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Accepting request 726430 from home:anag:branches:science

Browse Source 
- Update to version 1.10.5:
  * https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5-RELEASE.txt
- Bump fortran library soname, sonum_F from 100 to 102.
- Adjust library installation path, use %hpc_prefix/lib64 in x86_64 
  and %hpc_libdir in all other cases
- Patches refreshed:
  * hdf5-LD_LIBRARY_PATH.patch
  * hdf5-1.8.11-abort_unknown_host_config.patch
  * PPC64LE-Fix-long-double-handling.patch
  * hdf5-Remove-timestamps-from-binaries.patch
  * Disable-phdf5-tests.patch
- Patch disabled, upstream have changed the file that was being patched,
  while it could be ported, it's unknown if this patch is still needed.
  * hdf5-mpi.patch
- Patch removed, merged upstream
  * 0001-Fix-return-value-in-test_libver_bounds_open.patch

OBS-URL: https://build.opensuse.org/request/show/726430
OBS-URL: https://build.opensuse.org/package/show/science/hdf5?expand=0&rev=111
This commit is contained in:
Christian Goll 2019-09-03 07:57:43 +00:00 committed by Git OBS Bridge
parent 0abc2b716c
commit f5645d586f
10 changed files with 78 additions and 83 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

26
0001-Fix-return-value-in-test_libver_bounds_open.patch
View File

@ -1,26 +0,0 @@
From b24bae35dcd2733e7339f87da0f2681ee06439a8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Stefan=20Br=C3=BCns?= <stefan.bruens@rwth-aachen.de>
Date: Thu, 20 Sep 2018 20:36:13 +0200
Subject: [PATCH] Fix return value in test_libver_bounds_open
A return value is neither returned nor expected.
---
test/tfile.c | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/test/tfile.c b/test/tfile.c
index ad7f87f..d3134f8 100644
--- a/test/tfile.c
+++ b/test/tfile.c
@@ -4967,7 +4967,7 @@ test_libver_bounds_real(H5F_libver_t libver_create, unsigned oh_vers_create,
#define VERBFNAME "tverbounds_dspace.h5"
#define VERBDSNAME "dataset 1"
#define SPACE1_DIM1 3
-static int
+static void
test_libver_bounds_open(void)
{
hid_t file = -1; /* File ID */
--
2.19.0

45
Disable-phdf5-tests.patch
View File

@ -8,32 +8,29 @@ References:
Signed-off-by: Egbert Eich <eich@suse.com> Signed-off-by: Egbert Eich <eich@suse.com>
Signed-off-by: Egbert Eich <eich@suse.de> Signed-off-by: Egbert Eich <eich@suse.de>
--- ---
testpar/CMakeTests.cmake | 2 +- Index: hdf5-1.10.5/testpar/CMakeTests.cmake
testpar/Makefile.am | 2 +- ===================================================================
2 files changed, 2 insertions(+), 2 deletions(-) --- hdf5-1.10.5.orig/testpar/CMakeTests.cmake
diff --git a/testpar/CMakeTests.cmake b/testpar/CMakeTests.cmake +++ hdf5-1.10.5/testpar/CMakeTests.cmake
index 87470f3..ce2f2e4 100644 @@ -30,7 +30,7 @@ set (SKIP_testphdf5 "")
--- a/testpar/CMakeTests.cmake # set (SKIP_testphdf5 "${SKIP_testphdf5};-x;ecdsetw")
+++ b/testpar/CMakeTests.cmake #endif ()
@@ -16,7 +16,7 @@
##############################################################################
##############################################################################
-add_test (NAME TEST_PAR_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS}) -add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5})
+##add_test (NAME TEST_PAR_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS}) +## add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5})
set_tests_properties (MPI_TEST_testphdf5 PROPERTIES
foreach (testp ${H5P_TESTS}) FIXTURES_REQUIRED par_clear_testphdf5
add_test (NAME TEST_PAR_${testp} COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:${testp}> ${MPIEXEC_POSTFLAGS}) ENVIRONMENT "HDF5_ALARM_SECONDS=3600;srcdir=${HDF5_TEST_PAR_BINARY_DIR}"
diff --git a/testpar/Makefile.am b/testpar/Makefile.am Index: hdf5-1.10.5/testpar/Makefile.am
index 7262ca6..e9c8c4a 100644 ===================================================================
--- a/testpar/Makefile.am --- hdf5-1.10.5.orig/testpar/Makefile.am
+++ b/testpar/Makefile.am +++ hdf5-1.10.5/testpar/Makefile.am
@@ -23,7 +23,7 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test @@ -30,7 +30,7 @@ check_SCRIPTS = $(TEST_SCRIPT_PARA)
# Test programs. These are our main targets. # Test programs. These are our main targets.
# #
-TEST_PROG_PARA=t_mpi t_bigio testphdf5 t_cache t_cache_image t_pflush1 t_pflush2 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
+TEST_PROG_PARA=t_mpi t_bigio t_cache t_cache_image t_pflush1 t_pflush2 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
check_PROGRAMS = $(TEST_PROG_PARA)
# t_pflush1 and t_pflush2 are used by testpflush.sh
check_PROGRAMS = $(TEST_PROG_PARA) t_pflush1 t_pflush2

