From f5645d586f46c84eaa353117e40e8cb43517fc67d160f2531eadb7734c19a3f9 Mon Sep 17 00:00:00 2001 From: Christian Goll Date: Tue, 3 Sep 2019 07:57:43 +0000 Subject: [PATCH] Accepting request 726430 from home:anag:branches:science - 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 --- ...urn-value-in-test_libver_bounds_open.patch | 26 ----------- Disable-phdf5-tests.patch | 45 +++++++++---------- PPC64LE-Fix-long-double-handling.patch | 24 +++++----- hdf5-1.10.4.tar.bz2 | 3 -- hdf5-1.10.5.tar.bz2 | 3 ++ hdf5-1.8.11-abort_unknown_host_config.patch | 4 +- hdf5-LD_LIBRARY_PATH.patch | 10 ++--- hdf5-Remove-timestamps-from-binaries.patch | 8 ++-- hdf5.changes | 21 +++++++++ hdf5.spec | 17 ++++--- 10 files changed, 78 insertions(+), 83 deletions(-) delete mode 100644 0001-Fix-return-value-in-test_libver_bounds_open.patch delete mode 100644 hdf5-1.10.4.tar.bz2 create mode 100644 hdf5-1.10.5.tar.bz2 diff --git a/0001-Fix-return-value-in-test_libver_bounds_open.patch b/0001-Fix-return-value-in-test_libver_bounds_open.patch deleted file mode 100644 index f73c5b1..0000000 --- a/0001-Fix-return-value-in-test_libver_bounds_open.patch +++ /dev/null @@ -1,26 +0,0 @@ -From b24bae35dcd2733e7339f87da0f2681ee06439a8 Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Stefan=20Br=C3=BCns?= -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 - diff --git a/Disable-phdf5-tests.patch b/Disable-phdf5-tests.patch index c29b453..f55d46f 100644 --- a/Disable-phdf5-tests.patch +++ b/Disable-phdf5-tests.patch @@ -8,32 +8,29 @@ References: Signed-off-by: Egbert Eich Signed-off-by: Egbert Eich --- - testpar/CMakeTests.cmake | 2 +- - testpar/Makefile.am | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) -diff --git a/testpar/CMakeTests.cmake b/testpar/CMakeTests.cmake -index 87470f3..ce2f2e4 100644 ---- a/testpar/CMakeTests.cmake -+++ b/testpar/CMakeTests.cmake -@@ -16,7 +16,7 @@ - ############################################################################## - ############################################################################## +Index: hdf5-1.10.5/testpar/CMakeTests.cmake +=================================================================== +--- hdf5-1.10.5.orig/testpar/CMakeTests.cmake ++++ hdf5-1.10.5/testpar/CMakeTests.cmake +@@ -30,7 +30,7 @@ set (SKIP_testphdf5 "") + # set (SKIP_testphdf5 "${SKIP_testphdf5};-x;ecdsetw") + #endif () --add_test (NAME TEST_PAR_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $ ${MPIEXEC_POSTFLAGS}) -+##add_test (NAME TEST_PAR_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $ ${MPIEXEC_POSTFLAGS}) - - foreach (testp ${H5P_TESTS}) - add_test (NAME TEST_PAR_${testp} COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $ ${MPIEXEC_POSTFLAGS}) -diff --git a/testpar/Makefile.am b/testpar/Makefile.am -index 7262ca6..e9c8c4a 100644 ---- a/testpar/Makefile.am -+++ b/testpar/Makefile.am -@@ -23,7 +23,7 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test +-add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $ ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5}) ++## add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $ ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5}) + set_tests_properties (MPI_TEST_testphdf5 PROPERTIES + FIXTURES_REQUIRED par_clear_testphdf5 + ENVIRONMENT "HDF5_ALARM_SECONDS=3600;srcdir=${HDF5_TEST_PAR_BINARY_DIR}" +Index: hdf5-1.10.5/testpar/Makefile.am +=================================================================== +--- hdf5-1.10.5.orig/testpar/Makefile.am ++++ hdf5-1.10.5/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_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_pflush1 