Sync develop branch changes since 2/16 to hdf5_1_14 branch (#4058)

* Remove oneapi return value warning. (#4028)

* Replaced last sprintf with snprintf (#4007)

* Replaced last sprintf with snprintf

To have the size of the buffer, it was required to change a function signature, and change all users of it.

In most cases, determining the buffer size wasn't  trivial and so SIZE_MAX is passed. But at least this improves the infrastructure. Someone can later figure out the correct sizes.

* Test vlen sequence IO in API tests (#4027)

* Check argument for CMake REGEX FCMangle.h. (#4029)

* Replace deprecated Fortran 'include mpif.h' with 'USE mpi' (#4031)

With MPI 4.1 the use of the mpif.h include file has been deprecated. Codes
should transition to USE mpi or USE mpi_f08.

Signed-off-by: Christoph Niethammer <niethammer@hlrs.de>

* Fix H5F_get_access_plist to copy file locking settings (#4030)

H5F_get_access_plist previously did not copy over the file locking settings
from a file into the new File Access Property List that it creates. This would
make it difficult to match the file locking settings between an external file
and its parent file.

* Fix missing NOT from if check in HL folder (#4036)

* Fix the datatype passed to H5*exists_async APIs in tests. (#4033)

Add a new testing function to verify C_BOOL values.

* Add deb and rpm binaries to snapshots (#4035)

* Update and Add general INSTALL (#4016)

* Improve performance of flushing single objects (#4017)

Improve performance of flushing a single object, and remove metadata
cache flush markers

* Fix memory leak in H5LTopen_file_image when H5LT_FILE_IMAGE_DONT_COPY flag is used (#4021)

When the H5LT_FILE_IMAGE_DONT_COPY flag is passed to H5LTopen_file_image, the internally-allocated
udata structure gets leaked as the core file driver doesn't have a way to determine when or if it
needs to call the 'udata_free' callback. This has been fixed by freeing the udata structure when
the 'image_free' callback gets made during file close, where the file is holding the last reference
to the udata structure.

* Fix allocating too much memory in dset API test (#4041)

* Don't try to load general-19 warnings file for icc (#4042)

The Autools Classic Intel compiler configuration attempts to load a file
named `general-19` from the intel-warnings/classic directory, which does
not exist.

This removes the attempted load of the file.

* Remove unused AIX cross-compile cache overrides (#4043)

The ibm-aix Autotools config file had some unmaintained and unnecessary
Autoconf cache overrides. These have been removed.

* Consolidate Autotools linux files (#4044)

There are many architecture-specific linux files in the config
directory, all of which simply redirect to linux-gnulibc1.

This change renames linux-gnulibc1 to linux-gnu and deletes the more
specific files.

* Remove check for gettimeofday + tz in CMake (#4045)

This is not used in the library

* Remove limitations on preset generators (#4051)

* Fix issue with FAPL file locking setting inheriting test (#4053)

Fixes an issue where the HDF5_USE_FILE_LOCKING environment variable being
set can interfere with the file locking setting that the test expects to
be returned.

* Bump the github-actions group with 2 updates (#4054)

Bumps the github-actions group with 2 updates: [actions/download-artifact](https://github.com/actions/download-artifact) and [github/codeql-action](https://github.com/github/codeql-action).

* Fix VOL-compatibility issues in External Link API test  (#4039)

Fix link API tests with incorrect filename

* Add upddated cmake tools from source location (#4040)

* Add options to allow tools type selection and naming (#4046)

* Improve error messages when tools attempt to use non-enabled S3 and HDFS VFDs. (#4047)

* Correct several 1.15/1.15.0 references to 1.14/1.14.4.

