From b00eb29af8ede50cd30a516afcfc922757b23027 Mon Sep 17 00:00:00 2001
From: Deji Akingunola <dakingun@gmail.com>
Date: Wed, 24 Jul 2013 00:03:22 -0400
Subject: [PATCH 01/16] Rename mpich2 sub-packages to mpich and rebuild for
 mpich-3.0

---
 hdf5.spec | 114 +++++++++++++++++++++++++++++-------------------------
 1 file changed, 62 insertions(+), 52 deletions(-)

diff --git a/hdf5.spec b/hdf5.spec
index 4ce2023..99a4ae4 100644
--- a/hdf5.spec
+++ b/hdf5.spec
@@ -4,7 +4,7 @@
 # You need to recompile all users of HDF5 for each version change
 Name: hdf5
 Version: 1.8.10
-Release: 3%{?dist}
+Release: 4%{?dist}
 Summary: A general purpose library and file format for storing scientific data
 License: BSD
 Group: System Environment/Libraries
@@ -19,12 +19,12 @@ BuildRequires: krb5-devel, openssl-devel, zlib-devel, gcc-gfortran, time
 # Needed for mpi tests
 BuildRequires: openssh-clients
 
-%global with_mpich2 1
+%global with_mpich 1
 %global with_openmpi 1
 %if 0%{?rhel}
 %ifarch ppc64
 # No mpich2 on ppc64 in EL
-%global with_mpich2 0
+%global with_mpich 0
 %endif
 %endif
 %ifarch s390 s390x
@@ -32,8 +32,8 @@ BuildRequires: openssh-clients
 %global with_openmpi 0
 %endif
 
-%if %{with_mpich2}
-%global mpi_list mpich2
+%if %{with_mpich}
+%global mpi_list mpich
 %endif
 %if %{with_openmpi}
 %global mpi_list %{?mpi_list} openmpi
@@ -68,34 +68,40 @@ Requires: %{name}-devel = %{version}-%{release}
 HDF5 static libraries.
 
 
-%if %{with_mpich2}
-%package mpich2
-Summary: HDF5 mpich2 libraries
+%if %{with_mpich}
+%package mpich
+Summary: HDF5 mpich libraries
 Group: Development/Libraries
-Requires: mpich2
-BuildRequires: mpich2-devel
+Requires: mpich
+BuildRequires: mpich-devel
+Provides: %{name}-mpich2 = %{version}-%{release}
+Obsoletes: %{name}-mpich2 < 1.8.10-4
 
-%description mpich2
-HDF5 parallel mpich2 libraries
+%description mpich
+HDF5 parallel mpich libraries
 
 
-%package mpich2-devel
-Summary: HDF5 mpich2 development files
+%package mpich-devel
+Summary: HDF5 mpich development files
 Group: Development/Libraries
-Requires: %{name}-mpich2%{?_isa} = %{version}-%{release}
-Requires: mpich2
+Requires: %{name}-mpich%{?_isa} = %{version}-%{release}
+Requires: mpich
+Provides: %{name}-mpich2-devel = %{version}-%{release}
+Obsoletes: %{name}-mpich2-devel < 1.8.10-4
 
-%description mpich2-devel
-HDF5 parallel mpich2 development files
+%description mpich-devel
+HDF5 parallel mpich development files
 
 
-%package mpich2-static
-Summary: HDF5 mpich2 static libraries
+%package mpich-static
+Summary: HDF5 mpich static libraries
 Group: Development/Libraries
-Requires: %{name}-mpich2-devel%{?_isa} = %{version}-%{release}
+Requires: %{name}-mpich-devel%{?_isa} = %{version}-%{release}
+Provides: %{name}-mpich2-static = %{version}-%{release}
+Obsoletes: %{name}-mpich2-static < 1.8.10-4
 
-%description mpich2-static
-HDF5 parallel mpich2 static libraries
+%description mpich-static
+HDF5 parallel mpich static libraries
 %endif
 
 
@@ -302,42 +308,42 @@ done
 %defattr(-,root,root,-)
 %{_libdir}/*.a
 
-%if %{with_mpich2}
-%files mpich2
+%if %{with_mpich}
+%files mpich
 %defattr(-,root,root,-)
 %doc COPYING MANIFEST README.txt release_docs/RELEASE.txt
 %doc release_docs/HISTORY*.txt
-%{_libdir}/mpich2/bin/gif2h5
-%{_libdir}/mpich2/bin/h52gif
-%{_libdir}/mpich2/bin/h5copy
-%{_libdir}/mpich2/bin/h5debug
-%{_libdir}/mpich2/bin/h5diff
-%{_libdir}/mpich2/bin/h5dump
-%{_libdir}/mpich2/bin/h5import
-%{_libdir}/mpich2/bin/h5jam
-%{_libdir}/mpich2/bin/h5ls
-%{_libdir}/mpich2/bin/h5mkgrp
-%{_libdir}/mpich2/bin/h5redeploy
-%{_libdir}/mpich2/bin/h5repack
-%{_libdir}/mpich2/bin/h5perf
-%{_libdir}/mpich2/bin/h5perf_serial
-%{_libdir}/mpich2/bin/h5repart
-%{_libdir}/mpich2/bin/h5stat
-%{_libdir}/mpich2/bin/h5unjam
-%{_libdir}/mpich2/bin/ph5diff
-%{_libdir}/mpich2/lib/*.so.*
+%{_libdir}/mpich/bin/gif2h5
+%{_libdir}/mpich/bin/h52gif
+%{_libdir}/mpich/bin/h5copy
+%{_libdir}/mpich/bin/h5debug
+%{_libdir}/mpich/bin/h5diff
+%{_libdir}/mpich/bin/h5dump
+%{_libdir}/mpich/bin/h5import
+%{_libdir}/mpich/bin/h5jam
+%{_libdir}/mpich/bin/h5ls
+%{_libdir}/mpich/bin/h5mkgrp
+%{_libdir}/mpich/bin/h5redeploy
+%{_libdir}/mpich/bin/h5repack
+%{_libdir}/mpich/bin/h5perf
+%{_libdir}/mpich/bin/h5perf_serial
+%{_libdir}/mpich/bin/h5repart
+%{_libdir}/mpich/bin/h5stat
+%{_libdir}/mpich/bin/h5unjam
+%{_libdir}/mpich/bin/ph5diff
+%{_libdir}/mpich/lib/*.so.*
 
-%files mpich2-devel
+%files mpich-devel
 %defattr(-,root,root,-)
-%{_includedir}/mpich2-%{_arch}
-%{_libdir}/mpich2/bin/h5pcc
-%{_libdir}/mpich2/bin/h5pfc
-%{_libdir}/mpich2/lib/lib*.so
-%{_libdir}/mpich2/lib/lib*.settings
+%{_includedir}/mpich-%{_arch}
+%{_libdir}/mpich/bin/h5pcc
+%{_libdir}/mpich/bin/h5pfc
+%{_libdir}/mpich/lib/lib*.so
+%{_libdir}/mpich/lib/lib*.settings
 
-%files mpich2-static
+%files mpich-static
 %defattr(-,root,root,-)
-%{_libdir}/mpich2/lib/*.a
+%{_libdir}/mpich/lib/*.a
 %endif
 
 %if %{with_openmpi}
@@ -380,6 +386,10 @@ done
 
 
 %changelog
+* Wed Jul 24 2013 Deji Akingunola <dakingun@gmail.com> - 1.8.10-4
+- Rename mpich2 sub-packages to mpich and rebuild for mpich-3.0
+
+
 * Mon Mar 11 2013 Ralf Corsépius <corsepiu@fedoraproject.org> - 1.8.10-3
 - Remove %%config from %%{_sysconfdir}/rpm/macros.*
   (https://fedorahosted.org/fpc/ticket/259).