t_pflush2 t_pread t_pshutdown t_prestart t_init_term t_shapesame t_filters_parallel - - check_PROGRAMS = $(TEST_PROG_PARA) +-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 + # t_pflush1 and t_pflush2 are used by testpflush.sh + check_PROGRAMS = $(TEST_PROG_PARA) t_pflush1 t_pflush2 diff --git a/PPC64LE-Fix-long-double-handling.patch b/PPC64LE-Fix-long-double-handling.patch index 2044e17..87d0c7e 100644 --- a/PPC64LE-Fix-long-double-handling.patch +++ b/PPC64LE-Fix-long-double-handling.patch @@ -11,11 +11,11 @@ Signed-off-by: Egbert Eich hdf5-1.10.1/test/dt_arith.c | 26 ++++++++++++++++++++++++-- 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 082dbd4..9618a14 100644 ---- a/config/cmake/ConversionTests.c -+++ b/config/cmake/ConversionTests.c -@@ -34,6 +34,14 @@ int main(void) +Index: hdf5-1.10.5/config/cmake/ConversionTests.c +=================================================================== +--- hdf5-1.10.5.orig/config/cmake/ConversionTests.c ++++ hdf5-1.10.5/config/cmake/ConversionTests.c +@@ -34,6 +34,14 @@ int HDF_NO_UBSAN main(void) unsigned char s2[8]; int ret = 1; @@ -30,7 +30,7 @@ index 082dbd4..9618a14 100644 if(sizeof(long double) == 16 && sizeof(long) == 8) { /*make sure the long double type has 16 bytes in size and * 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]; int ret = 0; @@ -45,11 +45,11 @@ index 082dbd4..9618a14 100644 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, -diff --git a/hdf5-1.10.1/test/dt_arith.c b/hdf5-1.10.1/test/dt_arith.c -index 8f3e6e4..084b47c 100644 ---- a/test/dt_arith.c -+++ b/test/dt_arith.c -@@ -3051,7 +3051,18 @@ test_conv_flt_1 (const char *name, int run_test, hid_t src, hid_t dst) +Index: hdf5-1.10.5/test/dt_arith.c +=================================================================== +--- hdf5-1.10.5.orig/test/dt_arith.c ++++ hdf5-1.10.5/test/dt_arith.c +@@ -3051,7 +3051,18 @@ test_conv_flt_1 (const char *name, int r buf, saved, nelmts); #if H5_SIZEOF_LONG_DOUBLE!=H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE!=0 } else if(src_type == FLT_LDOUBLE) { @@ -69,7 +69,7 @@ index 8f3e6e4..084b47c 100644 buf, saved, nelmts); #endif } 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, buf, saved, nelmts); } else { diff --git a/hdf5-1.10.4.tar.bz2 b/hdf5-1.10.4.tar.bz2 deleted file mode 100644 index defab74..0000000 --- a/hdf5-1.10.4.tar.bz2 +++ /dev/null @@ -1,3 +0,0 @@ -version https://git-lfs.github.com/spec/v1 -oid sha256:1267ff06aaedc04ca25f7c6026687ea2884b837043431195f153401d942b28df -size 8598986 diff --git a/hdf5-1.10.5.tar.bz2 b/hdf5-1.10.5.tar.bz2 new file mode 100644 index 0000000..321b1a8 --- /dev/null +++ b/hdf5-1.10.5.tar.bz2 @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:68d6ea8843d2a106ec6a7828564c1689c7a85714a35d8efafa2fee20ca366f44 +size 8706317 diff --git a/hdf5-1.8.11-abort_unknown_host_config.patch b/hdf5-1.8.11-abort_unknown_host_config.patch index f9981c4..e8a65c0 100644 --- a/hdf5-1.8.11-abort_unknown_host_config.patch +++ b/hdf5-1.8.11-abort_unknown_host_config.patch @@ -2,7 +2,7 @@ Index: configure =================================================================== --- configure.orig +++ configure -@@ -4085,6 +4085,8 @@ done +@@ -4097,6 +4097,8 @@ done if test "X$host_config" != "Xnone"; then CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`" . $host_config @@ -15,7 +15,7 @@ Index: configure.ac =================================================================== --- configure.ac.orig +++ configure.ac -@@ -266,6 +266,8 @@ done +@@ -263,6 +263,8 @@ done if test "X$host_config" != "Xnone"; then CC_BASENAME="`echo $CC | cut -f1 -d' ' | xargs basename 2>/dev/null`" . $host_config diff --git a/hdf5-LD_LIBRARY_PATH.patch b/hdf5-LD_LIBRARY_PATH.patch index 3c32117..f1515fe 100644 --- a/hdf5-LD_LIBRARY_PATH.patch +++ b/hdf5-LD_LIBRARY_PATH.patch @@ -1,8 +1,8 @@ -Index: hdf5-1.10.0-patch1/src/Makefile.in +Index: hdf5-1.10.5/src/Makefile.in =================================================================== ---- hdf5-1.10.0-patch1.orig/src/Makefile.in -+++ hdf5-1.10.0-patch1/src/Makefile.in -@@ -1847,8 +1847,6 @@ help: +--- hdf5-1.10.5.orig/src/Makefile.in ++++ hdf5-1.10.5/src/Makefile.in +@@ -1873,8 +1873,6 @@ help: # Remove the generated .c file if errors occur unless HDF5_Make_Ignore # is set to ignore the error. H5Tinit.c: H5detect$(EXEEXT) @@ -11,7 +11,7 @@ Index: hdf5-1.10.0-patch1/src/Makefile.in $(RUNSERIAL) ./H5detect$(EXEEXT) > $@ || \ (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \ ($(RM) $@ ; exit 1) -@@ -1859,8 +1857,6 @@ H5Tinit.c: H5detect$(EXEEXT) +@@ -1885,8 +1883,6 @@ H5Tinit.c: H5detect$(EXEEXT) # Remove the generated .c file if errors occur unless HDF5_Make_Ignore # is set to ignore the error. H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings diff --git a/hdf5-Remove-timestamps-from-binaries.patch b/hdf5-Remove-timestamps-from-binaries.patch index 59120eb..9f8b70a 100644 --- a/hdf5-Remove-timestamps-from-binaries.patch +++ b/hdf5-Remove-timestamps-from-binaries.patch @@ -10,10 +10,10 @@ Signed-off-by: Egbert Eich --- src/H5detect.c | 15 --------------- 1 file changed, 15 deletions(-) -diff --git a/src/H5detect.c b/src/H5detect.c -index 4424009..f49774c 100644 ---- a/src/H5detect.c -+++ b/src/H5detect.c +Index: hdf5-1.10.5/src/H5detect.c +=================================================================== +--- hdf5-1.10.5.orig/src/H5detect.c ++++ hdf5-1.10.5/src/H5detect.c @@ -1245,21 +1245,6 @@ 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 */ diff --git a/hdf5.changes b/hdf5.changes index a38738b..56ec54a 100644 --- a/hdf5.changes +++ b/hdf5.changes @@ -1,3 +1,24 @@ +------------------------------------------------------------------- +Fri Aug 23 09:58:01 UTC 2019 - Ana Guerrero Lopez + +- 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 diff --git a/hdf5.spec b/hdf5.spec index 099be5c..5478565 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -33,8 +33,8 @@ %define use_sz2 0 -%define vers 1.10.4 -%define _vers 1_10_4 +%define vers 1.10.5 +%define _vers 1_10_5 %define short_ver 1.10 %define src_ver %{version} %define pname hdf5 @@ -181,7 +181,11 @@ ExclusiveArch: do_not_build %{?with_mpi:%global hpc_module_pname p%{pname}} %define my_prefix %hpc_prefix %define my_bindir %hpc_bindir + %ifarch x86_64 + %define my_libdir %hpc_prefix/lib64 + %else %define my_libdir %hpc_libdir + %endif %define my_incdir %hpc_includedir %define package_name %{hpc_package_name %_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. %define sonum 103 %define sonum_CXX 103 -%define sonum_F 100 +%define sonum_F 102 %define sonum_HL 100 %define sonum_HL_CXX 100 %define sonum_HL_F 100 @@ -233,9 +237,9 @@ Patch4: hdf5-1.8.10-tests-arm.patch %endif Patch5: PPC64LE-Fix-long-double-handling.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 -Patch9: 0001-Fix-return-value-in-test_libver_bounds_open.patch BuildRequires: fdupes %if 0%{?use_sz2} BuildRequires: libsz2-devel @@ -465,9 +469,8 @@ library packages. %endif %patch5 -p1 %patch6 -p1 -%patch7 -p1 +# %%patch7 -p1 %patch8 -p1 -%patch9 -p1 %if %{without hpc} # baselibs looks different for different flavors - generate it on the fly