diff --git a/.hdf5.metadata b/.hdf5.metadata index d4d6d66..976da32 100644 --- a/.hdf5.metadata +++ b/.hdf5.metadata @@ -1 +1,2 @@ -125b2dacb4fdac33f7bfbc7dfdeeb000ff68466b SOURCES/hdf5-1.10.7.tar.bz2 +5e11d91abe071858b0d9a4f3a202c1e6a0d27290 SOURCES/hdf5-1.10.6.tar.bz2 +2df4ecf6968914e55630ce180bdb529752cbbb46 SOURCES/hdf5_1.10.4+repack-1.debian.tar.xz diff --git a/SOURCES/hdf5-build.patch b/SOURCES/hdf5-build.patch index 66ba115..fcfe588 100644 --- a/SOURCES/hdf5-build.patch +++ b/SOURCES/hdf5-build.patch @@ -1,6 +1,6 @@ -diff -up hdf5-1.10.7/java/examples/datasets/JavaDatasetExample.sh.in.build hdf5-1.10.7/java/examples/datasets/JavaDatasetExample.sh.in ---- hdf5-1.10.7/java/examples/datasets/JavaDatasetExample.sh.in.build 2020-08-27 21:38:23.000000000 -0600 -+++ hdf5-1.10.7/java/examples/datasets/JavaDatasetExample.sh.in 2020-10-07 20:27:26.540707493 -0600 +diff -up hdf5-1.10.5/java/examples/datasets/JavaDatasetExample.sh.in.build hdf5-1.10.5/java/examples/datasets/JavaDatasetExample.sh.in +--- hdf5-1.10.5/java/examples/datasets/JavaDatasetExample.sh.in.build 2018-09-10 08:43:41.000000000 -0600 ++++ hdf5-1.10.5/java/examples/datasets/JavaDatasetExample.sh.in 2019-04-07 15:29:56.304854644 -0600 @@ -39,7 +39,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" BLDLIBDIR="$top_builddir/hdf5/lib" BLDDIR="." @@ -10,9 +10,9 @@ diff -up hdf5-1.10.7/java/examples/datasets/JavaDatasetExample.sh.in.build hdf5- TESTJARFILE=jar@PACKAGE_TARNAME@datasets.jar test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR -diff -up hdf5-1.10.7/java/examples/datasets/Makefile.am.build hdf5-1.10.7/java/examples/datasets/Makefile.am ---- hdf5-1.10.7/java/examples/datasets/Makefile.am.build 2020-08-27 21:38:23.000000000 -0600 -+++ hdf5-1.10.7/java/examples/datasets/Makefile.am 2020-10-07 20:27:26.540707493 -0600 +diff -up hdf5-1.10.5/java/examples/datasets/Makefile.am.build hdf5-1.10.5/java/examples/datasets/Makefile.am +--- hdf5-1.10.5/java/examples/datasets/Makefile.am.build 2018-09-03 20:54:44.000000000 -0600 ++++ hdf5-1.10.5/java/examples/datasets/Makefile.am 2019-04-07 15:29:56.305854652 -0600 @@ -27,7 +27,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -22,9 +22,9 @@ diff -up hdf5-1.10.7/java/examples/datasets/Makefile.am.build hdf5-1.10.7/java/e CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)datasets.jar -diff -up hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in.build hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in ---- hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in.build 2020-02-05 19:04:23.000000000 -0700 -+++ hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in 2020-10-07 20:27:26.541707501 -0600 +diff -up hdf5-1.10.5/java/examples/datatypes/JavaDatatypeExample.sh.in.build hdf5-1.10.5/java/examples/datatypes/JavaDatatypeExample.sh.in +--- hdf5-1.10.5/java/examples/datatypes/JavaDatatypeExample.sh.in.build 2018-09-10 08:43:41.000000000 -0600 ++++ hdf5-1.10.5/java/examples/datatypes/JavaDatatypeExample.sh.in 2019-04-07 15:29:56.305854652 -0600 @@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" BLDLIBDIR="$top_builddir/hdf5/lib" BLDDIR="." @@ -34,9 +34,9 @@ diff -up hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in.build hdf TESTJARFILE=jar@PACKAGE_TARNAME@datatypes.jar test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR -diff -up hdf5-1.10.7/java/examples/datatypes/Makefile.am.build hdf5-1.10.7/java/examples/datatypes/Makefile.am ---- hdf5-1.10.7/java/examples/datatypes/Makefile.am.build 2020-08-27 21:38:23.000000000 -0600 -+++ hdf5-1.10.7/java/examples/datatypes/Makefile.am 2020-10-07 20:27:26.541707501 -0600 +diff -up hdf5-1.10.5/java/examples/datatypes/Makefile.am.build hdf5-1.10.5/java/examples/datatypes/Makefile.am +--- hdf5-1.10.5/java/examples/datatypes/Makefile.am.build 2018-09-03 20:54:44.000000000 -0600 ++++ hdf5-1.10.5/java/examples/datatypes/Makefile.am 2019-04-07 15:29:56.306854659 -0600 @@ -27,7 +27,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -46,9 +46,9 @@ diff -up hdf5-1.10.7/java/examples/datatypes/Makefile.am.build hdf5-1.10.7/java/ CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)datatypes.jar -diff -up hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in.build hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in ---- hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in.build 2020-02-05 19:04:23.000000000 -0700 -+++ hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in 2020-10-07 20:27:26.541707501 -0600 +diff -up hdf5-1.10.5/java/examples/groups/JavaGroupExample.sh.in.build hdf5-1.10.5/java/examples/groups/JavaGroupExample.sh.in +--- hdf5-1.10.5/java/examples/groups/JavaGroupExample.sh.in.build 2018-09-10 08:43:41.000000000 -0600 ++++ hdf5-1.10.5/java/examples/groups/JavaGroupExample.sh.in 2019-04-07 15:29:56.306854659 -0600 @@ -37,7 +37,7 @@ BLDLIBDIR="$top_builddir/hdf5/lib" BLDITERDIR="./groups" BLDDIR="." @@ -58,9 +58,9 @@ diff -up hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in.build hdf5-1.10 TESTJARFILE=jar@PACKAGE_TARNAME@groups.jar test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR test -d $BLDITERDIR || mkdir -p $BLDITERDIR -diff -up hdf5-1.10.7/java/examples/groups/Makefile.am.build hdf5-1.10.7/java/examples/groups/Makefile.am ---- hdf5-1.10.7/java/examples/groups/Makefile.am.build 2020-08-27 21:38:23.000000000 -0600 -+++ hdf5-1.10.7/java/examples/groups/Makefile.am 2020-10-07 20:27:26.542707509 -0600 +diff -up hdf5-1.10.5/java/examples/groups/Makefile.am.build hdf5-1.10.5/java/examples/groups/Makefile.am +--- hdf5-1.10.5/java/examples/groups/Makefile.am.build 2018-09-03 20:54:44.000000000 -0600 ++++ hdf5-1.10.5/java/examples/groups/Makefile.am 2019-04-07 15:29:56.306854659 -0600 @@ -27,7 +27,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -70,9 +70,9 @@ diff -up hdf5-1.10.7/java/examples/groups/Makefile.am.build hdf5-1.10.7/java/exa CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)groups.jar -diff -up hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in.build hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in ---- hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in.build 2020-02-05 19:04:23.000000000 -0700 -+++ hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in 2020-10-07 20:27:26.542707509 -0600 +diff -up hdf5-1.10.5/java/examples/intro/JavaIntroExample.sh.in.build hdf5-1.10.5/java/examples/intro/JavaIntroExample.sh.in +--- hdf5-1.10.5/java/examples/intro/JavaIntroExample.sh.in.build 2018-09-10 08:43:41.000000000 -0600 ++++ hdf5-1.10.5/java/examples/intro/JavaIntroExample.sh.in 2019-04-07 15:29:56.307854667 -0600 @@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" BLDLIBDIR="$top_builddir/hdf5/lib" BLDDIR="." @@ -82,9 +82,9 @@ diff -up hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in.build hdf5-1.10. TESTJARFILE=jar@PACKAGE_TARNAME@intro.jar test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR -diff -up hdf5-1.10.7/java/examples/intro/Makefile.am.build hdf5-1.10.7/java/examples/intro/Makefile.am ---- hdf5-1.10.7/java/examples/intro/Makefile.am.build 2020-08-27 