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
2019-09-03 07:57:43 +00:00 · 2019-09-03 07:57:43 +00:00 · f5645d586f
commit f5645d586f
parent 0abc2b716c
10 changed files with 78 additions and 83 deletions
--- a/0001-Fix-return-value-in-test_libver_bounds_open.patch
+++ b/0001-Fix-return-value-in-test_libver_bounds_open.patch
@ -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
-
--- a/Disable-phdf5-tests.patch
+++ b/Disable-phdf5-tests.patch
@ -8,32 +8,29 @@ References:
 Signed-off-by: Egbert Eich <eich@suse.com>
 Signed-off-by: Egbert Eich <eich@suse.de>
 ---
- 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} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS})
-+##add_test (NAME TEST_PAR_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS})
- 
- foreach (testp ${H5P_TESTS})
-   add_test (NAME TEST_PAR_${testp} COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:${testp}> ${MPIEXEC_POSTFLAGS})
-diff --git a/testpar/Makefile.am b/testpar/Makefile.am
-index 7262ca6..e9c8c4a 100644
--- a/testpar/Makefile.am
-+++ b/testpar/Makefile.am
-@@ -23,7 +23,7 @@ AM_CPPFLAGS+=-I$(top_srcdir)/src -I$(top_srcdir)/test
+-add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5})
+## add_test (NAME MPI_TEST_testphdf5 COMMAND ${MPIEXEC_EXECUTABLE} ${MPIEXEC_NUMPROC_FLAG} ${MPIEXEC_MAX_NUMPROCS} ${MPIEXEC_PREFLAGS} $<TARGET_FILE:testphdf5> ${MPIEXEC_POSTFLAGS} ${SKIP_testphdf5})
+ set_tests_properties (MPI_TEST_testphdf5 PROPERTIES
+     FIXTURES_REQUIRED par_clear_testphdf5
+     ENVIRONMENT "HDF5_ALARM_SECONDS=3600;srcdir=${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
--- a/PPC64LE-Fix-long-double-handling.patch
+++ b/PPC64LE-Fix-long-double-handling.patch
@ -11,11 +11,11 @@ Signed-off-by: Egbert Eich <eich@suse.com>
 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 {
--- a/hdf5-1.10.4.tar.bz2
+++ b/hdf5-1.10.4.tar.bz2
@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:1267ff06aaedc04ca25f7c6026687ea2884b837043431195f153401d942b28df
-size 8598986
--- a/hdf5-1.10.5.tar.bz2
+++ b/hdf5-1.10.5.tar.bz2
@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:68d6ea8843d2a106ec6a7828564c1689c7a85714a35d8efafa2fee20ca366f44
+size 8706317
--- 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`"
   . $host_config
--- a/hdf5-LD_LIBRARY_PATH.patch
+++ b/hdf5-LD_LIBRARY_PATH.patch
@ -1,8 +1,8 @@
-Index: hdf5-1.10.0-patch1/src/Makefile.in
+Index: hdf5-1.10.5/src/Makefile.in
 ===================================================================
--- hdf5-1.10.0-patch1.orig/src/Makefile.in
-+++ hdf5-1.10.0-patch1/src/Makefile.in
-@@ -1847,8 +1847,6 @@ help:
+--- hdf5-1.10.5.orig/src/Makefile.in
+++ hdf5-1.10.5/src/Makefile.in
+@@ -1873,8 +1873,6 @@ help:
 # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
 # is set to ignore the error.
 H5Tinit.c: H5detect$(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
--- a/hdf5-Remove-timestamps-from-binaries.patch
+++ b/hdf5-Remove-timestamps-from-binaries.patch
@ -10,10 +10,10 @@ Signed-off-by: Egbert Eich <eich@suse.de>
 ---
 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 */
--- a/hdf5.changes
+++ b/hdf5.changes
@ -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>

--- 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