From 62bdcc0c86db1fcfe2d85dcddbf6ae7a24441ffb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Dan=20Hor=C3=A1k?= <dan@danny.cz>
Date: Fri, 30 Aug 2013 16:14:28 +0200
Subject: [PATCH 02/16] - disable parallel tests on s390(x)

---
 hdf5.spec | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/hdf5.spec b/hdf5.spec
index 99a4ae4..c3251af 100644
--- a/hdf5.spec
+++ b/hdf5.spec
@@ -4,7 +4,7 @@
 # You need to recompile all users of HDF5 for each version change
 Name: hdf5
 Version: 1.8.10
-Release: 4%{?dist}
+Release: 5%{?dist}
 Summary: A general purpose library and file format for storing scientific data
 License: BSD
 Group: System Environment/Libraries
@@ -256,6 +256,9 @@ EOF
 
 %check
 make -C build check
+# disable parallel tests on s390(x) - something gets wrong in DNS resolver in glibc
+# they are passed when run manually in mock
+%ifnarch s390 s390x
 export HDF5_Make_Ignore=yes
 for mpi in %{mpi_list}
 do
@@ -263,6 +266,7 @@ do
   make -C $mpi check
   module purge
 done
+%endif
 
 
 %post -p /sbin/ldconfig
@@ -386,6 +390,9 @@ done
 
 
 %changelog
+* Fri Aug 30 2013 Dan Horák <dan[at]danny.cz> - 1.8.10-5
+- disable parallel tests on s390(x)
+
 * Wed Jul 24 2013 Deji Akingunola <dakingun@gmail.com> - 1.8.10-4
 - Rename mpich2 sub-packages to mpich and rebuild for mpich-3.0
 

From 286a97d467fc8f72182c66026f5cc1f857d6167f Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@nwra.com>
Date: Tue, 4 Feb 2014 14:28:49 -0700
Subject: [PATCH 03/16] - Use parallel make - Limit number of processors to 4
 in parallel tests to avoid mpich issue with   oversubscription

---
 hdf5.spec | 13 ++++++++++---
 1 file changed, 10 insertions(+), 3 deletions(-)

diff --git a/hdf5.spec b/hdf5.spec
index 862404f..1f3d190 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: 1.8.12
-Release: 3%{?dist}
+Release: 4%{?dist}
 Summary: A general purpose library and file format for storing scientific data
 License: BSD
 Group: System Environment/Libraries
@@ -181,7 +181,7 @@ ln -s ../configure .
 %configure \
   %{configure_opts} \
   --enable-cxx
-make
+make %{?_smp_mflags}
 popd
 
 #MPI builds
@@ -203,7 +203,7 @@ do
     --includedir=%{_includedir}/$mpi-%{_arch} \
     --datarootdir=%{_libdir}/$mpi/share \
     --mandir=%{_libdir}/$mpi/share/man
-  make
+  make %{?_smp_mflags}
   module purge
   popd
 done
@@ -261,6 +261,8 @@ cp -p debian/man/*.1 ${RPM_BUILD_ROOT}%{_mandir}/man1/
 
 %check
 make -C build check
+# Limit to 4 processors to try to avoid oversubscribing
+export NPROCS=4
 # disable parallel tests on s390(x) - something gets wrong in DNS resolver in glibc
 # they are passed when run manually in mock
 %ifnarch s390 s390x
@@ -404,6 +406,11 @@ done
 
 
 %changelog
+* Tue Feb 4 2014 Orion Poplawski <orion@cora.nwra.com> 1.8.12-5
+- Use parallel make
+- Limit number of processors to 4 in parallel tests to avoid mpich issue with
+  oversubscription
+
 * Fri Jan 31 2014 Orion Poplawski <orion@cora.nwra.com> 1.8.12-4
 - Fix rpm macros install dir
 

From c96d985588b68f6e7628a0672ff48cb22181d4eb Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@nwra.com>
Date: Wed, 5 Feb 2014 11:11:24 -0700
Subject: [PATCH 04/16] Enable mpich on RHEL7

---
 hdf5.spec | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/hdf5.spec b/hdf5.spec
index 1f3d190..1efba98 100644
--- a/hdf5.spec
+++ b/hdf5.spec
@@ -28,9 +28,9 @@ BuildRequires: openssh-clients
 
 %global with_mpich 1
 %global with_openmpi 1
-%if 0%{?rhel}
+%if 0%{?rhel} <= 6
 %ifarch ppc64
-# No mpich2 on ppc64 in EL
+% No mpich2 on ppc64 in EL6
 %global with_mpich 0
 %endif
 %endif

From 149f02baf0b8ff02d7ba790e1ef8f2c45a631080 Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@cora.nwra.com>
Date: Thu, 6 Feb 2014 18:15:30 -0700
Subject: [PATCH 05/16] Work around a bug in mpich when hostname is not
 resovable

---
 hdf5.spec | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/hdf5.spec b/hdf5.spec
index 1efba98..422f983 100644
--- a/hdf5.spec
+++ b/hdf5.spec
@@ -188,6 +188,8 @@ popd
 export CC=mpicc
 export CXX=mpicxx
 export F9X=mpif90
+# Work around a bug in mpich when hostname is not resovable
+export RUNPARALLEL="mpiexec -np 4 -host localhost"
 for mpi in %{mpi_list}
 do
   mkdir $mpi

From 0d21f90329cbee5e1095d2c5c78aaaee8e1e0331 Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@cora.nwra.com>
Date: Wed, 4 Mar 2015 13:25:47 -0700
Subject: [PATCH 06/16] Change LD_LIBRARY_PATH patch to change
 configure.ac/Makefile.am since we are running autoreconf now

---
 hdf5-LD_LIBRARY_PATH.patch | 41 ++++++++++++++++++++++++--------------
 1 file changed, 26 insertions(+), 15 deletions(-)

diff --git a/hdf5-LD_LIBRARY_PATH.patch b/hdf5-LD_LIBRARY_PATH.patch
index f34ea69..e4025c1 100644
--- a/hdf5-LD_LIBRARY_PATH.patch
+++ b/hdf5-LD_LIBRARY_PATH.patch
@@ -1,20 +1,28 @@
-diff -up hdf5-1.8.10/configure.LD_LIBRARY_PATH hdf5-1.8.10/configure
---- hdf5-1.8.10/configure.LD_LIBRARY_PATH	2012-10-26 18:14:59.000000000 -0600
-+++ hdf5-1.8.10/configure	2012-11-14 08:56:52.695024834 -0700
-@@ -27496,9 +27496,6 @@ if ${hdf5_cv_printf_ll+:} false; then :
-   $as_echo_n "(cached) " >&6
- else
- 
+--- hdf5-1.8.12/configure.ac.LD_LIBRARY_PATH	2015-03-04 13:20:53.164831682 -0700
++++ hdf5-1.8.12/configure.ac	2015-03-04 13:23:17.852904172 -0700
+@@ -2342,14 +2342,9 @@
+ ## Try to figure out how to print `long long'.  Some machines use `%lld'
+ ## and others use `%qd'.  There may be more!  The final `l' is a
+ ## default in case none of the others work.
+-## Need to patch up LD_LIBRARY_PATH so that the execution can find all
+-## the dynamic library.  The correct way to do it should be updating
+-## LD_LIBRARY_PATH along with LDFLAGS or do it with the AC_TRY_RUN macro.
+ ##
+ AC_MSG_CHECKING([how to print long long])
+ AC_CACHE_VAL([hdf5_cv_printf_ll], [
 -LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo $AM_LDFLAGS $LDFLAGS | sed -e 's/-L/:/g' -e 's/ //g'`"
 -export LD_LIBRARY_PATH
--
+ 
  for hdf5_cv_printf_ll in l ll L q unknown; do
-    if test "$cross_compiling" = yes; then :
-   continue
-diff -up hdf5-1.8.10/src/Makefile.in.LD_LIBRARY_PATH hdf5-1.8.10/src/Makefile.in
---- hdf5-1.8.10/src/Makefile.in.LD_LIBRARY_PATH	2012-10-26 18:14:55.000000000 -0600
-+++ hdf5-1.8.10/src/Makefile.in	2012-11-14 08:55:35.197476914 -0700
-@@ -1327,8 +1327,6 @@ help:
+    AC_TRY_RUN([
+--- hdf5-1.8.12/src/Makefile.am.LD_LIBRARY_PATH	2013-11-21 08:13:52.000000000 -0700
++++ hdf5-1.8.12/src/Makefile.am	2015-03-04 13:22:19.355266916 -0700
+@@ -122,25 +122,17 @@
+ settings_DATA=libhdf5.settings
+ 
+ # Number format detection
+-# The LD_LIBRARY_PATH setting is a kludge.
+-# Things should have been all set during H5detect making.
  # Remove the generated .c file if errors occur unless HDF5_Make_Ignore
  # is set to ignore the error.
  H5Tinit.c: H5detect$(EXEEXT)
@@ -23,7 +31,10 @@ diff -up hdf5-1.8.10/src/Makefile.in.LD_LIBRARY_PATH hdf5-1.8.10/src/Makefile.in
  	$(RUNSERIAL) ./H5detect$(EXEEXT) > $@  ||                               \
  	    (test $$HDF5_Make_Ignore && echo "*** Error ignored") ||          \
  	    ($(RM) $@ ; exit 1)
-@@ -1339,8 +1337,6 @@ H5Tinit.c: H5detect$(EXEEXT)
+ 
+ # Build configuration header file generation
+-# The LD_LIBRARY_PATH setting is a kludge.
+-# Things should have been all set during H5make_libsettings making.
  # 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

From ba659edf4a537d394bc753ce33babc537ee75e13 Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@cora.nwra.com>
Date: Wed, 9 Dec 2015 21:45:25 -0700
Subject: [PATCH 07/16] Rebuild with openmpi 1.10.0

---
 hdf5.spec | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/hdf5.spec b/hdf5.spec
index 236ceb2..241cd1c 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: 1.8.12
-Release: 6%{?dist}
+Release: 7%{?dist}
 Summary: A general purpose library and file format for storing scientific data
 License: BSD
 Group: System Environment/Libraries
@@ -419,6 +419,9 @@ done
 
 
 %changelog
+* Wed Dec 9 2015 Orion Poplawski <orion@cora.nwra.com> - 1.8.12-7
+- Rebuild with openmpi 1.10.0
+
 * Wed Mar 4 2015 Orion Poplawski <orion@cora.nwra.com> - 1.8.12-6
 - Add patch to add ppc64le to config.guess (bug #1080122)
 - Add patch to fix long double conversions on ppc64le (bug #1078173)

From 8e69ef8615774ff2abb26eb4c0d693d0353287f9 Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@cora.nwra.com>
Date: Wed, 9 Dec 2015 21:46:17 -0700
Subject: [PATCH 08/16] Add bug #

---
 hdf5.spec | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/hdf5.spec b/hdf5.spec
index 241cd1c..3a2fc2b 100644
--- a/hdf5.spec
+++ b/hdf5.spec
@@ -420,7 +420,7 @@ done
 
 %changelog
 * Wed Dec 9 2015 Orion Poplawski <orion@cora.nwra.com> - 1.8.12-7
-- Rebuild with openmpi 1.10.0
+- Rebuild with openmpi 1.10.0 (bug #1290286)
 
 * Wed Mar 4 2015 Orion Poplawski <orion@cora.nwra.com> - 1.8.12-6
 - Add patch to add ppc64le to config.guess (bug #1080122)

From 92a96b1f666d72abb0127d07bc14c07f2763687f Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@cora.nwra.com>
Date: Thu, 15 Dec 2016 11:04:44 -0700
Subject: [PATCH 09/16] Add upstream patch to fix various Talos CVEs (bug
 #1397715)

Conflicts:
	hdf5.spec
---
 hdf5.spec             |   8 +-
 hdf51.8-CVE2016.patch | 280 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 287 insertions(+), 1 deletion(-)
 create mode 100644 hdf51.8-CVE2016.patch

diff --git a/hdf5.spec b/hdf5.spec
index 3a2fc2b..bc04847 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: 1.8.12
-Release: 7%{?dist}
+Release: 8%{?dist}
 Summary: A general purpose library and file format for storing scientific data
 License: BSD
 Group: System Environment/Libraries
@@ -26,6 +26,8 @@ Patch2: hdf5-aarch64.patch
 Patch3: hdf5-ldouble-ppc64le.patch
 # https://bugzilla.redhat.com/show_bug.cgi?id=1080122
 Patch4: hdf5-ppc64le.patch
+# Upstream patch for various Talos CVEs
+Patch5: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/talospatch/hdf51.8-CVE2016.patch
 
 BuildRequires: krb5-devel, openssl-devel, zlib-devel, gcc-gfortran, time
 # For patches/rpath
@@ -161,6 +163,7 @@ HDF5 parallel openmpi static libraries
 %patch2 -p1 -b .aarch64
 %patch3 -p1 -b .ldouble-ppc64le
 %patch4 -p1 -b .ppc64le
+%patch5 -p0 -b .CVE
 #This should be fixed in 1.8.7
 find \( -name '*.[ch]*' -o -name '*.f90' -o -name '*.txt' \) -exec chmod -x {} +
 autoreconf -f -i
@@ -419,6 +422,9 @@ done
 
 
 %changelog
+* Thu Dec 15 2016 Orion Poplawski <orion@cora.nwra.com> - 1.8.12-8
+- Add upstream patch to fix various Talos CVEs (bug #1397716)
+
 * Wed Dec 9 2015 Orion Poplawski <orion@cora.nwra.com> - 1.8.12-7
 - Rebuild with openmpi 1.10.0 (bug #1290286)
 
diff --git a/hdf51.8-CVE2016.patch b/hdf51.8-CVE2016.patch
new file mode 100644
index 0000000..da34e62
--- /dev/null
+++ b/hdf51.8-CVE2016.patch
@@ -0,0 +1,280 @@
+diff --git src/H5Ocache.c src/H5Ocache.c
+index 9057223..2aaf933 100644
+--- src/H5Ocache.c
++++ src/H5Ocache.c
+@@ -1134,6 +1134,10 @@ H5O_chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image,
+             HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "bad flag combination for message")
+         if((flags & H5O_MSG_FLAG_WAS_UNKNOWN) && !(flags & H5O_MSG_FLAG_MARK_IF_UNKNOWN))
+             HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "bad flag combination for message")
++        if((flags & H5O_MSG_FLAG_SHAREABLE)
++                && H5O_msg_class_g[id]
++                && !(H5O_msg_class_g[id]->share_flags & H5O_SHARE_IS_SHARABLE))
++            HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, FAIL, "message of unsharable class flagged as sharable")
+ 
+         /* Reserved bytes/creation index */
+         if(oh->version == H5O_VERSION_1)
+diff --git src/H5Odtype.c src/H5Odtype.c
+index 622a18e..67f2fca 100644
+--- src/H5Odtype.c
++++ src/H5Odtype.c
+@@ -310,7 +310,11 @@ H5O_dtype_decode_helper(H5F_t *f, unsigned *ioflags/*in,out*/, const uint8_t **p
+                     if(version == H5O_DTYPE_VERSION_1) {
+                         /* Decode the number of dimensions */
+                         ndims = *(*pp)++;
+-                        HDassert(ndims <= 4);
++
++                        /* Check that ndims is valid */
++                        if(ndims > 4)
++                            HGOTO_ERROR(H5E_DATATYPE, H5E_BADTYPE, FAIL, "invalid number of dimensions for array")
++
+                         *pp += 3;		/*reserved bytes */
+ 
+                         /* Skip dimension permutation */
+@@ -518,7 +522,8 @@ H5O_dtype_decode_helper(H5F_t *f, unsigned *ioflags/*in,out*/, const uint8_t **p
+             dt->shared->u.array.ndims = *(*pp)++;
+ 
+             /* Double-check the number of dimensions */
+-            HDassert(dt->shared->u.array.ndims <= H5S_MAX_RANK);
++            if(dt->shared->u.array.ndims > H5S_MAX_RANK)
++                HGOTO_ERROR(H5E_DATATYPE, H5E_CANTLOAD, FAIL, "too many dimensions for array datatype")
+ 
+             /* Skip reserved bytes, if version has them */
+             if(version < H5O_DTYPE_VERSION_3)
+diff --git src/H5Opkg.h src/H5Opkg.h
+index ff52537..2c8c5a0 100644
+--- src/H5Opkg.h
++++ src/H5Opkg.h
+@@ -201,6 +201,7 @@
+                                                                               \
+         /* Set the message's "shared info", if it's shareable */	      \
+         if((MSG)->flags & H5O_MSG_FLAG_SHAREABLE) {                           \
++            HDassert(msg_type->share_flags & H5O_SHARE_IS_SHARABLE);          \
+             H5O_UPDATE_SHARED((H5O_shared_t *)(MSG)->native, H5O_SHARE_TYPE_HERE, (F), msg_type->id, (MSG)->crt_idx, (OH)->chunk[0].addr) \
+         } /* end if */                                                        \
+                                                                               \
+diff --git src/H5Znbit.c src/H5Znbit.c
+index 38610b6..ddcf8fd 100644
+--- src/H5Znbit.c
++++ src/H5Znbit.c
+@@ -60,11 +60,11 @@ static void H5Z_nbit_decompress_one_nooptype(unsigned char *data, size_t data_of
+                        unsigned char *buffer, size_t *j, int *buf_len, unsigned size);
+ static void H5Z_nbit_decompress_one_atomic(unsigned char *data, size_t data_offset,
+                     unsigned char *buffer, size_t *j, int *buf_len, parms_atomic p);
+-static void H5Z_nbit_decompress_one_array(unsigned char *data, size_t data_offset,
++static herr_t H5Z__nbit_decompress_one_array(unsigned char *data, size_t data_offset,
+            unsigned char *buffer, size_t *j, int *buf_len, const unsigned parms[]);
+-static void H5Z_nbit_decompress_one_compound(unsigned char *data, size_t data_offset,
++static herr_t H5Z__nbit_decompress_one_compound(unsigned char *data, size_t data_offset,
+               unsigned char *buffer, size_t *j, int *buf_len, const unsigned parms[]);
+-static void H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer,
++static herr_t H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer,
+                                 const unsigned parms[]);
+ static void H5Z_nbit_compress_one_nooptype(unsigned char *data, size_t data_offset,
+                      unsigned char *buffer, size_t *j, int *buf_len, unsigned size);
+@@ -897,7 +897,8 @@ H5Z_filter_nbit(unsigned flags, size_t cd_nelmts, const unsigned cd_values[],
+             HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "memory allocation failed for nbit decompression")
+ 
+         /* decompress the buffer */
+-        H5Z_nbit_decompress(outbuf, d_nelmts, (unsigned char *)*buf, cd_values);
++        if(H5Z__nbit_decompress(outbuf, d_nelmts, (unsigned char *)*buf, cd_values) < 0)
++            HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, 0, "can't decompress buffer")
+     } /* end if */
+     /* output; compress */
+     else {
+@@ -1046,12 +1047,15 @@ H5Z_nbit_decompress_one_atomic(unsigned char *data, size_t data_offset,
+    }
+ }
+ 
+-static void
+-H5Z_nbit_decompress_one_array(unsigned char *data, size_t data_offset,
++static herr_t
++H5Z__nbit_decompress_one_array(unsigned char *data, size_t data_offset,
+            unsigned char *buffer, size_t *j, int *buf_len, const unsigned parms[])
+ {
+    unsigned i, total_size, base_class, base_size, n, begin_index;
+    parms_atomic p;
++   herr_t ret_value = SUCCEED; /* Return value */
++
++   FUNC_ENTER_STATIC
+ 
+    total_size = parms[parms_index++];
+    base_class = parms[parms_index++];
+@@ -1062,7 +1066,12 @@ H5Z_nbit_decompress_one_array(unsigned char *data, size_t data_offset,
+            p.order = parms[parms_index++];
+            p.precision = parms[parms_index++];
+            p.offset = parms[parms_index++];
+-           n = total_size/p.size;
++
++           /* Check values of precision and offset */
++           if(p.precision > p.size * 8 || (p.precision + p.offset) > p.size * 8)
++              HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "invalid datatype precision/offset")
++
++           n = total_size / p.size;
+            for(i = 0; i < n; i++)
+               H5Z_nbit_decompress_one_atomic(data, data_offset + i*p.size,
+                                              buffer, j, buf_len, p);
+@@ -1072,8 +1081,9 @@ H5Z_nbit_decompress_one_array(unsigned char *data, size_t data_offset,
+            n = total_size/base_size; /* number of base_type elements inside the array datatype */
+            begin_index = parms_index;
+            for(i = 0; i < n; i++) {
