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Accepting request 995074 from science

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- Update to version 1.12.2.
- Minor re-base of existing patches to apply cleanly.
- Drop upstreamed patch: hdf5-1.10.8-pr1494-fix-release-check-version.patch.

OBS-URL: https://build.opensuse.org/request/show/995074
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/hdf5?expand=0&rev=78
This commit is contained in:
Dominique Leuenberger 2022-08-15 17:58:21 +00:00 committed by Git OBS Bridge
commit 791ba5ef38
12 changed files with 77 additions and 191 deletions
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18
Disable-phdf5-tests.patch
View File

@ -8,11 +8,11 @@ References:
Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de>
---
Index: hdf5-1.10.5/testpar/CMakeTests.cmake
Index: hdf5-1.12.2/testpar/CMakeTests.cmake
===================================================================
--- hdf5-1.10.5.orig/testpar/CMakeTests.cmake
+++ hdf5-1.10.5/testpar/CMakeTests.cmake
@@ -43,7 +43,7 @@
--- hdf5-1.12.2.orig/testpar/CMakeTests.cmake
+++ hdf5-1.12.2/testpar/CMakeTests.cmake
@@ -43,7 +43,7 @@ foreach (skiptest ${SKIP_tests})
set (SKIP_testphdf5 "${SKIP_testphdf5};-x;${skiptest}")
endforeach ()
@ -21,16 +21,16 @@ Index: hdf5-1.10.5/testpar/CMakeTests.cmake
set_tests_properties (MPI_TEST_testphdf5 PROPERTIES
FIXTURES_REQUIRED par_clear_testphdf5
ENVIRONMENT "HDF5_ALARM_SECONDS=3600;srcdir=${HDF5_TEST_PAR_BINARY_DIR}"
Index: hdf5-1.10.5/testpar/Makefile.am
Index: hdf5-1.12.2/testpar/Makefile.am
===================================================================
--- hdf5-1.10.5.orig/testpar/Makefile.am
+++ hdf5-1.10.5/testpar/Makefile.am
--- hdf5-1.12.2.orig/testpar/Makefile.am
+++ hdf5-1.12.2/testpar/Makefile.am
@@ -30,7 +30,7 @@ check_SCRIPTS = $(TEST_SCRIPT_PARA)
# Test programs. These are our main targets.
#
-TEST_PROG_PARA=t_mpi t_bigio testphdf5 t_cache t_cache_image t_pread t_pshutdown t_prestart t_init_term t_shapesame t_filters_parallel
+TEST_PROG_PARA=t_mpi t_bigio t_cache t_cache_image t_pread t_pshutdown t_prestart t_init_term t_shapesame t_filters_parallel
-TEST_PROG_PARA=t_mpi t_bigio testphdf5 t_cache t_cache_image t_pread t_pshutdown t_prestart t_init_term t_shapesame t_filters_parallel t_2Gio
+TEST_PROG_PARA=t_mpi t_bigio t_cache t_cache_image t_pread t_pshutdown t_prestart t_init_term t_shapesame t_filters_parallel t_2Gio
# t_pflush1 and t_pflush2 are used by testpflush.sh
check_PROGRAMS = $(TEST_PROG_PARA) t_pflush1 t_pflush2