24
PPC64LE-Fix-long-double-handling.patch
View File

@ -11,11 +11,11 @@ Signed-off-by: Egbert Eich <eich@suse.com>
hdf5-1.10.1/test/dt_arith.c | 26 ++++++++++++++++++++++++-- hdf5-1.10.1/test/dt_arith.c | 26 ++++++++++++++++++++++++--
2 files changed, 40 insertions(+), 2 deletions(-) 2 files changed, 40 insertions(+), 2 deletions(-)
diff --git a/hdf5-1.10.1/config/cmake/ConversionTests.c b/hdf5-1.10.1/config/cmake/ConversionTests.c Index: hdf5-1.10.5/config/cmake/ConversionTests.c
index 082dbd4..9618a14 100644 ===================================================================
--- a/config/cmake/ConversionTests.c --- hdf5-1.10.5.orig/config/cmake/ConversionTests.c
+++ b/config/cmake/ConversionTests.c +++ hdf5-1.10.5/config/cmake/ConversionTests.c
@@ -34,6 +34,14 @@ int main(void) @@ -34,6 +34,14 @@ int HDF_NO_UBSAN main(void)
unsigned char s2[8]; unsigned char s2[8];
int ret = 1; int ret = 1;
@ -30,7 +30,7 @@ index 082dbd4..9618a14 100644
if(sizeof(long double) == 16 && sizeof(long) == 8) { if(sizeof(long double) == 16 && sizeof(long) == 8) {
/*make sure the long double type has 16 bytes in size and /*make sure the long double type has 16 bytes in size and
* 11 bits of exponent. If it is, * 11 bits of exponent. If it is,
@@ -157,6 +165,14 @@ int main(void) @@ -157,6 +165,14 @@ int HDF_NO_UBSAN main(void)
unsigned char s[16]; unsigned char s[16];
int ret = 0; int ret = 0;
@ -45,11 +45,11 @@ index 082dbd4..9618a14 100644
if(sizeof(long double) == 16) { if(sizeof(long double) == 16) {
/*make sure the long double type is the same as the failing type /*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, *which has 16 bytes in size and 11 bits of exponent. If it is,
diff --git a/hdf5-1.10.1/test/dt_arith.c b/hdf5-1.10.1/test/dt_arith.c Index: hdf5-1.10.5/test/dt_arith.c
index 8f3e6e4..084b47c 100644 ===================================================================
--- a/test/dt_arith.c --- hdf5-1.10.5.orig/test/dt_arith.c
+++ b/test/dt_arith.c +++ hdf5-1.10.5/test/dt_arith.c
@@ -3051,7 +3051,18 @@ test_conv_flt_1 (const char *name, int run_test, hid_t src, hid_t dst) @@ -3051,7 +3051,18 @@ test_conv_flt_1 (const char *name, int r
buf, saved, nelmts); buf, saved, nelmts);
#if H5_SIZEOF_LONG_DOUBLE!=H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE!=0 #if H5_SIZEOF_LONG_DOUBLE!=H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE!=0
} else if(src_type == FLT_LDOUBLE) { } else if(src_type == FLT_LDOUBLE) {
@ -69,7 +69,7 @@ index 8f3e6e4..084b47c 100644
buf, saved, nelmts); buf, saved, nelmts);
#endif #endif
} else } else
@@ -3712,7 +3723,18 @@ test_conv_int_fp(const char *name, int run_test, hid_t src, hid_t dst) @@ -3711,7 +3722,18 @@ test_conv_int_fp(const char *name, int r
INIT_FP_DENORM(long double, LDBL_MANT_DIG, src_size, src_nbits, sendian, dst_size, INIT_FP_DENORM(long double, LDBL_MANT_DIG, src_size, src_nbits, sendian, dst_size,
buf, saved, nelmts); buf, saved, nelmts);
} else { } else {

3
hdf5-1.10.4.tar.bz2
View File

@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:1267ff06aaedc04ca25f7c6026687ea2884b837043431195f153401d942b28df
size 8598986

3
hdf5-1.10.5.tar.bz2 Normal file
View File

@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:68d6ea8843d2a106ec6a7828564c1689c7a85714a35d8efafa2fee20ca366f44
size 8706317

4
hdf5-1.8.11-abort_unknown_host_config.patch
View File

@ -2,7 +2,7 @@ Index: configure
=================================================================== ===================================================================
--- configure.orig --- configure.orig
+++ configure +++ configure
@@ -4085,6 +4085,8 @@ done @@ -4097,6 +4097,8 @@ done
if test "X$host_config" != "Xnone"; then if test "X$host_config" != "Xnone"; then
CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`" CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
. $host_config . $host_config
@ -15,7 +15,7 @@ Index: configure.ac
=================================================================== ===================================================================
--- configure.ac.orig --- configure.ac.orig
+++ configure.ac +++ configure.ac
@@ -266,6 +266,8 @@ done @@ -263,6 +263,8 @@ done
if test "X$host_config" != "Xnone"; then if test "X$host_config" != "Xnone"; then
CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`" CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`"
. $host_config . $host_config

10
hdf5-LD_LIBRARY_PATH.patch
View File

@ -1,8 +1,8 @@
Index: hdf5-1.10.0-patch1/src/Makefile.in Index: hdf5-1.10.5/src/Makefile.in
=================================================================== ===================================================================
--- hdf5-1.10.0-patch1.orig/src/Makefile.in --- hdf5-1.10.5.orig/src/Makefile.in
+++ hdf5-1.10.0-patch1/src/Makefile.in +++ hdf5-1.10.5/src/Makefile.in
@@ -1847,8 +1847,6 @@ help: @@ -1873,8 +1873,6 @@ help:
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error. # is set to ignore the error.
H5Tinit.c: H5detect$(EXEEXT) H5Tinit.c: H5detect$(EXEEXT)
@ -11,7 +11,7 @@ Index: hdf5-1.10.0-patch1/src/Makefile.in
$(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \ $(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \
(test $$HDF5_Make_Ignore && echo "*** Error ignored") || \ (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \
($(RM) $@ ; exit 1) ($(RM) $@ ; exit 1)
@@ -1859,8 +1857,6 @@ H5Tinit.c: H5detect$(EXEEXT) @@ -1885,8 +1883,6 @@ H5Tinit.c: H5detect$(EXEEXT)
# Remove the generated .c file if errors occur unless HDF5_Make_Ignore # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
# is set to ignore the error. # is set to ignore the error.
H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings

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

@ -10,10 +10,10 @@ Signed-off-by: Egbert Eich <eich@suse.de>
--- ---
src/H5detect.c | 15 --------------- src/H5detect.c | 15 ---------------
1 file changed, 15 deletions(-) 1 file changed, 15 deletions(-)
diff --git a/src/H5detect.c b/src/H5detect.c Index: hdf5-1.10.5/src/H5detect.c
index 4424009..f49774c 100644 ===================================================================
--- a/src/H5detect.c --- hdf5-1.10.5.orig/src/H5detect.c
+++ b/src/H5detect.c +++ hdf5-1.10.5/src/H5detect.c
@@ -1245,21 +1245,6 @@ bit.\n"; @@ -1245,21 +1245,6 @@ bit.\n";
fprintf(rawoutstream, "/* Generated automatically by H5detect -- do not edit */\n\n\n"); fprintf(rawoutstream, "/* Generated automatically by H5detect -- do not edit */\n\n\n");
HDfputs(FileHeader, rawoutstream); /*the copyright notice--see top of this file */ HDfputs(FileHeader, rawoutstream); /*the copyright notice--see top of this file */

21
hdf5.changes
View File

@ -1,3 +1,24 @@
-------------------------------------------------------------------
Fri Aug 23 09:58:01 UTC 2019 - Ana Guerrero Lopez <aguerrero@suse.com>
- Update to version 1.10.5:
* https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.5/src/hdf5-1.10.5-RELEASE.txt
- Bump fortran library soname, sonum_F from 100 to 102.
- Adjust library installation path, use %hpc_prefix/lib64 in x86_64
and %hpc_libdir in all other cases
- Patches refreshed:
* hdf5-LD_LIBRARY_PATH.patch
* hdf5-1.8.11-abort_unknown_host_config.patch
* PPC64LE-Fix-long-double-handling.patch
* hdf5-Remove-timestamps-from-binaries.patch
* Disable-phdf5-tests.patch
- Patch disabled, upstream have changed the file that was being patched,
while it could be ported, it's unknown if this patch is still needed.
* hdf5-mpi.patch
- Patch removed, merged upstream
* 0001-Fix-return-value-in-test_libver_bounds_open.patch
------------------------------------------------------------------- -------------------------------------------------------------------
Thu Jul 4 11:45:55 UTC 2019 - Egbert Eich <eich@suse.com> Thu Jul 4 11:45:55 UTC 2019 - Egbert Eich <eich@suse.com>

17
hdf5.spec
View File

@ -33,8 +33,8 @@
%define use_sz2 0 %define use_sz2 0
%define vers 1.10.4 %define vers 1.10.5
%define _vers 1_10_4 %define _vers 1_10_5
%define short_ver 1.10 %define short_ver 1.10
%define src_ver %{version} %define src_ver %{version}
%define pname hdf5 %define pname hdf5
@ -181,7 +181,11 @@ ExclusiveArch: do_not_build
%{?with_mpi:%global hpc_module_pname p%{pname}} %{?with_mpi:%global hpc_module_pname p%{pname}}
%define my_prefix %hpc_prefix %define my_prefix %hpc_prefix
%define my_bindir %hpc_bindir %define my_bindir %hpc_bindir
%ifarch x86_64
%define my_libdir %hpc_prefix/lib64
%else
%define my_libdir %hpc_libdir %define my_libdir %hpc_libdir
%endif
%define my_incdir %hpc_includedir %define my_incdir %hpc_includedir
%define package_name %{hpc_package_name %_vers} %define package_name %{hpc_package_name %_vers}
%define libname(l:s:) lib%{pname}%{-l*}%{hpc_package_name_tail %{?_vers}} %define libname(l:s:) lib%{pname}%{-l*}%{hpc_package_name_tail %{?_vers}}
@ -210,7 +214,7 @@ ExclusiveArch: do_not_build
# do not match the so numbers that are actually built. # do not match the so numbers that are actually built.
%define sonum 103 %define sonum 103
%define sonum_CXX 103 %define sonum_CXX 103
%define sonum_F 100 %define sonum_F 102
%define sonum_HL 100 %define sonum_HL 100
%define sonum_HL_CXX 100 %define sonum_HL_CXX 100
%define sonum_HL_F 100 %define sonum_HL_F 100
@ -233,9 +237,9 @@ Patch4: hdf5-1.8.10-tests-arm.patch
%endif %endif
Patch5: PPC64LE-Fix-long-double-handling.patch Patch5: PPC64LE-Fix-long-double-handling.patch
Patch6: hdf5-Remove-timestamps-from-binaries.patch Patch6: hdf5-Remove-timestamps-from-binaries.patch
Patch7: hdf5-mpi.patch # Could be ported but it's unknown if it's still needed
# Patch7: hdf5-mpi.patch
Patch8: Disable-phdf5-tests.patch Patch8: Disable-phdf5-tests.patch
Patch9: 0001-Fix-return-value-in-test_libver_bounds_open.patch
BuildRequires: fdupes BuildRequires: fdupes
%if 0%{?use_sz2} %if 0%{?use_sz2}
BuildRequires: libsz2-devel BuildRequires: libsz2-devel
@ -465,9 +469,8 @@ library packages.
%endif %endif
%patch5 -p1 %patch5 -p1
%patch6 -p1 %patch6 -p1
%patch7 -p1 # %%patch7 -p1
%patch8 -p1 %patch8 -p1
%patch9 -p1
%if %{without hpc} %if %{without hpc}
# baselibs looks different for different flavors - generate it on the fly # baselibs looks different for different flavors - generate it on the fly