+-              H5Z_nbit_decompress_one_array(data, data_offset + i*base_size,
+-                                            buffer, j, buf_len, parms);
++              if(H5Z__nbit_decompress_one_array(data, data_offset + i * base_size,
++                                            buffer, j, buf_len, parms) < 0)
++                 HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress array")
+               parms_index = begin_index;
+            }
+            break;
+@@ -1082,8 +1092,9 @@ H5Z_nbit_decompress_one_array(unsigned char *data, size_t data_offset,
+            n = total_size/base_size; /* number of base_type elements inside the array datatype */
+            begin_index = parms_index;
+            for(i = 0; i < n; i++) {
+-              H5Z_nbit_decompress_one_compound(data, data_offset + i*base_size,
+-                                               buffer, j, buf_len, parms);
++              if(H5Z__nbit_decompress_one_compound(data, data_offset + i * base_size,
++                                               buffer, j, buf_len, parms) < 0)
++                 HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress compound")
+               parms_index = begin_index;
+            }
+            break;
+@@ -1094,51 +1105,76 @@ H5Z_nbit_decompress_one_array(unsigned char *data, size_t data_offset,
+       default:
+           HDassert(0 && "This Should never be executed!");
+    } /* end switch */
++
++done:
++    FUNC_LEAVE_NOAPI(ret_value)
+ }
+ 
+-static void
+-H5Z_nbit_decompress_one_compound(unsigned char *data, size_t data_offset,
++static herr_t
++H5Z__nbit_decompress_one_compound(unsigned char *data, size_t data_offset,
+               unsigned char *buffer, size_t *j, int *buf_len, const unsigned parms[])
+ {
+-   unsigned i, nmembers, member_offset, member_class, size;
++   unsigned i, nmembers, member_offset, member_class, member_size, used_size = 0, size;
+    parms_atomic p;
++   herr_t ret_value = SUCCEED; /* Return value */
+ 
+-   parms_index++; /* skip total size of compound datatype */
++   FUNC_ENTER_STATIC
++
++   size = parms[parms_index++];
+    nmembers = parms[parms_index++];
+ 
+    for(i = 0; i < nmembers; i++) {
+       member_offset = parms[parms_index++];
+       member_class = parms[parms_index++];
++
++      /* Check for overflow */
++      member_size = parms[parms_index];
++      used_size += member_size;
++      if(used_size > size)
++         HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "compound member offset overflowed compound size")
+       switch(member_class) {
+          case H5Z_NBIT_ATOMIC:
+-              p.size = parms[parms_index++];
++              p.size = member_size;
++              /* Advance past member size */
++              parms_index++;
+               p.order = parms[parms_index++];
+               p.precision = parms[parms_index++];
+               p.offset = parms[parms_index++];
++
++              /* Check values of precision and offset */
++              if(p.precision > p.size * 8 || (p.precision + p.offset) > p.size * 8)
++                 HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "invalid datatype precision/offset")
++
+               H5Z_nbit_decompress_one_atomic(data, data_offset + member_offset,
+                                              buffer, j, buf_len, p);
+               break;
+          case H5Z_NBIT_ARRAY:
+-              H5Z_nbit_decompress_one_array(data, data_offset + member_offset,
+-                                            buffer, j, buf_len, parms);
++              if(H5Z__nbit_decompress_one_array(data, data_offset + member_offset,
++                                            buffer, j, buf_len, parms) < 0)
++                 HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress array")
+               break;
+          case H5Z_NBIT_COMPOUND:
+-              H5Z_nbit_decompress_one_compound(data, data_offset+member_offset,
+-                                               buffer, j, buf_len, parms);
++              if(H5Z__nbit_decompress_one_compound(data, data_offset+member_offset,
++                                            buffer, j, buf_len, parms) < 0)
++                 HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress compound")
+               break;
+          case H5Z_NBIT_NOOPTYPE:
+-              size = parms[parms_index++];
++              /* Advance past member size */
++              parms_index++;
+               H5Z_nbit_decompress_one_nooptype(data, data_offset+member_offset,
+-                                               buffer, j, buf_len, size);
++                                               buffer, j, buf_len, member_size);
+               break;
+           default:
+               HDassert(0 && "This Should never be executed!");
+       } /* end switch */
+    }
++
++done:
++    FUNC_LEAVE_NOAPI(ret_value)
+ }
+ 
+-static void
+-H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer,
++static herr_t
++H5Z__nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffer,
+                                 const unsigned parms[])
+ {
+    /* i: index of data, j: index of buffer,
+@@ -1146,6 +1182,9 @@ H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffe
+    size_t i, j, size;
+    int buf_len;
+    parms_atomic p;
++   herr_t ret_value = SUCCEED; /* Return value */
++
++   FUNC_ENTER_STATIC
+ 
+    /* may not have to initialize to zeros */
+    for(i = 0; i < d_nelmts*parms[4]; i++) data[i] = 0;
+@@ -1161,6 +1200,11 @@ H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffe
+            p.order = parms[5];
+            p.precision = parms[6];
+            p.offset = parms[7];
++
++           /* Check values of precision and offset */
++           if(p.precision > p.size * 8 || (p.precision + p.offset) > p.size * 8)
++              HGOTO_ERROR(H5E_PLINE, H5E_BADTYPE, FAIL, "invalid datatype precision/offset")
++
+            for(i = 0; i < d_nelmts; i++) {
+               H5Z_nbit_decompress_one_atomic(data, i*p.size, buffer, &j, &buf_len, p);
+            }
+@@ -1169,7 +1213,8 @@ H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffe
+            size = parms[4];
+            parms_index = 4;
+            for(i = 0; i < d_nelmts; i++) {
+-              H5Z_nbit_decompress_one_array(data, i*size, buffer, &j, &buf_len, parms);
++              if(H5Z__nbit_decompress_one_array(data, i*size, buffer, &j, &buf_len, parms) < 0)
++                 HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress array")
+               parms_index = 4;
+            }
+            break;
+@@ -1177,13 +1222,17 @@ H5Z_nbit_decompress(unsigned char *data, unsigned d_nelmts, unsigned char *buffe
+            size = parms[4];
+            parms_index = 4;
+            for(i = 0; i < d_nelmts; i++) {
+-              H5Z_nbit_decompress_one_compound(data, i*size, buffer, &j, &buf_len, parms);
++              if(H5Z__nbit_decompress_one_compound(data, i*size, buffer, &j, &buf_len, parms) < 0)
++                 HGOTO_ERROR(H5E_PLINE, H5E_CANTFILTER, FAIL, "can't decompress compound")
+               parms_index = 4;
+            }
+            break;
+       default:
+           HDassert(0 && "This Should never be executed!");
+    } /* end switch */
++
++done:
++    FUNC_LEAVE_NOAPI(ret_value)
+ }
+ 
+ static void H5Z_nbit_compress_one_byte(unsigned char *data, size_t data_offset, int k, int begin_i,

From a6dc238336b71e63902a24605593fceb412b8e5a Mon Sep 17 00:00:00 2001
From: Christoph Junghans <junghans@votca.org>
Date: Tue, 15 Aug 2017 10:54:14 -0600
Subject: [PATCH 10/16] enable szip support through libaec

---
 hdf5.spec | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/hdf5.spec b/hdf5.spec
index bc04847..4fb09db 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: 1.8.12
-Release: 8%{?dist}
+Release: 9%{?dist}
 Summary: A general purpose library and file format for storing scientific data
 License: BSD
 Group: System Environment/Libraries
@@ -35,6 +35,7 @@ BuildRequires: automake
 BuildRequires: libtool
 # Needed for mpi tests
 BuildRequires: openssh-clients
+BuildRequires: libaec-devel
 
 %global with_mpich 1
 %global with_openmpi 1
@@ -70,6 +71,7 @@ grids. You can also mix and match them in HDF5 files according to your needs.
 Summary: HDF5 development files
 Group: Development/Libraries
 Requires: %{name} = %{version}-%{release}
+Requires: libaec-devel%{?_isa}
 Requires: zlib-devel
 
 %description devel
@@ -179,6 +181,7 @@ autoreconf -f -i
   --enable-fortran2003 \\\
   --enable-hl \\\
   --enable-shared \\\
+  --with-szlib \\\
 %{nil}
 # --enable-cxx and --enable-parallel flags are incompatible
 # --with-mpe=DIR          Use MPE instrumentation [default=no]
@@ -422,6 +425,9 @@ done
 
 
 %changelog
+* Tue Aug 15 2017 Christoph Junghans <junghans@votca.org> - 1.8.12-9
+- enable szip support through libaec
+
 * Thu Dec 15 2016 Orion Poplawski <orion@cora.nwra.com> - 1.8.12-8
 - Add upstream patch to fix various Talos CVEs (bug #1397716)
 

From b2141638381d00355dba2dc186cb2f2f771e5598 Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@nwra.com>
Date: Thu, 17 Aug 2017 11:52:56 -0600
Subject: [PATCH 11/16] Fixup mpi-devel package requires

---
 hdf5.spec | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

diff --git a/hdf5.spec b/hdf5.spec
index 4fb09db..b029f03 100644
--- a/hdf5.spec
+++ b/hdf5.spec
@@ -72,7 +72,7 @@ Summary: HDF5 development files
 Group: Development/Libraries
 Requires: %{name} = %{version}-%{release}
 Requires: libaec-devel%{?_isa}
-Requires: zlib-devel
+Requires: zlib-devel%{?_isa}
 
 %description devel
 HDF5 development headers and libraries.
@@ -103,7 +103,9 @@ HDF5 parallel mpich libraries
 Summary: HDF5 mpich development files
 Group: Development/Libraries
 Requires: %{name}-mpich%{?_isa} = %{version}-%{release}
-Requires: mpich
+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
 
@@ -138,7 +140,9 @@ HDF5 parallel openmpi libraries
 Summary: HDF5 openmpi development files
 Group: Development/Libraries
 Requires: %{name}-openmpi%{_isa} = %{version}-%{release}
-Requires: openmpi-devel
+Requires: libaec-devel%{?_isa}
+Requires: zlib-devel%{?_isa}
+Requires: openmpi-devel%{?_isa}
 
 %description openmpi-devel
 HDF5 parallel openmpi development files

From 7b71654b92bd1169b6263043dcd43927efd7f830 Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@nwra.com>
Date: Tue, 22 Aug 2017 15:41:19 -0600
Subject: [PATCH 12/16] RHEL doesn't provide mpich-devel%{_isa}

---
 hdf5.spec | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/hdf5.spec b/hdf5.spec
index b029f03..cd0292b 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: 1.8.12
-Release: 9%{?dist}
+Release: 10%{?dist}
 Summary: A general purpose library and file format for storing scientific data
 License: BSD
 Group: System Environment/Libraries
@@ -105,7 +105,8 @@ Group: Development/Libraries
 Requires: %{name}-mpich%{?_isa} = %{version}-%{release}
 Requires: libaec-devel%{?_isa}
 Requires: zlib-devel%{?_isa}
-Requires: mpich-devel%{?_isa}
+# RHEL doesn't provide with %{_isa}
+Requires: mpich-devel
 Provides: %{name}-mpich2-devel = %{version}-%{release}
 Obsoletes: %{name}-mpich2-devel < 1.8.11-4
 
@@ -429,6 +430,9 @@ done
 
 
 %changelog
+* Tue Aug 22 2017 Orion Poplawski <orion@nwra.com> - 1.8.12-10
+- RHEL doesn't provide mpich-devel%%{_isa}
+
 * Tue Aug 15 2017 Christoph Junghans <junghans@votca.org> - 1.8.12-9
 - enable szip support through libaec
 

From 8f36faddbd8ebd5a872c522154ce9533bd4742df Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@nwra.com>
Date: Tue, 7 May 2019 21:02:50 -0600
Subject: [PATCH 13/16] Build an openmpi3 version on el7

---
 hdf5.spec | 76 +++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 74 insertions(+), 2 deletions(-)

diff --git a/hdf5.spec b/hdf5.spec
index cd0292b..adc23f9 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: 1.8.12
-Release: 10%{?dist}
+Release: 11%{?dist}
 Summary: A general purpose library and file format for storing scientific data
 License: BSD
 Group: System Environment/Libraries
@@ -54,9 +54,11 @@ BuildRequires: libaec-devel
 %global mpi_list mpich
 %endif
 %if %{with_openmpi}
-%global mpi_list %{?mpi_list} openmpi
+%global mpi_list %{?mpi_list} openmpi %{?el7:openmpi3}
 %endif
 
+%{?el7:%global ompi3 1}
+
 %description
 HDF5 is a general purpose library and file format for storing scientific data.
 HDF5 can store two primary objects: datasets and groups. A dataset is
@@ -156,6 +158,38 @@ Requires: %{name}-openmpi-devel%{?_isa} = %{version}-%{release}
 
 %description openmpi-static
 HDF5 parallel openmpi static libraries
+
+%if 0%{?ompi3}
+%package openmpi3
+Summary: HDF5 openmpi3 libraries
+Group: Development/Libraries
+Requires: openmpi3
+BuildRequires: openmpi3-devel
+
+%description openmpi3
+HDF5 parallel openmpi3 libraries
+
+
+%package openmpi3-devel
+Summary: HDF5 openmpi3 development files
+Group: Development/Libraries
+Requires: %{name}-openmpi3%{_isa} = %{version}-%{release}
+Requires: libaec-devel%{?_isa}
+Requires: zlib-devel%{?_isa}
+Requires: openmpi3-devel%{?_isa}
+
+%description openmpi3-devel
+HDF5 parallel openmpi3 development files
+
+
+%package openmpi3-static
+Summary: HDF5 openmpi3 static libraries
+Group: Development/Libraries
+Requires: %{name}-openmpi3-devel%{?_isa} = %{version}-%{release}
+
+%description openmpi3-static
+HDF5 parallel openmpi3 static libraries
+%endif
 %endif
 
 
@@ -426,10 +460,48 @@ done
 
 %files openmpi-static
 %{_libdir}/openmpi/lib/*.a
+
+%if 0%{?ompi3}
+%files openmpi3
+%doc COPYING MANIFEST README.txt release_docs/RELEASE.txt
+%doc release_docs/HISTORY*.txt
+%{_libdir}/openmpi3/bin/gif2h5
+%{_libdir}/openmpi3/bin/h52gif
+%{_libdir}/openmpi3/bin/h5copy
+%{_libdir}/openmpi3/bin/h5debug
+%{_libdir}/openmpi3/bin/h5diff
+%{_libdir}/openmpi3/bin/h5dump
+%{_libdir}/openmpi3/bin/h5import
+%{_libdir}/openmpi3/bin/h5jam
+%{_libdir}/openmpi3/bin/h5ls
+%{_libdir}/openmpi3/bin/h5mkgrp
+%{_libdir}/openmpi3/bin/h5perf
+%{_libdir}/openmpi3/bin/h5perf_serial
+%{_libdir}/openmpi3/bin/h5redeploy
+%{_libdir}/openmpi3/bin/h5repack
+%{_libdir}/openmpi3/bin/h5repart
+%{_libdir}/openmpi3/bin/h5stat
+%{_libdir}/openmpi3/bin/h5unjam
+%{_libdir}/openmpi3/bin/ph5diff
+%{_libdir}/openmpi3/lib/*.so.*
+
+%files openmpi3-devel
+%{_includedir}/openmpi3-%{_arch}
+%{_libdir}/openmpi3/bin/h5pcc
+%{_libdir}/openmpi3/bin/h5pfc
+%{_libdir}/openmpi3/lib/lib*.so
+%{_libdir}/openmpi3/lib/lib*.settings
+
+%files openmpi3-static
+%{_libdir}/openmpi3/lib/*.a
+%endif
 %endif
 
 
 %changelog
+* Sun Apr 28 2019 Dave Love <loveshack@fedoraproject.org> - 1.8.12-11
+- Build an openmpi3 version on el7
+
 * Tue Aug 22 2017 Orion Poplawski <orion@nwra.com> - 1.8.12-10
 - RHEL doesn't provide mpich-devel%%{_isa}
 

From eab17a925299ee32d3b76eb950341ad0f8397276 Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@nwra.com>
Date: Wed, 8 May 2019 12:36:37 -0600
Subject: [PATCH 14/16] No openmpi3 for ppc64

---
 hdf5.spec | 24 +++++++++++-------------
 1 file changed, 11 insertions(+), 13 deletions(-)

diff --git a/hdf5.spec b/hdf5.spec
index adc23f9..00fbff2 100644
--- a/hdf5.spec
+++ b/hdf5.spec
@@ -39,25 +39,23 @@ BuildRequires: libaec-devel
 
 %global with_mpich 1
 %global with_openmpi 1
-%if 0%{?rhel} <= 6
+
 %ifarch ppc64
-% No mpich2 on ppc64 in EL6
-%global with_mpich 0
-%endif
-%endif
-%ifarch s390 s390x
-# No openmpi on s390(x)
-%global with_openmpi 0
+# No openmpi3 on ppc64
+%global with_openmpi3 0
+%else
+%global with_openmpi3 1
 %endif
 
 %if %{with_mpich}
 %global mpi_list mpich
 %endif
 %if %{with_openmpi}
-%global mpi_list %{?mpi_list} openmpi %{?el7:openmpi3}
+%global mpi_list %{?mpi_list} openmpi
+%endif
+%if 0%{?with_openmpi3}
+%global mpi_list %{?mpi_list} openmpi3
 %endif
-
-%{?el7:%global ompi3 1}
 
 %description
 HDF5 is a general purpose library and file format for storing scientific data.
@@ -159,7 +157,7 @@ Requires: %{name}-openmpi-devel%{?_isa} = %{version}-%{release}
 %description openmpi-static
 HDF5 parallel openmpi static libraries
 
-%if 0%{?ompi3}
+%if 0%{?with_openmpi3}
 %package openmpi3
 Summary: HDF5 openmpi3 libraries
 Group: Development/Libraries
@@ -461,7 +459,7 @@ done
 %files openmpi-static
 %{_libdir}/openmpi/lib/*.a
 
-%if 0%{?ompi3}
+%if 0%{?with_openmpi3}
 %files openmpi3
 %doc COPYING MANIFEST README.txt release_docs/RELEASE.txt
 %doc release_docs/HISTORY*.txt

From dd4311a91110f77c2e688acbfb7fd1ab7e5d2195 Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@nwra.com>
Date: Mon, 25 Jan 2021 19:08:20 -0700
Subject: [PATCH 15/16] Drop compiling with -O0

---
 hdf5.spec | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/hdf5.spec b/hdf5.spec
index 00fbff2..745cec6 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: 1.8.12
-Release: 11%{?dist}
+Release: 12%{?dist}
 Summary: A general purpose library and file format for storing scientific data
 License: BSD
 Group: System Environment/Libraries
@@ -228,7 +228,6 @@ autoreconf -f -i
 export CC=gcc
 export CXX=g++
 export F9X=gfortran
-export CFLAGS="${RPM_OPT_FLAGS/O2/O0}"
 mkdir build
 pushd build
 ln -s ../configure .
@@ -497,6 +496,9 @@ done
 
 
 %changelog
+* Tue Jan 26 2021 Orion Poplawski <orion@nwra.com> - 1.8.12-12
+- Drop compiling with -O0
+
 * Sun Apr 28 2019 Dave Love <loveshack@fedoraproject.org> - 1.8.12-11
 - Build an openmpi3 version on el7
 

From 593c3ccc3f53f712678d7cdac5ef607464cb85b7 Mon Sep 17 00:00:00 2001
From: Orion Poplawski <orion@nwra.com>
Date: Sun, 26 Jan 2020 19:17:09 -0700
Subject: [PATCH 16/16] Remove Fedora build flags from h5cc/h5c++/h5fc
 (bz#1980549)

---
 hdf5-wrappers.patch | 109 ++++++++++++++++++++++++++++++++++++++++++++
 hdf5.spec           |   9 +++-
 2 files changed, 117 insertions(+), 1 deletion(-)
 create mode 100644 hdf5-wrappers.patch

diff --git a/hdf5-wrappers.patch b/hdf5-wrappers.patch
new file mode 100644
index 0000000..bcda52d
--- /dev/null
+++ b/hdf5-wrappers.patch
@@ -0,0 +1,109 @@
+diff -up hdf5-1.8.12/c++/src/h5c++.in.wrappers hdf5-1.8.12/c++/src/h5c++.in
+--- hdf5-1.8.12/c++/src/h5c++.in.wrappers	2013-11-21 08:14:01.000000000 -0700
++++ hdf5-1.8.12/c++/src/h5c++.in	2021-09-15 20:14:40.123641057 -0600
+@@ -89,10 +89,10 @@ 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
+ # to the user's flags.
+-H5BLD_CXXFLAGS="@AM_CXXFLAGS@ @CXXFLAGS@"
++H5BLD_CXXFLAGS=
+ H5BLD_CPPFLAGS="@AM_CPPFLAGS@ @CPPFLAGS@"
+-H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
+-H5BLD_LIBS="@LIBS@"
++H5BLD_LDFLAGS=
++H5BLD_LIBS=
+ 
+ CXX="${HDF5_CXX:-$CXXBASE}"
+ CXXLINKER="${HDF5_CLINKER:-$CXXLINKERBASE}"
+@@ -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
+@@ -387,7 +388,7 @@ if test "x$do_link" = "xyes"; then
+   # from the hdf5 build. The order of the flags is intended to give precedence
+   # to the user's flags.
+ 
+-  $SHOW $CXXLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CXXFLAGS $CXXFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args $shared_link
++  $SHOW $CXXLINKER $H5BLD_CPPFLAGS $CPPFLAGS $H5BLD_CXXFLAGS $CXXFLAGS $LDFLAGS $clibpath $link_objs $LIBS $link_args
+ 
+   status=$?
+ fi
+diff -up hdf5-1.8.12/fortran/src/h5fc.in.wrappers hdf5-1.8.12/fortran/src/h5fc.in
+--- hdf5-1.8.12/fortran/src/h5fc.in.wrappers	2013-11-21 08:14:04.000000000 -0700
++++ hdf5-1.8.12/fortran/src/h5fc.in	2021-09-15 20:14:40.123641057 -0600
+@@ -85,11 +85,11 @@ FLINKERBASE="@FC@"
+ # libraries in $link_args, followed by any external library paths and libraries 
+ # from AM_LDFLAGS, LDFLAGS, AM_LIBS or LIBS carried in from the hdf5 build.
+ # The order of the flags is intended to give precedence to the user's flags.
+-H5BLD_FCFLAGS="@AM_FCFLAGS@ @FCFLAGS@"
++H5BLD_FCFLAGS=
+ F9XMODFLAG="@F9XMODFLAG@"
+ F9XSUFFIXFLAG="@F9XSUFFIXFLAG@"
+-H5BLD_LDFLAGS="@AM_LDFLAGS@ @LDFLAGS@"
+-H5BLD_LIBS="@LIBS@"
++H5BLD_LDFLAGS=
++H5BLD_LIBS=
+ 
+ FC="${HDF5_FC:-$FCBASE}"
+ FLINKER="${HDF5_FLINKER:-$FLINKERBASE}"
+@@ -101,7 +101,8 @@ LIBS="${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="${HDF5_USE_SHLIB:-no}"
+ else
+@@ -365,7 +366,7 @@ if test "x$do_link" = "xyes"; then
+   # 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
++  $SHOW $FLINKER $FCFLAGS $H5BLD_FCFLAGS $F9XSUFFIXFLAG $LDFLAGS $fmodules $link_objs $LIBS $link_args
+   status=$?
+ fi
+ 
+diff -up hdf5-1.8.12/tools/misc/h5cc.in.wrappers hdf5-1.8.12/tools/misc/h5cc.in
+--- hdf5-1.8.12/tools/misc/h5cc.in.wrappers	2013-11-21 08:13:59.000000000 -0700
++++ hdf5-1.8.12/tools/misc/h5cc.in	2021-09-15 20:14:40.123641057 -0600
+@@ -91,10 +91,10 @@ 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}"
+@@ -107,7 +107,8 @@ 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
+@@ -394,7 +395,7 @@ 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 745cec6..1b92f69 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: 1.8.12
-Release: 12%{?dist}
+Release: 13%{?dist}
 Summary: A general purpose library and file format for storing scientific data
 License: BSD
 Group: System Environment/Libraries
@@ -28,6 +28,9 @@ Patch3: hdf5-ldouble-ppc64le.patch
 Patch4: hdf5-ppc64le.patch
 # Upstream patch for various Talos CVEs
 Patch5: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8/talospatch/hdf51.8-CVE2016.patch
+# Remove Fedora build flags from h5cc/h5c++/h5fc
+# https://bugzilla.redhat.com/show_bug.cgi?id=1794625
+Patch6: hdf5-wrappers.patch
 
 BuildRequires: krb5-devel, openssl-devel, zlib-devel, gcc-gfortran, time
 # For patches/rpath
@@ -203,6 +206,7 @@ HDF5 parallel openmpi3 static libraries
 %patch3 -p1 -b .ldouble-ppc64le
 %patch4 -p1 -b .ppc64le
 %patch5 -p0 -b .CVE
+%patch6 -p1 -b .wrappers
 #This should be fixed in 1.8.7
 find \( -name '*.[ch]*' -o -name '*.f90' -o -name '*.txt' \) -exec chmod -x {} +
 autoreconf -f -i
@@ -496,6 +500,9 @@ done
 
 
 %changelog
+* Wed Sep 15 2021 Orion Poplawski <orion@nwra.com> - 1.8.12-13
+- Remove Fedora build flags from h5cc/h5c++/h5fc (bz#1980549)
+
 * Tue Jan 26 2021 Orion Poplawski <orion@nwra.com> - 1.8.12-12
 - Drop compiling with -O0