21:38:23.000000000 -0600 -+++ hdf5-1.10.7/java/examples/intro/Makefile.am 2020-10-07 20:27:26.542707509 -0600 +diff -up hdf5-1.10.5/java/examples/intro/Makefile.am.build hdf5-1.10.5/java/examples/intro/Makefile.am +--- hdf5-1.10.5/java/examples/intro/Makefile.am.build 2018-09-03 20:54:44.000000000 -0600 ++++ hdf5-1.10.5/java/examples/intro/Makefile.am 2019-04-07 15:29:56.307854667 -0600 @@ -27,7 +27,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -94,9 +94,9 @@ diff -up hdf5-1.10.7/java/examples/intro/Makefile.am.build hdf5-1.10.7/java/exam CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)intro.jar -diff -up hdf5-1.10.7/java/src/Makefile.am.build hdf5-1.10.7/java/src/Makefile.am ---- hdf5-1.10.7/java/src/Makefile.am.build 2020-09-04 15:50:58.000000000 -0600 -+++ hdf5-1.10.7/java/src/Makefile.am 2020-10-07 20:27:26.542707509 -0600 +diff -up hdf5-1.10.5/java/src/Makefile.am.build hdf5-1.10.5/java/src/Makefile.am +--- hdf5-1.10.5/java/src/Makefile.am.build 2018-09-03 20:54:44.000000000 -0600 ++++ hdf5-1.10.5/java/src/Makefile.am 2019-04-07 15:29:56.308854675 -0600 @@ -33,8 +33,8 @@ JAVAROOT = .classes classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -108,21 +108,21 @@ diff -up hdf5-1.10.7/java/src/Makefile.am.build hdf5-1.10.7/java/src/Makefile.am pkgpath = hdf/hdf5lib CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$$CLASSPATH -diff -up hdf5-1.10.7/java/test/junit.sh.in.build hdf5-1.10.7/java/test/junit.sh.in ---- hdf5-1.10.7/java/test/junit.sh.in.build 2020-09-04 15:50:58.000000000 -0600 -+++ hdf5-1.10.7/java/test/junit.sh.in 2020-10-07 22:14:59.047682005 -0600 -@@ -46,7 +46,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" +diff -up hdf5-1.10.5/java/test/junit.sh.in.build hdf5-1.10.5/java/test/junit.sh.in +--- hdf5-1.10.5/java/test/junit.sh.in.build 2019-02-18 13:19:25.000000000 -0700 ++++ hdf5-1.10.5/java/test/junit.sh.in 2019-04-07 15:30:29.450114380 -0600 +@@ -43,7 +43,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" + BLDLIBDIR="$top_builddir/hdf5/lib" BLDDIR="." - BLDLIBDIR="$BLDDIR/testlibs" HDFTEST_HOME="$top_srcdir/java/test" -JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar +JARFILE=@PACKAGE_TARNAME@.jar TESTJARFILE=jar@PACKAGE_TARNAME@test.jar test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR -diff -up hdf5-1.10.7/java/test/Makefile.am.build hdf5-1.10.7/java/test/Makefile.am ---- hdf5-1.10.7/java/test/Makefile.am.build 2020-09-04 15:50:58.000000000 -0600 -+++ hdf5-1.10.7/java/test/Makefile.am 2020-10-07 20:27:26.543707517 -0600 +diff -up hdf5-1.10.5/java/test/Makefile.am.build hdf5-1.10.5/java/test/Makefile.am +--- hdf5-1.10.5/java/test/Makefile.am.build 2019-02-16 15:41:11.000000000 -0700 ++++ hdf5-1.10.5/java/test/Makefile.am 2019-04-07 15:29:56.309854683 -0600 @@ -27,7 +27,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) diff --git a/SOURCES/hdf5-warning.patch b/SOURCES/hdf5-warning.patch index 25ff9e4..a4c8197 100644 --- a/SOURCES/hdf5-warning.patch +++ b/SOURCES/hdf5-warning.patch @@ -1,7 +1,7 @@ -diff -up hdf5-1.10.7/testpar/t_cache.c.warning hdf5-1.10.7/testpar/t_cache.c ---- hdf5-1.10.7/testpar/t_cache.c.warning 2020-09-04 15:50:58.000000000 -0600 -+++ hdf5-1.10.7/testpar/t_cache.c 2020-10-07 20:23:01.877566435 -0600 -@@ -80,8 +80,8 @@ long local_pins = 0; +diff -up hdf5-1.10.4/testpar/t_cache.c.warning hdf5-1.10.4/testpar/t_cache.c +--- hdf5-1.10.4/testpar/t_cache.c.warning 2018-09-10 08:43:41.000000000 -0600 ++++ hdf5-1.10.4/testpar/t_cache.c 2018-11-24 08:08:37.333832898 -0700 +@@ -79,8 +79,8 @@ long local_pins = 0; /* the following fields are used by the server process only */ @@ -12,7 +12,7 @@ diff -up hdf5-1.10.7/testpar/t_cache.c.warning hdf5-1.10.7/testpar/t_cache.c /***************************************************************************** -@@ -176,8 +176,8 @@ struct datum +@@ -175,8 +175,8 @@ struct datum hbool_t local_pinned; hbool_t cleared; hbool_t flushed; @@ -23,7 +23,16 @@ diff -up hdf5-1.10.7/testpar/t_cache.c.warning hdf5-1.10.7/testpar/t_cache.c int index; struct H5AC_aux_t * aux_ptr; }; -@@ -2445,12 +2445,12 @@ static herr_t +@@ -2197,7 +2197,7 @@ serve_entry_reads_request(struct mssg_t + reply.base_addr = target_addr; + reply.len = 0; + reply.ver = 0; +- reply.count = (long)(data[target_index].reads); ++ reply.count = data[target_index].reads; + reply.magic = MSSG_MAGIC; + } + } +@@ -2446,12 +2446,12 @@ static herr_t datum_image_len(const void *thing, size_t *image_len) { int idx; @@ -38,25 +47,25 @@ diff -up hdf5-1.10.7/testpar/t_cache.c.warning hdf5-1.10.7/testpar/t_cache.c idx = addr_to_datum_index(entry_ptr->base_addr); -@@ -4612,7 +4612,7 @@ verify_entry_reads(haddr_t addr, +@@ -4615,7 +4615,7 @@ verify_entry_reads(haddr_t addr, int expected_entry_reads) { hbool_t success = TRUE; -- int reported_entry_reads = 0; +- int reported_entry_reads; + unsigned reported_entry_reads = 0; struct mssg_t mssg; if ( success ) { -@@ -4719,7 +4719,7 @@ verify_entry_writes(haddr_t addr, +@@ -4722,7 +4722,7 @@ verify_entry_writes(haddr_t addr, int expected_entry_writes) { hbool_t success = TRUE; -- int reported_entry_writes = 0; +- int reported_entry_writes; + unsigned reported_entry_writes = 0; struct mssg_t mssg; if ( success ) { -@@ -4824,7 +4824,7 @@ static hbool_t +@@ -4827,7 +4827,7 @@ static hbool_t verify_total_reads(int expected_total_reads) { hbool_t success = TRUE; /* will set to FALSE if appropriate. */ diff --git a/SOURCES/hdf5-wrappers.patch b/SOURCES/hdf5-wrappers.patch index ff721bb..34f903e 100644 --- a/SOURCES/hdf5-wrappers.patch +++ b/SOURCES/hdf5-wrappers.patch @@ -1,42 +1,6 @@ -diff -up hdf5-1.10.7/bin/h5cc.in.wrappers hdf5-1.10.7/bin/h5cc.in ---- hdf5-1.10.7/bin/h5cc.in.wrappers 2020-10-07 20:24:29.127283333 -0600 -+++ hdf5-1.10.7/bin/h5cc.in 2020-10-07 20:27:05.289536904 -0600 -@@ -89,10 +89,10 @@ CLINKERBASE="@CC@" - # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in - # from the hdf5 build. The order of the flags is intended to give precedence - # to the user's flags. --H5BLD_CFLAGS="@AM_CFLAGS@ @CFLAGS@" -+H5BLD_CFLAGS= - H5BLD_CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@" --H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@" --H5BLD_LIBS="@LIBS@" -+H5BLD_LDFLAGS= -+H5BLD_LIBS= - - CC="${HDF5_CC:-$CCBASE}" - CLINKER="${HDF5_CLINKER:-$CLINKERBASE}" -@@ -105,7 +105,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}" - # available library is shared, it will be used by default. The user can - # override either default, although choosing an unavailable library will result - # in link errors. --STATIC_AVAILABLE="@enable_static@" -+# Fedora prefers shared libraries -+STATIC_AVAILABLE=no - if test "${STATIC_AVAILABLE}" = "yes"; then - USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}" - else -@@ -385,7 +386,7 @@ if test "x$do_link" = "xyes"; then - # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in - # from the hdf5 build. The order of the flags is intended to give precedence - # to the user's flags. -- $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link -+ $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args - status=$? - fi - -diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in ---- hdf5-1.10.7/c++/src/h5c++.in.wrappers 2020-08-27 21:38:23.000000000 -0600 -+++ hdf5-1.10.7/c++/src/h5c++.in 2020-10-07 20:24:29.126283325 -0600 +diff -up hdf5-1.10.5/c++/src/h5c++.in.wrappers hdf5-1.10.5/c++/src/h5c++.in +--- hdf5-1.10.5/c++/src/h5c++.in.wrappers 2018-09-03 20:54:43.000000000 -0600 ++++ hdf5-1.10.5/c++/src/h5c++.in 2020-01-26 19:14:11.243718498 -0700 @@ -87,10 +87,10 @@ CXXLINKERBASE="@CXX@" # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in # from the hdf5 build. The order of the flags is intended to give precedence @@ -70,11 +34,11 @@ diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in status=$? fi -diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.in ---- hdf5-1.10.7/fortran/src/h5fc.in.wrappers 2020-08-27 21:38:23.000000000 -0600 -+++ hdf5-1.10.7/fortran/src/h5fc.in 2020-10-07 20:25:53.793962985 -0600 +diff -up hdf5-1.10.5/fortran/src/h5fc.in.wrappers hdf5-1.10.5/fortran/src/h5fc.in +--- hdf5-1.10.5/fortran/src/h5fc.in.wrappers 2018-09-03 20:54:44.000000000 -0600 ++++ hdf5-1.10.5/fortran/src/h5fc.in 2020-01-26 19:14:18.699761737 -0700 @@ -83,11 +83,11 @@ FLINKERBASE="@FC@" - # libraries in $link_args, followed by any external library paths and libraries + # libraries in $link_args, followed by any external library paths and libraries # from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build. # The order of the flags is intended to give precedence to the user's flags. -H5BLD_FCFLAGS="@AM_FCFLAGS@ @FCFLAGS@" @@ -99,7 +63,7 @@ diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.i USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}" else @@ -363,7 +364,7 @@ if test "x$do_link" = "xyes"; then - # libraries in $link_args, followed by any external library paths and libraries + # libraries in $link_args, followed by any external library paths and libraries # from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build. # The order of the flags is intended to give precedence to the user's flags. - $SHOW $FLINKER $FCFLAGS $H5BLD_FCFLAGS $F9XSUFFIXFLAG $LDFLAGS $fmodules $link_objs $LIBS $link_args $shared_link @@ -107,3 +71,39 @@ diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.i status=$? fi +diff -up hdf5-1.10.5/bin//h5cc.in.wrappers hdf5-1.10.5/tools/src/misc/h5cc.in +--- hdf5-1.10.5/bin/h5cc.in.wrappers 2018-09-03 20:54:44.000000000 -0600 ++++ hdf5-1.10.5/bin/h5cc.in 2020-01-26 19:13:58.079642156 -0700 +@@ -89,10 +89,10 @@ CLINKERBASE="@CC@" + # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in + # from the hdf5 build. The order of the flags is intended to give precedence + # to the user's flags. +-H5BLD_CFLAGS="@AM_CFLAGS@ @CFLAGS@" ++H5BLD_CFLAGS= + H5BLD_CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@" +-H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@" +-H5BLD_LIBS="@LIBS@" ++H5BLD_LDFLAGS= ++H5BLD_LIBS= + + CC="${HDF5_CC:-$CCBASE}" + CLINKER="${HDF5_CLINKER:-$CLINKERBASE}" +@@ -105,7 +105,8 @@ LIBS="${HDF5_LIBS:-$LIBSBASE}" + # available library is shared, it will be used by default. The user can + # override either default, although choosing an unavailable library will result + # in link errors. +-STATIC_AVAILABLE="@enable_static@" ++# Fedora prefers shared libraries ++STATIC_AVAILABLE=no + if test "${STATIC_AVAILABLE}" = "yes"; then + USE_SHARED_LIB="${HDF5_USE_SHLIB:-no}" + else +@@ -392,7 +393,7 @@ if test "x$do_link" = "xyes"; then + # paths and libraries from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in + # from the hdf5 build. The order of the flags is intended to give precedence + # to the user's flags. +- $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link ++ $SHOW $CLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CFLAGS $CFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args + status=$? + fi + diff --git a/SPECS/hdf5.spec b/SPECS/hdf5.spec index 0a7e2f5..48537ba 100644 --- a/SPECS/hdf5.spec +++ b/SPECS/hdf5.spec @@ -3,13 +3,11 @@ # Patch version? %global snaprel %{nil} -## WARNING: Wait for netcdf 4.8.0 ! - # NOTE: Try not to release new versions to released versions of Fedora # You need to recompile all users of HDF5 for each version change Name: hdf5 -Version: 1.10.7 -Release: 2%{?dist} +Version: 1.10.6 +Release: 5%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -17,7 +15,7 @@ URL: https://portal.hdfgroup.org/display/HDF5/HDF5 Source0: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-%{version}/src/hdf5-%{version}.tar.bz2 Source1: h5comp # For man pages -Source2: hdf5_1.10.6+repack-2.debian.tar.xz +Source2: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.10.4+repack-1.debian.tar.xz Patch0: hdf5-LD_LIBRARY_PATH.patch # Fix some warnings Patch2: hdf5-warning.patch @@ -164,8 +162,6 @@ HDF5 parallel openmpi static libraries %patch5 -p1 -b .wrappers # Replace jars with system versions -# hamcrest-core is obsoleted in hamcrest-2.2 -# Junit tests are failing with junit-4.13.1 %if 0%{?rhel} >= 9 || 0%{?fedora} > 34 find . ! -name junit.jar -name "*.jar" -delete ln -s %{_javadir}/hamcrest/hamcrest.jar java/lib/hamcrest-core.jar @@ -313,19 +309,20 @@ mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ %check make -C build check -#export HDF5_Make_Ignore=yes +export HDF5_Make_Ignore=yes export OMPI_MCA_rmaps_base_oversubscribe=1 +# MPI Tests are hanging +%if 0 +# t_cache_image appears to be hanging, others taking very long on s390x +%ifnarch s390x for mpi in %{?mpi_list} do module load mpi/$mpi-%{_arch} -# i686 & s390x mpich - testphdf5: malloc.c:4189: _int_malloc: Assertion `(unsigned long) (size) >= (unsigned long) (nb)' failed. -%ifarch armv7hl %{ix86} s390x - make -C $mpi check || : -%else make -C $mpi check -%endif module purge done +%endif +%endif %ldconfig_scriptlets @@ -353,8 +350,6 @@ done %{_bindir}/h5stat %{_bindir}/h5unjam %{_bindir}/h5watch -%{_bindir}/mirror_server -%{_bindir}/mirror_server_stop %{_libdir}/libhdf5.so.103* %{_libdir}/libhdf5_cpp.so.103* %{_libdir}/libhdf5_fortran.so.102* @@ -425,8 +420,6 @@ done %{_libdir}/mpich/bin/h5stat %{_libdir}/mpich/bin/h5unjam %{_libdir}/mpich/bin/h5watch -%{_libdir}/mpich/bin/mirror_server -%{_libdir}/mpich/bin/mirror_server_stop %{_libdir}/mpich/bin/ph5diff %{_libdir}/mpich/lib/*.so.10* @@ -470,8 +463,6 @@ done %{_libdir}/openmpi/bin/h5stat %{_libdir}/openmpi/bin/h5unjam %{_libdir}/openmpi/bin/h5watch -%{_libdir}/openmpi/bin/mirror_server -%{_libdir}/openmpi/bin/mirror_server_stop %{_libdir}/openmpi/bin/ph5diff %{_libdir}/openmpi/lib/*.so.10* @@ -492,20 +483,6 @@ done %changelog -* Mon Aug 30 2021 Orion Poplawski - 1.10.7-2 -- Fix typo in h5fc (bz#1998879) - -* Mon Aug 09 2021 Orion Poplawski - 1.10.7-1 -- Update to 1.10.7 - -* Thu Jul 29 2021 Antonio Trande - 1.10.6-7 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild -- Use bundled junit -- Fix hamcrest symlinks in Fedora 35+ - -* Sun May 30 2021 Orion Poplawski - 1.10.6-6 -- Handle junit versions better - * Tue Jan 26 2021 Fedora Release Engineering - 1.10.6-5 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild