Sync 1.14 branch with develop

.github/workflows/linux-auto-aocc-ompi.yml

@@ -0,0 +1,66 @@
+name: linux autotools aocc ompi
+
+on:
+  push:
+  pull_request:  
+    branches:
+      - hdf5_1_14
+    paths-ignore:
+      - '.github/CODEOWNERS'
+      - '.github/FUNDING.yml'
+      - 'doc/**'
+      - 'release_docs/**'
+      - 'ACKNOWLEDGEMENTS'
+      - 'COPYING**'
+      - '**.md'
+
+# Using concurrency to cancel any in-progress job or run
+concurrency:
+  group: ${{ github.workflow }}-${{ github.sha || github.event.pull_request.number }}
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install System dependencies
+        run: |
+          sudo apt update
+          sudo apt install -y libaec-dev zlib1g-dev automake autoconf libcurl4-openssl-dev libjpeg-dev wget curl bzip2 m4 flex bison cmake libzip-dev doxygen openssl libtool libtool-bin build-essential libncurses-dev libquadmath0 libstdc++6 libxml2
+      - name: Install AOCC 4.1.0
+        run: |
+          wget https://download.amd.com/developer/eula/aocc/aocc-4-1/aocc-compiler-4.1.0.tar
+          tar -xvf aocc-compiler-4.1.0.tar
+          cd aocc-compiler-4.1.0
+          bash install.sh
+          source /home/runner/work/hdf5/hdf5/setenv_AOCC.sh
+          which clang
+          which flang
+          clang -v
+      - name: Install OpenMPI 4.1.5
+        run: |
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib
+          wget https://download.open-mpi.org/release/open-mpi/v4.1/openmpi-4.1.5.tar.gz
+          tar zxvf openmpi-4.1.5.tar.gz
+          cd openmpi-4.1.5
+          ./configure CC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/clang FC=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/bin/flang --prefix=/usr/local
+          make
+          sudo make install
+      - name: Install HDF5
+        env:
+          NPROCS: 2      
+        run: |
+          export LD_LIBRARY_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib/openmpi:/usr/local/lib
+          export LD_RUN_PATH=/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib:/usr/local/lib/openmpi:/usr/local/lib
+          export PATH=/usr/local/bin:$PATH
+          ./autogen.sh
+          ./configure --prefix=/tmp  --enable-parallel --enable-shared CC=/usr/local/bin/mpicc LDFLAGS="-L/home/runner/work/hdf5/hdf5/aocc-compiler-4.1.0/lib -L/usr/local/lib/openmpi"
+          make -j
+          make check -j
+          make install
+          make uninstall

CMakeFilters.cmake

@@ -85,12 +85,7 @@ if (HDF5_ENABLE_Z_LIB_SUPPORT)
         set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_LIBRARIES})
       endif ()
     else ()
-      if (BUILD_ZLIB_WITH_FETCHCONTENT)
-        # Only tgz files available
-        ORIGINAL_ZLIB_LIBRARY ("TGZ")
-        message (VERBOSE "HDF5_ZLIB is built from fetch content")
-        set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY})
-      elseif (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
+      if (HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "GIT" OR HDF5_ALLOW_EXTERNAL_SUPPORT MATCHES "TGZ")
         EXTERNAL_ZLIB_LIBRARY (${HDF5_ALLOW_EXTERNAL_SUPPORT})
         message (VERBOSE "Filter HDF5_ZLIB is built")
         set (LINK_COMP_LIBS ${LINK_COMP_LIBS} ${ZLIB_STATIC_LIBRARY})

config/clang-cxxflags

@@ -47,6 +47,7 @@ load_clang_arguments()
     done)
     IFS=' ' echo "$*"
 }
+
 # Get the compiler version in a way that works for clang++
 # unless a compiler version is already known
 #