* Ignore HDF5Examples/CMakeUserPresets.json

1 files changed, 0 insertions, 401 deletions

diff --git a/config/linux-gnulibc1 b/config/linux-gnulibc1
deleted file mode 100644
index b4139ee..0000000
--- a/config/linux-gnulibc1
+++ /dev/null
@@ -1,401 +0,0 @@
-#							-*- 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
-# help@hdfgroup.org.
-
-
-# This file is part of the HDF5 build script.  It is processed shortly
-# after configure starts and defines, among other things, flags for
-# the various compile modes.
-#
-# See BlankForm in this directory for details.
-
-# The default compiler is `gcc'.
-if test -z "$CC"; then
-    if test "X-$enable_parallel" = "X-yes"; then
-	# default to use mpicc which is the defacto MPI compiler name
-	CC=mpicc
-	CC_BASENAME=mpicc
-    else
-	CC=gcc
-	CC_BASENAME=gcc
-    fi
-fi
-
-# Figure out GNU C compiler flags
-. $srcdir/config/gnu-flags
-
-# Figure out PGI C compiler flags
-. $srcdir/config/pgi-flags
-
-# Figure out CCE C compiler flags
-. $srcdir/config/cce-flags
-
-# Figure out Intel oneAPI C compiler flags
-. $srcdir/config/oneapi-flags
-
-# Figure out Intel classic C compiler flags
-. $srcdir/config/intel-flags
-
-# Figure out Clang C compiler flags
-. $srcdir/config/clang-flags
-
-# Figure out NVHPC C compiler flags
-. $srcdir/config/nvidia-flags
-
-# Use default Fortran 90 compiler according to what C compiler is used.
-if test "X-" = "X-$FC"; then
-    case $CC_BASENAME in
-        gcc*)
-            FC=gfortran
-            FC_BASENAME=gfortran
-            ;;
-        pgcc*)
-            FC=pgf90
-            FC_BASENAME=pgf90
-            ;;
-        nvc*)
-            FC=nvfortran
-            FC_BASENAME=nvfortran
-            ;;
-        icx*)
-            FC=ifx
-            FC_BASENAME=ifx
-            ;;
-        icc*)
-            FC=ifort
-            FC_BASENAME=ifort
-            ;;
-        mpicc*)
-            FC=mpif90
-            FC_BASENAME=mpif90
-            ;;
-        clang*)
-            # clang has no fortran compiler. Use gfortran.
-            FC=gfortran
-            FC_BASENAME=gfortran
-            ;;
-    esac
-else
-    case $FC in
-        # The PGI and Intel compilers are automatically detected below
-        ifc*|ifort*|pgf90*|nvfortran*)
-            ;;
-
-        *f95*)
-            # Figure out which compiler we are using: pgf90 or Absoft f95
-            RM='rm -f'
-            tmpfile=/tmp/cmpver.$$
-            $FC -V >$tmpfile
-            if test -s "$tmpfile"; then 
-                if( grep -s 'Absoft' $tmpfile > /dev/null) then
-                    FC_BASENAME=f95
-                fi 
-                if( grep -s 'pgf90' $tmpfile > /dev/null) then
-                    FC_BASENAME=pgf90
-                fi 
-            fi
-            $RM $tmpfile
-            fc_version_info=`$FC -V | grep Absoft`
-            ;;
-         # The NAG compiler
-	 *nagfor*|*nagftn*)
-            RM='rm -f'
-            tmpfile=/tmp/cmpver.$$
-            $FC -V >& $tmpfile
-            if test -s "$tmpfile"; then
-                if( grep -s 'NAG Fortran' $tmpfile > /dev/null) then
-                    FC_BASENAME=nagfor
-                fi
-            fi
-            fc_version_info=`grep "NAG Fortran" $tmpfile`
-            echo "compiler '$FC' is $fc_version_info"
-            $RM $tmpfile
-	    ;;
-         *)
-            ;;
-    esac
-fi
-
-# Figure out GNU FC compiler flags
-. $srcdir/config/gnu-fflags
-
-# Figure out PGI FC compiler flags
-. $srcdir/config/pgi-fflags
-
-# Figure out CCE FC compiler flags
-. $srcdir/config/cce-fflags
-
-# Figure out Intel oneAPI FC compiler flags
-. $srcdir/config/oneapi-fflags
-
-# Figure out Intel classic FC compiler flags
-. $srcdir/config/intel-fflags
-
-# Figure out Clang FC compiler flags
-. $srcdir/config/clang-fflags
-
-# Figure out NVHPC FC compiler flags
-. $srcdir/config/nvidia-fflags
-
-case $FC_BASENAME in
-    #
-    # Absoft compiler
-    #
-    f95)
-        # Set required flag for compiling C stubs
-        H5_CFLAGS="$H5_CFLAGS"
-
-        F9XSUFFIXFLAG=""
-        H5_FCFLAGS="$H5_FCFLAGS"
-        FSEARCH_DIRS=""
-
-        # Production
-        PROD_FCFLAGS=
-
-        # Debug
-        DEBUG_FCFLAGS=
-
-        # Symbols
-        SYMBOLS_FCFLAGS="-g"
-        NO_SYMBOLS_FCFLAGS="-s"
-
-        # Profiling
-        PROFILE_FCFLAGS="-pg"
-
-        # Optimization
-        HIGH_OPT_FCFLAGS="-O"
-        DEBUG_OPT_FCFLAGS=
-        NO_OPT_FCFLAGS=
-
-        f9x_flags_set=yes
-        ;;
-#
-#   NAG compiler
-#
-    nagfor)
-
-        F9XSUFFIXFLAG=""
-        AM_FCFLAGS="$AM_FCFLAGS"
-        FSEARCH_DIRS=""
-
-        # Production
-        PROD_FCFLAGS=
-
-        # Debug
-        DEBUG_FCFLAGS="-C"
-
-        # Symbols
-        SYMBOLS_FCFLAGS="-g"
-        NO_SYMBOLS_FCFLAGS="-s"
-
-        # Profiling
-        PROFILE_FCFLAGS="-pg"
-
-        # Optimization
-        HIGH_OPT_FCFLAGS="-O"
-        DEBUG_OPT_FCFLAGS="-O0"
-        NO_OPT_FCFLAGS="-O0"
-
-        f9x_flags_set=yes
-        ;;
-
-esac  
-
-# The default C++ compiler
-
-# The default compiler is `g++'.
-if test -z "$CXX"; then
-  CXX=g++
-  CXX_BASENAME=g++
-fi
-
-# Figure out Intel oneAPI CXX compiler flags
-. $srcdir/config/oneapi-cxxflags
-
-# Figure out Intel classic CXX compiler flags
-# Do this ahead of GNU to avoid icpc being detected as g++
-. $srcdir/config/intel-cxxflags
-
-# Figure out GNU CXX compiler flags
-. $srcdir/config/gnu-cxxflags
-
-# Figure out PGI CXX compiler flags
-. $srcdir/config/pgi-cxxflags
-
-# Figure out Clang CXX compiler flags
-. $srcdir/config/clang-cxxflags
-
-# Figure out NVHPC CXX compiler flags
-. $srcdir/config/nvidia-cxxflags
-
-# compiler version strings
-
-# check if the compiler_version_info is already set
-if test -z "$cc_version_info"; then
-
-case $CC in
-    # whatever matches *pgcc* will also match *gcc*, so this one must come first
-    *pgcc*)
-        cc_version_info=`$CC $CFLAGS $H5_CFLAGS -V 2>&1 | grep 'pgcc'`
-        ;;
-
-    *gcc*)
-        cc_version_info=`$CC $CFLAGS $H5_CFLAGS --version 2>&1 | grep -v 'PathScale' |\
-            grep 'GCC' | sed 's/\(.*(GCC) [-a-z0-9\. ]*\).*/\1/'`
-        ;;
-    # this must come before *icc* for the same reason
-    *mpicc*)
-        cc_version_info=`$CC $CCFLAGS $H5_CCFLAGS -v 2>&1 | grep 'version' |\
-            sed 's/^[a-z0-9]* for //' |\
-            sed 's/\"/\\\"/g' |\
-            sed 's/^\([a-z]* \)/ built with \1/1'`
-        cc_version_info=`echo $cc_version_info`
-        ;;
-
-    *nvc*)
-        cc_version_info=`$CC $CFLAGS $H5_CFLAGS -V 2>&1 | grep 'nvc'`
-        ;;
-
-    *icx*)
-        cc_version_info=`$CC $CCFLAGS $H5_CCFLAGS -V 2>&1 | grep 'Version' |\
-            sed 's/\(Intel.* Compiler\).*\( Version [a-z0-9\.]*\).*\( Build [0-9]*\)/\1\2\3/'`
-        ;;
-
-    *icc*)
-        cc_version_info=`$CC $CCFLAGS $H5_CCFLAGS -V 2>&1 | grep 'Version' |\
-            sed 's/\(Intel.* Compiler\).*\( Version [a-z0-9\.]*\).*\( Build [0-9]*\)/\1\2\3/'`
-        ;;
-
-    *clang*)
-        cc_version_info="`$CC $CFLAGS $H5_CFLAGS --version 2>&1 |\
-            grep 'clang version' | sed 's/.*clang version \([-a-z0-9\.]*\).*/\1/'`"
-        ;;
-
-    *)
-        echo "No match to get cc_version_info for $CC"
-        ;;
-esac
-
-fi
-
-# get fortran version info
-# check if the compiler_version_info is already set
-if test -z "$fc_version_info"; then
-case $FC in
-    *gfortran*)
-        fc_version_info=`$FC $FCFLAGS $H5_FCFLAGS --version 2>&1 |\
-            grep 'GCC' | sed 's/\(.*(GCC) [-a-z0-9\. ]*\).*/\1/'`
-        ;;
-
-    *mpif90*)
-        fc_version_info=`$FC $FCFLAGS $H5_FCFLAGS -v 2>&1 | grep 'version' |\
-            sed 's/^[a-z0-9]* for //' |\
-            sed 's/\"/\\\"/g' |\
-            sed 's/^\([a-z]* \)/ built with \1/1'`
-        fc_version_info=`echo $fc_version_info`
-        ;;
-
-    *ifx*)
-        fc_version_info=`$FC $FCFLAGS $H5_FCFLAGS -V 2>&1 | grep 'Version' |\
-            sed 's/\(Intel.* Compiler\).*\( Version [a-z0-9\.]*\).*\( Build [0-9]*\)/\1\2\3/'`
-        ;;
-
-    *ifc*|*ifort*)
-        fc_version_info=`$FC $FCFLAGS $H5_FCFLAGS -V 2>&1 | grep 'Version' |\
-            sed 's/\(Intel.* Compiler\).*\( Version [a-z0-9\.]*\).*\( Build [0-9]*\)/\1\2\3/'`
-        ;;
-
-    *f95*)
-        # Figure out which compiler we are using: pgf90 or Absoft f95
-        RM='rm -f'
-        tmpfile=/tmp/cmpver.$$
-        $FC -V >$tmpfile
-        if test -s "$tmpfile"; then 
-            if( grep -s 'Absoft' $tmpfile > /dev/null) then
-                FC_BASENAME=f95
-            fi 
-        fi
-        $RM $tmpfile
-        fc_version_info=`$FC -V | grep Absoft`
-        ;;
-
-    *g95*)
-        fc_version_info=`$FC $FCFLAGS $H5_FCFLAGS --version 2>&1 |\
-            grep 'GCC'` 
-        ;;
-
-    *pgf90*)
-        fc_version_info=`$FC $FCFLAGS $H5_FCFLAGS -V 2>&1 | grep 'pgf90'`
-        ;;
-
-    *nvfortran*)
-        fc_version_info=`$FC $FCFLAGS $H5_FCFLAGS -V 2>&1 | grep 'nvfortran'`
-        ;;
-
-    *nagfor*|*nagftn*)
-        RM='rm -f'
-        tmpfile=/tmp/cmpver.$$
-        $FC -V >& $tmpfile
-        if test -s "$tmpfile"; then
-           if( grep -s 'NAG Fortran' $tmpfile > /dev/null) then
-               FC_BASENAME=nagfor
-           fi
-        fi
-        fc_version_info=`grep "NAG Fortran" $tmpfile`
-        $RM $tmpfile
-        echo "compiler '$FC' is $fc_version_info"
-	;;
-
-     *)
-        echo "No match to get fc_version_info for $FC"
-        ;;
-esac
-fi
-
-# get c++ version info
-# check if the compiler_version_info is already set
-if test -z "$cxx_version_info"; then
-case $CXX in
-    *nvc++*)
-        cxx_version_info=`$CXX $CXXFLAGS $H5_CXXFLAGS -V 2>&1 | grep 'nvc++'`
-        ;;
-    *pgc++*)
-        cxx_version_info=`$CXX $CXXFLAGS $H5_CXXFLAGS -V 2>&1 | grep 'pgc++'`
-        ;;
-    *g++*)
-        cxx_version_info=`$CXX $CXXFLAGS $H5_CXXFLAGS --version 2>&1 |\
-            grep 'GCC' | sed 's/\(.*(GCC) [-a-z0-9\. ]*\).*/\1/'`
-        ;;
-    *icpx*)
-        cxx_version_info=`$CXX $CXXFLAGS $H5_CXXFLAGS -V 2>&1 | grep 'Version' |\
-            sed 's/\(Intel.* Compiler\).*\( Version [a-z0-9\.]*\).*\( Build [0-9]*\)/\1\2\3/'`
-        ;;
-    *icpc*)
-        cxx_version_info=`$CXX $CXXFLAGS $H5_CXXFLAGS -V 2>&1 | grep 'Version' |\
-            sed 's/\(Intel.* Compiler\).*\( Version [a-z0-9\.]*\).*\( Build [0-9]*\)/\1\2\3/'`
-        ;;
-    *mpicxx*)
-        cxx_version_info=`$CXX $CXXFLAGS $H5_CXXFLAGS -v 2>&1 | grep 'version' |\
-            sed 's/^[a-z0-9]* for //' |\
-            sed 's/^\([a-z]* \)/ built with \1/1'`
-        cxx_version_info=`echo $cxx_version_info`
-        ;; 
-
-    *clang++*)
-        cxx_version_info="`$CXX $CXXFLAGS $H5_CXXFLAGS --version 2>&1 |\
-            grep 'clang version' | sed 's/.*clang version \([-a-z0-9\.]*\).*/\1/'`"
-        ;;
-
-    *)
-        echo "No match to get cxx_version_info for $CXX"
-        ;;
-esac
-fi