 # Generate file from template.
 CONFIGURE_FILE("${CMAKE_CURRENT_SOURCE_DIR}/libpio.settings.in"

configure.ac

@@ -56,13 +56,35 @@ else
     fi
   done
 fi
+
 if test -n "$cc_version_info"; then
   CC_VERSION="$CC_VERSION ( $cc_version_info)"
 fi
 
 # Find and learn about the Fortran compiler.
 AC_PROG_FC
 
+# Compiler with version information. This consists of the full path
+# name of the compiler and the reported version number.
+AC_SUBST([FC_VERSION])
+# Strip anything that looks like a flag off of $FC
+FC_NOFLAGS=`echo $FC | sed 's/ -.*//'`
+
+if `echo $FC_NOFLAGS | grep ^/ >/dev/null 2>&1`; then
+  FC_VERSION="$FC"
+else
+  FC_VERSION="$FC";
+  for x in `echo $PATH | sed -e 's/:/ /g'`; do
+    if test -x $x/$FC_NOFLAGS; then
+      FC_VERSION="$x/$FC"
+      break
+    fi
+  done
+fi
+if test -n "$fc_version_info"; then
+  FC_VERSION="$FC_VERSION ( $fc_version_info)"
+fi
+
 # Always use malloc in autotools builds.
 AC_DEFINE([PIO_USE_MALLOC], [1], [use malloc for memory])
 
@@ -185,6 +207,7 @@ if test -z "$DOXYGEN" -a "x$enable_docs" = xyes; then
    AC_MSG_ERROR([Doxygen not found but --enable-docs used.])
 fi
 
+AC_MSG_NOTICE([processing doxyfile])
 # If building docs, process Doxyfile.in into Doxyfile.
 if test "x$enable_docs" = xyes; then
    AC_SUBST([CMAKE_CURRENT_SOURCE_DIR], ["."])
@@ -201,6 +224,7 @@ if test "x$enable_docs" = xyes; then
    AC_CONFIG_FILES([doc/Doxyfile])
 fi
 
+AC_MSG_NOTICE([setting flags])
 # NetCDF (at least classic) is required for PIO to build.
 AC_DEFINE([_NETCDF], [1], [netCDF classic library available])
 
@@ -235,29 +259,45 @@ if test x$ac_cv_lib_pnetcdf_ncmpi_create = xyes; then
    AC_DEFINE([USE_PNETCDF_VARN_ON_READ], [1], [defined by CMake build])
 fi
 
-# Do we have a parallel build of netCDF-4?
+# Do we have netCDF-4?
+AC_COMPILE_IFELSE([AC_LANG_PROGRAM([#include "netcdf_meta.h"],
+[[#if !NC_HAS_NC4
+# error
+#endif]
+])], [have_netcdf4=yes], [have_netcdf4=no])
+AC_MSG_CHECKING([whether netCDF provides netCDF/HDF5])
+AC_MSG_RESULT([${have_netcdf4}])
+
+# Do we have a parallel build of netCDF-4? (Really we should be
+# checking NC_HAS_PARALLEL4, but that was only recently introduced, so
+# we will go with NC_HAS_PARALLEL.)
 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([#include "netcdf_meta.h"],
 [[#if !NC_HAS_PARALLEL
 # error
 #endif]
 ])], [have_netcdf_par=yes], [have_netcdf_par=no])
+AC_MSG_CHECKING([whether netCDF provides parallel I/O for netCDF/HDF5])
+AC_MSG_RESULT([${have_netcdf_par}])
 
 # Do we have szip?
 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([#include "netcdf_meta.h"],
 [[#if !NC_HAS_SZIP_WRITE
 # error
 #endif]
 ])], [have_szip_write=yes], [have_szip_write=no])
+AC_MSG_CHECKING([whether netCDF provides szip write capability])
+AC_MSG_RESULT([${have_szip_write}])
 
 # Do we have parallel filter support?
 AC_COMPILE_IFELSE([AC_LANG_PROGRAM([#include "netcdf_meta.h"],
 [[#if !NC_HAS_PAR_FILTERS
 # error
 #endif]
 ])], [have_par_filters=yes], [have_par_filters=no])
+AC_MSG_CHECKING([whether netCDF provides parallel filter support])
+AC_MSG_RESULT([${have_par_filters}])
 
-AC_MSG_CHECKING([whether netCDF provides parallel IO])
-AC_MSG_RESULT([${have_netcdf_par}])
+# Set some build settings for when netcdf-4 is supported.
 if test x$have_netcdf_par = xyes; then
   AC_DEFINE([_NETCDF4],[1],[Does netCDF library provide netCDF-4 with parallel access])
 fi
@@ -356,21 +396,25 @@ AC_DEFUN([AX_SET_META],[
 AX_SET_META([PIO_HAS_SZIP_WRITE],[$have_szip_write],[yes])
 AX_SET_META([PIO_HAS_PNETCDF],[$enable_pnetcdf],[yes])
 AX_SET_META([PIO_HAS_PAR_FILTERS], [$have_par_filters],[yes])
+AX_SET_META([PIO_HAS_NETCDF4], [$have_netcdf4],[yes])
+AX_SET_META([PIO_HAS_NETCDF4_PAR], [$have_netcdf_par],[yes])
 
 # Create output variables from various shell variables, for use in
 # generating libpio.settings.
 AC_SUBST([enable_shared])
 AC_SUBST([enable_static])
 AC_SUBST([CFLAGS])
 AC_SUBST([CPPFLAGS])
+AC_SUBST([FFLAGS])
+AC_SUBST([FCFLAGS])
 AC_SUBST([LDFLAGS])
-AC_SUBST([AM_CFLAGS])
-AC_SUBST([AM_CPPFLAGS])
-AC_SUBST([AM_LDFLAGS])
+AC_SUBST([FPPFLAGS]) # ignored by autotools
 AC_SUBST(HAS_PNETCDF,[$enable_pnetcdf])
 AC_SUBST(HAS_LOGGING, [$enable_logging])
 AC_SUBST(HAS_SZIP_WRITE, [$have_szip_write])
 AC_SUBST([HAS_PAR_FILTERS], [$have_par_filters])
+AC_SUBST([HAS_NETCDF4], [$have_netcdf4])
+AC_SUBST([HAS_NETCDF4_PAR], [$have_netcdf_par])
 
 # Create the build summary file. 
 AC_CONFIG_FILES([libpio.settings

libpio.settings.in

@@ -19,9 +19,16 @@ Shared Library:		@enable_shared@
 Static Library:		@enable_static@
 Extra libraries:	@LIBS@
 
+Fortran Compiler:       @FC_VERSION@
+FFLAGS:                 @FFLAGS@
+FCFLAGS:                @FCFLAGS@
+FPPFLAGS:               @FPPFLAGS@
+
 # Features
 --------
 PnetCDF Support:	@HAS_PNETCDF@
-SZIP Write Support:     @HAS_SZIP_WRITE@
-Parallel Filters:       @HAS_PAR_FILTERS@
+SZIP Write Support:	@HAS_SZIP_WRITE@
+Parallel Filters:	@HAS_PAR_FILTERS@
+NetCDF/HDF5 Support:	@HAS_NETCDF4@
+NetCDF/HDF5 Par I/O:	@HAS_NETCDF4_PAR@
 

src/CMakeLists.txt

@@ -34,8 +34,14 @@ endif ()
 
 # Build the C library
 add_subdirectory (clib)
+set(CFLAGS ${CFLAGS}  PARENT_SCOPE)
+set(CPPFLAGS ${CPPFLAGS} PARENT_SCOPE)
+
 
 # Build the Fortran library
 if (PIO_ENABLE_FORTRAN)
   add_subdirectory (flib)
+  set(FFLAGS ${FFLAGS} PARENT_SCOPE)
+  set(FCFLAGS ${FCFLAGS} PARENT_SCOPE)
+  set(FPPFLAGS ${FPPFLAGS} PARENT_SCOPE)
 endif ()