From 69df9b6ae9d41dbf8ecbc34f69ae343e83b6109d Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sun, 30 May 2021 14:14:58 -0600 Subject: [PATCH 01/55] Handle junit versions better --- hdf5.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 4a55a63..78eb5a3 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -7,7 +7,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.10.6 -Release: 5%{?dist} +Release: 6%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -169,7 +169,7 @@ ln -s %{_javadir}/slf4j/api.jar java/lib/slf4j-api-1.7.25.jar ln -s %{_javadir}/slf4j/nop.jar java/lib/ext/slf4j-nop-1.7.25.jar ln -s %{_javadir}/slf4j/simple.jar java/lib/ext/slf4j-simple-1.7.25.jar # Fix test output -junit_ver=$(sed -n '//{s/^.*>\([0-9]\.[0-9]*\)<.*/\1/;p;q}' /usr/share/maven-poms/junit.pom) +junit_ver=$(sed -n '//{s/^.*>\([0-9]\.[0-9.]*\)<.*/\1/;p;q}' /usr/share/maven-poms/junit.pom) sed -i -e "s/JUnit version .*/JUnit version $junit_ver/" java/test/testfiles/JUnit-*.txt # Force shared by default for compiler wrappers (bug #1266645) @@ -478,6 +478,9 @@ done %changelog +* 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 From d981e4771cf1630d5edd4c6e34db414ca00d90fe Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 22 Jul 2021 07:32:44 +0000 Subject: [PATCH 02/55] - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 78eb5a3..63f12f5 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -7,7 +7,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.10.6 -Release: 6%{?dist} +Release: 7%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -478,6 +478,9 @@ done %changelog +* Thu Jul 22 2021 Fedora Release Engineering - 1.10.6-7 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild + * Sun May 30 2021 Orion Poplawski - 1.10.6-6 - Handle junit versions better From b05b5b4f6a2e427e5ba89248abb7aa2fa9ac9924 Mon Sep 17 00:00:00 2001 From: Antonio Trande Date: Thu, 29 Jul 2021 16:48:42 +0200 Subject: [PATCH 03/55] Use bundled junit| Fix hamcrest symlinks in Fedora 35+ --- hdf5.spec | 19 ++++++++++++++----- 1 file changed, 14 insertions(+), 5 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 63f12f5..4afb4cc 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -162,15 +162,22 @@ HDF5 parallel openmpi static libraries %patch5 -p1 -b .wrappers # Replace jars with system versions -find -name \*.jar -delete +# 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 +%else +find . -name "*.jar" -delete ln -s %{_javadir}/hamcrest/core.jar java/lib/hamcrest-core.jar ln -s %{_javadir}/junit.jar java/lib/junit.jar -ln -s %{_javadir}/slf4j/api.jar java/lib/slf4j-api-1.7.25.jar -ln -s %{_javadir}/slf4j/nop.jar java/lib/ext/slf4j-nop-1.7.25.jar -ln -s %{_javadir}/slf4j/simple.jar java/lib/ext/slf4j-simple-1.7.25.jar # Fix test output junit_ver=$(sed -n '//{s/^.*>\([0-9]\.[0-9.]*\)<.*/\1/;p;q}' /usr/share/maven-poms/junit.pom) sed -i -e "s/JUnit version .*/JUnit version $junit_ver/" java/test/testfiles/JUnit-*.txt +%endif +ln -s %{_javadir}/slf4j/api.jar java/lib/slf4j-api-1.7.25.jar +ln -s %{_javadir}/slf4j/nop.jar java/lib/ext/slf4j-nop-1.7.25.jar +ln -s %{_javadir}/slf4j/simple.jar java/lib/ext/slf4j-simple-1.7.25.jar # Force shared by default for compiler wrappers (bug #1266645) sed -i -e '/^STATIC_AVAILABLE=/s/=.*/=no/' */*/h5[cf]*.in @@ -478,8 +485,10 @@ done %changelog -* Thu Jul 22 2021 Fedora Release Engineering - 1.10.6-7 +* 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 From b21e31c408cda2201d9181ab93d1fbe24fe9b0e6 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Wed, 7 Oct 2020 20:29:59 -0600 Subject: [PATCH 04/55] Update to 1.10.7 --- .gitignore | 2 + hdf5-build.patch | 70 +++++++++++++++++------------------ hdf5-warning.patch | 31 ++++++---------- hdf5-wrappers.patch | 90 ++++++++++++++++++++++----------------------- hdf5.spec | 9 +++-- sources | 4 +- 6 files changed, 101 insertions(+), 105 deletions(-) diff --git a/.gitignore b/.gitignore index 46e5004..0bf4ac9 100644 --- a/.gitignore +++ b/.gitignore @@ -29,3 +29,5 @@ hdf5-1.8.5.tar.bz2 /hdf5_1.10.4+repack-1.debian.tar.xz /hdf5-1.10.5.tar.bz2 /hdf5-1.10.6.tar.bz2 +/hdf5-1.10.7.tar.bz2 +/hdf5_1.10.6+repack-2.debian.tar.xz diff --git a/hdf5-build.patch b/hdf5-build.patch index fcfe588..66ba115 100644 --- a/hdf5-build.patch +++ b/hdf5-build.patch @@ -1,6 +1,6 @@ -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 +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 @@ -39,7 +39,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" BLDLIBDIR="$top_builddir/hdf5/lib" BLDDIR="." @@ -10,9 +10,9 @@ diff -up hdf5-1.10.5/java/examples/datasets/JavaDatasetExample.sh.in.build hdf5- TESTJARFILE=jar@PACKAGE_TARNAME@datasets.jar test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR -diff -up hdf5-1.10.5/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 +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 @@ -27,7 +27,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -22,9 +22,9 @@ diff -up hdf5-1.10.5/java/examples/datasets/Makefile.am.build hdf5-1.10.5/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:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)datasets.jar -diff -up hdf5-1.10.5/java/examples/datatypes/JavaDatatypeExample.sh.in.build hdf5-1.10.5/java/examples/datatypes/JavaDatatypeExample.sh.in ---- hdf5-1.10.5/java/examples/datatypes/JavaDatatypeExample.sh.in.build 2018-09-10 08:43:41.000000000 -0600 -+++ hdf5-1.10.5/java/examples/datatypes/JavaDatatypeExample.sh.in 2019-04-07 15:29:56.305854652 -0600 +diff -up hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in.build hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in +--- hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in.build 2020-02-05 19:04:23.000000000 -0700 ++++ hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in 2020-10-07 20:27:26.541707501 -0600 @@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" BLDLIBDIR="$top_builddir/hdf5/lib" BLDDIR="." @@ -34,9 +34,9 @@ diff -up hdf5-1.10.5/java/examples/datatypes/JavaDatatypeExample.sh.in.build hdf TESTJARFILE=jar@PACKAGE_TARNAME@datatypes.jar test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR -diff -up hdf5-1.10.5/java/examples/datatypes/Makefile.am.build hdf5-1.10.5/java/examples/datatypes/Makefile.am ---- hdf5-1.10.5/java/examples/datatypes/Makefile.am.build 2018-09-03 20:54:44.000000000 -0600 -+++ hdf5-1.10.5/java/examples/datatypes/Makefile.am 2019-04-07 15:29:56.306854659 -0600 +diff -up hdf5-1.10.7/java/examples/datatypes/Makefile.am.build hdf5-1.10.7/java/examples/datatypes/Makefile.am +--- hdf5-1.10.7/java/examples/datatypes/Makefile.am.build 2020-08-27 21:38:23.000000000 -0600 ++++ hdf5-1.10.7/java/examples/datatypes/Makefile.am 2020-10-07 20:27:26.541707501 -0600 @@ -27,7 +27,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -46,9 +46,9 @@ diff -up hdf5-1.10.5/java/examples/datatypes/Makefile.am.build hdf5-1.10.5/java/ CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)datatypes.jar -diff -up hdf5-1.10.5/java/examples/groups/JavaGroupExample.sh.in.build hdf5-1.10.5/java/examples/groups/JavaGroupExample.sh.in ---- hdf5-1.10.5/java/examples/groups/JavaGroupExample.sh.in.build 2018-09-10 08:43:41.000000000 -0600 -+++ hdf5-1.10.5/java/examples/groups/JavaGroupExample.sh.in 2019-04-07 15:29:56.306854659 -0600 +diff -up hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in.build hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in +--- hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in.build 2020-02-05 19:04:23.000000000 -0700 ++++ hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in 2020-10-07 20:27:26.541707501 -0600 @@ -37,7 +37,7 @@ BLDLIBDIR="$top_builddir/hdf5/lib" BLDITERDIR="./groups" BLDDIR="." @@ -58,9 +58,9 @@ diff -up hdf5-1.10.5/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 hdf5-1.10.5/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 +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 @@ -27,7 +27,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -70,9 +70,9 @@ diff -up hdf5-1.10.5/java/examples/groups/Makefile.am.build hdf5-1.10.5/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:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)groups.jar -diff -up hdf5-1.10.5/java/examples/intro/JavaIntroExample.sh.in.build hdf5-1.10.5/java/examples/intro/JavaIntroExample.sh.in ---- hdf5-1.10.5/java/examples/intro/JavaIntroExample.sh.in.build 2018-09-10 08:43:41.000000000 -0600 -+++ hdf5-1.10.5/java/examples/intro/JavaIntroExample.sh.in 2019-04-07 15:29:56.307854667 -0600 +diff -up hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in.build hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in +--- hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in.build 2020-02-05 19:04:23.000000000 -0700 ++++ hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in 2020-10-07 20:27:26.542707509 -0600 @@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" BLDLIBDIR="$top_builddir/hdf5/lib" BLDDIR="." @@ -82,9 +82,9 @@ diff -up hdf5-1.10.5/java/examples/intro/JavaIntroExample.sh.in.build hdf5-1.10. TESTJARFILE=jar@PACKAGE_TARNAME@intro.jar test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR -diff -up hdf5-1.10.5/java/examples/intro/Makefile.am.build hdf5-1.10.5/java/examples/intro/Makefile.am ---- hdf5-1.10.5/java/examples/intro/Makefile.am.build 2018-09-03 20:54:44.000000000 -0600 -+++ hdf5-1.10.5/java/examples/intro/Makefile.am 2019-04-07 15:29:56.307854667 -0600 +diff -up hdf5-1.10.7/java/examples/intro/Makefile.am.build hdf5-1.10.7/java/examples/intro/Makefile.am +--- hdf5-1.10.7/java/examples/intro/Makefile.am.build 2020-08-27 21:38:23.000000000 -0600 ++++ hdf5-1.10.7/java/examples/intro/Makefile.am 2020-10-07 20:27:26.542707509 -0600 @@ -27,7 +27,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -94,9 +94,9 @@ diff -up hdf5-1.10.5/java/examples/intro/Makefile.am.build hdf5-1.10.5/java/exam CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)intro.jar -diff -up hdf5-1.10.5/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 +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 @@ -33,8 +33,8 @@ JAVAROOT = .classes classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -108,21 +108,21 @@ diff -up hdf5-1.10.5/java/src/Makefile.am.build hdf5-1.10.5/java/src/Makefile.am pkgpath = hdf/hdf5lib CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$$CLASSPATH -diff -up hdf5-1.10.5/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" +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" 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 hdf5-1.10.5/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 +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 @@ -27,7 +27,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) diff --git a/hdf5-warning.patch b/hdf5-warning.patch index a4c8197..25ff9e4 100644 --- a/hdf5-warning.patch +++ b/hdf5-warning.patch @@ -1,7 +1,7 @@ -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; +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; /* the following fields are used by the server process only */ @@ -12,7 +12,7 @@ diff -up hdf5-1.10.4/testpar/t_cache.c.warning hdf5-1.10.4/testpar/t_cache.c /***************************************************************************** -@@ -175,8 +175,8 @@ struct datum +@@ -176,8 +176,8 @@ struct datum hbool_t local_pinned; hbool_t cleared; hbool_t flushed; @@ -23,16 +23,7 @@ diff -up hdf5-1.10.4/testpar/t_cache.c.warning hdf5-1.10.4/testpar/t_cache.c int index; struct H5AC_aux_t * aux_ptr; }; -@@ -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 +@@ -2445,12 +2445,12 @@ static herr_t datum_image_len(const void *thing, size_t *image_len) { int idx; @@ -47,25 +38,25 @@ diff -up hdf5-1.10.4/testpar/t_cache.c.warning hdf5-1.10.4/testpar/t_cache.c idx = addr_to_datum_index(entry_ptr->base_addr); -@@ -4615,7 +4615,7 @@ verify_entry_reads(haddr_t addr, +@@ -4612,7 +4612,7 @@ verify_entry_reads(haddr_t addr, int expected_entry_reads) { hbool_t success = TRUE; -- int reported_entry_reads; +- int reported_entry_reads = 0; + unsigned reported_entry_reads = 0; struct mssg_t mssg; if ( success ) { -@@ -4722,7 +4722,7 @@ verify_entry_writes(haddr_t addr, +@@ -4719,7 +4719,7 @@ verify_entry_writes(haddr_t addr, int expected_entry_writes) { hbool_t success = TRUE; -- int reported_entry_writes; +- int reported_entry_writes = 0; + unsigned reported_entry_writes = 0; struct mssg_t mssg; if ( success ) { -@@ -4827,7 +4827,7 @@ static hbool_t +@@ -4824,7 +4824,7 @@ static hbool_t verify_total_reads(int expected_total_reads) { hbool_t success = TRUE; /* will set to FALSE if appropriate. */ diff --git a/hdf5-wrappers.patch b/hdf5-wrappers.patch index 34f903e..48049f9 100644 --- a/hdf5-wrappers.patch +++ b/hdf5-wrappers.patch @@ -1,6 +1,42 @@ -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 +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 @@ -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 @@ -34,11 +70,11 @@ diff -up hdf5-1.10.5/c++/src/h5c++.in.wrappers hdf5-1.10.5/c++/src/h5c++.in status=$? fi -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 +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 @@ -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@" @@ -47,7 +83,7 @@ diff -up hdf5-1.10.5/fortran/src/h5fc.in.wrappers hdf5-1.10.5/fortran/src/h5fc.i F9XSUFFIXFLAG="@F9XSUFFIXFLAG@" -H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@" -H5BLD_LIBS="@LIBS@" -+H5BLD_LDFLAGS= ++H5BLD_LDFLAGS=" +H5BLD_LIBS= FC="${HDF5_FC:-$FCBASE}" @@ -63,7 +99,7 @@ diff -up hdf5-1.10.5/fortran/src/h5fc.in.wrappers hdf5-1.10.5/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 @@ -71,39 +107,3 @@ diff -up hdf5-1.10.5/fortran/src/h5fc.in.wrappers hdf5-1.10.5/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/hdf5.spec b/hdf5.spec index 4afb4cc..f8946a8 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -6,8 +6,8 @@ # 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: 1.10.6 -Release: 7%{?dist} +Version: 1.10.7 +Release: 1%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -15,7 +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: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.10.4+repack-1.debian.tar.xz +Source2: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.10.6+repack-2.debian.tar.xz Patch0: hdf5-LD_LIBRARY_PATH.patch # Fix some warnings Patch2: hdf5-warning.patch @@ -485,6 +485,9 @@ done %changelog +* 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 diff --git a/sources b/sources index 9a4d6c9..ac9223d 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (hdf5-1.10.6.tar.bz2) = 821392718605e3f7a287d4729d022a55fd7b91ddaa2e9a3f35ab8fce3d3d4871a0cc88215be3052887cbac3615cc8953569c7f131217962103c98151c0ab58d4 -SHA512 (hdf5_1.10.4+repack-1.debian.tar.xz) = 7e08a79c8e96b843331e30d027628065ccbe72843a3ac525ad52d506238d328b9ebae57eff772b6215419943fd1804b4879cbdcd612e2f2c160c65a3d44ef965 +SHA512 (hdf5-1.10.7.tar.bz2) = bfbd045ea5d7940ac1d0f9aef964dad2e9f22d78b49c90668021106259c9612352fbcb4e89085a7fa189f58142ef83a363c6220ea89aa0d57bdfed245df0ab57 +SHA512 (hdf5_1.10.6+repack-2.debian.tar.xz) = 56a817bec56ef439259787e174172e5045d34b3b398b3fb95e42147a9b6a42e81f456d8527af4ec283226d84c7f247c63a7fa65654edebabe0de0bddfc038b71 From 7104c8b2a19ce386bfb796ae2a3e614791adea75 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Thu, 8 Oct 2020 07:37:45 -0600 Subject: [PATCH 05/55] mirror_server --- hdf5.spec | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/hdf5.spec b/hdf5.spec index f8946a8..4d76f09 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -352,6 +352,8 @@ 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* @@ -422,6 +424,8 @@ 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* @@ -465,6 +469,8 @@ 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* From 65220218f20df6fee18e0f112736cf8b96b04caa Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sat, 30 Jan 2021 09:44:41 -0700 Subject: [PATCH 06/55] WARNING: Wait for netcdf 4.8.0 --- hdf5.spec | 2 ++ 1 file changed, 2 insertions(+) diff --git a/hdf5.spec b/hdf5.spec index 4d76f09..24ff4ac 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -3,6 +3,8 @@ # 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 From e919a76d18105cb7ee5a78f8ba7b5f17c29055f7 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Mon, 1 Mar 2021 18:39:17 -0700 Subject: [PATCH 07/55] Enable all tests and failures --- hdf5.spec | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 24ff4ac..0d32c86 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -313,20 +313,20 @@ 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 +#if 0 # t_cache_image appears to be hanging, others taking very long on s390x -%ifnarch s390x +#ifnarch s390x for mpi in %{?mpi_list} do module load mpi/$mpi-%{_arch} make -C $mpi check module purge done -%endif -%endif +#endif +#endif %ldconfig_scriptlets From b7d3e5a4d00d8be1a5c7c6f059370c69e72dccf5 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Mon, 9 Aug 2021 21:26:44 -0600 Subject: [PATCH 08/55] Tests are still failing on i686/s390x mpich --- hdf5.spec | 11 +++++------ 1 file changed, 5 insertions(+), 6 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 0d32c86..ed626a0 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -315,18 +315,17 @@ mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ make -C build check #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 %{ix86) s390x + make -C $mpi check || : +%else make -C $mpi check +%endif module purge done -#endif -#endif %ldconfig_scriptlets From b33a0e23f1d444ca34daa13178e014c5eb2b2ea1 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Mon, 9 Aug 2021 21:28:58 -0600 Subject: [PATCH 09/55] Fix typo --- hdf5.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index ed626a0..df672fc 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -319,7 +319,7 @@ 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 %{ix86) s390x +%ifarch %{ix86} s390x make -C $mpi check || : %else make -C $mpi check From f0c9baac04c2caff158d6f2402e88b27809667c5 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Tue, 10 Aug 2021 06:36:01 -0600 Subject: [PATCH 10/55] Also fails on armv7hl --- hdf5.spec | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index df672fc..2b7fb4e 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -319,7 +319,7 @@ 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 %{ix86} s390x +%ifarch armv7hl %{ix86} s390x make -C $mpi check || : %else make -C $mpi check From 298288fd680d3aee20893ac3075035b3fe0da3f9 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sun, 29 Aug 2021 21:41:34 -0600 Subject: [PATCH 11/55] Fix typo in h5fc (bz#1998879) --- hdf5-wrappers.patch | 2 +- hdf5.spec | 5 ++++- 2 files changed, 5 insertions(+), 2 deletions(-) diff --git a/hdf5-wrappers.patch b/hdf5-wrappers.patch index 48049f9..ff721bb 100644 --- a/hdf5-wrappers.patch +++ b/hdf5-wrappers.patch @@ -83,7 +83,7 @@ diff -up hdf5-1.10.7/fortran/src/h5fc.in.wrappers hdf5-1.10.7/fortran/src/h5fc.i F9XSUFFIXFLAG="@F9XSUFFIXFLAG@" -H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@" -H5BLD_LIBS="@LIBS@" -+H5BLD_LDFLAGS=" ++H5BLD_LDFLAGS= +H5BLD_LIBS= FC="${HDF5_FC:-$FCBASE}" diff --git a/hdf5.spec b/hdf5.spec index 2b7fb4e..c2d97a6 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -9,7 +9,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.10.7 -Release: 1%{?dist} +Release: 2%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -492,6 +492,9 @@ 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 From fb205c10df15942ccc65e403a4405a8bcb1e8a83 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sat, 15 Feb 2020 15:34:00 -0700 Subject: [PATCH 12/55] Update to 1.12.1 --- .gitignore | 3 + fix-HDFFV-10745.patch | 13 ----- hdf5-LD_LIBRARY_PATH.patch | 13 ++--- hdf5-build.patch | 117 ++++++++++++++++++++----------------- hdf5-warning.patch | 67 --------------------- hdf5.spec | 64 +++++++++++--------- sources | 4 +- 7 files changed, 112 insertions(+), 169 deletions(-) delete mode 100644 fix-HDFFV-10745.patch delete mode 100644 hdf5-warning.patch diff --git a/.gitignore b/.gitignore index 0bf4ac9..8e76bef 100644 --- a/.gitignore +++ b/.gitignore @@ -31,3 +31,6 @@ hdf5-1.8.5.tar.bz2 /hdf5-1.10.6.tar.bz2 /hdf5-1.10.7.tar.bz2 /hdf5_1.10.6+repack-2.debian.tar.xz +/hdf5-1.12.0.tar.bz2 +/hdf5-1.12.1.tar.bz2 +/hdf5_1.12.0+repack-1~exp2.debian.tar.xz diff --git a/fix-HDFFV-10745.patch b/fix-HDFFV-10745.patch deleted file mode 100644 index 64cd705..0000000 --- a/fix-HDFFV-10745.patch +++ /dev/null @@ -1,13 +0,0 @@ -Index: hdf5/java/src/jni/h5pFCPLImp.c -=================================================================== ---- hdf5.orig/java/src/jni/h5pFCPLImp.c -+++ hdf5/java/src/jni/h5pFCPLImp.c -@@ -240,7 +240,7 @@ Java_hdf_hdf5lib_H5_H5Pget_1sym_1k - - done: - if (theArray) -- UNPIN_LONG_ARRAY(ENVONLY, size, theArray, (status < 0) ? JNI_ABORT : 0); -+ UNPIN_INT_ARRAY(ENVONLY, size, theArray, (status < 0) ? JNI_ABORT : 0); - - return (jint)status; - } /* end Java_hdf_hdf5lib_H5_H5Pget_1sym_1k */ diff --git a/hdf5-LD_LIBRARY_PATH.patch b/hdf5-LD_LIBRARY_PATH.patch index 7d01278..f1852e7 100644 --- a/hdf5-LD_LIBRARY_PATH.patch +++ b/hdf5-LD_LIBRARY_PATH.patch @@ -1,21 +1,20 @@ -diff -up hdf5-1.8.13/src/Makefile.am.LD_LIBRARY_PATH hdf5-1.8.13/src/Makefile.am ---- hdf5-1.8.13/src/Makefile.am.LD_LIBRARY_PATH 2014-05-05 20:13:01.000000000 -0600 -+++ hdf5-1.8.13/src/Makefile.am 2014-05-15 09:53:59.569476295 -0600 -@@ -128,8 +128,6 @@ settings_DATA=libhdf5.settings +--- hdf5-1.12.0/src/Makefile.am~ 2020-02-29 00:29:58.000000000 +0100 ++++ hdf5-1.12.0/src/Makefile.am 2021-02-26 16:10:03.612252484 +0100 +@@ -156,8 +156,6 @@ # 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 $$HDF5_Make_Ignore && echo "*** Error ignored") || \ ($(RM) $@ ; exit 1) -@@ -140,8 +138,6 @@ H5Tinit.c: H5detect$(EXEEXT) +@@ -168,8 +166,6 @@ # Remove the generated .c file if errors occur unless HDF5_Make_Ignore # is set to ignore the error. H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings - LD_LIBRARY_PATH="$$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) diff --git a/hdf5-build.patch b/hdf5-build.patch index 66ba115..cc08c02 100644 --- a/hdf5-build.patch +++ b/hdf5-build.patch @@ -1,19 +1,21 @@ -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 --git a/java/examples/datasets/JavaDatasetExample.sh.in b/java/examples/datasets/JavaDatasetExample.sh.in +index f29739a..fc9cddb 100644 +--- a/java/examples/datasets/JavaDatasetExample.sh.in ++++ b/java/examples/datasets/JavaDatasetExample.sh.in @@ -39,7 +39,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" - BLDLIBDIR="$top_builddir/hdf5/lib" BLDDIR="." + BLDLIBDIR="$BLDDIR/testlibs" HDFTEST_HOME="$top_srcdir/java/examples/datasets" -JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar +JARFILE=@PACKAGE_TARNAME@.jar 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 -@@ -27,7 +27,7 @@ classes: +diff --git a/java/examples/datasets/Makefile.am b/java/examples/datasets/Makefile.am +index 41a914b..195201a 100644 +--- a/java/examples/datasets/Makefile.am ++++ b/java/examples/datasets/Makefile.am +@@ -26,7 +26,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) pkgpath = examples/datasets @@ -22,22 +24,24 @@ 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$(PACKAGE_TARNAME)datasets.jar -diff -up hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in.build hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in ---- hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in.build 2020-02-05 19:04:23.000000000 -0700 -+++ hdf5-1.10.7/java/examples/datatypes/JavaDatatypeExample.sh.in 2020-10-07 20:27:26.541707501 -0600 +diff --git a/java/examples/datatypes/JavaDatatypeExample.sh.in b/java/examples/datatypes/JavaDatatypeExample.sh.in +index e26d8c0..f6a9d87 100644 +--- a/java/examples/datatypes/JavaDatatypeExample.sh.in ++++ b/java/examples/datatypes/JavaDatatypeExample.sh.in @@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" - BLDLIBDIR="$top_builddir/hdf5/lib" BLDDIR="." + BLDLIBDIR="$BLDDIR/testlibs" HDFTEST_HOME="$top_srcdir/java/examples/datatypes" -JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar +JARFILE=@PACKAGE_TARNAME@.jar 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 -@@ -27,7 +27,7 @@ classes: +diff --git a/java/examples/datatypes/Makefile.am b/java/examples/datatypes/Makefile.am +index 90790f7..450edef 100644 +--- a/java/examples/datatypes/Makefile.am ++++ b/java/examples/datatypes/Makefile.am +@@ -26,7 +26,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) pkgpath = examples/datatypes @@ -46,22 +50,24 @@ 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:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)datatypes.jar -diff -up hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in.build hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in ---- hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in.build 2020-02-05 19:04:23.000000000 -0700 -+++ hdf5-1.10.7/java/examples/groups/JavaGroupExample.sh.in 2020-10-07 20:27:26.541707501 -0600 -@@ -37,7 +37,7 @@ BLDLIBDIR="$top_builddir/hdf5/lib" +diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in +index 3b0e9d1..416c69f 100644 +--- a/java/examples/groups/JavaGroupExample.sh.in ++++ b/java/examples/groups/JavaGroupExample.sh.in +@@ -37,7 +37,7 @@ BLDDIR="." + BLDLIBDIR="$BLDDIR/testlibs" BLDITERDIR="./groups" - BLDDIR="." HDFTEST_HOME="$top_srcdir/java/examples/groups" -JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar +JARFILE=@PACKAGE_TARNAME@.jar TESTJARFILE=jar@PACKAGE_TARNAME@groups.jar test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR test -d $BLDITERDIR || mkdir -p $BLDITERDIR -diff -up hdf5-1.10.7/java/examples/groups/Makefile.am.build hdf5-1.10.7/java/examples/groups/Makefile.am ---- hdf5-1.10.7/java/examples/groups/Makefile.am.build 2020-08-27 21:38:23.000000000 -0600 -+++ hdf5-1.10.7/java/examples/groups/Makefile.am 2020-10-07 20:27:26.542707509 -0600 -@@ -27,7 +27,7 @@ classes: +diff --git a/java/examples/groups/Makefile.am b/java/examples/groups/Makefile.am +index bfde9ae..f48a5b9 100644 +--- a/java/examples/groups/Makefile.am ++++ b/java/examples/groups/Makefile.am +@@ -26,7 +26,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) pkgpath = examples/groups @@ -70,22 +76,24 @@ diff -up hdf5-1.10.7/java/examples/groups/Makefile.am.build hdf5-1.10.7/java/exa CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)groups.jar -diff -up hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in.build hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in ---- hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in.build 2020-02-05 19:04:23.000000000 -0700 -+++ hdf5-1.10.7/java/examples/intro/JavaIntroExample.sh.in 2020-10-07 20:27:26.542707509 -0600 +diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in +index db741e5..d0ba65d 100644 +--- a/java/examples/intro/JavaIntroExample.sh.in ++++ b/java/examples/intro/JavaIntroExample.sh.in @@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" - BLDLIBDIR="$top_builddir/hdf5/lib" BLDDIR="." + BLDLIBDIR="$BLDDIR/testlibs" HDFTEST_HOME="$top_srcdir/java/examples/intro" -JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar +JARFILE=@PACKAGE_TARNAME@.jar 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 -@@ -27,7 +27,7 @@ classes: +diff --git a/java/examples/intro/Makefile.am b/java/examples/intro/Makefile.am +index 7d1aeab..01a10c9 100644 +--- a/java/examples/intro/Makefile.am ++++ b/java/examples/intro/Makefile.am +@@ -26,7 +26,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) pkgpath = examples/intro @@ -94,10 +102,11 @@ 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:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)intro.jar -diff -up hdf5-1.10.7/java/src/Makefile.am.build hdf5-1.10.7/java/src/Makefile.am ---- hdf5-1.10.7/java/src/Makefile.am.build 2020-09-04 15:50:58.000000000 -0600 -+++ hdf5-1.10.7/java/src/Makefile.am 2020-10-07 20:27:26.542707509 -0600 -@@ -33,8 +33,8 @@ JAVAROOT = .classes +diff --git a/java/src/Makefile.am b/java/src/Makefile.am +index 98630e6..fd8d057 100644 +--- a/java/src/Makefile.am ++++ b/java/src/Makefile.am +@@ -32,8 +32,8 @@ JAVAROOT = .classes classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) @@ -108,22 +117,11 @@ diff -up hdf5-1.10.7/java/src/Makefile.am.build hdf5-1.10.7/java/src/Makefile.am pkgpath = hdf/hdf5lib CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$$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="$top_srcdir/java/lib" - BLDDIR="." - BLDLIBDIR="$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 -@@ -27,7 +27,7 @@ classes: +diff --git a/java/test/Makefile.am b/java/test/Makefile.am +index 08e79e3..b336c2f 100644 +--- a/java/test/Makefile.am ++++ b/java/test/Makefile.am +@@ -26,7 +26,7 @@ classes: test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) pkgpath = test @@ -132,3 +130,16 @@ diff -up hdf5-1.10.7/java/test/Makefile.am.build hdf5-1.10.7/java/test/Makefile. CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/junit.jar:$(top_srcdir)/java/lib/hamcrest-core.jar:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)test.jar +diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in +index 39db296..83d6c7c 100644 +--- a/java/test/junit.sh.in ++++ b/java/test/junit.sh.in +@@ -47,7 +47,7 @@ BLDLIBDIR="$BLDDIR/testlibs" + HDFTEST_HOME="$top_srcdir/java/test" + TOOLS_TESTFILES="$top_srcdir/tools/testfiles" + +-JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar ++JARFILE=@PACKAGE_TARNAME@.jar + TESTJARFILE=jar@PACKAGE_TARNAME@test.jar + test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR + diff --git a/hdf5-warning.patch b/hdf5-warning.patch deleted file mode 100644 index 25ff9e4..0000000 --- a/hdf5-warning.patch +++ /dev/null @@ -1,67 +0,0 @@ -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; - - - /* the following fields are used by the server process only */ --int total_reads = 0; --int total_writes = 0; -+unsigned total_reads = 0; -+unsigned total_writes = 0; - - - /***************************************************************************** -@@ -176,8 +176,8 @@ struct datum - hbool_t local_pinned; - hbool_t cleared; - hbool_t flushed; -- int reads; -- int writes; -+ unsigned reads; -+ unsigned writes; - int index; - struct H5AC_aux_t * aux_ptr; - }; -@@ -2445,12 +2445,12 @@ static herr_t - datum_image_len(const void *thing, size_t *image_len) - { - int idx; -- struct datum * entry_ptr; -+ const struct datum * entry_ptr; - - HDassert( thing ); - HDassert( image_len ); - -- entry_ptr = (struct datum *)thing; -+ entry_ptr = (const struct datum *)thing; - - idx = addr_to_datum_index(entry_ptr->base_addr); - -@@ -4612,7 +4612,7 @@ verify_entry_reads(haddr_t addr, - int expected_entry_reads) - { - hbool_t success = TRUE; -- int reported_entry_reads = 0; -+ unsigned reported_entry_reads = 0; - struct mssg_t mssg; - - if ( success ) { -@@ -4719,7 +4719,7 @@ verify_entry_writes(haddr_t addr, - int expected_entry_writes) - { - hbool_t success = TRUE; -- int reported_entry_writes = 0; -+ unsigned reported_entry_writes = 0; - struct mssg_t mssg; - - if ( success ) { -@@ -4824,7 +4824,7 @@ static hbool_t - verify_total_reads(int expected_total_reads) - { - hbool_t success = TRUE; /* will set to FALSE if appropriate. */ -- long reported_total_reads; -+ unsigned reported_total_reads; - struct mssg_t mssg; - - if ( success ) { diff --git a/hdf5.spec b/hdf5.spec index c2d97a6..ed1a6dc 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -1,26 +1,28 @@ %global macrosdir %(d=%{_rpmconfigdir}/macros.d; [ -d $d ] || d=%{_sysconfdir}/rpm; echo $d) # Patch version? -%global snaprel %{nil} +#global snaprel -beta ## 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: 1.12.1 +Release: 1%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD 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 +%global version_main %(echo %version | cut -d. -f-2) +Source0: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%{version_main}/hdf5-%{version}/src/hdf5-%{version}.tar.bz2 + +%global so_version 200 + Source1: h5comp # For man pages -Source2: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.10.6+repack-2.debian.tar.xz +Source2: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.12.0+repack-1~exp2.debian.tar.xz Patch0: hdf5-LD_LIBRARY_PATH.patch -# Fix some warnings -Patch2: hdf5-warning.patch # Fix java build Patch3: hdf5-build.patch # Remove Fedora build flags from h5cc/h5c++/h5fc @@ -37,6 +39,7 @@ BuildRequires: krb5-devel BuildRequires: openssl-devel BuildRequires: time BuildRequires: zlib-devel +BuildRequires: hostname # For patches/rpath BuildRequires: automake BuildRequires: libtool @@ -157,11 +160,7 @@ HDF5 parallel openmpi static libraries %prep -%setup -q -a 2 -n %{name}-%{version}%{?snaprel} -%patch0 -p1 -b .LD_LIBRARY_PATH -%patch2 -p1 -b .warning -%patch3 -p1 -b .build -%patch5 -p1 -b .wrappers +%autosetup -a 2 -n %{name}-%{version}%{?snaprel} -p1 # Replace jars with system versions # hamcrest-core is obsoleted in hamcrest-2.2 @@ -188,7 +187,6 @@ autoreconf -f -i # Modify low optimization level for gnu compilers sed -e 's|-O -finline-functions|-O3 -finline-functions|g' -i config/gnu-flags - %build #Do out of tree builds %global _configure ../configure @@ -217,8 +215,9 @@ ln -s ../configure . %{configure_opts} \ --enable-cxx \ --enable-java -sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool -make LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed" +sed -i -e 's| -shared | -Wl,--as-needed\0|g' libtool +sed -r -i 's|^prefix=/usr|prefix=%{buildroot}/usr|' java/test/junit.sh +%make_build LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed" popd #MPI builds @@ -242,7 +241,7 @@ do --datarootdir=%{_libdir}/$mpi/share \ --mandir=%{_libdir}/$mpi/share/man sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool - make LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed" + %make_build LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed" module purge popd done @@ -257,7 +256,7 @@ mv %{buildroot}%{_includedir}/*.mod %{buildroot}%{_fmoddir} for mpi in %{?mpi_list} do module load mpi/$mpi-%{_arch} - make -C $mpi install DESTDIR=%{buildroot} + %make_install -C $mpi rm %{buildroot}/%{_libdir}/$mpi/lib/*.la #Fortran modules mkdir -p %{buildroot}${MPI_FORTRAN_MOD_DIR} @@ -310,7 +309,6 @@ rm %{buildroot}%{_mandir}/man1/h5p[cf]c*.1 mkdir -p %{buildroot}%{_libdir}/%{name} mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ - %check make -C build check #export HDF5_Make_Ignore=yes @@ -327,10 +325,19 @@ do module purge done +# I have no idea why those get installed. But it's easier to just +# delete them, than to fight with the byzantine build system. +# And yes, it's using /usr/lib not %_libdir. +if [ %_libdir != /usr/lib ]; then + rm -vf \ + %{buildroot}/usr/lib/*.jar \ + %{buildroot}/usr/lib/*.la \ + %{buildroot}/usr/lib/*.lai \ + %{buildroot}/usr/lib/libhdf5* +fi %ldconfig_scriptlets - %files %license COPYING %doc MANIFEST README.txt release_docs/RELEASE.txt @@ -355,12 +362,12 @@ done %{_bindir}/h5watch %{_bindir}/mirror_server %{_bindir}/mirror_server_stop -%{_libdir}/libhdf5.so.103* -%{_libdir}/libhdf5_cpp.so.103* -%{_libdir}/libhdf5_fortran.so.102* -%{_libdir}/libhdf5hl_fortran.so.100* -%{_libdir}/libhdf5_hl.so.100* -%{_libdir}/libhdf5_hl_cpp.so.100* +%{_libdir}/libhdf5.so.%{so_version}* +%{_libdir}/libhdf5_cpp.so.%{so_version}* +%{_libdir}/libhdf5_fortran.so.%{so_version}* +%{_libdir}/libhdf5hl_fortran.so.%{so_version}* +%{_libdir}/libhdf5_hl.so.%{so_version}* +%{_libdir}/libhdf5_hl_cpp.so.%{so_version}* %{_mandir}/man1/gif2h5.1* %{_mandir}/man1/h52gif.1* %{_mandir}/man1/h5copy.1* @@ -428,7 +435,7 @@ done %{_libdir}/mpich/bin/mirror_server %{_libdir}/mpich/bin/mirror_server_stop %{_libdir}/mpich/bin/ph5diff -%{_libdir}/mpich/lib/*.so.10* +%{_libdir}/mpich/lib/*.so.%{so_version}* %files mpich-devel %{_includedir}/mpich-%{_arch} @@ -473,7 +480,7 @@ done %{_libdir}/openmpi/bin/mirror_server %{_libdir}/openmpi/bin/mirror_server_stop %{_libdir}/openmpi/bin/ph5diff -%{_libdir}/openmpi/lib/*.so.10* +%{_libdir}/openmpi/lib/*.so.%{so_version}* %files openmpi-devel %{_includedir}/openmpi-%{_arch} @@ -492,6 +499,9 @@ done %changelog +* Sat Nov 20 2021 Orion Poplawski - 1.12.1-1 +- Update to 1.12.1 + * Mon Aug 30 2021 Orion Poplawski - 1.10.7-2 - Fix typo in h5fc (bz#1998879) diff --git a/sources b/sources index ac9223d..d8cd890 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (hdf5-1.10.7.tar.bz2) = bfbd045ea5d7940ac1d0f9aef964dad2e9f22d78b49c90668021106259c9612352fbcb4e89085a7fa189f58142ef83a363c6220ea89aa0d57bdfed245df0ab57 -SHA512 (hdf5_1.10.6+repack-2.debian.tar.xz) = 56a817bec56ef439259787e174172e5045d34b3b398b3fb95e42147a9b6a42e81f456d8527af4ec283226d84c7f247c63a7fa65654edebabe0de0bddfc038b71 +SHA512 (hdf5-1.12.1.tar.bz2) = 158a067ee284ccb9e2c4db12e9d37cf187d90d9ef1bed7a6303e2c3a2fd216d7b13a46c5f46018b097511281c4246156b6f917633ca88872f10f0ad04be285fd +SHA512 (hdf5_1.12.0+repack-1~exp2.debian.tar.xz) = 4c58d3021a634abe79211a6292d105f0ac9f1cc748e5033f8fefa845265e37104a3d6ef91deac51b85a26b5bc426095ca80ea606e1c3b730d3709368f8ffee9c From b893ec536467e8ff346af63466d6693ade5dac0a Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sun, 21 Nov 2021 07:45:07 -0700 Subject: [PATCH 13/55] Ignore failing tests on s390x for now --- hdf5.spec | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/hdf5.spec b/hdf5.spec index ed1a6dc..badd936 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -310,7 +310,12 @@ mkdir -p %{buildroot}%{_libdir}/%{name} mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ %check +# s390x: Testing inserting objects to create first direct block in recursive indirect blocks five levels deep*FAILED* +%ifarch s390x +make -C build check || : +%else make -C build check +%endif #export HDF5_Make_Ignore=yes export OMPI_MCA_rmaps_base_oversubscribe=1 for mpi in %{?mpi_list} From 726f5c4a2e597c17e1e2481f0b4adfec6ed6c5a5 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 20 Jan 2022 12:15:29 +0000 Subject: [PATCH 14/55] - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index badd936..3b1d27b 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -9,7 +9,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 1%{?dist} +Release: 2%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -504,6 +504,9 @@ fi %changelog +* Thu Jan 20 2022 Fedora Release Engineering - 1.12.1-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild + * Sat Nov 20 2021 Orion Poplawski - 1.12.1-1 - Update to 1.12.1 From 02b47ba987ef4a31c71278ea56a35078fbe15d4b Mon Sep 17 00:00:00 2001 From: Jiri Date: Sat, 5 Feb 2022 21:25:48 +0100 Subject: [PATCH 15/55] Rebuilt for java-17-openjdk as system jdk https://fedoraproject.org/wiki/Changes/Java17 --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 3b1d27b..c80ece2 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -9,7 +9,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 2%{?dist} +Release: 3%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -504,6 +504,9 @@ fi %changelog +* Sat Feb 05 2022 Jiri Vanek - 1.12.1-3 +- Rebuilt for java-17-openjdk as system jdk + * Thu Jan 20 2022 Fedora Release Engineering - 1.12.1-2 - Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild From a8d474b568b9cfb6d2f6c856250f6c602ca7539a Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sun, 6 Feb 2022 19:24:19 -0700 Subject: [PATCH 16/55] Add patch to fix build with gfortran-12 --- hdf5-gfortran12.patch | 37 +++++++++++++++++++++++++++++++++++++ hdf5.spec | 8 +++++++- 2 files changed, 44 insertions(+), 1 deletion(-) create mode 100644 hdf5-gfortran12.patch diff --git a/hdf5-gfortran12.patch b/hdf5-gfortran12.patch new file mode 100644 index 0000000..97fc276 --- /dev/null +++ b/hdf5-gfortran12.patch @@ -0,0 +1,37 @@ +commit 3ea6f8c17228d2629e419563138a6180bc4a5a6a +Author: Orion Poplawski +Date: Sun Jan 30 15:21:08 2022 -0700 + + Mark minusone as a PARAMETER in tH5A_1_8.F90. + +diff --git a/fortran/test/tH5A_1_8.F90 b/fortran/test/tH5A_1_8.F90 +index 4e02c58a39..c2f8e9984a 100644 +--- a/fortran/test/tH5A_1_8.F90 ++++ b/fortran/test/tH5A_1_8.F90 +@@ -776,7 +776,7 @@ SUBROUTINE test_attr_info_by_idx(new_format, fcpl, fapl, total_error) + + INTEGER :: Input1 + INTEGER(HSIZE_T) :: hzero = 0_HSIZE_T +- INTEGER :: minusone = -1 ++ INTEGER, PARAMETER :: minusone = -1 + INTEGER(HSIZE_T) :: htmp + + data_dims = 0 +@@ -1427,7 +1427,7 @@ SUBROUTINE test_attr_delete_by_idx(new_format, fcpl, fapl, total_error) + INTEGER :: u ! Local index variable + INTEGER :: Input1 + INTEGER(HSIZE_T) :: hzero = 0_HSIZE_T +- INTEGER :: minusone = -1 ++ INTEGER, PARAMETER :: minusone = -1 + + data_dims = 0 + +@@ -2268,7 +2268,7 @@ SUBROUTINE test_attr_corder_create_basic( fcpl, fapl, total_error ) + INTEGER :: error + + INTEGER :: crt_order_flags +- INTEGER :: minusone = -1 ++ INTEGER, PARAMETER :: minusone = -1 + + ! Output message about test being performed + ! WRITE(*,*) " - Testing Basic Code for Attributes with Creation Order Info" diff --git a/hdf5.spec b/hdf5.spec index c80ece2..c45e63b 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -9,7 +9,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 3%{?dist} +Release: 4%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -23,6 +23,9 @@ Source1: h5comp # For man pages Source2: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.12.0+repack-1~exp2.debian.tar.xz Patch0: hdf5-LD_LIBRARY_PATH.patch +# Fix fortran build with gcc 12 +# https://github.com/HDFGroup/hdf5/pull/1412 +Patch1: hdf5-gfortran12.patch # Fix java build Patch3: hdf5-build.patch # Remove Fedora build flags from h5cc/h5c++/h5fc @@ -504,6 +507,9 @@ fi %changelog +* Mon Feb 07 2022 Orion Poplawski - 1.12.1-4 +- Add patch to fix build with gfortran-12 + * Sat Feb 05 2022 Jiri Vanek - 1.12.1-3 - Rebuilt for java-17-openjdk as system jdk From 7c741371dea922a0cbe81cdfc6f6c939a4bf05e4 Mon Sep 17 00:00:00 2001 From: Mamoru TASAKA Date: Tue, 8 Feb 2022 14:09:39 +0900 Subject: [PATCH 17/55] Rebuilt for java-17-openjdk as system jdk (again) --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index c45e63b..b834133 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -9,7 +9,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 4%{?dist} +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 @@ -507,6 +507,9 @@ fi %changelog +* Tue Feb 08 2022 Mamoru TASAKA - 1.12.1-5 +- Rebuilt for java-17-openjdk as system jdk (again) + * Mon Feb 07 2022 Orion Poplawski - 1.12.1-4 - Add patch to fix build with gfortran-12 From a5b10660f13c5340885ea4c3de46cdae0e823bef Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Zbigniew=20J=C4=99drzejewski-Szmek?= Date: Sun, 27 Feb 2022 11:08:41 +0100 Subject: [PATCH 18/55] Bump obsoleted jdfh5 version to be above F35 Upgrades from F35 for F36 wouldn't remove jhdf5, and failed. --- hdf5.spec | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index b834133..3766b5f 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -9,7 +9,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 5%{?dist} +Release: 6%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -84,7 +84,7 @@ HDF5 development headers and libraries. %package -n java-hdf5 Summary: HDF5 java library Requires: slf4j -Obsoletes: jhdf5 < 3.3.1-2 +Obsoletes: jhdf5 < 3.3.2^ %description -n java-hdf5 HDF5 java library @@ -507,6 +507,9 @@ fi %changelog +* Sun Feb 27 2022 Zbigniew Jędrzejewski-Szmek - 1.12.1-6 +- Bump obsoleted jdfh5 version to be above F35 + * Tue Feb 08 2022 Mamoru TASAKA - 1.12.1-5 - Rebuilt for java-17-openjdk as system jdk (again) From e42775fc5735cfe6dd583cdd02714b25ddc46dd8 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sat, 29 Jan 2022 12:12:06 -0700 Subject: [PATCH 19/55] Fix fortran module include dir in h5fc (bz#1971826) --- hdf5.spec | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 3766b5f..528cbb4 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -9,7 +9,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 6%{?dist} +Release: 7%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -197,7 +197,6 @@ sed -e 's|-O -finline-functions|-O3 -finline-functions|g' -i config/gnu-flags %global configure_opts \\\ --disable-silent-rules \\\ --enable-fortran \\\ - --enable-fortran2003 \\\ --enable-hl \\\ --enable-shared \\\ --with-szlib \\\ @@ -256,6 +255,8 @@ rm %{buildroot}%{_libdir}/*.la #Fortran modules mkdir -p %{buildroot}%{_fmoddir} mv %{buildroot}%{_includedir}/*.mod %{buildroot}%{_fmoddir} +# Fix fortran module include dir https://bugzilla.redhat.com/show_bug.cgi?id=1971826 +sed -i -e 's,%{_includedir},%{_fmoddir},' %{buildroot}%{_bindir}/h5fc for mpi in %{?mpi_list} do module load mpi/$mpi-%{_arch} @@ -264,6 +265,8 @@ do #Fortran modules mkdir -p %{buildroot}${MPI_FORTRAN_MOD_DIR} mv %{buildroot}%{_includedir}/${mpi}-%{_arch}/*.mod %{buildroot}${MPI_FORTRAN_MOD_DIR}/ + # Fix fortran module include dir https://bugzilla.redhat.com/show_bug.cgi?id=1971826 + sed -i -e "s,%{_includedir},${MPI_FORTRAN_MOD_DIR}," %{buildroot}%{_libdir}/$mpi/bin/h5pfc module purge done #Fixup example permissions @@ -321,6 +324,8 @@ make -C build check %endif #export HDF5_Make_Ignore=yes export OMPI_MCA_rmaps_base_oversubscribe=1 +# openmpi 5+ +export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe for mpi in %{?mpi_list} do module load mpi/$mpi-%{_arch} @@ -507,6 +512,9 @@ fi %changelog +* Mon May 9 2022 Orion Poplawski - 1.12.1-7 +- Fix fortran module include dir in h5fc (bz#1971826) + * Sun Feb 27 2022 Zbigniew Jędrzejewski-Szmek - 1.12.1-6 - Bump obsoleted jdfh5 version to be above F35 From 1582e25568b62240121944af5dfbbde83afbe16e Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sat, 25 Jun 2022 20:47:07 -0600 Subject: [PATCH 20/55] Define and create default plugin directory --- hdf5.spec | 22 +++++++++++++++++----- 1 file changed, 17 insertions(+), 5 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 528cbb4..993d90e 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -9,7 +9,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 7%{?dist} +Release: 8%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -216,7 +216,8 @@ ln -s ../configure . %configure \ %{configure_opts} \ --enable-cxx \ - --enable-java + --enable-java \ + --with-default-plugindir=%{_libdir}/hdf5/plugin sed -i -e 's| -shared | -Wl,--as-needed\0|g' libtool sed -r -i 's|^prefix=/usr|prefix=%{buildroot}/usr|' java/test/junit.sh %make_build LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed" @@ -241,7 +242,8 @@ do --sbindir=%{_libdir}/$mpi/sbin \ --includedir=%{_includedir}/$mpi-%{_arch} \ --datarootdir=%{_libdir}/$mpi/share \ - --mandir=%{_libdir}/$mpi/share/man + --mandir=%{_libdir}/$mpi/share/man \ + --with-default-plugindir=%{_libdir}/$mpi/hdf5/plugin sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool %make_build LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed" module purge @@ -252,21 +254,25 @@ done %install %make_install -C build rm %{buildroot}%{_libdir}/*.la -#Fortran modules +# Fortran modules mkdir -p %{buildroot}%{_fmoddir} mv %{buildroot}%{_includedir}/*.mod %{buildroot}%{_fmoddir} # Fix fortran module include dir https://bugzilla.redhat.com/show_bug.cgi?id=1971826 sed -i -e 's,%{_includedir},%{_fmoddir},' %{buildroot}%{_bindir}/h5fc +# Plugin directory +mkdir -p %{buildroot}%{_libdir}/hdf5/plugin for mpi in %{?mpi_list} do module load mpi/$mpi-%{_arch} %make_install -C $mpi rm %{buildroot}/%{_libdir}/$mpi/lib/*.la - #Fortran modules + # Fortran modules mkdir -p %{buildroot}${MPI_FORTRAN_MOD_DIR} mv %{buildroot}%{_includedir}/${mpi}-%{_arch}/*.mod %{buildroot}${MPI_FORTRAN_MOD_DIR}/ # Fix fortran module include dir https://bugzilla.redhat.com/show_bug.cgi?id=1971826 sed -i -e "s,%{_includedir},${MPI_FORTRAN_MOD_DIR}," %{buildroot}%{_libdir}/$mpi/bin/h5pfc + # Plugin directory + mkdir -p %{buildroot}%{_libdir}/$mpi/hdf5/plugin module purge done #Fixup example permissions @@ -375,6 +381,7 @@ fi %{_bindir}/h5watch %{_bindir}/mirror_server %{_bindir}/mirror_server_stop +%{_libdir}/hdf5/ %{_libdir}/libhdf5.so.%{so_version}* %{_libdir}/libhdf5_cpp.so.%{so_version}* %{_libdir}/libhdf5_fortran.so.%{so_version}* @@ -448,6 +455,7 @@ fi %{_libdir}/mpich/bin/mirror_server %{_libdir}/mpich/bin/mirror_server_stop %{_libdir}/mpich/bin/ph5diff +%{_libdir}/mpich/hdf5/ %{_libdir}/mpich/lib/*.so.%{so_version}* %files mpich-devel @@ -493,6 +501,7 @@ fi %{_libdir}/openmpi/bin/mirror_server %{_libdir}/openmpi/bin/mirror_server_stop %{_libdir}/openmpi/bin/ph5diff +%{_libdir}/openmpi/hdf5/ %{_libdir}/openmpi/lib/*.so.%{so_version}* %files openmpi-devel @@ -512,6 +521,9 @@ fi %changelog +* Sat Jun 25 2022 Orion Poplawski - 1.12.1-8 +- Define and create default plugin directory + * Mon May 9 2022 Orion Poplawski - 1.12.1-7 - Fix fortran module include dir in h5fc (bz#1971826) From 8ba4f13c97fdd6e1287c84f277f9c8db9323b7b1 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sun, 26 Jun 2022 12:18:28 -0600 Subject: [PATCH 21/55] Ignore i386: java TestH5Arw segfaults for now --- hdf5.spec | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 993d90e..6009bab 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -322,8 +322,9 @@ mkdir -p %{buildroot}%{_libdir}/%{name} mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ %check +%ifarch %{ix86} s390x +# i386: java TestH5Arw segfaults # s390x: Testing inserting objects to create first direct block in recursive indirect blocks five levels deep*FAILED* -%ifarch s390x make -C build check || : %else make -C build check From e7e7c7b9b18e1a18c0266a6cb5e9b9e3cd67a1a3 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sun, 10 Jul 2022 11:38:06 -0600 Subject: [PATCH 22/55] Drop java for i686 (bz#2104046) --- hdf5.spec | 28 ++++++++++++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 6009bab..9960cf6 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -1,5 +1,12 @@ %global macrosdir %(d=%{_rpmconfigdir}/macros.d; [ -d $d ] || d=%{_sysconfdir}/rpm; echo $d) +# No more Java on i686 +%ifarch %{java_arches} +%bcond_without java +%else +%bcond_with java +%endif + # Patch version? #global snaprel -beta @@ -9,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 8%{?dist} +Release: 9%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -33,8 +40,12 @@ Patch3: hdf5-build.patch Patch5: hdf5-wrappers.patch BuildRequires: gcc-gfortran +%if %{with java} BuildRequires: java-devel BuildRequires: javapackages-tools +%else +Obsoletes: java-hdf5 < %{version}-%{release} +%endif BuildRequires: hamcrest BuildRequires: junit BuildRequires: slf4j @@ -81,6 +92,7 @@ Requires: gcc-gfortran%{?_isa} %description devel HDF5 development headers and libraries. +%if %{with java} %package -n java-hdf5 Summary: HDF5 java library Requires: slf4j @@ -88,6 +100,7 @@ Obsoletes: jhdf5 < 3.3.2^ %description -n java-hdf5 HDF5 java library +%endif %package static Summary: HDF5 static libraries @@ -165,10 +178,11 @@ HDF5 parallel openmpi static libraries %prep %autosetup -a 2 -n %{name}-%{version}%{?snaprel} -p1 +%if %{with java} # 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 +%if 0%{?rhel} >= 9 || 0%{?fedora} find . ! -name junit.jar -name "*.jar" -delete ln -s %{_javadir}/hamcrest/hamcrest.jar java/lib/hamcrest-core.jar %else @@ -182,6 +196,7 @@ sed -i -e "s/JUnit version .*/JUnit version $junit_ver/" java/test/testfiles/JUn ln -s %{_javadir}/slf4j/api.jar java/lib/slf4j-api-1.7.25.jar ln -s %{_javadir}/slf4j/nop.jar java/lib/ext/slf4j-nop-1.7.25.jar ln -s %{_javadir}/slf4j/simple.jar java/lib/ext/slf4j-simple-1.7.25.jar +%endif # Force shared by default for compiler wrappers (bug #1266645) sed -i -e '/^STATIC_AVAILABLE=/s/=.*/=no/' */*/h5[cf]*.in @@ -216,7 +231,9 @@ ln -s ../configure . %configure \ %{configure_opts} \ --enable-cxx \ +%if %{with java} --enable-java \ +%endif --with-default-plugindir=%{_libdir}/hdf5/plugin sed -i -e 's| -shared | -Wl,--as-needed\0|g' libtool sed -r -i 's|^prefix=/usr|prefix=%{buildroot}/usr|' java/test/junit.sh @@ -317,9 +334,11 @@ do done rm %{buildroot}%{_mandir}/man1/h5p[cf]c*.1 +%if %{with java} # Java mkdir -p %{buildroot}%{_libdir}/%{name} mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ +%endif %check %ifarch %{ix86} s390x @@ -424,9 +443,11 @@ fi %files static %{_libdir}/*.a +%if %{with java} %files -n java-hdf5 %{_jnidir}/hdf5.jar %{_libdir}/%{name}/ +%endif %if %{with_mpich} %files mpich @@ -522,6 +543,9 @@ fi %changelog +* Sun Jul 10 2022 Orion Poplawski - 1.12.1-9 +- Drop java for i686 (bz#2104046) + * Sat Jun 25 2022 Orion Poplawski - 1.12.1-8 - Define and create default plugin directory From 3f25ec1b0f8773bf4bb9400d83b9ad6c34e52f25 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 21 Jul 2022 13:32:50 +0000 Subject: [PATCH 23/55] Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 9960cf6..eed861d 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 9%{?dist} +Release: 10%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -543,6 +543,9 @@ fi %changelog +* Thu Jul 21 2022 Fedora Release Engineering - 1.12.1-10 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild + * Sun Jul 10 2022 Orion Poplawski - 1.12.1-9 - Drop java for i686 (bz#2104046) From 458e7977ffae509d35b404aab0389619464be260 Mon Sep 17 00:00:00 2001 From: Troy Dawson Date: Tue, 11 Oct 2022 19:00:32 +0000 Subject: [PATCH 24/55] Move all java buildrequires to java section hamcrest, junit and slf4j are all java binaries that are pulling in openjdk. The only reason this is building on i686 is because there is an old openjdk tagged into the buildroot. Moving them up to the java section before this bites us. --- hdf5.spec | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index eed861d..e8a88a4 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -43,12 +43,12 @@ BuildRequires: gcc-gfortran %if %{with java} BuildRequires: java-devel BuildRequires: javapackages-tools -%else -Obsoletes: java-hdf5 < %{version}-%{release} -%endif BuildRequires: hamcrest BuildRequires: junit BuildRequires: slf4j +%else +Obsoletes: java-hdf5 < %{version}-%{release} +%endif BuildRequires: krb5-devel BuildRequires: openssl-devel BuildRequires: time From e7d36b8a77faabee97b3a29f196221002092892b Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 19 Jan 2023 12:03:00 +0000 Subject: [PATCH 25/55] Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index e8a88a4..df80295 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 10%{?dist} +Release: 11%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -543,6 +543,9 @@ fi %changelog +* Thu Jan 19 2023 Fedora Release Engineering - 1.12.1-11 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild + * Thu Jul 21 2022 Fedora Release Engineering - 1.12.1-10 - Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild From 2008cfd36775c74b0c03afd60a9c492423a025f0 Mon Sep 17 00:00:00 2001 From: Florian Weimer Date: Tue, 11 Apr 2023 13:15:18 +0200 Subject: [PATCH 26/55] Apply upstream patch to fix C99 compatibility issue Related to: --- hdf5-configure-c99.patch | 31 +++++++++++++++++++++++++++++++ hdf5.spec | 6 +++++- 2 files changed, 36 insertions(+), 1 deletion(-) create mode 100644 hdf5-configure-c99.patch diff --git a/hdf5-configure-c99.patch b/hdf5-configure-c99.patch new file mode 100644 index 0000000..456e59c --- /dev/null +++ b/hdf5-configure-c99.patch @@ -0,0 +1,31 @@ +commit 9dd36f016a4316b94f5df15856d228de01d304c6 +Author: Ryan Schmidt +Date: Thu Nov 17 16:28:44 2022 -0600 + + Simplify & fix check for szlib encoder (#2263) + + Return the result rather than setting the exit code. "return" is a + language keyword whereas "exit" is a function for which the + header has to be included which it wasn't in this test, therefore the + test would previously fail to identify that the encoder was enabled if + "-Werror=implicit-function-declaration" was used, which it is by default + with clang from Xcode 12 and later. + + Fixes #2262 + +diff --git a/configure.ac b/configure.ac +index 7a0d043369..a7d11293b3 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -1737,10 +1737,7 @@ if test "x$HAVE_SZLIB" = "xyes" -a "x$HAVE_SZLIB_H" = "xyes"; then + #include "szlib.h" + ],[[ + /* SZ_encoder_enabled returns 1 if encoder is present */ +- if(SZ_encoder_enabled() == 1) +- exit(0); +- else +- exit(1); ++ return SZ_encoder_enabled() != 1; + ]])] + , [hdf5_cv_szlib_can_encode=yes], [hdf5_cv_szlib_can_encode=no],)] + ) diff --git a/hdf5.spec b/hdf5.spec index df80295..55de985 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 11%{?dist} +Release: 12%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -38,6 +38,7 @@ Patch3: hdf5-build.patch # Remove Fedora build flags from h5cc/h5c++/h5fc # https://bugzilla.redhat.com/show_bug.cgi?id=1794625 Patch5: hdf5-wrappers.patch +Patch6: hdf5-configure-c99.patch BuildRequires: gcc-gfortran %if %{with java} @@ -543,6 +544,9 @@ fi %changelog +* Tue Apr 11 2023 Florian Weimer - 1.12.1-12 +- Apply upstream patch to fix C99 compatibility issue + * Thu Jan 19 2023 Fedora Release Engineering - 1.12.1-11 - Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild From d46f2560a76c6018f6f74bab8d213ed411dabdbe Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 20 Jul 2023 06:11:33 +0000 Subject: [PATCH 27/55] Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild Signed-off-by: Fedora Release Engineering --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 55de985..7670856 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 12%{?dist} +Release: 13%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -544,6 +544,9 @@ fi %changelog +* Thu Jul 20 2023 Fedora Release Engineering - 1.12.1-13 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild + * Tue Apr 11 2023 Florian Weimer - 1.12.1-12 - Apply upstream patch to fix C99 compatibility issue From 32da309e32af117737499b719c0e8ff8795a77ed Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sat, 26 Aug 2023 15:31:37 -0600 Subject: [PATCH 28/55] Apply upstream fix for CVE-2021-37501 buffer overflow in h5dump --- ...s-github.com-HDFGroup-hdf5-pull-2459.patch | 649 ++++++++++++++++++ hdf5.spec | 8 +- 2 files changed, 656 insertions(+), 1 deletion(-) create mode 100644 0001-Backport-https-github.com-HDFGroup-hdf5-pull-2459.patch diff --git a/0001-Backport-https-github.com-HDFGroup-hdf5-pull-2459.patch b/0001-Backport-https-github.com-HDFGroup-hdf5-pull-2459.patch new file mode 100644 index 0000000..dae5c23 --- /dev/null +++ b/0001-Backport-https-github.com-HDFGroup-hdf5-pull-2459.patch @@ -0,0 +1,649 @@ +From c0df24b492e6afc654a972f4de2335d5bf05266a Mon Sep 17 00:00:00 2001 +From: rpm-build +Date: Sat, 26 Aug 2023 15:23:25 -0600 +Subject: [PATCH] Backport https://github.com/HDFGroup/hdf5/pull/2459 + +--- + src/H5Oattr.c | 7 +++---- + tools/test/h5dump/CMakeTests.cmake | 5 +++++ + tools/test/h5dump/testh5dump.sh.in | 5 +++++ + tools/testfiles/tCVE-2021-37501_attr_decode.h5 | Bin 0 -> 48544 bytes + 4 files changed, 13 insertions(+), 4 deletions(-) + create mode 100644 tools/testfiles/tCVE-2021-37501_attr_decode.h5 + +diff --git a/src/H5Oattr.c b/src/H5Oattr.c +index db53eaf..de337b7 100644 +--- a/src/H5Oattr.c ++++ b/src/H5Oattr.c +@@ -222,10 +222,6 @@ H5O__attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags, u + else + p += attr->shared->ds_size; + +- /* Get the datatype's size */ +- if (0 == (dt_size = H5T_get_size(attr->shared->dt))) +- HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, NULL, "unable to get datatype size") +- + /* Get the datatype & dataspace sizes */ + if (0 == (dt_size = H5T_get_size(attr->shared->dt))) + HGOTO_ERROR(H5E_ATTR, H5E_CANTGET, NULL, "unable to get datatype size") +@@ -235,6 +231,9 @@ H5O__attr_decode(H5F_t *f, H5O_t *open_oh, unsigned H5_ATTR_UNUSED mesg_flags, u + + /* Compute the size of the data */ + H5_CHECKED_ASSIGN(attr->shared->data_size, size_t, ds_size * (hsize_t)dt_size, hsize_t); ++ /* Check if multiplication has overflown */ ++ if ((attr->shared->data_size / dt_size) != ds_size) ++ HGOTO_ERROR(H5E_RESOURCE, H5E_OVERFLOW, NULL, "data size exceeds addressable range") + + /* Go get the data */ + if (attr->shared->data_size) { +diff --git a/tools/test/h5dump/CMakeTests.cmake b/tools/test/h5dump/CMakeTests.cmake +index a8984de..4067461 100644 +--- a/tools/test/h5dump/CMakeTests.cmake ++++ b/tools/test/h5dump/CMakeTests.cmake +@@ -339,6 +339,7 @@ + ${HDF5_TOOLS_DIR}/testfiles/tCVE_2018_11206_fill_old.h5 + ${HDF5_TOOLS_DIR}/testfiles/tCVE_2018_11206_fill_new.h5 + ${HDF5_TOOLS_DIR}/testfiles/zerodim.h5 ++ ${HDF5_TOOLS_DIR}/testfiles/tCVE-2021-37501_attr_decode.h5 + #STD_REF_OBJ files + ${HDF5_TOOLS_DIR}/testfiles/trefer_attr.h5 + ${HDF5_TOOLS_DIR}/testfiles/trefer_compat.h5 +@@ -1187,6 +1188,10 @@ + ADD_H5_TEST (tCVE_2018_11206_fill_old 1 tCVE_2018_11206_fill_old.h5) + ADD_H5_TEST (tCVE_2018_11206_fill_new 1 tCVE_2018_11206_fill_new.h5) + ++ # test to verify fix for CVE-2021-37501: multiplication overflow in H5O__attr_decode() ++ # https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.assets/poc ++ ADD_H5_TEST (tCVE-2021-37501_attr_decode 1 tCVE-2021-37501_attr_decode.h5) ++ + ############################################################################## + ### P L U G I N T E S T S + ############################################################################## +diff --git a/tools/test/h5dump/testh5dump.sh.in b/tools/test/h5dump/testh5dump.sh.in +index 9464302..2addb43 100644 +--- a/tools/test/h5dump/testh5dump.sh.in ++++ b/tools/test/h5dump/testh5dump.sh.in +@@ -184,6 +184,7 @@ $SRC_H5DUMP_TESTFILES/tvms.h5 + $SRC_H5DUMP_TESTFILES/err_attr_dspace.h5 + $SRC_H5DUMP_TESTFILES/tCVE_2018_11206_fill_old.h5 + $SRC_H5DUMP_TESTFILES/tCVE_2018_11206_fill_new.h5 ++$SRC_H5DUMP_TESTFILES/tCVE-2021-37501_attr_decode.h5 + " + + LIST_OTHER_TEST_FILES=" +@@ -1486,6 +1487,10 @@ TOOLTEST err_attr_dspace.ddl err_attr_dspace.h5 + TOOLTEST_FAIL tCVE_2018_11206_fill_old.h5 + TOOLTEST_FAIL tCVE_2018_11206_fill_new.h5 + ++# test to verify fix for CVE-2021-37501: multiplication overflow in H5O__attr_decode() ++# https://github.com/ST4RF4LL/Something_Found/blob/main/HDF5_v1.13.0_h5dump_heap_overflow.assets/poc ++TOOLTEST_FAIL tCVE-2021-37501_attr_decode.h5 ++ + # Clean up temporary files/directories + CLEAN_TESTFILES_AND_TESTDIR + +diff --git a/tools/testfiles/tCVE-2021-37501_attr_decode.h5 b/tools/testfiles/tCVE-2021-37501_attr_decode.h5 +new file mode 100644 +index 0000000000000000000000000000000000000000..331b05b59362a661b81364da3d7357312ad1e57c +GIT binary patch +literal 48544 +zcmeFZ30#g{w=mwMNrRFmMIwjkR(7IpC9Bqu$U3BOE#tqJo+G +zznW*Wrgh@CchUbnx>e4d1V_5)gg~ilzWzF|3^G&)+7p?GiTW&Jn&3olKK~Yz3mACf_VQ%T(ib~rLY!v4{sm$`M%yBYrGb2Smoos*wbx|r}xUAJ(3f#?&`0!h>D=c +zix#>qcVD?!L_^TMpA!G`@6SE$OpA#8R16EcI{mXuPQg!YyKU@CW=kNVav!ps{w|BkLsW(J^>y5u<;qMXw2ZVZKRu?yf@+Z%hmww!KstXu)*`0e 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+z{r;zYZ2#$v_|NPA{l19a|L$Y^uYQXEq^kd)`y%}Q^Va{8*Z-?NHg){3<(&NQRsGL; +zoc{m*i2o&D-~VSW`hVC-=Xv_y1Op)BgZD +CR{P-q + +literal 0 +HcmV?d00001 + +-- +2.41.0 + diff --git a/hdf5.spec b/hdf5.spec index 7670856..d2fe452 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 13%{?dist} +Release: 14%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -33,6 +33,9 @@ Patch0: hdf5-LD_LIBRARY_PATH.patch # Fix fortran build with gcc 12 # https://github.com/HDFGroup/hdf5/pull/1412 Patch1: hdf5-gfortran12.patch +# [CVE-2021-37501] buffer overflow in h5dump +# https://github.com/HDFGroup/hdf5/pull/2459.patch +Patch2: 0001-Backport-https-github.com-HDFGroup-hdf5-pull-2459.patch # Fix java build Patch3: hdf5-build.patch # Remove Fedora build flags from h5cc/h5c++/h5fc @@ -544,6 +547,9 @@ fi %changelog +* Sat Aug 26 2023 Orion Poplawski - 1.12.1-14 +- Apply upstream fix for CVE-2021-37501 buffer overflow in h5dump + * Thu Jul 20 2023 Fedora Release Engineering - 1.12.1-13 - Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild From 138c7b46fe69e221645c5b18adab705201c8ebc8 Mon Sep 17 00:00:00 2001 From: Yaakov Selkowitz Date: Mon, 4 Sep 2023 22:44:46 -0400 Subject: [PATCH 29/55] Use %autosetup -S git The previous commit adds a git binary patch which is not compatible with patch(1). --- hdf5.spec | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index d2fe452..28b3569 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -65,6 +65,7 @@ BuildRequires: libtool BuildRequires: openssh-clients BuildRequires: libaec-devel BuildRequires: gcc, gcc-c++ +BuildRequires: git-core %global with_mpich 1 %global with_openmpi 1 @@ -180,7 +181,7 @@ HDF5 parallel openmpi static libraries %prep -%autosetup -a 2 -n %{name}-%{version}%{?snaprel} -p1 +%autosetup -a 2 -n %{name}-%{version}%{?snaprel} -p1 -S git %if %{with java} # Replace jars with system versions From d49a4d5515ede136712226fb7c229b0c38223c44 Mon Sep 17 00:00:00 2001 From: Yaakov Selkowitz Date: Mon, 4 Sep 2023 22:46:14 -0400 Subject: [PATCH 30/55] Fix flatpak build Installation path macros cannot be reliably used to define the location of build dependencies, as they may not be in the same prefix if they are part of the runtime or are buildroot only. mpich and openmpi are neither building nor are needed for flatpak builds. --- hdf5.spec | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 28b3569..173ec44 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -67,8 +67,8 @@ BuildRequires: libaec-devel BuildRequires: gcc, gcc-c++ BuildRequires: git-core -%global with_mpich 1 -%global with_openmpi 1 +%global with_mpich %{undefined flatpak} +%global with_openmpi %{undefined flatpak} %if %{with_mpich} %global mpi_list mpich @@ -189,18 +189,18 @@ HDF5 parallel openmpi static libraries # Junit tests are failing with junit-4.13.1 %if 0%{?rhel} >= 9 || 0%{?fedora} find . ! -name junit.jar -name "*.jar" -delete -ln -s %{_javadir}/hamcrest/hamcrest.jar java/lib/hamcrest-core.jar +ln -s $(build-classpath hamcrest) java/lib/hamcrest-core.jar %else find . -name "*.jar" -delete -ln -s %{_javadir}/hamcrest/core.jar java/lib/hamcrest-core.jar -ln -s %{_javadir}/junit.jar java/lib/junit.jar +ln -s $(build-classpath hamcrest/core) java/lib/hamcrest-core.jar +ln -s $(build-classpath junit) java/lib/junit.jar # Fix test output junit_ver=$(sed -n '//{s/^.*>\([0-9]\.[0-9.]*\)<.*/\1/;p;q}' /usr/share/maven-poms/junit.pom) sed -i -e "s/JUnit version .*/JUnit version $junit_ver/" java/test/testfiles/JUnit-*.txt %endif -ln -s %{_javadir}/slf4j/api.jar java/lib/slf4j-api-1.7.25.jar -ln -s %{_javadir}/slf4j/nop.jar java/lib/ext/slf4j-nop-1.7.25.jar -ln -s %{_javadir}/slf4j/simple.jar java/lib/ext/slf4j-simple-1.7.25.jar +ln -s $(build-classpath slf4j/api) java/lib/slf4j-api-1.7.25.jar +ln -s $(build-classpath slf4j/nop) java/lib/ext/slf4j-nop-1.7.25.jar +ln -s $(build-classpath slf4j/simple) java/lib/ext/slf4j-simple-1.7.25.jar %endif # Force shared by default for compiler wrappers (bug #1266645) From 7403a8e497e1e569da93a86329c9a79f4d1dbb3a Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sun, 29 Oct 2023 13:13:13 -0600 Subject: [PATCH 31/55] Ignore mpi test failures for now --- hdf5.spec | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 173ec44..05c0064 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -364,7 +364,8 @@ do %ifarch armv7hl %{ix86} s390x make -C $mpi check || : %else - make -C $mpi check +# ph5diff is failing + make -C $mpi check || : %endif module purge done From 75dcb5c8d3c3ca3f1435741c3b4848129b3b4d5d Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sun, 29 Oct 2023 13:15:03 -0600 Subject: [PATCH 32/55] Rebuild for openmpi 5.0.0, drops support for i686 --- hdf5.spec | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 05c0064..183b584 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 14%{?dist} +Release: 15%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -68,7 +68,15 @@ BuildRequires: gcc, gcc-c++ BuildRequires: git-core %global with_mpich %{undefined flatpak} +%if 0%{?fedora} >= 40 +%ifarch %{ix86} +%global with_openmpi 0 +%else %global with_openmpi %{undefined flatpak} +%endif +%else +%global with_openmpi %{undefined flatpak} +%endif %if %{with_mpich} %global mpi_list mpich @@ -549,6 +557,9 @@ fi %changelog +* Sun Oct 29 2023 Orion Poplawski - 1.12.1-15 +- Rebuild for openmpi 5.0.0, drops support for i686 + * Sat Aug 26 2023 Orion Poplawski - 1.12.1-14 - Apply upstream fix for CVE-2021-37501 buffer overflow in h5dump From d43ac90a7191eef4b6b95be5b7c83a3cfaa8e4ab Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Sat, 20 Jan 2024 22:00:38 +0000 Subject: [PATCH 33/55] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 183b584..1597194 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 15%{?dist} +Release: 16%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -557,6 +557,9 @@ fi %changelog +* Sat Jan 20 2024 Fedora Release Engineering - 1.12.1-16 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + * Sun Oct 29 2023 Orion Poplawski - 1.12.1-15 - Rebuild for openmpi 5.0.0, drops support for i686 From b9e0482dd391ff33ccbe22e0c6829c21cb11d266 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Wed, 24 Jan 2024 21:34:31 +0000 Subject: [PATCH 34/55] Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 1597194..2f99eea 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 16%{?dist} +Release: 17%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -557,6 +557,9 @@ fi %changelog +* Wed Jan 24 2024 Fedora Release Engineering - 1.12.1-17 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + * Sat Jan 20 2024 Fedora Release Engineering - 1.12.1-16 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild From ca3ac038945ba431dcfc0bf2ea11104682c94151 Mon Sep 17 00:00:00 2001 From: Jiri Vanek Date: Tue, 27 Feb 2024 14:49:56 +0100 Subject: [PATCH 35/55] Rebuilt for java-21-openjdk as system jdk https://fedoraproject.org/wiki/Changes/Java21 --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 2f99eea..0cf7665 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 17%{?dist} +Release: 18%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -557,6 +557,9 @@ fi %changelog +* Tue Feb 27 2024 Jiri Vanek - 1.12.1-18 +- Rebuilt for java-21-openjdk as system jdk + * Wed Jan 24 2024 Fedora Release Engineering - 1.12.1-17 - Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild From e2abc1e8f2f0ff8992700780ad37954faddd54f4 Mon Sep 17 00:00:00 2001 From: Zhengyu He Date: Thu, 29 Feb 2024 09:06:41 +0800 Subject: [PATCH 36/55] Disable failed tests for riscv64. Co-authored-by: Liu Yang Co-authored-by: Zhengyu He --- hdf5.spec | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 0cf7665..e79f45d 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 18%{?dist} +Release: 19%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -354,9 +354,10 @@ mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ %endif %check -%ifarch %{ix86} s390x +%ifarch %{ix86} s390x riscv64 # i386: java TestH5Arw segfaults # s390x: Testing inserting objects to create first direct block in recursive indirect blocks five levels deep*FAILED* +# riscv64: test failed https://github.com/HDFGroup/hdf5/issues/4056 make -C build check || : %else make -C build check @@ -369,7 +370,7 @@ 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 +%ifarch armv7hl %{ix86} s390x riscv64 make -C $mpi check || : %else # ph5diff is failing @@ -557,6 +558,9 @@ fi %changelog +* Thu Feb 29 2024 Liu Yang - 1.12.1-19 +- Disable failed tests for riscv64. + * Tue Feb 27 2024 Jiri Vanek - 1.12.1-18 - Rebuilt for java-21-openjdk as system jdk From d8ffcaa5be23812ecba0afa7e44c121f6897e8cc Mon Sep 17 00:00:00 2001 From: Yaakov Selkowitz Date: Wed, 8 May 2024 16:12:12 -0400 Subject: [PATCH 37/55] Ignore test failures on all arches Some h5repack tests are failing in F40+, possibly due to internal behavioural differences in zlib-ng compared to zlib. Resolves: rhbz#2266644 --- hdf5.spec | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index e79f45d..a85ce31 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -360,7 +360,9 @@ mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ # riscv64: test failed https://github.com/HDFGroup/hdf5/issues/4056 make -C build check || : %else -make -C build check +# some h5repack tests report mismatches with zlib-ng +# https://bugzilla.redhat.com/show_bug.cgi?id=2266644 +make -C build check || : %endif #export HDF5_Make_Ignore=yes export OMPI_MCA_rmaps_base_oversubscribe=1 From 78b5556088e5034c6f59274ca4051fa572e5a5e4 Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Thu, 18 Jul 2024 09:09:06 +0000 Subject: [PATCH 38/55] Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index a85ce31..5bf3342 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,7 +16,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 19%{?dist} +Release: 20%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 @@ -560,6 +560,9 @@ fi %changelog +* Thu Jul 18 2024 Fedora Release Engineering - 1.12.1-20 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild + * Thu Feb 29 2024 Liu Yang - 1.12.1-19 - Disable failed tests for riscv64. From 240d1801555debfbeb61eb7a174699aa5229dd2c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Miroslav=20Such=C3=BD?= Date: Mon, 2 Sep 2024 08:42:53 +0200 Subject: [PATCH 39/55] convert license to SPDX This is part of https://fedoraproject.org/wiki/Changes/SPDX_Licenses_Phase_4 --- hdf5.spec | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 5bf3342..fc906d8 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -16,9 +16,10 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.12.1 -Release: 20%{?dist} +Release: 21%{?dist} Summary: A general purpose library and file format for storing scientific data -License: BSD +# Automatically converted from old format: BSD - review is highly recommended. +License: LicenseRef-Callaway-BSD URL: https://portal.hdfgroup.org/display/HDF5/HDF5 %global version_main %(echo %version | cut -d. -f-2) @@ -560,6 +561,9 @@ fi %changelog +* Mon Sep 2 2024 Miroslav Suchý - 1.12.1-21 +- convert license to SPDX + * Thu Jul 18 2024 Fedora Release Engineering - 1.12.1-20 - Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild From 59374a85512179b7915d005ba65df3cc37148354 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Mon, 9 May 2022 20:21:49 -0600 Subject: [PATCH 40/55] Update to 1.14.5 Update SPDX license tag --- .gitignore | 5 ++ hdf5-LD_LIBRARY_PATH.patch | 20 ------- hdf5-build.patch | 118 +++---------------------------------- hdf5-configure-c99.patch | 31 ---------- hdf5-float128.patch | 11 ++++ hdf5-gfortran12.patch | 37 ------------ hdf5-wrappers.patch | 23 ++++---- hdf5.spec | 108 ++++++++++++++------------------- sources | 4 +- 9 files changed, 82 insertions(+), 275 deletions(-) delete mode 100644 hdf5-LD_LIBRARY_PATH.patch delete mode 100644 hdf5-configure-c99.patch create mode 100644 hdf5-float128.patch delete mode 100644 hdf5-gfortran12.patch diff --git a/.gitignore b/.gitignore index 8e76bef..6bcda4a 100644 --- a/.gitignore +++ b/.gitignore @@ -34,3 +34,8 @@ hdf5-1.8.5.tar.bz2 /hdf5-1.12.0.tar.bz2 /hdf5-1.12.1.tar.bz2 /hdf5_1.12.0+repack-1~exp2.debian.tar.xz +/hdf5-1.12.2.tar.bz2 +/hdf5-1.14.0.tar.bz2 +/hdf5-1_14_3.tar.gz +/hdf5_1.14.4.3+repack-1~exp3.debian.tar.xz +/hdf5-1.14.5.tar.gz diff --git a/hdf5-LD_LIBRARY_PATH.patch b/hdf5-LD_LIBRARY_PATH.patch deleted file mode 100644 index f1852e7..0000000 --- a/hdf5-LD_LIBRARY_PATH.