config/clang-fflags

@@ -0,0 +1,139 @@
+#                            -*- shell-script -*-
+#
+# Copyright by The HDF Group.
+# All rights reserved.
+#
+# This file is part of HDF5.  The full HDF5 copyright notice, including
+# terms governing use, modification, and redistribution, is contained in
+# the COPYING file, which can be found at the root of the source code
+# distribution tree, or in https://www.hdfgroup.org/licenses.
+# If you do not have access to either file, you may request a copy from
+# [email protected].
+
+
+# This file should be sourced into configure if the compiler is the
+# Clang Fortran compiler (flang) or a derivative.  It is careful not to do
+# anything if the compiler is not Clang; otherwise 'cc_flags_set' is set
+# to 'yes'
+#
+
+# Get the compiler version in a way that works for clang
+# unless a compiler version is already known
+#
+#   cc_vendor:    The compiler name: flang
+#   cc_version:   Version number: 6.0.0, 7.3.0, ... 10.0.1
+#
+if test "X-" = "X-$f9x_flags_set"; then
+    # flang -v will return version number following "clang"
+    f9x_version="`$FC $FCFLAGS $H5_FCFLAGS -v 2>&1 |\
+        grep 'clang version' | sed 's/.*clang version \([-a-z0-9\.]*\).*/\1/'`"
+    if test -n "$f9x_version"; then
+        f9x_vendor="flang"
+    fi
+    if test "X-" != "X-$f9x_version"; then
+
+        # Get the compiler version numbers
+        f9x_vers_major=`echo $f9x_version | cut -f1 -d.`
+        f9x_vers_minor=`echo $f9x_version | cut -f2 -d.`
+        f9x_vers_patch=`echo $f9x_version | cut -f3 -d.`
+        test -n "$f9x_vers_major" || f9x_vers_major=0
+        test -n "$f9x_vers_minor" || f9x_vers_minor=0
+        test -n "$f9x_vers_patch" || f9x_vers_patch=0
+    fi
+fi
+
+if test "X-flang" = "X-$f9x_vendor"; then
+
+    echo "compiler '$FC' is $f9x_vendor-$f9x_version"
+
+    FC_BASENAME=flang
+    F9XSUFFIXFLAG=""
+    FSEARCH_DIRS=""
+
+    ###############################
+    # Architecture-specific flags #
+    ###############################
+
+    arch=
+    # Nothing currently. (Uncomment code below and modify to add any)
+    #case "$host_os-$host_cpu" in
+    #    *-i686)
+    #        arch="-march=i686"
+    #        ;;
+    #esac
+
+    H5_FCFLAGS="$H5_FCFLAGS $arch"
+
+    ##############
+    # Production #
+    ##############
+
+    PROD_FCFLAGS=
+
+    #########
+    # Debug #
+    #########
+
+    DEBUG_FCFLAGS=
+
+    ########################
+    # Enhanced Diagnostics #
+    ########################
+
+    NO_DIAGS_FCFLAGS=
+    DIAGS_FCFLAGS=
+
+    ###########
+    # Symbols #
+    ###########
+
+    NO_SYMBOLS_FCFLAGS=
+    SYMBOLS_FCFLAGS=
+
+    #############
+    # Profiling #
+    #############
+
+    PROFILE_FCFLAGS=
+
+    ################
+    # Optimization #
+    ################
+
+    HIGH_OPT_FCFLAGS="-O3"
+    NO_OPT_FCFLAGS="-O0"
+    DEBUG_OPT_FCFLAGS="-O0"
+
+    ############
+    # Warnings #
+    ############
+
+    ###########
+    # General #
+    ###########
+
+    # We don't use OpenMP, so don't link to it
+    H5_FCFLAGS="$H5_FCFLAGS -nomp"
+
+    ######################
+    # Developer warnings #
+    ######################
+
+    NO_DEVELOPER_WARNING_FCFLAGS=
+    DEVELOPER_WARNING_FCFLAGS=
+
+    #############################
+    # Version-specific warnings #
+    #############################
+
+    #################
+    # Flags are set #
+    #################
+    f9x_flags_set=yes
+fi
+
+# Clear f9x info if no flags set
+if test "X$f9x_flags_set" = "X"; then
+    f9x_vendor=
+    f9x_version=
+fi

config/cmake/HDFFortranCompilerFlags.cmake

@@ -52,6 +52,11 @@ if (CMAKE_Fortran_COMPILER_ID STREQUAL "GNU" AND NOT CMAKE_Fortran_COMPILER_VERS
   endif ()
 endif ()
 
+if (CMAKE_Fortran_COMPILER_ID STREQUAL "NAG")
+    message (STATUS "... Select IEEE floating-point mode full")
+    list (APPEND HDF5_CMAKE_Fortran_FLAGS "-ieee=full")
+endif ()
+
 if (NOT MSVC AND NOT MINGW)
   # General flags
   if (CMAKE_Fortran_COMPILER_ID STREQUAL "Intel")

config/linux-gnulibc1

@@ -92,7 +92,7 @@ else
             fc_version_info=`$FC -V | grep Absoft`
             ;;
          # The NAG compiler
-	 nagfor*|nagftn*)
+	 *nagfor*|*nagftn*)
             RM='rm -f'
             tmpfile=/tmp/cmpver.$$
             $FC -V >& $tmpfile
@@ -122,6 +122,9 @@ fi
 # Figure out Intel FC compiler flags
 . $srcdir/config/intel-fflags
 
+# Figure out Clang FC compiler flags
+. $srcdir/config/clang-fflags
+
 case $FC_BASENAME in
     #
     # Absoft compiler
@@ -163,7 +166,7 @@ case $FC_BASENAME in
         # NOTE: The default is -ieee=stop, which will cause problems
         #       when the H5T module performs floating-point type
         #       introspection
-        H5_FCFLAGS="$H5_FCFLAGS -ieee=full"
+        AM_FCFLAGS="$AM_FCFLAGS -ieee=full"
         FSEARCH_DIRS=""
 
         # Production

configure.ac

@@ -4225,15 +4225,18 @@ if test "X$HDF_FORTRAN" = "Xyes"; then
       ;;
   esac
 
-  ### libtool does not pass the correct argument linking (-Wl,-Wl,,) for the NAG Fortran compiler
+  ### libtool does not pass the correct linker options for some Fortran compilers
   ### on Linux (other OSs have not been tested).
-  ### Therefore, detect if we are using the NAG Fortran compiler, and replace the wl="-Wl," for Fortran to
-  ### wl="-Wl,-Wl,," in the libtool file. (HDFFV-10037)
   case "`uname`" in
     Linux*)
+      ### NAG Fortran needs to replace "-Wl," with "-Wl,-Wl,," (HDFFV-10037)
       if test "X$FC_BASENAME" = "Xnagfor"; then
          cat libtool | awk '/BEGIN LIBTOOL TAG CONFIG: FC/{flag=1}flag&&/wl=/{$NF="wl=\"-Wl,-Wl,,\"";flag=0}1' > libtool.tmp && mv -f libtool.tmp libtool && chmod 755 libtool
       fi
+      ### Flang needs to replace "", with "-Wl," (avoids unknown option: -soname issues)
+      if test "X$FC_BASENAME" = "Xflang"; then
+         cat libtool | awk '/BEGIN LIBTOOL TAG CONFIG: FC/{flag=1}flag&&/wl=/{$NF="wl=\"-Wl,\"";flag=0}1' > libtool.tmp && mv -f libtool.tmp libtool && chmod 755 libtool
+      fi
       ;;
   esac
 fi

fortran/examples/CMakeLists.txt

@@ -35,9 +35,12 @@ set (F2003_examples
 
 foreach (example ${examples})
   add_executable (f90_ex_${example} ${HDF5_F90_EXAMPLES_SOURCE_DIR}/${example}.f90)
-  target_compile_options(f90_ex_${example} PRIVATE $<$<STREQUAL:"x${CMAKE_Fortran_SIMULATE_ID}","xMSVC">:${WIN_COMPILE_FLAGS}>)
-#  set_property(TARGET f90_ex_${example} APPEND PROPERTY LINK_FLAGS $<$<STREQUAL:"x${CMAKE_Fortran_SIMULATE_ID}","xMSVC">:"-SUBSYSTEM:CONSOLE">)
-#  set_property(TARGET f90_ex_${example} APPEND PROPERTY LINK_FLAGS $<$<STREQUAL:"x${CMAKE_Fortran_SIMULATE_ID}","xMSVC">:${WIN_LINK_FLAGS}>)
+  target_compile_options(f90_ex_${example}
+      PRIVATE
+          "${HDF5_CMAKE_Fortran_FLAGS}"
+          "$<$<STREQUAL:x${CMAKE_Fortran_SIMULATE_ID},xMSVC>:${WIN_COMPILE_FLAGS}>")
+#  set_property(TARGET f90_ex_${example} APPEND PROPERTY LINK_FLAGS "$<$<STREQUAL:x${CMAKE_Fortran_SIMULATE_ID},xMSVC>:-SUBSYSTEM:CONSOLE>")
+#  set_property(TARGET f90_ex_${example} APPEND PROPERTY LINK_FLAGS "$<$<STREQUAL:x${CMAKE_Fortran_SIMULATE_ID},xMSVC>:${WIN_LINK_FLAGS}>")
   if(MSVC)
     set_property(TARGET f90_ex_${example} PROPERTY LINK_FLAGS "/SUBSYSTEM:CONSOLE ${WIN_LINK_FLAGS}")
   endif()
@@ -76,9 +79,12 @@ endforeach ()
 
 foreach (example ${F2003_examples})
   add_executable (f03_ex_${example} ${HDF5_F90_EXAMPLES_SOURCE_DIR}/${example}.f90)
-  target_compile_options(f03_ex_${example} PRIVATE $<$<STREQUAL:"x${CMAKE_Fortran_SIMULATE_ID}","xMSVC">:${WIN_COMPILE_FLAGS}>)
-#  set_property(TARGET f03_ex_${example} APPEND PROPERTY LINK_FLAGS $<$<STREQUAL:"x${CMAKE_Fortran_SIMULATE_ID}","xMSVC">:"-SUBSYSTEM:CONSOLE">)
-#  set_property(TARGET f03_ex_${example} APPEND PROPERTY LINK_FLAGS $<$<STREQUAL:"x${CMAKE_Fortran_SIMULATE_ID}","xMSVC">:${WIN_LINK_FLAGS}>)
+  target_compile_options(f03_ex_${example}
+      PRIVATE
+          "${HDF5_CMAKE_Fortran_FLAGS}"
+          "$<$<STREQUAL:x${CMAKE_Fortran_SIMULATE_ID},xMSVC>:${WIN_COMPILE_FLAGS}>")
+#  set_property(TARGET f03_ex_${example} APPEND PROPERTY LINK_FLAGS "$<$<STREQUAL:x${CMAKE_Fortran_SIMULATE_ID},xMSVC>:-SUBSYSTEM:CONSOLE>")
+#  set_property(TARGET f03_ex_${example} APPEND PROPERTY LINK_FLAGS $<$<STREQUAL:"$<$<STREQUAL:x${CMAKE_Fortran_SIMULATE_ID},xMSVC>:${WIN_LINK_FLAGS}>")
   if(MSVC)
     set_property(TARGET f03_ex_${example} PROPERTY LINK_FLAGS "/SUBSYSTEM:CONSOLE ${WIN_LINK_FLAGS}")
   endif()
@@ -117,9 +123,12 @@ endforeach ()
 
 if (H5_HAVE_PARALLEL AND MPI_Fortran_FOUND)
   add_executable (f90_ex_ph5example ${HDF5_F90_EXAMPLES_SOURCE_DIR}/ph5example.f90)
-  target_compile_options(f90_ex_ph5example PRIVATE $<$<STREQUAL:"x${CMAKE_Fortran_SIMULATE_ID}","xMSVC">:${WIN_COMPILE_FLAGS}>)
-#  set_property(TARGET f90_ex_ph5example APPEND PROPERTY LINK_FLAGS $<$<STREQUAL:"x${CMAKE_Fortran_SIMULATE_ID}","xMSVC">:"-SUBSYSTEM:CONSOLE">)
-#  set_property(TARGET f90_ex_ph5example APPEND PROPERTY LINK_FLAGS $<$<STREQUAL:"x${CMAKE_Fortran_SIMULATE_ID}","xMSVC">:${WIN_LINK_FLAGS}>)
+  target_compile_options(f90_ex_ph5example
+      PRIVATE
+          "${HDF5_CMAKE_Fortran_FLAGS}"
+          "$<$<STREQUAL:x${CMAKE_Fortran_SIMULATE_ID},xMSVC>:${WIN_COMPILE_FLAGS}>")
+#  set_property(TARGET f90_ex_ph5example APPEND PROPERTY LINK_FLAGS "$<$<STREQUAL:x${CMAKE_Fortran_SIMULATE_ID},xMSVC>:-SUBSYSTEM:CONSOLE>")
+#  set_property(TARGET f90_ex_ph5example APPEND PROPERTY LINK_FLAGS "$<$<STREQUAL:x${CMAKE_Fortran_SIMULATE_ID},xMSVC>:${WIN_LINK_FLAGS}>")
   if(MSVC)
     set_property(TARGET f90_ex_ph5example PROPERTY LINK_FLAGS "/SUBSYSTEM:CONSOLE ${WIN_LINK_FLAGS}")
   endif()

fortran/examples/ph5example.f90

@@ -16,10 +16,10 @@
      PROGRAM DATASET
 
      USE HDF5 ! This module contains all necessary modules
+     USE MPI
 
      IMPLICIT NONE
 
-     INCLUDE 'mpif.h'
      CHARACTER(LEN=10), PARAMETER :: default_fname = "sds.h5"  ! Default name
      CHARACTER(LEN=8), PARAMETER :: dsetname = "IntArray" ! Dataset name
 
@@ -72,10 +72,8 @@ PROGRAM DATASET
      CALL h5pset_fapl_mpio_f(plist_id, comm, info, error)
 
      !
-     ! Figure out the filename to use.  If your system does not support
-     ! getenv, comment that statement with this,
-     ! filename = ""
-     CALL getenv("HDF5_PARAPREFIX", filename)
+     ! Figure out the filename to use.
+     CALL get_environment_variable("HDF5_PARAPREFIX", filename)
      fnamelen = LEN_TRIM(filename)
      if ( fnamelen == 0 ) then
 	filename = default_fname