21
PPC64LE-Fix-long-double-handling.patch
View File

@ -11,10 +11,10 @@ Signed-off-by: Egbert Eich <eich@suse.com>
hdf5-1.10.1/test/dt_arith.c | 26 ++++++++++++++++++++++++--
2 files changed, 40 insertions(+), 2 deletions(-)
Index: hdf5-1.10.8/config/cmake/ConversionTests.c
Index: hdf5-1.12.2/config/cmake/ConversionTests.c
===================================================================
--- hdf5-1.10.8.orig/config/cmake/ConversionTests.c
+++ hdf5-1.10.8/config/cmake/ConversionTests.c
--- hdf5-1.12.2.orig/config/cmake/ConversionTests.c
+++ hdf5-1.12.2/config/cmake/ConversionTests.c
@@ -34,6 +34,14 @@ int HDF_NO_UBSAN main(void)
unsigned char s2[8];
int ret = 1;
@ -45,12 +45,12 @@ Index: hdf5-1.10.8/config/cmake/ConversionTests.c
if(sizeof(long double) == 16) {
/*make sure the long double type is the same as the failing type
*which has 16 bytes in size and 11 bits of exponent. If it is,
Index: hdf5-1.10.8/test/dt_arith.c
Index: hdf5-1.12.2/test/dt_arith.c
===================================================================
--- hdf5-1.10.8.orig/test/dt_arith.c
+++ hdf5-1.10.8/test/dt_arith.c
@@ -3040,7 +3040,18 @@ test_conv_flt_1(const char *name, int ru
#if H5_SIZEOF_LONG_DOUBLE != H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE != 0
--- hdf5-1.12.2.orig/test/dt_arith.c
+++ hdf5-1.12.2/test/dt_arith.c
@@ -3036,7 +3036,19 @@ test_conv_flt_1(const char *name, int ru
#if H5_SIZEOF_LONG_DOUBLE != H5_SIZEOF_DOUBLE
}
else if (src_type == FLT_LDOUBLE) {
- INIT_FP_SPECIAL(src_size, src_nbits, sendian, LDBL_MANT_DIG, dst_size, buf, saved, nelmts);
@ -65,11 +65,12 @@ Index: hdf5-1.10.8/test/dt_arith.c
+ override the mantissa size. */
+ mant_dig = 52;
+ }
+ INIT_FP_SPECIAL(src_size, src_nbits, sendian, mant_dig, dst_size, buf, saved, nelmts);
+ INIT_FP_SPECIAL(src_size, src_nbits, sendian, mant_dig, dst_size,
+ buf, saved, nelmts);
#endif
}
else
@@ -3750,7 +3761,18 @@ test_conv_int_fp(const char *name, int r
@@ -3736,7 +3748,18 @@ test_conv_int_fp(const char *name, int r
nelmts);
}
else {

127
hdf5-1.10.8-pr1494-fix-release-check-version.patch
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@ -1,127 +0,0 @@
From 5595f1be4085006f62ebc603bf3fa52020205e48 Mon Sep 17 00:00:00 2001
From: Allen Byrne <byrn@hdfgroup.org>
Date: Fri, 11 Mar 2022 14:11:31 -0600
Subject: [PATCH 1/2] Fix release check version logic #1438
---
config/cmake/scripts/HDF5config.cmake | 2 +-
release_docs/RELEASE.txt | 17 +++++++++++++++++
src/H5.c | 14 ++++++--------
test/CMakeTests.cmake | 2 +-
4 files changed, 25 insertions(+), 10 deletions(-)
Index: hdf5-1.10.8/release_docs/RELEASE.txt
===================================================================
--- hdf5-1.10.8.orig/release_docs/RELEASE.txt
+++ hdf5-1.10.8/release_docs/RELEASE.txt
@@ -274,7 +274,23 @@ New Features
(ADB - 2020/09/24)
Library:
- --------
+ - Issue #1436 identified a problem with the H5_VERS_RELEASE check in the
+ H5check_version function.
+
+ Investigating the original fix, #812, we discovered some inconsistencies
+ with a new block added to check H5_VERS_RELEASE for incompatibilities.
+ This new block was not using the new warning text dealing with the
+ H5_VERS_RELEASE check and would cause the warning to be duplicated.
+
+ By removing the H5_VERS_RELEASE argument in the first check for
+ H5_VERS_MAJOR and H5_VERS_MINOR, the second check would only check
+ the H5_VERS_RELEASE for incompatible release versions. This adheres
+ to the statement that except for the develop branch, all release versions
+ in a major.minor maintenance branch should be compatible. The prerequisite
+ is that an application will not use any APIs not present in all release versions.
+
+ (ADB - 2022/03/11, #1438)
+
- Change how the release part of version, in major.minor.release is checked
for compatibility
Index: hdf5-1.10.8/src/H5.c
===================================================================
--- hdf5-1.10.8.orig/src/H5.c
+++ hdf5-1.10.8/src/H5.c
@@ -821,6 +821,7 @@ H5check_version(unsigned majnum, unsigne
static int checked = 0; /* If we've already checked the version info */
static unsigned int disable_version_check = 0; /* Set if the version check should be disabled */
static const char * version_mismatch_warning = VERSION_MISMATCH_WARNING;
+ static const char * release_mismatch_warning = RELEASE_MISMATCH_WARNING;
herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API_NOINIT_NOERR_NOFS
@@ -841,10 +842,7 @@ H5check_version(unsigned majnum, unsigne
}
/* H5_VERS_MAJOR and H5_VERS_MINOR must match */
- /* Cast relnum to int to avoid warning for unsigned < 0 comparison
- * in first release versions */
- if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum || H5_VERS_RELEASE > (int)relnum) {
-
+ if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum) {
switch (disable_version_check) {
case 0:
HDfprintf(stderr, "%s%s", version_mismatch_warning,
@@ -879,7 +877,7 @@ H5check_version(unsigned majnum, unsigne
break;
} /* end switch */
- } /* end if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum || H5_VERS_RELEASE > relnum) */
+ } /* end if (H5_VERS_MAJOR != majnum || H5_VERS_MINOR != minnum) */
/* H5_VERS_RELEASE should be compatible, we will only add checks for exceptions */
if (H5_VERS_RELEASE != relnum) {
@@ -889,7 +887,7 @@ H5check_version(unsigned majnum, unsigne
switch (disable_version_check) {
case 0:
HDfprintf(
- stderr, "%s%s", version_mismatch_warning,
+ stderr, "%s%s", release_mismatch_warning,
"You can, at your own risk, disable this warning by setting the environment\n"
"variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.\n"
"Setting it to 2 or higher will suppress the warning messages totally.\n");
@@ -908,7 +906,7 @@ H5check_version(unsigned majnum, unsigne
"%s'HDF5_DISABLE_VERSION_CHECK' "
"environment variable is set to %d, application will\n"
"continue at your own risk.\n",
- version_mismatch_warning, disable_version_check);
+ release_mismatch_warning, disable_version_check);
/* Mention the versions we are referring to */
HDfprintf(stderr, "Headers are %u.%u.%u, library is %u.%u.%u\n", majnum, minnum,
relnum, (unsigned)H5_VERS_MAJOR, (unsigned)H5_VERS_MINOR,
@@ -986,7 +984,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5close
*
- * Purpose: Terminate the library and release all resources.
+ * Purpose: Terminate the library and release all resources.
*
* Return: Non-negative on success/Negative on failure
*
Index: hdf5-1.10.8/test/CMakeTests.cmake
===================================================================
--- hdf5-1.10.8.orig/test/CMakeTests.cmake
+++ hdf5-1.10.8/test/CMakeTests.cmake
@@ -704,7 +704,7 @@ set_tests_properties (H5TEST-tcheck_vers
WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST
WILL_FAIL "true"
)
-# release + 1 should pass
+# release + 1 should pass on non-develop branches
add_test (NAME H5TEST-tcheck_version-release COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:tcheck_version> "-tr")
set_tests_properties (H5TEST-tcheck_version-release PROPERTIES
WORKING_DIRECTORY ${HDF5_TEST_BINARY_DIR}/H5TEST
Index: hdf5-1.10.8/config/cmake/scripts/HDF5config.cmake
===================================================================
--- hdf5-1.10.8.orig/config/cmake/scripts/HDF5config.cmake
+++ hdf5-1.10.8/config/cmake/scripts/HDF5config.cmake
@@ -163,7 +163,7 @@ if (NOT DEFINED HPC)
set (SITE_COMPILER_NAME "vs2012")
set (SITE_COMPILER_VERSION "11")
else ()
- message (FATAL_ERROR "Invalid BUILD_GENERATOR must be - Unix, VS2017, or VS201764, VS2015, VS201564, VS2013, VS201364")
+ message (FATAL_ERROR "Invalid BUILD_GENERATOR must be - Unix, VS2017, VS201764, VS2015, VS201564, VS2013, VS201364")
endif ()
## Set the following to unique id your computer ##
set (CTEST_SITE "WIN7${BUILD_GENERATOR}.XXXX")

3
hdf5-1.10.8.tar.bz2
View File

@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:66ec544b195a4cb9f6ffed034fd82e52429d6112747c2996ab69853f606e546b
size 9517067

BIN
hdf5-1.12.2.tar.bz2 (Stored with Git LFS) Normal file
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Binary file not shown.

22
hdf5-1.8.10-tests-arm.patch
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@ -1,10 +1,12 @@
--- ./test/testhdf5.c.orig 2012-05-09 17:05:49.000000000 +0200
+++ ./test/testhdf5.c 2012-06-20 19:22:33.332532223 +0200
@@ -57,7 +57,6 @@ main(int argc, char *argv[])
AddTest("coords", test_coords, cleanup_coords, "Dataspace coordinates", NULL);
AddTest("sohm", test_sohm, cleanup_sohm, "Shared Object Header Messages", NULL);
AddTest("attr", test_attr, cleanup_attr, "Attributes", NULL);
- AddTest("select", test_select, cleanup_select, "Selections", NULL);
AddTest("time", test_time, cleanup_time, "Time Datatypes", NULL);
AddTest("reference", test_reference, cleanup_reference, "References", NULL);
AddTest("vltypes", test_vltypes, cleanup_vltypes, "Variable-Length Datatypes", NULL);
Index: hdf5-1.12.2/test/testhdf5.c
===================================================================
--- hdf5-1.12.2.orig/test/testhdf5.c
+++ hdf5-1.12.2/test/testhdf5.c
@@ -53,7 +53,6 @@ main(int argc, char *argv[])
AddTest("coords", test_coords, cleanup_coords, "Dataspace coordinates", NULL);
AddTest("sohm", test_sohm, cleanup_sohm, "Shared Object Header Messages", NULL);
AddTest("attr", test_attr, cleanup_attr, "Attributes", NULL);
- AddTest("select", test_select, cleanup_select, "Selections", NULL);
AddTest("time", test_time, cleanup_time, "Time Datatypes", NULL);
AddTest("ref_deprec", test_reference_deprec, cleanup_reference_deprec, "Deprecated References", NULL);
AddTest("ref", test_reference, cleanup_reference, "References", NULL);

4
hdf5-1.8.11-abort_unknown_host_config.patch
View File

@ -2,7 +2,7 @@ Index: configure
===================================================================
--- configure.orig
+++ configure
@@ -4286,6 +4286,8 @@ done
@@ -4343,6 +4343,8 @@ done
if test "X$host_config" != "Xnone"; then
CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
. $host_config
@ -15,7 +15,7 @@ Index: configure.ac
===================================================================
--- configure.ac.orig
+++ configure.ac
@@ -294,6 +294,8 @@ done
@@ -330,6 +330,8 @@ done
if test "X$host_config" != "Xnone"; then
CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
. $host_config

14
hdf5-LD_LIBRARY_PATH.patch
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@ -1,22 +1,22 @@
Index: hdf5-1.10.8/src/Makefile.in
Index: hdf5-1.12.2/src/Makefile.in
===================================================================
--- hdf5-1.10.8.orig/src/Makefile.in
+++ hdf5-1.10.8/src/Makefile.in
@@ -1990,8 +1990,6 @@ help:
--- hdf5-1.12.2.orig/src/Makefile.in
+++ hdf5-1.12.2/src/Makefile.in
@@ -1998,8 +1998,6 @@ help:
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5Tinit.c: H5detect$(EXEEXT)
- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
- sed -e 's/-L/:/g' -e 's/ //g'`" \
$(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \
$(RUNSERIAL) ./H5detect$(EXEEXT) $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)
@@ -2002,8 +2000,6 @@ H5Tinit.c: H5detect$(EXEEXT)
@@ -2010,8 +2008,6 @@ H5Tinit.c: H5detect$(EXEEXT)
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error.
H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings
- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \
- sed -e 's/-L/:/g' -e 's/ //g'`" \
$(RUNSERIAL) ./H5make_libsettings$(EXEEXT) > $@ || \
$(RUNSERIAL) ./H5make_libsettings$(EXEEXT) $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1)

8
hdf5-Remove-timestamps-from-binaries.patch
View File

@ -10,11 +10,11 @@ Signed-off-by: Egbert Eich <eich@suse.de>
---
src/H5detect.c | 15 ---------------
1 file changed, 15 deletions(-)
Index: hdf5-1.10.8/src/H5detect.c
Index: hdf5-1.12.2/src/H5detect.c
===================================================================
--- hdf5-1.10.8.orig/src/H5detect.c
+++ hdf5-1.10.8/src/H5detect.c
@@ -1190,22 +1190,6 @@ bit.\n";
--- hdf5-1.12.2.orig/src/H5detect.c
+++ hdf5-1.12.2/src/H5detect.c
@@ -1224,22 +1224,6 @@ bit.\n";
fprintf(rawoutstream, "/* Generated automatically by H5detect -- do not edit */\n\n\n");
HDfputs(FileHeader, rawoutstream); /*the copyright notice--see top of this file */

14
hdf5.changes
View File

@ -1,3 +1,17 @@
-------------------------------------------------------------------
Wed Jul 27 23:42:38 UTC 2022 - Atri Bhattacharya <badshah400@gmail.com>
- Update to version 1.12.2:
See <https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.12/hdf5-1.12.2/src/hdf5-1.12.2-RELEASE.txt>.
- Minor re-base of existing patches to apply cleanly:
* hdf5-LD_LIBRARY_PATH.patch
* hdf5-1.8.11-abort_unknown_host_config.patch
* hdf5-Remove-timestamps-from-binaries.patch
* hdf5-mpi.patch
* Disable-phdf5-tests.patch
- Drop upstreamed patch:
hdf5-1.10.8-pr1494-fix-release-check-version.patch.
-------------------------------------------------------------------
Wed May 4 06:39:53 UTC 2022 - Egbert Eich <eich@suse.com>

22
hdf5.spec
View File

@ -34,9 +34,9 @@
%define use_sz2 0
%define vers 1.10.8
%define _vers 1_10_8
%define short_ver 1.10
%define short_ver 1.12
%define vers %{short_ver}.2
%define _vers %( echo %{vers} | tr '.' '_' )
%define src_ver %{version}
%define pname hdf5
%global _lto_cflags %{_lto_cflags} -ffat-lto-objects
@ -436,8 +436,6 @@ Patch6: hdf5-Remove-timestamps-from-binaries.patch
# Could be ported but it's unknown if it's still needed
Patch7: hdf5-mpi.patch
Patch8: Disable-phdf5-tests.patch
# boo#1179521, boo#1196682, gh#HDFGroup/hdf5#1494
Patch9: hdf5-1.10.8-pr1494-fix-release-check-version.patch
# Imported from Fedora, strip flags from h5cc wrapper
Patch10: hdf5-wrappers.patch
BuildRequires: fdupes
@ -680,7 +678,6 @@ library packages.
%patch6 -p1
# %%patch7 -p1
%patch8 -p1
%patch9 -p1
%patch10 -p1
%if %{without hpc}
@ -775,7 +772,8 @@ export MPICXX=mpicxx
%if 0%{?use_sz2}
--with-szlib \
%endif
--with-pthread
--with-pthread \
%{nil}
make V=1 %{?_smp_mflags}
@ -941,15 +939,13 @@ export HDF5_Make_Ignore=yes
%{my_bindir}/h5repart
%{my_bindir}/h5stat
%{my_bindir}/h5unjam
%{my_bindir}/mirror_server
%{my_bindir}/mirror_server_stop
%files -n %{libname -s %{sonum}}
%doc ACKNOWLEDGMENTS README.txt
%doc ACKNOWLEDGMENTS README.md
%mylicense COPYING
##
%if %{without mpi}
%doc release_docs/HISTORY-1_8_0-1_10_0.txt
%doc release_docs/HISTORY-1_10_0-1_12_0.txt
%doc release_docs/RELEASE.txt
%endif
%defattr(0755,root,root)
@ -1000,9 +996,9 @@ export HDF5_Make_Ignore=yes
%files devel
##
%{?with_hpc:%dir %{my_incdir}}
%doc release_docs/HISTORY-1_0-1_8_0_rc3.txt
%doc release_docs/HISTORY-1_10_0-1_12_0.txt
%doc release_docs/RELEASE.txt
%doc ACKNOWLEDGMENTS README.txt
%doc ACKNOWLEDGMENTS README.md
%{?with_hpc:%{hpc_pkgconfig_file -n hdf5}}
%{?with_hpc:%{hpc_pkgconfig_file -N -n hdf5_hl}}
%{?with_hpc:%{hpc_pkgconfig_file -N -n hdf5_fortran}}

12
so_versions
View File

@ -1,6 +1,6 @@
%define sonum 103
%define sonum_CXX 103
%define sonum_F 102
%define sonum_HL 100
%define sonum_HL_CXX 100
%define sonum_HL_F 100
%define sonum 200
%define sonum_CXX 200
%define sonum_F 200
%define sonum_HL 200
%define sonum_HL_CXX 200
%define sonum_HL_F 200