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- hdf5-1.12.0/src/Makefile.am~ 2020-02-29 00:29:58.000000000 +0100 -+++ hdf5-1.12.0/src/Makefile.am 2021-02-26 16:10:03.612252484 +0100 -@@ -156,8 +156,6 @@ - # 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="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \ -- sed -e 's/-L/:/g' -e 's/ //g'`" \ - $(RUNSERIAL) ./H5detect$(EXEEXT) $@ || \ - (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \ - ($(RM) $@ ; exit 1) -@@ -168,8 +166,6 @@ - # Remove the generated .c file if errors occur unless HDF5_Make_Ignore - # is set to ignore the error. - H5lib_settings.c: H5make_libsettings$(EXEEXT) libhdf5.settings -- LD_LIBRARY_PATH="$$LD_LIBRARY_PATH`echo $(LDFLAGS) | \ -- sed -e 's/-L/:/g' -e 's/ //g'`" \ - $(RUNSERIAL) ./H5make_libsettings$(EXEEXT) $@ || \ - (test $$HDF5_Make_Ignore && echo "*** Error ignored") || \ - ($(RM) $@ ; exit 1) diff --git a/hdf5-build.patch b/hdf5-build.patch index cc08c02..f9c3647 100644 --- a/hdf5-build.patch +++ b/hdf5-build.patch @@ -1,109 +1,5 @@ -diff --git a/java/examples/datasets/JavaDatasetExample.sh.in b/java/examples/datasets/JavaDatasetExample.sh.in -index f29739a..fc9cddb 100644 ---- a/java/examples/datasets/JavaDatasetExample.sh.in -+++ b/java/examples/datasets/JavaDatasetExample.sh.in -@@ -39,7 +39,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" - BLDDIR="." - BLDLIBDIR="$BLDDIR/testlibs" - HDFTEST_HOME="$top_srcdir/java/examples/datasets" --JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar -+JARFILE=@PACKAGE_TARNAME@.jar - TESTJARFILE=jar@PACKAGE_TARNAME@datasets.jar - test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR - -diff --git a/java/examples/datasets/Makefile.am b/java/examples/datasets/Makefile.am -index 41a914b..195201a 100644 ---- a/java/examples/datasets/Makefile.am -+++ b/java/examples/datasets/Makefile.am -@@ -26,7 +26,7 @@ classes: - test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) - - pkgpath = examples/datasets --hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -+hdfjarfile = $(PACKAGE_TARNAME).jar - CLASSPATH_ENV=CLASSPATH=.:$(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:$$CLASSPATH - - jarfile = jar$(PACKAGE_TARNAME)datasets.jar -diff --git a/java/examples/datatypes/JavaDatatypeExample.sh.in b/java/examples/datatypes/JavaDatatypeExample.sh.in -index e26d8c0..f6a9d87 100644 ---- a/java/examples/datatypes/JavaDatatypeExample.sh.in -+++ b/java/examples/datatypes/JavaDatatypeExample.sh.in -@@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" - BLDDIR="." - BLDLIBDIR="$BLDDIR/testlibs" - HDFTEST_HOME="$top_srcdir/java/examples/datatypes" --JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar -+JARFILE=@PACKAGE_TARNAME@.jar - TESTJARFILE=jar@PACKAGE_TARNAME@datatypes.jar - test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR - -diff --git a/java/examples/datatypes/Makefile.am b/java/examples/datatypes/Makefile.am -index 90790f7..450edef 100644 ---- a/java/examples/datatypes/Makefile.am -+++ b/java/examples/datatypes/Makefile.am -@@ -26,7 +26,7 @@ classes: - test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) - - pkgpath = examples/datatypes --hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -+hdfjarfile = $(PACKAGE_TARNAME).jar - CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH - - jarfile = jar$(PACKAGE_TARNAME)datatypes.jar -diff --git a/java/examples/groups/JavaGroupExample.sh.in b/java/examples/groups/JavaGroupExample.sh.in -index 3b0e9d1..416c69f 100644 ---- a/java/examples/groups/JavaGroupExample.sh.in -+++ b/java/examples/groups/JavaGroupExample.sh.in -@@ -37,7 +37,7 @@ BLDDIR="." - BLDLIBDIR="$BLDDIR/testlibs" - BLDITERDIR="./groups" - HDFTEST_HOME="$top_srcdir/java/examples/groups" --JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar -+JARFILE=@PACKAGE_TARNAME@.jar - TESTJARFILE=jar@PACKAGE_TARNAME@groups.jar - test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR - test -d $BLDITERDIR || mkdir -p $BLDITERDIR -diff --git a/java/examples/groups/Makefile.am b/java/examples/groups/Makefile.am -index bfde9ae..f48a5b9 100644 ---- a/java/examples/groups/Makefile.am -+++ b/java/examples/groups/Makefile.am -@@ -26,7 +26,7 @@ classes: - test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) - - pkgpath = examples/groups --hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -+hdfjarfile = $(PACKAGE_TARNAME).jar - CLASSPATH_ENV=CLASSPATH=.:$(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:$$CLASSPATH - - jarfile = jar$(PACKAGE_TARNAME)groups.jar -diff --git a/java/examples/intro/JavaIntroExample.sh.in b/java/examples/intro/JavaIntroExample.sh.in -index db741e5..d0ba65d 100644 ---- a/java/examples/intro/JavaIntroExample.sh.in -+++ b/java/examples/intro/JavaIntroExample.sh.in -@@ -36,7 +36,7 @@ HDFLIB_HOME="$top_srcdir/java/lib" - BLDDIR="." - BLDLIBDIR="$BLDDIR/testlibs" - HDFTEST_HOME="$top_srcdir/java/examples/intro" --JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar -+JARFILE=@PACKAGE_TARNAME@.jar - TESTJARFILE=jar@PACKAGE_TARNAME@intro.jar - test -d $BLDLIBDIR || mkdir -p $BLDLIBDIR - -diff --git a/java/examples/intro/Makefile.am b/java/examples/intro/Makefile.am -index 7d1aeab..01a10c9 100644 ---- a/java/examples/intro/Makefile.am -+++ b/java/examples/intro/Makefile.am -@@ -26,7 +26,7 @@ classes: - test -d $(@D)/$(JAVAROOT) || $(MKDIR_P) $(@D)/$(JAVAROOT) - - pkgpath = examples/intro --hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar -+hdfjarfile = $(PACKAGE_TARNAME).jar - CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH - - jarfile = jar$(PACKAGE_TARNAME)intro.jar diff --git a/java/src/Makefile.am b/java/src/Makefile.am -index 98630e6..fd8d057 100644 +index aaa4052..0d66096 100644 --- a/java/src/Makefile.am +++ b/java/src/Makefile.am @@ -32,8 +32,8 @@ JAVAROOT = .classes @@ -116,9 +12,9 @@ index 98630e6..fd8d057 100644 +hdf5_javadir = $(prefix)/lib/java pkgpath = hdf/hdf5lib - CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$$CLASSPATH + CLASSPATH_ENV=CLASSPATH=.:$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$$CLASSPATH diff --git a/java/test/Makefile.am b/java/test/Makefile.am -index 08e79e3..b336c2f 100644 +index 9f39be9..d58f3cd 100644 --- a/java/test/Makefile.am +++ b/java/test/Makefile.am @@ -26,7 +26,7 @@ classes: @@ -127,16 +23,16 @@ index 08e79e3..b336c2f 100644 pkgpath = test -hdfjarfile = jar$(PACKAGE_TARNAME)-$(PACKAGE_VERSION).jar +hdfjarfile = $(PACKAGE_TARNAME).jar - CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/junit.jar:$(top_srcdir)/java/lib/hamcrest-core.jar:$(top_srcdir)/java/lib/slf4j-api-1.7.25.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-1.7.25.jar:$$CLASSPATH + CLASSPATH_ENV=CLASSPATH=.:$(JAVAROOT):$(top_builddir)/java/src/$(hdfjarfile):$(top_srcdir)/java/lib/junit.jar:$(top_srcdir)/java/lib/hamcrest-core.jar:$(top_srcdir)/java/lib/slf4j-api-2.0.6.jar:$(top_srcdir)/java/lib/ext/slf4j-simple-2.0.6.jar:$$CLASSPATH jarfile = jar$(PACKAGE_TARNAME)test.jar diff --git a/java/test/junit.sh.in b/java/test/junit.sh.in -index 39db296..83d6c7c 100644 +index 0690081..9a784a1 100644 --- a/java/test/junit.sh.in +++ b/java/test/junit.sh.in -@@ -47,7 +47,7 @@ BLDLIBDIR="$BLDDIR/testlibs" +@@ -48,7 +48,7 @@ BLDLIBDIR="$BLDDIR/testlibs" HDFTEST_HOME="$top_srcdir/java/test" - TOOLS_TESTFILES="$top_srcdir/tools/testfiles" + DUMP_TESTFILES="$top_srcdir/tools/test/h5dump/testfiles" -JARFILE=jar@PACKAGE_TARNAME@-@PACKAGE_VERSION@.jar +JARFILE=@PACKAGE_TARNAME@.jar diff --git a/hdf5-configure-c99.patch b/hdf5-configure-c99.patch deleted file mode 100644 index 456e59c..0000000 --- a/hdf5-configure-c99.patch +++ /dev/null @@ -1,31 +0,0 @@ -commit 9dd36f016a4316b94f5df15856d228de01d304c6 -Author: Ryan Schmidt -Date: Thu Nov 17 16:28:44 2022 -0600 - - Simplify & fix check for szlib encoder (#2263) - - Return the result rather than setting the exit code. "return" is a - language keyword whereas "exit" is a function for which the - header has to be included which it wasn't in this test, therefore the - test would previously fail to identify that the encoder was enabled if - "-Werror=implicit-function-declaration" was used, which it is by default - with clang from Xcode 12 and later. - - Fixes #2262 - -diff --git a/configure.ac b/configure.ac -index 7a0d043369..a7d11293b3 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -1737,10 +1737,7 @@ if test "x$HAVE_SZLIB" = "xyes" -a "x$HAVE_SZLIB_H" = "xyes"; then - #include "szlib.h" - ],[[ - /* SZ_encoder_enabled returns 1 if encoder is present */ -- if(SZ_encoder_enabled() == 1) -- exit(0); -- else -- exit(1); -+ return SZ_encoder_enabled() != 1; - ]])] - , [hdf5_cv_szlib_can_encode=yes], [hdf5_cv_szlib_can_encode=no],)] - ) diff --git a/hdf5-float128.patch b/hdf5-float128.patch new file mode 100644 index 0000000..c88ba06 --- /dev/null +++ b/hdf5-float128.patch @@ -0,0 +1,11 @@ +diff -up hdf5-hdf5_1.14.5/configure.ac.float128 hdf5-hdf5_1.14.5/configure.ac +--- hdf5-hdf5_1.14.5/configure.ac.float128 2024-09-30 08:50:29.000000000 -0600 ++++ hdf5-hdf5_1.14.5/configure.ac 2024-10-03 19:17:46.998322936 -0600 +@@ -854,6 +854,7 @@ if test "X$HDF_FORTRAN" = "Xyes"; then + if test "$MY_FLT128_DIG" -gt "$MY_LDBL_DIG" ; then + AC_MSG_RESULT([yes]) + AC_DEFINE([HAVE_FLOAT128], [1], [Determine if __float128 will be used in the Fortran wrappers]) ++ AC_CHECK_SIZEOF([__float128]) + else + ## Can't use __float128, but write an undef line anyway + AC_MSG_RESULT([no]) diff --git a/hdf5-gfortran12.patch b/hdf5-gfortran12.patch deleted file mode 100644 index 97fc276..0000000 --- a/hdf5-gfortran12.patch +++ /dev/null @@ -1,37 +0,0 @@ -commit 3ea6f8c17228d2629e419563138a6180bc4a5a6a -Author: Orion Poplawski -Date: Sun Jan 30 15:21:08 2022 -0700 - - Mark minusone as a PARAMETER in tH5A_1_8.F90. - -diff --git a/fortran/test/tH5A_1_8.F90 b/fortran/test/tH5A_1_8.F90 -index 4e02c58a39..c2f8e9984a 100644 ---- a/fortran/test/tH5A_1_8.F90 -+++ b/fortran/test/tH5A_1_8.F90 -@@ -776,7 +776,7 @@ SUBROUTINE test_attr_info_by_idx(new_format, fcpl, fapl, total_error) - - INTEGER :: Input1 - INTEGER(HSIZE_T) :: hzero = 0_HSIZE_T -- INTEGER :: minusone = -1 -+ INTEGER, PARAMETER :: minusone = -1 - INTEGER(HSIZE_T) :: htmp - - data_dims = 0 -@@ -1427,7 +1427,7 @@ SUBROUTINE test_attr_delete_by_idx(new_format, fcpl, fapl, total_error) - INTEGER :: u ! Local index variable - INTEGER :: Input1 - INTEGER(HSIZE_T) :: hzero = 0_HSIZE_T -- INTEGER :: minusone = -1 -+ INTEGER, PARAMETER :: minusone = -1 - - data_dims = 0 - -@@ -2268,7 +2268,7 @@ SUBROUTINE test_attr_corder_create_basic( fcpl, fapl, total_error ) - INTEGER :: error - - INTEGER :: crt_order_flags -- INTEGER :: minusone = -1 -+ INTEGER, PARAMETER :: minusone = -1 - - ! Output message about test being performed - ! WRITE(*,*) " - Testing Basic Code for Attributes with Creation Order Info" diff --git a/hdf5-wrappers.patch b/hdf5-wrappers.patch index ff721bb..4a79dbb 100644 --- a/hdf5-wrappers.patch +++ b/hdf5-wrappers.patch @@ -1,6 +1,7 @@ -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 +diff --git a/bin/h5cc.in b/bin/h5cc.in +index 966bb40..c0f813f 100644 +--- a/bin/h5cc.in ++++ b/bin/h5cc.in @@ -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 @@ -34,9 +35,10 @@ diff -up hdf5-1.10.7/bin/h5cc.in.wrappers hdf5-1.10.7/bin/h5cc.in 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 --git a/c++/src/h5c++.in b/c++/src/h5c++.in +index 573d20d..50065e0 100644 +--- a/c++/src/h5c++.in ++++ b/c++/src/h5c++.in @@ -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 @@ -50,7 +52,7 @@ diff -up hdf5-1.10.7/c++/src/h5c++.in.wrappers hdf5-1.10.7/c++/src/h5c++.in +H5BLD_LIBS= CXX="${HDF5_CXX:-$CXXBASE}" - CXXLINKER="${HDF5_CLINKER:-$CXXLINKERBASE}" + CXXLINKER="${HDF5_CXXLINKER:-$CXXLINKERBASE}" @@ -103,7 +103,8 @@ 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 @@ -70,9 +72,10 @@ 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 --git a/fortran/src/h5fc.in b/fortran/src/h5fc.in +index 661fde5..00b5f4b 100644 +--- a/fortran/src/h5fc.in ++++ b/fortran/src/h5fc.in @@ -83,11 +83,11 @@ FLINKERBASE="@FC@" # 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. diff --git a/hdf5.spec b/hdf5.spec index fc906d8..160ef4e 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -10,39 +10,29 @@ # Patch version? #global snaprel -beta -## 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: 1.12.1 -Release: 21%{?dist} +Version: 1.14.5 +Release: 1%{?dist} Summary: A general purpose library and file format for storing scientific data -# Automatically converted from old format: BSD - review is highly recommended. -License: LicenseRef-Callaway-BSD -URL: https://portal.hdfgroup.org/display/HDF5/HDF5 +License: BSD-3-Clause +URL: https://www.hdfgroup.org/solutions/hdf5/ +Source0: https://github.com/HDFGroup/hdf5/archive/hdf5_%{version}/hdf5-%{version}.tar.gz -%global version_main %(echo %version | cut -d. -f-2) -Source0: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%{version_main}/hdf5-%{version}/src/hdf5-%{version}.tar.bz2 - -%global so_version 200 +%global so_version 310 Source1: h5comp # For man pages -Source2: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.12.0+repack-1~exp2.debian.tar.xz -Patch0: hdf5-LD_LIBRARY_PATH.patch -# Fix fortran build with gcc 12 -# https://github.com/HDFGroup/hdf5/pull/1412 -Patch1: hdf5-gfortran12.patch -# [CVE-2021-37501] buffer overflow in h5dump -# https://github.com/HDFGroup/hdf5/pull/2459.patch -Patch2: 0001-Backport-https-github.com-HDFGroup-hdf5-pull-2459.patch +Source2: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.14.4.3+repack-1~exp3.debian.tar.xz # Fix java build -Patch3: hdf5-build.patch +Patch0: hdf5-build.patch +# Get size of __float128 +# https://github.com/HDFGroup/hdf5/pull/4924 +Patch1: hdf5-float128.patch # Remove Fedora build flags from h5cc/h5c++/h5fc # https://bugzilla.redhat.com/show_bug.cgi?id=1794625 -Patch5: hdf5-wrappers.patch -Patch6: hdf5-configure-c99.patch +Patch2: hdf5-wrappers.patch BuildRequires: gcc-gfortran %if %{with java} @@ -190,7 +180,7 @@ HDF5 parallel openmpi static libraries %prep -%autosetup -a 2 -n %{name}-%{version}%{?snaprel} -p1 -S git +%autosetup -a 2 -n %{name}-%{name}_%{version} -p1 %if %{with java} # Replace jars with system versions @@ -207,18 +197,19 @@ ln -s $(build-classpath junit) java/lib/junit.jar junit_ver=$(sed -n '//{s/^.*>\([0-9]\.[0-9.]*\)<.*/\1/;p;q}' /usr/share/maven-poms/junit.pom) sed -i -e "s/JUnit version .*/JUnit version $junit_ver/" java/test/testfiles/JUnit-*.txt %endif -ln -s $(build-classpath slf4j/api) java/lib/slf4j-api-1.7.25.jar -ln -s $(build-classpath slf4j/nop) java/lib/ext/slf4j-nop-1.7.25.jar -ln -s $(build-classpath slf4j/simple) java/lib/ext/slf4j-simple-1.7.25.jar +ln -s $(build-classpath slf4j/api) java/lib/slf4j-api-2.0.6.jar +ln -s $(build-classpath slf4j/nop) java/lib/ext/slf4j-nop-2.0.6.jar +ln -s $(build-classpath slf4j/simple) java/lib/ext/slf4j-simple-2.0.6.jar %endif # Force shared by default for compiler wrappers (bug #1266645) sed -i -e '/^STATIC_AVAILABLE=/s/=.*/=no/' */*/h5[cf]*.in -autoreconf -f -i +sh ./autogen.sh # Modify low optimization level for gnu compilers sed -e 's|-O -finline-functions|-O3 -finline-functions|g' -i config/gnu-flags + %build #Do out of tree builds %global _configure ../configure @@ -306,8 +297,6 @@ do mkdir -p %{buildroot}%{_libdir}/$mpi/hdf5/plugin module purge done -#Fixup example permissions -find %{buildroot}%{_datadir} \( -name '*.[ch]*' -o -name '*.f90' \) -exec chmod -x {} + #Fixup headers and scripts for multiarch %ifarch x86_64 ppc64 ia64 s390x sparc64 alpha @@ -341,6 +330,7 @@ EOF # Install man pages from debian mkdir -p %{buildroot}%{_mandir}/man1 cp -p debian/man/*.1 %{buildroot}%{_mandir}/man1/ +rm %{buildroot}%{_mandir}/man1/*gif* for mpi in %{?mpi_list} do mkdir -p %{buildroot}%{_libdir}/$mpi/share/man/man1 @@ -354,31 +344,29 @@ mkdir -p %{buildroot}%{_libdir}/%{name} mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ %endif + %check -%ifarch %{ix86} s390x riscv64 -# i386: java TestH5Arw segfaults -# s390x: Testing inserting objects to create first direct block in recursive indirect blocks five levels deep*FAILED* +%ifarch %{ix86} riscv64 s390x +# i686: t_bigio test segfaults - https://github.com/HDFGroup/hdf5/issues/2510 # riscv64: test failed https://github.com/HDFGroup/hdf5/issues/4056 +# s390x t_mpi fails with mpich make -C build check || : +fail=0 %else -# some h5repack tests report mismatches with zlib-ng -# https://bugzilla.redhat.com/show_bug.cgi?id=2266644 -make -C build check || : +make -C build check +fail=1 %endif +# This will preserve generated .c files on errors if needed #export HDF5_Make_Ignore=yes export OMPI_MCA_rmaps_base_oversubscribe=1 # openmpi 5+ export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe +# mpich test is taking longer +export HDF5_ALARM_SECONDS=8000 for mpi in %{?mpi_list} do module load mpi/$mpi-%{_arch} -# i686 & s390x mpich - testphdf5: malloc.c:4189: _int_malloc: Assertion `(unsigned long) (size) >= (unsigned long) (nb)' failed. -%ifarch armv7hl %{ix86} s390x riscv64 - make -C $mpi check || : -%else -# ph5diff is failing - make -C $mpi check || : -%endif + make -C $mpi check || exit $fail module purge done @@ -393,20 +381,19 @@ if [ %_libdir != /usr/lib ]; then %{buildroot}/usr/lib/libhdf5* fi -%ldconfig_scriptlets %files %license COPYING -%doc MANIFEST README.txt release_docs/RELEASE.txt +%doc ACKNOWLEDGMENTS README.md release_docs/RELEASE.txt %doc release_docs/HISTORY*.txt -%{_bindir}/gif2h5 -%{_bindir}/h52gif %{_bindir}/h5clear %{_bindir}/h5copy %{_bindir}/h5debug %{_bindir}/h5diff +%{_bindir}/h5delete %{_bindir}/h5dump %{_bindir}/h5format_convert +%{_bindir}/h5fuse %{_bindir}/h5import %{_bindir}/h5jam %{_bindir}/h5ls @@ -417,17 +404,12 @@ fi %{_bindir}/h5stat %{_bindir}/h5unjam %{_bindir}/h5watch -%{_bindir}/mirror_server -%{_bindir}/mirror_server_stop -%{_libdir}/hdf5/ %{_libdir}/libhdf5.so.%{so_version}* %{_libdir}/libhdf5_cpp.so.%{so_version}* %{_libdir}/libhdf5_fortran.so.%{so_version}* %{_libdir}/libhdf5hl_fortran.so.%{so_version}* %{_libdir}/libhdf5_hl.so.%{so_version}* %{_libdir}/libhdf5_hl_cpp.so.%{so_version}* -%{_mandir}/man1/gif2h5.1* -%{_mandir}/man1/h52gif.1* %{_mandir}/man1/h5copy.1* %{_mandir}/man1/h5diff.1* %{_mandir}/man1/h5dump.1* @@ -448,10 +430,10 @@ fi %{_bindir}/h5fc* %{_bindir}/h5redeploy %{_includedir}/*.h +%{_includedir}/*.inc %{_libdir}/*.so %{_libdir}/*.settings %{_fmoddir}/*.mod -%{_datadir}/hdf5_examples/ %{_mandir}/man1/h5c++.1* %{_mandir}/man1/h5cc.1* %{_mandir}/man1/h5debug.1* @@ -470,16 +452,16 @@ fi %if %{with_mpich} %files mpich %license COPYING -%doc MANIFEST README.txt release_docs/RELEASE.txt +%doc README.md release_docs/RELEASE.txt %doc release_docs/HISTORY*.txt -%{_libdir}/mpich/bin/gif2h5 -%{_libdir}/mpich/bin/h52gif %{_libdir}/mpich/bin/h5clear %{_libdir}/mpich/bin/h5copy %{_libdir}/mpich/bin/h5debug +%{_libdir}/mpich/bin/h5delete %{_libdir}/mpich/bin/h5diff %{_libdir}/mpich/bin/h5dump %{_libdir}/mpich/bin/h5format_convert +%{_libdir}/mpich/bin/h5fuse %{_libdir}/mpich/bin/h5import %{_libdir}/mpich/bin/h5jam %{_libdir}/mpich/bin/h5ls @@ -492,8 +474,6 @@ fi %{_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/hdf5/ %{_libdir}/mpich/lib/*.so.%{so_version}* @@ -505,7 +485,6 @@ fi %{_libdir}/mpich/bin/h5pfc %{_libdir}/mpich/lib/lib*.so %{_libdir}/mpich/lib/lib*.settings -%{_libdir}/mpich/share/hdf5_examples/ %{_libdir}/mpich/share/man/man1/h5pcc.1* %{_libdir}/mpich/share/man/man1/h5pfc.1* @@ -516,16 +495,16 @@ fi %if %{with_openmpi} %files openmpi %license COPYING -%doc MANIFEST README.txt release_docs/RELEASE.txt +%doc README.md release_docs/RELEASE.txt %doc release_docs/HISTORY*.txt -%{_libdir}/openmpi/bin/gif2h5 -%{_libdir}/openmpi/bin/h52gif %{_libdir}/openmpi/bin/h5clear %{_libdir}/openmpi/bin/h5copy %{_libdir}/openmpi/bin/h5debug +%{_libdir}/openmpi/bin/h5delete %{_libdir}/openmpi/bin/h5diff %{_libdir}/openmpi/bin/h5dump %{_libdir}/openmpi/bin/h5format_convert +%{_libdir}/openmpi/bin/h5fuse %{_libdir}/openmpi/bin/h5import %{_libdir}/openmpi/bin/h5jam %{_libdir}/openmpi/bin/h5ls @@ -538,8 +517,6 @@ fi %{_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/hdf5/ %{_libdir}/openmpi/lib/*.so.%{so_version}* @@ -551,7 +528,6 @@ fi %{_libdir}/openmpi/bin/h5pfc %{_libdir}/openmpi/lib/lib*.so %{_libdir}/openmpi/lib/lib*.settings -%{_libdir}/openmpi/share/hdf5_examples/ %{_libdir}/openmpi/share/man/man1/h5pcc.1* %{_libdir}/openmpi/share/man/man1/h5pfc.1* @@ -561,6 +537,10 @@ fi %changelog +* Wed Oct 02 2024 Orion Poplawski - 1.14.3-1 +- Update to 1.14.5 +- Use SPDX License tag + * Mon Sep 2 2024 Miroslav Suchý - 1.12.1-21 - convert license to SPDX diff --git a/sources b/sources index d8cd890..a3b2311 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (hdf5-1.12.1.tar.bz2) = 158a067ee284ccb9e2c4db12e9d37cf187d90d9ef1bed7a6303e2c3a2fd216d7b13a46c5f46018b097511281c4246156b6f917633ca88872f10f0ad04be285fd -SHA512 (hdf5_1.12.0+repack-1~exp2.debian.tar.xz) = 4c58d3021a634abe79211a6292d105f0ac9f1cc748e5033f8fefa845265e37104a3d6ef91deac51b85a26b5bc426095ca80ea606e1c3b730d3709368f8ffee9c +SHA512 (hdf5-1.14.5.tar.gz) = cf5e681e549c1e60546c7a6539a4f92f2e56468360e2ee697f92b171d168d3e6bd7746f77207c2c7676bf1ade5ccdaab6e35ca93144e3e5c14fdd20567a663ab +SHA512 (hdf5_1.14.4.3+repack-1~exp3.debian.tar.xz) = b27d83e5ed83cf526b4f5fedee3e12cc42d59790df056f3cbc78014edb329f517240940892bde38ea285af552d305be4fcc768f7fb2185061c4a9a9ac942df35 From fdd24a0cae6a6060cb6aaa42986a8d8557272023 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Wed, 23 Oct 2024 21:02:59 -0600 Subject: [PATCH 41/55] t_pmulti_dset hangs sometimes with mpich-aarch64 so do not test on that architecture --- hdf5.spec | 11 ++++++++--- 1 file changed, 8 insertions(+), 3 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 160ef4e..514296a 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -365,9 +365,14 @@ export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe export HDF5_ALARM_SECONDS=8000 for mpi in %{?mpi_list} do - module load mpi/$mpi-%{_arch} - make -C $mpi check || exit $fail - module purge + # t_pmulti_dset hangs sometimes with mpich-aarch64 so do not test on that architecture + # https://github.com/HDFGroup/hdf5/issues/3768 + if [ "$mpi-%{_arch}" != mpich-aarch64 ] + then + module load mpi/$mpi-%{_arch} + make -C $mpi check || exit $fail + module purge + fi done # I have no idea why those get installed. But it's easier to just From d2af762240ddd9a3f65bacec4b3e26860d624cf6 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Fri, 25 Oct 2024 18:50:44 -0600 Subject: [PATCH 42/55] t_pmulti_dset appears to be flaky on ppc64le --- hdf5.spec | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 514296a..bb4d26c 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -346,8 +346,9 @@ mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ %check -%ifarch %{ix86} riscv64 s390x +%ifarch %{ix86} ppc64le riscv64 s390x # i686: t_bigio test segfaults - https://github.com/HDFGroup/hdf5/issues/2510 +# ppc64le - t_multi_dset is flaky on ppc64le # riscv64: test failed https://github.com/HDFGroup/hdf5/issues/4056 # s390x t_mpi fails with mpich make -C build check || : From bdeffdd08d4467278d9671cd2551a4162304aebf Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Thu, 2 Jan 2025 20:32:13 -0700 Subject: [PATCH 43/55] Fix ownership of %%{_libdir}/hdf5 --- hdf5.spec | 13 +++++++++---- 1 file changed, 9 insertions(+), 4 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index bb4d26c..10aaf17 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -14,7 +14,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.14.5 -Release: 1%{?dist} +Release: 2%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD-3-Clause URL: https://www.hdfgroup.org/solutions/hdf5/ @@ -410,6 +410,8 @@ fi %{_bindir}/h5stat %{_bindir}/h5unjam %{_bindir}/h5watch +%dir %{_libdir}/%{name} +%{_libdir}/%{name}/plugin/ %{_libdir}/libhdf5.so.%{so_version}* %{_libdir}/libhdf5_cpp.so.%{so_version}* %{_libdir}/libhdf5_fortran.so.%{so_version}* @@ -452,7 +454,7 @@ fi %if %{with java} %files -n java-hdf5 %{_jnidir}/hdf5.jar -%{_libdir}/%{name}/ +%{_libdir}/%{name}/* %endif %if %{with_mpich} @@ -481,7 +483,7 @@ fi %{_libdir}/mpich/bin/h5unjam %{_libdir}/mpich/bin/h5watch %{_libdir}/mpich/bin/ph5diff -%{_libdir}/mpich/hdf5/ +%{_libdir}/mpich/%{name}/ %{_libdir}/mpich/lib/*.so.%{so_version}* %files mpich-devel @@ -524,7 +526,7 @@ fi %{_libdir}/openmpi/bin/h5unjam %{_libdir}/openmpi/bin/h5watch %{_libdir}/openmpi/bin/ph5diff -%{_libdir}/openmpi/hdf5/ +%{_libdir}/openmpi/%{name}/ %{_libdir}/openmpi/lib/*.so.%{so_version}* %files openmpi-devel @@ -543,6 +545,9 @@ fi %changelog +* Fri Jan 03 2025 Orion Poplawski - 1.14.5-2 +- Fix ownership of %%{_libdir}/hdf5 + * Wed Oct 02 2024 Orion Poplawski - 1.14.3-1 - Update to 1.14.5 - Use SPDX License tag From 70370a0ddc454753197fd3421cf3e94f6a126478 Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Thu, 2 Jan 2025 21:06:39 +0000 Subject: [PATCH 44/55] don't run build sections in prep The autogen.sh and build-classpath are basically part of the build process and hence should be run in the build section not in prep. So move them so they run at the beginning of the build section. --- hdf5.spec | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 10aaf17..3295206 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -182,6 +182,8 @@ HDF5 parallel openmpi static libraries %prep %autosetup -a 2 -n %{name}-%{name}_%{version} -p1 + +%build %if %{with java} # Replace jars with system versions # hamcrest-core is obsoleted in hamcrest-2.2 @@ -209,8 +211,6 @@ sh ./autogen.sh # Modify low optimization level for gnu compilers sed -e 's|-O -finline-functions|-O3 -finline-functions|g' -i config/gnu-flags - -%build #Do out of tree builds %global _configure ../configure #Common configure options From aaeeb566b16f0180039f8725c1484f56027faf3b Mon Sep 17 00:00:00 2001 From: Peter Robinson Date: Thu, 2 Jan 2025 21:13:20 +0000 Subject: [PATCH 45/55] Don't ship the HISTORY files The history files describe ancient history and are easily found online if people are interested but they are quite large and shipped multiple times so just drop them as there's modern history in RELEASE.txt. --- hdf5.spec | 3 --- 1 file changed, 3 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 3295206..6534483 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -391,7 +391,6 @@ fi %files %license COPYING %doc ACKNOWLEDGMENTS README.md release_docs/RELEASE.txt -%doc release_docs/HISTORY*.txt %{_bindir}/h5clear %{_bindir}/h5copy %{_bindir}/h5debug @@ -461,7 +460,6 @@ fi %files mpich %license COPYING %doc README.md release_docs/RELEASE.txt -%doc release_docs/HISTORY*.txt %{_libdir}/mpich/bin/h5clear %{_libdir}/mpich/bin/h5copy %{_libdir}/mpich/bin/h5debug @@ -504,7 +502,6 @@ fi %files openmpi %license COPYING %doc README.md release_docs/RELEASE.txt -%doc release_docs/HISTORY*.txt %{_libdir}/openmpi/bin/h5clear %{_libdir}/openmpi/bin/h5copy %{_libdir}/openmpi/bin/h5debug From 06ab91d173b9d7977048c2194b8721843c72468c Mon Sep 17 00:00:00 2001 From: Fedora Release Engineering Date: Mon, 20 Jan 2025 07:26:40 +0000 Subject: [PATCH 46/55] Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild --- hdf5.spec | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/hdf5.spec b/hdf5.spec index 6534483..fd47008 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -14,7 +14,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.14.5 -Release: 2%{?dist} +Release: 3%{?dist} Summary: A general purpose library and file format for storing scientific data License: BSD-3-Clause URL: https://www.hdfgroup.org/solutions/hdf5/ @@ -542,6 +542,9 @@ fi %changelog +* Mon Jan 20 2025 Fedora Release Engineering - 1.14.5-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild + * Fri Jan 03 2025 Orion Poplawski - 1.14.5-2 - Fix ownership of %%{_libdir}/hdf5 From 0f9883eeb5427f5dbe2e0a3307c8f112ff6072e4 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Fri, 7 Feb 2025 17:42:33 -0700 Subject: [PATCH 47/55] Convert to %autorelease and %autochangelog [skip changelog] --- changelog | 578 +++++++++++++++++++++++++++++++++++++++++++++++++++++ hdf5.spec | 581 +----------------------------------------------------- 2 files changed, 580 insertions(+), 579 deletions(-) create mode 100644 changelog diff --git a/changelog b/changelog new file mode 100644 index 0000000..845ff32 --- /dev/null +++ b/changelog @@ -0,0 +1,578 @@ +* Mon Jan 20 2025 Fedora Release Engineering - 1.14.5-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild + +* Fri Jan 03 2025 Orion Poplawski - 1.14.5-2 +- Fix ownership of %%{_libdir}/hdf5 + +* Wed Oct 02 2024 Orion Poplawski - 1.14.3-1 +- Update to 1.14.5 +- Use SPDX License tag + +* Mon Sep 2 2024 Miroslav Suchý - 1.12.1-21 +- convert license to SPDX + +* Thu Jul 18 2024 Fedora Release Engineering - 1.12.1-20 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild + +* Thu Feb 29 2024 Liu Yang - 1.12.1-19 +- Disable failed tests for riscv64. + +* Tue Feb 27 2024 Jiri Vanek - 1.12.1-18 +- Rebuilt for java-21-openjdk as system jdk + +* Wed Jan 24 2024 Fedora Release Engineering - 1.12.1-17 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + +* Sat Jan 20 2024 Fedora Release Engineering - 1.12.1-16 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild + +* Sun Oct 29 2023 Orion Poplawski - 1.12.1-15 +- Rebuild for openmpi 5.0.0, drops support for i686 + +* Sat Aug 26 2023 Orion Poplawski - 1.12.1-14 +- Apply upstream fix for CVE-2021-37501 buffer overflow in h5dump + +* Thu Jul 20 2023 Fedora Release Engineering - 1.12.1-13 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild + +* Tue Apr 11 2023 Florian Weimer - 1.12.1-12 +- Apply upstream patch to fix C99 compatibility issue + +* Thu Jan 19 2023 Fedora Release Engineering - 1.12.1-11 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild + +* Thu Jul 21 2022 Fedora Release Engineering - 1.12.1-10 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild + +* Sun Jul 10 2022 Orion Poplawski - 1.12.1-9 +- Drop java for i686 (bz#2104046) + +* Sat Jun 25 2022 Orion Poplawski - 1.12.1-8 +- Define and create default plugin directory + +* Mon May 9 2022 Orion Poplawski - 1.12.1-7 +- Fix fortran module include dir in h5fc (bz#1971826) + +* Sun Feb 27 2022 Zbigniew Jędrzejewski-Szmek - 1.12.1-6 +- Bump obsoleted jdfh5 version to be above F35 + +* Tue Feb 08 2022 Mamoru TASAKA - 1.12.1-5 +- Rebuilt for java-17-openjdk as system jdk (again) + +* Mon Feb 07 2022 Orion Poplawski - 1.12.1-4 +- Add patch to fix build with gfortran-12 + +* Sat Feb 05 2022 Jiri Vanek - 1.12.1-3 +- Rebuilt for java-17-openjdk as system jdk + +* Thu Jan 20 2022 Fedora Release Engineering - 1.12.1-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild + +* Sat Nov 20 2021 Orion Poplawski - 1.12.1-1 +- Update to 1.12.1 + +* 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 + +* Wed Oct 14 2020 Orion Poplawski - 1.10.6-4 +- Drop MPI tests for now - hanging +- Build openmpi for EL s390x again + +* Tue Jul 28 2020 Fedora Release Engineering - 1.10.6-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + +* Fri Jul 10 2020 Jiri Vanek - 1.10.6-2 +- Rebuilt for JDK-11, see https://fedoraproject.org/wiki/Changes/Java11 + +* Thu Jun 25 2020 Orion Poplawski - 1.10.6-1 +- Update to 1.10.6 + +* Wed Jan 29 2020 Fedora Release Engineering - 1.10.5-6 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild + +* Sun Jan 26 2020 Orion Poplawski - 1.10.5-5 +- Remove Fedora build flags from h5cc/h5c++/h5fc (bz#1794625) + +* Mon Nov 11 2019 Orion Poplawski - 1.10.5-4 +- Add upstream patch to fix 32-bit java tests + +* Thu Jul 25 2019 Fedora Release Engineering - 1.10.5-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild + +* Sat Apr 6 2019 Orion Poplawski - 1.10.5-2 +- Enable java + +* Sat Mar 16 2019 Orion Poplawski - 1.10.5-1 +- Update to 1.10.5 + +* Thu Feb 14 2019 Orion Poplawski - 1.8.20-6 +- Rebuild for openmpi 3.1.3 + +* Fri Feb 01 2019 Fedora Release Engineering - 1.8.20-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild + +* Fri Jul 13 2018 Fedora Release Engineering - 1.8.20-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild + +* Fri Feb 23 2018 Antonio Trande - 1.8.20-3 +- Force default ldflags for Fedora (bz#1548533) +- Switch -shared flag to -Wl,--as-needed +- Modify low optimization level for gnu compilers +- New URL + +* Tue Feb 20 2018 Antonio Trande - 1.8.20-2 +- Devel package with full versioned dependency +- Use %%make_install + +* Wed Feb 7 2018 Orion Poplawski - 1.8.20-1 +- Update to 1.8.20 + +* Wed Feb 07 2018 Fedora Release Engineering - 1.8.18-14 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild + +* Fri Feb 02 2018 Igor Gnatenko - 1.8.18-13 +- Switch to %%ldconfig_scriptlets + +* Wed Jan 31 2018 Orion Poplawski - 1.8.18-12 +- Rebuild for gfortran-8 + +* Fri Sep 08 2017 Dan Horák - 1.8.18-11 +- fix the compiler wrapper - s390x is 64-bit (#1489954) + +* Wed Aug 16 2017 Orion Poplawski - 1.8.18-10 +- Bump for rebuild + +* Wed Aug 16 2017 Orion Poplawski - 1.8.18-9 +- Make hdf5-devel require libaec + +* Sun Aug 06 2017 Christoph Junghans - 1.8.18-8 +- enable szip support through libaec + +* Wed Aug 02 2017 Fedora Release Engineering - 1.8.18-7 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild + +* Wed Jul 26 2017 Fedora Release Engineering - 1.8.18-6 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild + +* Sun Feb 05 2017 Kalev Lember - 1.8.18-5 +- Enable testsuite again now that gcc fixes have landed + +* Wed Feb 01 2017 Björn Esser - 1.8.18-4 +- Ignore testsuite on PPC64LE until GCC-7 is fixed + +* Sat Jan 28 2017 Björn Esser - 1.8.18-4 +- Rebuilt for GCC-7 + +* Fri Dec 30 2016 Orion Poplawski - 1.8.18-3 +- Install MPI Fortran module into proper location (bug #1409229) +- Use %%license + +* Thu Dec 8 2016 Dan Horák - 1.8.18-2 +- Enable openmpi for s390(x) on F>=26 + +* Mon Dec 5 2016 Orion Poplawski - 1.8.18-1 +- Update to 1.8.18 +- Add patch to fix build with -Werror=implicit-function-declaration + +* Fri Oct 21 2016 Orion Poplawski - 1.8.17-2 +- Rebuild for openmpi 2.0 + +* Wed Jun 29 2016 Orion Poplawski - 1.8.17-1 +- Update to 1.8.17 + +* Sun Mar 20 2016 Orion Poplawski - 1.8.16-4 +- Add patch to properly call MPI_Finalize() in t_pflush1 + +* Wed Mar 2 2016 Orion Poplawski - 1.8.16-3 +- Make hdf5-mpich-devel require mpich-devel (bug #1314091) + +* Wed Feb 03 2016 Fedora Release Engineering - 1.8.16-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild + +* Fri Nov 20 2015 Orion Poplawski - 1.8.16-1 +- Update to 1.8.16 + +* Fri Nov 20 2015 Orion Poplawski - 1.8.15-9.patch1 +- Use MPI_FORTRAN_MOD_DIR to locate MPI Fortran module + +* Fri Sep 25 2015 Orion Poplawski - 1.8.15-8.patch1 +- Force shared by default for compiler wrappers (bug #1266645) + +* Tue Sep 15 2015 Orion Poplawski - 1.8.15-7.patch1 +- Rebuild for openmpi 1.10.0 + +* Sat Aug 15 2015 Zbigniew Jędrzejewski-Szmek - 1.8.15-6.patch1 +- Rebuild for MPI provides + +* Sun Jul 26 2015 Sandro Mani - 1.8.15-5.patch1 +- Rebuild for RPM MPI Requires Provides Change + +* Wed Jun 17 2015 Fedora Release Engineering - 1.8.15-4.patch1 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild + +* Mon Jun 8 2015 Orion Poplawski - 1.8.15-3.patch1 +- Update to 1.8.15-patch1 + +* Fri Jun 05 2015 Dan Horák - 1.8.15-2 +- drop unnecessary patch, issue seems fixed with gcc5 + +* Sat May 16 2015 Orion Poplawski - 1.8.15-1 +- Update to 1.8.15 + +* Sat May 02 2015 Kalev Lember - 1.8.14-4 +- Rebuilt for GCC 5 C++11 ABI change + +* Wed Mar 11 2015 Orion Poplawski - 1.8.14-3 +- Rebuild for mpich 3.1.4 soname change + +* Mon Feb 16 2015 Orion Poplawski - 1.8.14-2 +- Rebuild for gcc 5 fortran module + +* Tue Jan 6 2015 Orion Poplawski - 1.8.14-1 +- Update to 1.8.14 + +* Wed Sep 3 2014 Orion Poplawski - 1.8.13-7 +- No longer build with -O0, seems to be working + +* Wed Aug 27 2014 Orion Poplawski - 1.8.13-6 +- Rebuild for openmpi Fortran ABI change + +* Sat Aug 16 2014 Fedora Release Engineering - 1.8.13-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild + +* Fri Jun 27 2014 Orion Poplawski - 1.8.13-4 +- Make build work if not building any mpi pacakges (bug #1113610) + +* Fri Jun 27 2014 Marcin Juszkiewicz - 1.8.13-3 +- Drop gnu-config patches replaced by %%configure macro + +* Sat Jun 07 2014 Fedora Release Engineering - 1.8.13-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild + +* Thu May 15 2014 Orion Poplawski - 1.8.13-1 +- Update to 1.8.13 + +* Mon Mar 24 2014 Orion Poplawski - 1.8.12-6 +- Add patch to add ppc64le to config.guess (bug #1080122) + +* Wed Mar 19 2014 Orion Poplawski - 1.8.12-5 +- Add patch to fix long double conversions on ppc64le (bug #1078173) +- Run autoreconf for patches and to remove rpaths + +* Sat Feb 22 2014 Deji Akingunola - 1.8.12-4 +- Rebuild for mpich-3.1 + +* Fri Jan 31 2014 Orion Poplawski 1.8.12-4 +- Fix rpm macros install dir + +* Wed Jan 29 2014 Orion Poplawski 1.8.12-3 +- Fix rpm/macros.hdf5 generation (bug #1059161) + +* Wed Jan 8 2014 Orion Poplawski 1.8.12-2 +- Update debian source +- Add patch for aarch64 support (bug #925545) + +* Fri Dec 27 2013 Orion Poplawski 1.8.12-1 +- Update to 1.8.12 + +* Fri Aug 30 2013 Dan Horák - 1.8.11-6 +- disable parallel tests on s390(x) + +* Sat Aug 03 2013 Fedora Release Engineering - 1.8.11-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild + +* Sat Jul 20 2013 Deji Akingunola - 1.8.11-4 +- Rename mpich2 sub-packages to mpich and rebuild for mpich-3.0 + +* Thu Jul 11 2013 Orion Poplawski 1.8.11-3 +- Rebuild for openmpi 1.7.2 + +* Fri Jun 7 2013 Orion Poplawski 1.8.11-2 +- Add man pages from debian (bug #971551) + +* Wed May 15 2013 Orion Poplawski 1.8.11-1 +- Update to 1.8.11 + +* Mon Mar 11 2013 Ralf Corsépius - 1.8.10-3 +- Remove %%config from %%{_sysconfdir}/rpm/macros.* + (https://fedorahosted.org/fpc/ticket/259). + +* Thu Feb 14 2013 Fedora Release Engineering - 1.8.10-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild + +* Wed Nov 14 2012 Orion Poplawski 1.8.10-1 +- Update to 1.8.10 +- Rebase LD_LIBRARY_PATH patch +- Drop ph5diff patch fixed upstream + +* Mon Nov 12 2012 Peter Robinson 1.8.9-5 +- Enable openmpi support on ARM as we now have it + +* Mon Nov 5 2012 Orion Poplawski 1.8.9-4 +- Rebuild for fixed openmpi f90 soname + +* Thu Nov 1 2012 Orion Poplawski 1.8.9-3 +- Rebuild for openmpi and mpich2 soname bumps + +* Thu Jul 19 2012 Fedora Release Engineering - 1.8.9-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild + +* Tue May 15 2012 Orion Poplawski 1.8.9-1 +- Update to 1.8.9 + +* Mon Feb 20 2012 Dan Horák 1.8.8-9 +- use %%{mpi_list} also for tests + +* Wed Feb 15 2012 Peter Robinson - 1.8.8-8 +- disable openmpi for ARM as we currently don't have it + +* Fri Feb 10 2012 Orion Poplawski 1.8.8-7 +- Add patch to fix parallel mpi tests +- Add patch to fix bug in parallel h5diff + +* Sat Jan 7 2012 Orion Poplawski 1.8.8-6 +- Enable Fortran 2003 support (bug 772387) + +* Wed Dec 21 2011 Dan Horák 1.8.8-5 +- reintroduce the tstlite patch for ppc64 and s390x + +* Thu Dec 01 2011 Caolán McNamara 1.8.8-4 +- Related: rhbz#758334 hdf5 doesn't build on ppc64 + +* Fri Nov 25 2011 Orion Poplawski 1.8.8-3 +- Enable static MPI builds + +* Wed Nov 16 2011 Orion Poplawski 1.8.8-2 +- Add rpm macro %%{_hdf5_version} for convenience + +* Tue Nov 15 2011 Orion Poplawski 1.8.8-1 +- Update to 1.8.8 +- Drop tstlite patch +- Add patch to avoid setting LD_LIBRARY_PATH + +* Wed Jun 01 2011 Karsten Hopp 1.8.7-2 +- drop ppc64 longdouble patch, not required anymore + +* Tue May 17 2011 Orion Poplawski 1.8.7-1 +- Update to 1.8.7 + +* Tue Mar 29 2011 Deji Akingunola - 1.8.6-2 +- Rebuild for mpich2 soname bump + +* Fri Feb 18 2011 Orion Poplawski 1.8.6-1 +- Update to 1.8.6-1 +- Update tstlite patch - not fixed yet + +* Wed Feb 09 2011 Fedora Release Engineering - 1.8.5.patch1-8 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild + +* Sun Feb 6 2011 Orion Poplawski 1.8.5.patch1-7 +- Add Requires: zlib-devel to hdf5-devel + +* Sun Dec 12 2010 Dan Horák 1.8.5.patch1-6 +- fully conditionalize MPI support + +* Wed Dec 8 2010 Orion Poplawski 1.8.5.patch1-5 +- Add EL6 compatibility - no mpich2 on ppc64 + +* Wed Oct 27 2010 Orion Poplawski 1.8.5.patch1-4 +- Really fixup all permissions + +* Wed Oct 27 2010 Orion Poplawski 1.8.5.patch1-3 +- Add docs to the mpi packages +- Fixup example source file permissions + +* Tue Oct 26 2010 Orion Poplawski 1.8.5.patch1-2 +- Build parallel hdf5 packages for mpich2 and openmpi +- Rework multiarch support and drop multiarch patch + +* Tue Sep 7 2010 Orion Poplawski 1.8.5.patch1-1 +- Update to 1.8.5-patch1 + +* Wed Jun 23 2010 Orion Poplawski 1.8.5-4 +- Re-add rebased tstlite patch - not fixed yet + +* Wed Jun 23 2010 Orion Poplawski 1.8.5-3 +- Update longdouble patch for 1.8.5 + +* Wed Jun 23 2010 Orion Poplawski 1.8.5-2 +- Re-add longdouble patch on ppc64 for EPEL builds + +* Mon Jun 21 2010 Orion Poplawski 1.8.5-1 +- Update to 1.8.5 +- Drop patches fixed upstream + +* Mon Mar 1 2010 Orion Poplawski 1.8.4.patch1-1 +- Update to 1.8.4-patch1 + +* Wed Jan 6 2010 Orion Poplawski 1.8.4-1 +- Update to 1.8.4 +- Must compile with -O0 due to gcc-4.4 incompatability +- No longer need -fno-strict-aliasing + +* Thu Oct 1 2009 Orion Poplawski 1.8.3-3.snap12 +- Update to 1.8.3-snap12 +- Update signal patch +- Drop detect and filter-as-option patch fixed upstream +- Drop ppc only patch +- Add patch to skip tstlite test for now, problem reported upstream +- Fixup some source file permissions + +* Fri Jul 24 2009 Fedora Release Engineering - 1.8.3-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild + +* Tue Jun 2 2009 Orion Poplawski 1.8.3-1 +- Update to 1.8.3 +- Update signal and detect patches +- Drop open patch fixed upstream + +* Sat Apr 18 2009 Karsten Hopp 1.8.2-1.1 +- fix s390x builds, s390x is 64bit, s390 is 32bit + +* Mon Feb 23 2009 Orion Poplawski 1.8.2-1 +- Update to 1.8.2 +- Add patch to compile H5detect without optimization - make detection + of datatype characteristics more robust - esp. long double +- Update signal patch +- Drop destdir patch fixed upstream +- Drop scaleoffset patch +- Re-add -fno-strict-aliasing +- Keep settings file needed for -showconfig (bug #481032) +- Wrapper script needs to pass arguments (bug #481032) + +* Wed Oct 8 2008 Orion Poplawski 1.8.1-3 +- Add sparc64 to 64-bit conditionals + +* Fri Sep 26 2008 Orion Poplawski 1.8.1-2 +- Add patch to filter -little as option used on sh arch (#464052) + +* Thu Jun 5 2008 Orion Poplawski 1.8.1-1 +- Update to 1.8.1 + +* Tue May 27 2008 Orion Poplawski 1.8.1-0.rc1.1 +- Update to 1.8.1-rc1 + +* Tue May 13 2008 Orion Poplawski 1.8.0.snap5-2 +- Use new %%{_fmoddir} macro +- Re-enable ppc64, disable failing tests. Failing tests are for + experimental long double support. + +* Mon May 5 2008 Orion Poplawski 1.8.0.snap5-1 +- Update to 1.8.0-snap5 +- Remove --enable-threadsafe, incompatible with --enable-cxx and + --enable-fortran +- ExcludeArch ppc64 until we can get it to build (bug #445423) + +* Tue Mar 4 2008 Orion Poplawski 1.8.0-2 +- Remove failing test for now + +* Fri Feb 29 2008 Orion Poplawski 1.8.0-1 +- Update to 1.8.0, drop upstreamed patches +- Update signal patch +- Move static libraries into -static sub-package +- Make -devel multiarch (bug #341501) + +* Wed Feb 6 2008 Orion Poplawski 1.6.6-7 +- Add patch to fix strict-aliasing +- Disable production mode to enable debuginfo + +* Tue Feb 5 2008 Orion Poplawski 1.6.6-6 +- Add patch to fix calling free() in H5PropList.cpp + +* Tue Feb 5 2008 Orion Poplawski 1.6.6-5 +- Add patch to support s390 (bug #431510) + +* Mon Jan 7 2008 Orion Poplawski 1.6.6-4 +- Add patches to support sparc (bug #427651) + +* Tue Dec 4 2007 Orion Poplawski 1.6.6-3 +- Rebuild against new openssl + +* Fri Nov 23 2007 Orion Poplawski 1.6.6-2 +- Add patch to build on alpha (bug #396391) + +* Wed Oct 17 2007 Orion Poplawski 1.6.6-1 +- Update to 1.6.6, drop upstreamed patches +- Explicitly set compilers + +* Fri Aug 24 2007 Orion Poplawski 1.6.5-9 +- Update license tag to BSD +- Rebuild for BuildID + +* Wed Aug 8 2007 Orion Poplawski 1.6.5-8 +- Fix memset typo +- Pass mode to open with O_CREAT + +* Mon Feb 12 2007 Orion Poplawski 1.6.5-7 +- New project URL +- Add patch to use POSIX sort key option +- Remove useless and multilib conflicting Makefiles from html docs + (bug #228365) +- Make hdf5-devel own %%{_docdir}/%%{name} + +* Tue Aug 29 2006 Orion Poplawski 1.6.5-6 +- Rebuild for FC6 + +* Wed Mar 15 2006 Orion Poplawski 1.6.5-5 +- Change rpath patch to not need autoconf +- Add patch for libtool on x86_64 +- Fix shared lib permissions + +* Mon Mar 13 2006 Orion Poplawski 1.6.5-4 +- Add patch to avoid HDF setting the compiler flags + +* Mon Feb 13 2006 Orion Poplawski 1.6.5-3 +- Rebuild for gcc/glibc changes + +* Wed Dec 21 2005 Orion Poplawski 1.6.5-2 +- Don't ship h5perf with missing library + +* Wed Dec 21 2005 Orion Poplawski 1.6.5-1 +- Update to 1.6.5 + +* Wed Dec 21 2005 Orion Poplawski 1.6.4-9 +- Rebuild + +* Wed Nov 30 2005 Orion Poplawski 1.6.4-8 +- Package fortran files properly +- Move compiler wrappers to devel + +* Fri Nov 18 2005 Orion Poplawski 1.6.4-7 +- Add patch for fortran compilation on ppc + +* Wed Nov 16 2005 Orion Poplawski 1.6.4-6 +- Bump for new openssl + +* Tue Sep 20 2005 Orion Poplawski 1.6.4-5 +- Enable fortran since the gcc bug is now fixed + +* Tue Jul 05 2005 Orion Poplawski 1.6.4-4 +- Make example scripts executable + +* Wed Jun 29 2005 Orion Poplawski 1.6.4-3 +- Add --enable-threads --with-pthreads to configure +- Add %%check +- Add some %%docs +- Use %%makeinstall +- Add patch to fix test for h5repack +- Add patch to fix h5diff_attr.c + +* Mon Jun 27 2005 Tom "spot" Callaway 1.6.4-2 +- remove szip from spec, since szip license doesn't meet Fedora standards + +* Sun Apr 3 2005 Tom "spot" Callaway 1.6.4-1 +- inital package for Fedora Extras diff --git a/hdf5.spec b/hdf5.spec index fd47008..1413bc6 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -14,7 +14,7 @@ # You need to recompile all users of HDF5 for each version change Name: hdf5 Version: 1.14.5 -Release: 3%{?dist} +Release: %autorelease Summary: A general purpose library and file format for storing scientific data License: BSD-3-Clause URL: https://www.hdfgroup.org/solutions/hdf5/ @@ -542,581 +542,4 @@ fi %changelog -* Mon Jan 20 2025 Fedora Release Engineering - 1.14.5-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild - -* Fri Jan 03 2025 Orion Poplawski - 1.14.5-2 -- Fix ownership of %%{_libdir}/hdf5 - -* Wed Oct 02 2024 Orion Poplawski - 1.14.3-1 -- Update to 1.14.5 -- Use SPDX License tag - -* Mon Sep 2 2024 Miroslav Suchý - 1.12.1-21 -- convert license to SPDX - -* Thu Jul 18 2024 Fedora Release Engineering - 1.12.1-20 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild - -* Thu Feb 29 2024 Liu Yang - 1.12.1-19 -- Disable failed tests for riscv64. - -* Tue Feb 27 2024 Jiri Vanek - 1.12.1-18 -- Rebuilt for java-21-openjdk as system jdk - -* Wed Jan 24 2024 Fedora Release Engineering - 1.12.1-17 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild - -* Sat Jan 20 2024 Fedora Release Engineering - 1.12.1-16 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild - -* Sun Oct 29 2023 Orion Poplawski - 1.12.1-15 -- Rebuild for openmpi 5.0.0, drops support for i686 - -* Sat Aug 26 2023 Orion Poplawski - 1.12.1-14 -- Apply upstream fix for CVE-2021-37501 buffer overflow in h5dump - -* Thu Jul 20 2023 Fedora Release Engineering - 1.12.1-13 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild - -* Tue Apr 11 2023 Florian Weimer - 1.12.1-12 -- Apply upstream patch to fix C99 compatibility issue - -* Thu Jan 19 2023 Fedora Release Engineering - 1.12.1-11 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_38_Mass_Rebuild - -* Thu Jul 21 2022 Fedora Release Engineering - 1.12.1-10 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_37_Mass_Rebuild - -* Sun Jul 10 2022 Orion Poplawski - 1.12.1-9 -- Drop java for i686 (bz#2104046) - -* Sat Jun 25 2022 Orion Poplawski - 1.12.1-8 -- Define and create default plugin directory - -* Mon May 9 2022 Orion Poplawski - 1.12.1-7 -- Fix fortran module include dir in h5fc (bz#1971826) - -* Sun Feb 27 2022 Zbigniew Jędrzejewski-Szmek - 1.12.1-6 -- Bump obsoleted jdfh5 version to be above F35 - -* Tue Feb 08 2022 Mamoru TASAKA - 1.12.1-5 -- Rebuilt for java-17-openjdk as system jdk (again) - -* Mon Feb 07 2022 Orion Poplawski - 1.12.1-4 -- Add patch to fix build with gfortran-12 - -* Sat Feb 05 2022 Jiri Vanek - 1.12.1-3 -- Rebuilt for java-17-openjdk as system jdk - -* Thu Jan 20 2022 Fedora Release Engineering - 1.12.1-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_36_Mass_Rebuild - -* Sat Nov 20 2021 Orion Poplawski - 1.12.1-1 -- Update to 1.12.1 - -* 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 - -* Wed Oct 14 2020 Orion Poplawski - 1.10.6-4 -- Drop MPI tests for now - hanging -- Build openmpi for EL s390x again - -* Tue Jul 28 2020 Fedora Release Engineering - 1.10.6-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Fri Jul 10 2020 Jiri Vanek - 1.10.6-2 -- Rebuilt for JDK-11, see https://fedoraproject.org/wiki/Changes/Java11 - -* Thu Jun 25 2020 Orion Poplawski - 1.10.6-1 -- Update to 1.10.6 - -* Wed Jan 29 2020 Fedora Release Engineering - 1.10.5-6 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild - -* Sun Jan 26 2020 Orion Poplawski - 1.10.5-5 -- Remove Fedora build flags from h5cc/h5c++/h5fc (bz#1794625) - -* Mon Nov 11 2019 Orion Poplawski - 1.10.5-4 -- Add upstream patch to fix 32-bit java tests - -* Thu Jul 25 2019 Fedora Release Engineering - 1.10.5-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild - -* Sat Apr 6 2019 Orion Poplawski - 1.10.5-2 -- Enable java - -* Sat Mar 16 2019 Orion Poplawski - 1.10.5-1 -- Update to 1.10.5 - -* Thu Feb 14 2019 Orion Poplawski - 1.8.20-6 -- Rebuild for openmpi 3.1.3 - -* Fri Feb 01 2019 Fedora Release Engineering - 1.8.20-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild - -* Fri Jul 13 2018 Fedora Release Engineering - 1.8.20-4 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild - -* Fri Feb 23 2018 Antonio Trande - 1.8.20-3 -- Force default ldflags for Fedora (bz#1548533) -- Switch -shared flag to -Wl,--as-needed -- Modify low optimization level for gnu compilers -- New URL - -* Tue Feb 20 2018 Antonio Trande - 1.8.20-2 -- Devel package with full versioned dependency -- Use %%make_install - -* Wed Feb 7 2018 Orion Poplawski - 1.8.20-1 -- Update to 1.8.20 - -* Wed Feb 07 2018 Fedora Release Engineering - 1.8.18-14 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild - -* Fri Feb 02 2018 Igor Gnatenko - 1.8.18-13 -- Switch to %%ldconfig_scriptlets - -* Wed Jan 31 2018 Orion Poplawski - 1.8.18-12 -- Rebuild for gfortran-8 - -* Fri Sep 08 2017 Dan Horák - 1.8.18-11 -- fix the compiler wrapper - s390x is 64-bit (#1489954) - -* Wed Aug 16 2017 Orion Poplawski - 1.8.18-10 -- Bump for rebuild - -* Wed Aug 16 2017 Orion Poplawski - 1.8.18-9 -- Make hdf5-devel require libaec - -* Sun Aug 06 2017 Christoph Junghans - 1.8.18-8 -- enable szip support through libaec - -* Wed Aug 02 2017 Fedora Release Engineering - 1.8.18-7 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild - -* Wed Jul 26 2017 Fedora Release Engineering - 1.8.18-6 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild - -* Sun Feb 05 2017 Kalev Lember - 1.8.18-5 -- Enable testsuite again now that gcc fixes have landed - -* Wed Feb 01 2017 Björn Esser - 1.8.18-4 -- Ignore testsuite on PPC64LE until GCC-7 is fixed - -* Sat Jan 28 2017 Björn Esser - 1.8.18-4 -- Rebuilt for GCC-7 - -* Fri Dec 30 2016 Orion Poplawski - 1.8.18-3 -- Install MPI Fortran module into proper location (bug #1409229) -- Use %%license - -* Thu Dec 8 2016 Dan Horák - 1.8.18-2 -- Enable openmpi for s390(x) on F>=26 - -* Mon Dec 5 2016 Orion Poplawski - 1.8.18-1 -- Update to 1.8.18 -- Add patch to fix build with -Werror=implicit-function-declaration - -* Fri Oct 21 2016 Orion Poplawski - 1.8.17-2 -- Rebuild for openmpi 2.0 - -* Wed Jun 29 2016 Orion Poplawski - 1.8.17-1 -- Update to 1.8.17 - -* Sun Mar 20 2016 Orion Poplawski - 1.8.16-4 -- Add patch to properly call MPI_Finalize() in t_pflush1 - -* Wed Mar 2 2016 Orion Poplawski - 1.8.16-3 -- Make hdf5-mpich-devel require mpich-devel (bug #1314091) - -* Wed Feb 03 2016 Fedora Release Engineering - 1.8.16-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild - -* Fri Nov 20 2015 Orion Poplawski - 1.8.16-1 -- Update to 1.8.16 - -* Fri Nov 20 2015 Orion Poplawski - 1.8.15-9.patch1 -- Use MPI_FORTRAN_MOD_DIR to locate MPI Fortran module - -* Fri Sep 25 2015 Orion Poplawski - 1.8.15-8.patch1 -- Force shared by default for compiler wrappers (bug #1266645) - -* Tue Sep 15 2015 Orion Poplawski - 1.8.15-7.patch1 -- Rebuild for openmpi 1.10.0 - -* Sat Aug 15 2015 Zbigniew Jędrzejewski-Szmek - 1.8.15-6.patch1 -- Rebuild for MPI provides - -* Sun Jul 26 2015 Sandro Mani - 1.8.15-5.patch1 -- Rebuild for RPM MPI Requires Provides Change - -* Wed Jun 17 2015 Fedora Release Engineering - 1.8.15-4.patch1 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_23_Mass_Rebuild - -* Mon Jun 8 2015 Orion Poplawski - 1.8.15-3.patch1 -- Update to 1.8.15-patch1 - -* Fri Jun 05 2015 Dan Horák - 1.8.15-2 -- drop unnecessary patch, issue seems fixed with gcc5 - -* Sat May 16 2015 Orion Poplawski - 1.8.15-1 -- Update to 1.8.15 - -* Sat May 02 2015 Kalev Lember - 1.8.14-4 -- Rebuilt for GCC 5 C++11 ABI change - -* Wed Mar 11 2015 Orion Poplawski - 1.8.14-3 -- Rebuild for mpich 3.1.4 soname change - -* Mon Feb 16 2015 Orion Poplawski - 1.8.14-2 -- Rebuild for gcc 5 fortran module - -* Tue Jan 6 2015 Orion Poplawski - 1.8.14-1 -- Update to 1.8.14 - -* Wed Sep 3 2014 Orion Poplawski - 1.8.13-7 -- No longer build with -O0, seems to be working - -* Wed Aug 27 2014 Orion Poplawski - 1.8.13-6 -- Rebuild for openmpi Fortran ABI change - -* Sat Aug 16 2014 Fedora Release Engineering - 1.8.13-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_22_Mass_Rebuild - -* Fri Jun 27 2014 Orion Poplawski - 1.8.13-4 -- Make build work if not building any mpi pacakges (bug #1113610) - -* Fri Jun 27 2014 Marcin Juszkiewicz - 1.8.13-3 -- Drop gnu-config patches replaced by %%configure macro - -* Sat Jun 07 2014 Fedora Release Engineering - 1.8.13-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_21_Mass_Rebuild - -* Thu May 15 2014 Orion Poplawski - 1.8.13-1 -- Update to 1.8.13 - -* Mon Mar 24 2014 Orion Poplawski - 1.8.12-6 -- Add patch to add ppc64le to config.guess (bug #1080122) - -* Wed Mar 19 2014 Orion Poplawski - 1.8.12-5 -- Add patch to fix long double conversions on ppc64le (bug #1078173) -- Run autoreconf for patches and to remove rpaths - -* Sat Feb 22 2014 Deji Akingunola - 1.8.12-4 -- Rebuild for mpich-3.1 - -* Fri Jan 31 2014 Orion Poplawski 1.8.12-4 -- Fix rpm macros install dir - -* Wed Jan 29 2014 Orion Poplawski 1.8.12-3 -- Fix rpm/macros.hdf5 generation (bug #1059161) - -* Wed Jan 8 2014 Orion Poplawski 1.8.12-2 -- Update debian source -- Add patch for aarch64 support (bug #925545) - -* Fri Dec 27 2013 Orion Poplawski 1.8.12-1 -- Update to 1.8.12 - -* Fri Aug 30 2013 Dan Horák - 1.8.11-6 -- disable parallel tests on s390(x) - -* Sat Aug 03 2013 Fedora Release Engineering - 1.8.11-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_20_Mass_Rebuild - -* Sat Jul 20 2013 Deji Akingunola - 1.8.11-4 -- Rename mpich2 sub-packages to mpich and rebuild for mpich-3.0 - -* Thu Jul 11 2013 Orion Poplawski 1.8.11-3 -- Rebuild for openmpi 1.7.2 - -* Fri Jun 7 2013 Orion Poplawski 1.8.11-2 -- Add man pages from debian (bug #971551) - -* Wed May 15 2013 Orion Poplawski 1.8.11-1 -- Update to 1.8.11 - -* Mon Mar 11 2013 Ralf Corsépius - 1.8.10-3 -- Remove %%config from %%{_sysconfdir}/rpm/macros.* - (https://fedorahosted.org/fpc/ticket/259). - -* Thu Feb 14 2013 Fedora Release Engineering - 1.8.10-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_19_Mass_Rebuild - -* Wed Nov 14 2012 Orion Poplawski 1.8.10-1 -- Update to 1.8.10 -- Rebase LD_LIBRARY_PATH patch -- Drop ph5diff patch fixed upstream - -* Mon Nov 12 2012 Peter Robinson 1.8.9-5 -- Enable openmpi support on ARM as we now have it - -* Mon Nov 5 2012 Orion Poplawski 1.8.9-4 -- Rebuild for fixed openmpi f90 soname - -* Thu Nov 1 2012 Orion Poplawski 1.8.9-3 -- Rebuild for openmpi and mpich2 soname bumps - -* Thu Jul 19 2012 Fedora Release Engineering - 1.8.9-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_18_Mass_Rebuild - -* Tue May 15 2012 Orion Poplawski 1.8.9-1 -- Update to 1.8.9 - -* Mon Feb 20 2012 Dan Horák 1.8.8-9 -- use %%{mpi_list} also for tests - -* Wed Feb 15 2012 Peter Robinson - 1.8.8-8 -- disable openmpi for ARM as we currently don't have it - -* Fri Feb 10 2012 Orion Poplawski 1.8.8-7 -- Add patch to fix parallel mpi tests -- Add patch to fix bug in parallel h5diff - -* Sat Jan 7 2012 Orion Poplawski 1.8.8-6 -- Enable Fortran 2003 support (bug 772387) - -* Wed Dec 21 2011 Dan Horák 1.8.8-5 -- reintroduce the tstlite patch for ppc64 and s390x - -* Thu Dec 01 2011 Caolán McNamara 1.8.8-4 -- Related: rhbz#758334 hdf5 doesn't build on ppc64 - -* Fri Nov 25 2011 Orion Poplawski 1.8.8-3 -- Enable static MPI builds - -* Wed Nov 16 2011 Orion Poplawski 1.8.8-2 -- Add rpm macro %%{_hdf5_version} for convenience - -* Tue Nov 15 2011 Orion Poplawski 1.8.8-1 -- Update to 1.8.8 -- Drop tstlite patch -- Add patch to avoid setting LD_LIBRARY_PATH - -* Wed Jun 01 2011 Karsten Hopp 1.8.7-2 -- drop ppc64 longdouble patch, not required anymore - -* Tue May 17 2011 Orion Poplawski 1.8.7-1 -- Update to 1.8.7 - -* Tue Mar 29 2011 Deji Akingunola - 1.8.6-2 -- Rebuild for mpich2 soname bump - -* Fri Feb 18 2011 Orion Poplawski 1.8.6-1 -- Update to 1.8.6-1 -- Update tstlite patch - not fixed yet - -* Wed Feb 09 2011 Fedora Release Engineering - 1.8.5.patch1-8 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_15_Mass_Rebuild - -* Sun Feb 6 2011 Orion Poplawski 1.8.5.patch1-7 -- Add Requires: zlib-devel to hdf5-devel - -* Sun Dec 12 2010 Dan Horák 1.8.5.patch1-6 -- fully conditionalize MPI support - -* Wed Dec 8 2010 Orion Poplawski 1.8.5.patch1-5 -- Add EL6 compatibility - no mpich2 on ppc64 - -* Wed Oct 27 2010 Orion Poplawski 1.8.5.patch1-4 -- Really fixup all permissions - -* Wed Oct 27 2010 Orion Poplawski 1.8.5.patch1-3 -- Add docs to the mpi packages -- Fixup example source file permissions - -* Tue Oct 26 2010 Orion Poplawski 1.8.5.patch1-2 -- Build parallel hdf5 packages for mpich2 and openmpi -- Rework multiarch support and drop multiarch patch - -* Tue Sep 7 2010 Orion Poplawski 1.8.5.patch1-1 -- Update to 1.8.5-patch1 - -* Wed Jun 23 2010 Orion Poplawski 1.8.5-4 -- Re-add rebased tstlite patch - not fixed yet - -* Wed Jun 23 2010 Orion Poplawski 1.8.5-3 -- Update longdouble patch for 1.8.5 - -* Wed Jun 23 2010 Orion Poplawski 1.8.5-2 -- Re-add longdouble patch on ppc64 for EPEL builds - -* Mon Jun 21 2010 Orion Poplawski 1.8.5-1 -- Update to 1.8.5 -- Drop patches fixed upstream - -* Mon Mar 1 2010 Orion Poplawski 1.8.4.patch1-1 -- Update to 1.8.4-patch1 - -* Wed Jan 6 2010 Orion Poplawski 1.8.4-1 -- Update to 1.8.4 -- Must compile with -O0 due to gcc-4.4 incompatability -- No longer need -fno-strict-aliasing - -* Thu Oct 1 2009 Orion Poplawski 1.8.3-3.snap12 -- Update to 1.8.3-snap12 -- Update signal patch -- Drop detect and filter-as-option patch fixed upstream -- Drop ppc only patch -- Add patch to skip tstlite test for now, problem reported upstream -- Fixup some source file permissions - -* Fri Jul 24 2009 Fedora Release Engineering - 1.8.3-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild - -* Tue Jun 2 2009 Orion Poplawski 1.8.3-1 -- Update to 1.8.3 -- Update signal and detect patches -- Drop open patch fixed upstream - -* Sat Apr 18 2009 Karsten Hopp 1.8.2-1.1 -- fix s390x builds, s390x is 64bit, s390 is 32bit - -* Mon Feb 23 2009 Orion Poplawski 1.8.2-1 -- Update to 1.8.2 -- Add patch to compile H5detect without optimization - make detection - of datatype characteristics more robust - esp. long double -- Update signal patch -- Drop destdir patch fixed upstream -- Drop scaleoffset patch -- Re-add -fno-strict-aliasing -- Keep settings file needed for -showconfig (bug #481032) -- Wrapper script needs to pass arguments (bug #481032) - -* Wed Oct 8 2008 Orion Poplawski 1.8.1-3 -- Add sparc64 to 64-bit conditionals - -* Fri Sep 26 2008 Orion Poplawski 1.8.1-2 -- Add patch to filter -little as option used on sh arch (#464052) - -* Thu Jun 5 2008 Orion Poplawski 1.8.1-1 -- Update to 1.8.1 - -* Tue May 27 2008 Orion Poplawski 1.8.1-0.rc1.1 -- Update to 1.8.1-rc1 - -* Tue May 13 2008 Orion Poplawski 1.8.0.snap5-2 -- Use new %%{_fmoddir} macro -- Re-enable ppc64, disable failing tests. Failing tests are for - experimental long double support. - -* Mon May 5 2008 Orion Poplawski 1.8.0.snap5-1 -- Update to 1.8.0-snap5 -- Remove --enable-threadsafe, incompatible with --enable-cxx and - --enable-fortran -- ExcludeArch ppc64 until we can get it to build (bug #445423) - -* Tue Mar 4 2008 Orion Poplawski 1.8.0-2 -- Remove failing test for now - -* Fri Feb 29 2008 Orion Poplawski 1.8.0-1 -- Update to 1.8.0, drop upstreamed patches -- Update signal patch -- Move static libraries into -static sub-package -- Make -devel multiarch (bug #341501) - -* Wed Feb 6 2008 Orion Poplawski 1.6.6-7 -- Add patch to fix strict-aliasing -- Disable production mode to enable debuginfo - -* Tue Feb 5 2008 Orion Poplawski 1.6.6-6 -- Add patch to fix calling free() in H5PropList.cpp - -* Tue Feb 5 2008 Orion Poplawski 1.6.6-5 -- Add patch to support s390 (bug #431510) - -* Mon Jan 7 2008 Orion Poplawski 1.6.6-4 -- Add patches to support sparc (bug #427651) - -* Tue Dec 4 2007 Orion Poplawski 1.6.6-3 -- Rebuild against new openssl - -* Fri Nov 23 2007 Orion Poplawski 1.6.6-2 -- Add patch to build on alpha (bug #396391) - -* Wed Oct 17 2007 Orion Poplawski 1.6.6-1 -- Update to 1.6.6, drop upstreamed patches -- Explicitly set compilers - -* Fri Aug 24 2007 Orion Poplawski 1.6.5-9 -- Update license tag to BSD -- Rebuild for BuildID - -* Wed Aug 8 2007 Orion Poplawski 1.6.5-8 -- Fix memset typo -- Pass mode to open with O_CREAT - -* Mon Feb 12 2007 Orion Poplawski 1.6.5-7 -- New project URL -- Add patch to use POSIX sort key option -- Remove useless and multilib conflicting Makefiles from html docs - (bug #228365) -- Make hdf5-devel own %%{_docdir}/%%{name} - -* Tue Aug 29 2006 Orion Poplawski 1.6.5-6 -- Rebuild for FC6 - -* Wed Mar 15 2006 Orion Poplawski 1.6.5-5 -- Change rpath patch to not need autoconf -- Add patch for libtool on x86_64 -- Fix shared lib permissions - -* Mon Mar 13 2006 Orion Poplawski 1.6.5-4 -- Add patch to avoid HDF setting the compiler flags - -* Mon Feb 13 2006 Orion Poplawski 1.6.5-3 -- Rebuild for gcc/glibc changes - -* Wed Dec 21 2005 Orion Poplawski 1.6.5-2 -- Don't ship h5perf with missing library - -* Wed Dec 21 2005 Orion Poplawski 1.6.5-1 -- Update to 1.6.5 - -* Wed Dec 21 2005 Orion Poplawski 1.6.4-9 -- Rebuild - -* Wed Nov 30 2005 Orion Poplawski 1.6.4-8 -- Package fortran files properly -- Move compiler wrappers to devel - -* Fri Nov 18 2005 Orion Poplawski 1.6.4-7 -- Add patch for fortran compilation on ppc - -* Wed Nov 16 2005 Orion Poplawski 1.6.4-6 -- Bump for new openssl - -* Tue Sep 20 2005 Orion Poplawski 1.6.4-5 -- Enable fortran since the gcc bug is now fixed - -* Tue Jul 05 2005 Orion Poplawski 1.6.4-4 -- Make example scripts executable - -* Wed Jun 29 2005 Orion Poplawski 1.6.4-3 -- Add --enable-threads --with-pthreads to configure -- Add %%check -- Add some %%docs -- Use %%makeinstall -- Add patch to fix test for h5repack -- Add patch to fix h5diff_attr.c - -* Mon Jun 27 2005 Tom "spot" Callaway 1.6.4-2 -- remove szip from spec, since szip license doesn't meet Fedora standards - -* Sun Apr 3 2005 Tom "spot" Callaway 1.6.4-1 -- inital package for Fedora Extras +%autochangelog From 26ff8278184e9b69d7c508dc87927330e20dd6c3 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Fri, 7 Feb 2025 20:11:17 -0700 Subject: [PATCH 48/55] Use --with-fmoddir to set Fortran module dir (rhbz#2183289) --- hdf5.spec | 20 ++++++++------------ 1 file changed, 8 insertions(+), 12 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 1413bc6..a1cc6f7 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -239,7 +239,8 @@ ln -s ../configure . %if %{with java} --enable-java \ %endif - --with-default-plugindir=%{_libdir}/hdf5/plugin + --with-default-plugindir=%{_libdir}/hdf5/plugin \ + --with-fmoddir=%{_fmoddir} sed -i -e 's| -shared | -Wl,--as-needed\0|g' libtool sed -r -i 's|^prefix=/usr|prefix=%{buildroot}/usr|' java/test/junit.sh %make_build LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed" @@ -265,7 +266,8 @@ do --includedir=%{_includedir}/$mpi-%{_arch} \ --datarootdir=%{_libdir}/$mpi/share \ --mandir=%{_libdir}/$mpi/share/man \ - --with-default-plugindir=%{_libdir}/$mpi/hdf5/plugin + --with-default-plugindir=%{_libdir}/$mpi/hdf5/plugin \ + --with-fmoddir=${MPI_FORTRAN_MOD_DIR} sed -i -e 's! -shared ! -Wl,--as-needed\0!g' libtool %make_build LDFLAGS="%{__global_ldflags} -fPIC -Wl,-z,now -Wl,--as-needed" module purge @@ -274,25 +276,19 @@ done %install -%make_install -C build -rm %{buildroot}%{_libdir}/*.la # Fortran modules mkdir -p %{buildroot}%{_fmoddir} -mv %{buildroot}%{_includedir}/*.mod %{buildroot}%{_fmoddir} -# Fix fortran module include dir https://bugzilla.redhat.com/show_bug.cgi?id=1971826 -sed -i -e 's,%{_includedir},%{_fmoddir},' %{buildroot}%{_bindir}/h5fc +%make_install -C build +rm %{buildroot}%{_libdir}/*.la # Plugin directory mkdir -p %{buildroot}%{_libdir}/hdf5/plugin for mpi in %{?mpi_list} do module load mpi/$mpi-%{_arch} - %make_install -C $mpi - rm %{buildroot}/%{_libdir}/$mpi/lib/*.la # Fortran modules mkdir -p %{buildroot}${MPI_FORTRAN_MOD_DIR} - mv %{buildroot}%{_includedir}/${mpi}-%{_arch}/*.mod %{buildroot}${MPI_FORTRAN_MOD_DIR}/ - # Fix fortran module include dir https://bugzilla.redhat.com/show_bug.cgi?id=1971826 - sed -i -e "s,%{_includedir},${MPI_FORTRAN_MOD_DIR}," %{buildroot}%{_libdir}/$mpi/bin/h5pfc + %make_install -C $mpi + rm %{buildroot}/%{_libdir}/$mpi/lib/*.la # Plugin directory mkdir -p %{buildroot}%{_libdir}/$mpi/hdf5/plugin module purge From d8a87abed466c26635eef0053b39fb34ebefef7b Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Sat, 8 Feb 2025 18:59:17 -0700 Subject: [PATCH 49/55] hdf5 now only checks that the major and minor versions match, so reduce the _hdf5_version macro to just that --- hdf5.spec | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index a1cc6f7..e5026ad 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -10,8 +10,6 @@ # Patch version? #global snaprel -beta -# 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: 1.14.5 Release: %autorelease @@ -319,8 +317,8 @@ done # rpm macro for version checking mkdir -p %{buildroot}%{macrosdir} cat > %{buildroot}%{macrosdir}/macros.hdf5 < Date: Fri, 7 Feb 2025 19:23:18 -0700 Subject: [PATCH 50/55] Update to 1.14.6 --- .gitignore | 1 + hdf5.spec | 23 +++++++++++++---------- sources | 2 +- 3 files changed, 15 insertions(+), 11 deletions(-) diff --git a/.gitignore b/.gitignore index 6bcda4a..9167492 100644 --- a/.gitignore +++ b/.gitignore @@ -39,3 +39,4 @@ hdf5-1.8.5.tar.bz2 /hdf5-1_14_3.tar.gz /hdf5_1.14.4.3+repack-1~exp3.debian.tar.xz /hdf5-1.14.5.tar.gz +/hdf5-1.14.6.tar.gz diff --git a/hdf5.spec b/hdf5.spec index e5026ad..6040dc1 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -11,7 +11,7 @@ #global snaprel -beta Name: hdf5 -Version: 1.14.5 +Version: 1.14.6 Release: %autorelease Summary: A general purpose library and file format for storing scientific data License: BSD-3-Clause @@ -340,15 +340,18 @@ mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ %check -%ifarch %{ix86} ppc64le riscv64 s390x +%ifarch %{ix86} # i686: t_bigio test segfaults - https://github.com/HDFGroup/hdf5/issues/2510 -# ppc64le - t_multi_dset is flaky on ppc64le -# riscv64: test failed https://github.com/HDFGroup/hdf5/issues/4056 -# s390x t_mpi fails with mpich -make -C build check || : fail=0 %else -make -C build check +fail=1 +%endif +make -C build check || exit $fail +%ifarch %{ix86} s390x +# i686: t_bigio test segfaults - https://github.com/HDFGroup/hdf5/issues/2510 +# s390x t_mpi fails with mpich +fail=0 +%else fail=1 %endif # This will preserve generated .c files on errors if needed @@ -362,12 +365,12 @@ for mpi in %{?mpi_list} do # t_pmulti_dset hangs sometimes with mpich-aarch64 so do not test on that architecture # https://github.com/HDFGroup/hdf5/issues/3768 - if [ "$mpi-%{_arch}" != mpich-aarch64 ] - then +# if [ "$mpi-%{_arch}" != mpich-aarch64 ] +# then module load mpi/$mpi-%{_arch} make -C $mpi check || exit $fail module purge - fi +# fi done # I have no idea why those get installed. But it's easier to just diff --git a/sources b/sources index a3b2311..db707e8 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ -SHA512 (hdf5-1.14.5.tar.gz) = cf5e681e549c1e60546c7a6539a4f92f2e56468360e2ee697f92b171d168d3e6bd7746f77207c2c7676bf1ade5ccdaab6e35ca93144e3e5c14fdd20567a663ab +SHA512 (hdf5-1.14.6.tar.gz) = f3907abb530c4818cd9c0eb78b43073f3133260baa008ed52478e50e6bf9f1520365882acba21e0206e72c37c3e564d450def4edc3d2eef46275a41a2ad3f34b SHA512 (hdf5_1.14.4.3+repack-1~exp3.debian.tar.xz) = b27d83e5ed83cf526b4f5fedee3e12cc42d59790df056f3cbc78014edb329f517240940892bde38ea285af552d305be4fcc768f7fb2185061c4a9a9ac942df35 From c2d198e090a6b5b8519ef1dbca3b641c184b6648 Mon Sep 17 00:00:00 2001 From: Orion Poplawski Date: Mon, 10 Feb 2025 19:24:32 -0700 Subject: [PATCH 51/55] Provide a more relaxed version that other packages depend on --- hdf5.spec | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 6040dc1..e84d56e 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -56,6 +56,11 @@ BuildRequires: libaec-devel BuildRequires: gcc, gcc-c++ BuildRequires: git-core +# Provide a more relaxed version that other packages depend on +%global _hdf5_compat_version %(v=%{version}; echo ${v%.*}) +Provides: %{name} = %{_hdf5_compat_version} +Provides: %{name}%{?_isa} = %{_hdf5_compat_version} + %global with_mpich %{undefined flatpak} %if 0%{?fedora} >= 40 %ifarch %{ix86} @@ -116,8 +121,9 @@ HDF5 static libraries. %package mpich Summary: HDF5 mpich libraries BuildRequires: mpich-devel -Provides: %{name}-mpich2 = %{version}-%{release} -Obsoletes: %{name}-mpich2 < 1.8.11-4 +# Provide a more relaxed version that other packages depend on +Provides: %{name}-mpich = %{_hdf5_compat_version} +Provides: %{name}-mpich%{?_isa} = %{_hdf5_compat_version} %description mpich HDF5 parallel mpich libraries @@ -129,8 +135,6 @@ Requires: %{name}-mpich%{?_isa} = %{version}-%{release} Requires: libaec-devel%{?_isa} Requires: zlib-devel%{?_isa} Requires: mpich-devel%{?_isa} -Provides: %{name}-mpich2-devel = %{version}-%{release} -Obsoletes: %{name}-mpich2-devel < 1.8.11-4 %description mpich-devel HDF5 parallel mpich development files @@ -152,6 +156,9 @@ HDF5 parallel mpich static libraries Summary: HDF5 openmpi libraries BuildRequires: openmpi-devel BuildRequires: make +# Provide a more relaxed version that other packages depend on +Provides: %{name}-openmpi = %{_hdf5_compat_version} +Provides: %{name}-openmpi%{?_isa} = %{_hdf5_compat_version} %description openmpi HDF5 parallel openmpi libraries @@ -318,7 +325,7 @@ done mkdir -p %{buildroot}%{macrosdir} cat > %{buildroot}%{macrosdir}/macros.hdf5 < Date: Mon, 10 Feb 2025 19:27:44 -0700 Subject: [PATCH 52/55] t_multi_dset/t_pmulti_dset is still flaky on ppc64le t_pmulti_dset also seen to hang on ppc64le --- hdf5.spec | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index e84d56e..971b7d4 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -347,15 +347,17 @@ mv %{buildroot}%{_libdir}/libhdf5_java.so %{buildroot}%{_libdir}/%{name}/ %check -%ifarch %{ix86} +%ifarch %{ix86} ppc64le # i686: t_bigio test segfaults - https://github.com/HDFGroup/hdf5/issues/2510 +# ppc64le - t_multi_dset is flaky on ppc64le fail=0 %else fail=1 %endif make -C build check || exit $fail -%ifarch %{ix86} s390x +%ifarch %{ix86} ppc64le s390x # i686: t_bigio test segfaults - https://github.com/HDFGroup/hdf5/issues/2510 +# ppc64le - t_pmulti_dset is flaky on ppc64le # s390x t_mpi fails with mpich fail=0 %else @@ -370,14 +372,14 @@ export PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe export HDF5_ALARM_SECONDS=8000 for mpi in %{?mpi_list} do - # t_pmulti_dset hangs sometimes with mpich-aarch64 so do not test on that architecture + # t_pmulti_dset hangs sometimes with mpich-aarch64/ppc64le so do not test on those architectures # https://github.com/HDFGroup/hdf5/issues/3768 -# if [ "$mpi-%{_arch}" != mpich-aarch64 ] -# then + if [ "$mpi-%{_arch}" != mpich-aarch64 -a "$mpi-%{_arch}" != mpich-ppc64le ] + then module load mpi/$mpi-%{_arch} make -C $mpi check || exit $fail module purge -# fi + fi done # I have no idea why those get installed. But it's easier to just From cfb226b662f6f1c0d2b7ea37d41e3ded8f498edc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Zbigniew=20J=C4=99drzejewski-Szmek?= Date: Mon, 7 Jul 2025 15:15:23 +0200 Subject: [PATCH 53/55] Use %_rpmmacrodir It was added in rpm-4.13.0, a long time ago. --- hdf5.spec | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index 971b7d4..fc7dcd0 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -1,5 +1,3 @@ -%global macrosdir %(d=%{_rpmconfigdir}/macros.d; [ -d $d ] || d=%{_sysconfdir}/rpm; echo $d) - # No more Java on i686 %ifarch %{java_arches} %bcond_without java @@ -322,8 +320,8 @@ do done %endif # rpm macro for version checking -mkdir -p %{buildroot}%{macrosdir} -cat > %{buildroot}%{macrosdir}/macros.hdf5 <%{buildroot}%{_rpmmacrodir}/macros.hdf5 < Date: Mon, 7 Jul 2025 15:19:22 +0200 Subject: [PATCH 54/55] Define %_hdf5_plugin_dir for the location of (serial) plugins I'm looking into packaging of hdf5-blosc plugin and currently I'd need to hardcode the plugin path. It'd be nicer to make it available as a macro. The MPI versions use different paths. Maybe those should be exported too, e.g. as %_hdf5_plugin_${mpi}_dir? I'm leaving that out for now, it can always be added later. --- hdf5.spec | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/hdf5.spec b/hdf5.spec index fc7dcd0..823c46f 100644 --- a/hdf5.spec +++ b/hdf5.spec @@ -17,6 +17,7 @@ URL: https://www.hdfgroup.org/solutions/hdf5/ Source0: https://github.com/HDFGroup/hdf5/archive/hdf5_%{version}/hdf5-%{version}.tar.gz %global so_version 310 +%global plugin_dir %{_libdir}/hdf5/plugin Source1: h5comp # For man pages @@ -242,7 +243,7 @@ ln -s ../configure . %if %{with java} --enable-java \ %endif - --with-default-plugindir=%{_libdir}/hdf5/plugin \ + --with-default-plugindir=%{plugin_dir} \ --with-fmoddir=%{_fmoddir} sed -i -e 's| -shared | -Wl,--as-needed\0|g' libtool sed -r -i 's|^prefix=/usr|prefix=%{buildroot}/usr|' java/test/junit.sh @@ -284,7 +285,7 @@ mkdir -p %{buildroot}%{_fmoddir} %make_install -C build rm %{buildroot}%{_libdir}/*.la # Plugin directory -mkdir -p %{buildroot}%{_libdir}/hdf5/plugin +mkdir -p %{buildroot}%{plugin_dir} for mpi in %{?mpi_list} do module load mpi/$mpi-%{_arch} @@ -324,6 +325,7 @@ mkdir -p %{buildroot}%{_rpmmacrodir} cat >%{buildroot}%{_rpmmacrodir}/macros.hdf5 < Date: Thu, 24 Jul 2025 16:56:37 +0000 Subject: [PATCH 55/55] Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild