Update to 1.10.5

epel9
Orion Poplawski 6 years ago committed by Orion Poplawski
parent 0fc70b9d21
commit 458d98e201

5
.gitignore vendored

@ -23,3 +23,8 @@ hdf5-1.8.5.tar.bz2
/hdf5_1.8.16+docs-8.debian.tar.xz /hdf5_1.8.16+docs-8.debian.tar.xz
/hdf5-1.8.18.tar.bz2 /hdf5-1.8.18.tar.bz2
/hdf5-1.8.20.tar.bz2 /hdf5-1.8.20.tar.bz2
/hdf5-1.10.3.tar.bz2
/hdf5_1.10.2+repack-1~exp1.debian.tar.xz
/hdf5-1.10.4.tar.bz2
/hdf5_1.10.4+repack-1.debian.tar.xz
/hdf5-1.10.5.tar.bz2

@ -1,75 +0,0 @@
diff -up hdf5-1.8.16/configure.ac.ldouble-ppc64le hdf5-1.8.16/configure.ac
--- hdf5-1.8.16/configure.ac.ldouble-ppc64le 2015-11-13 09:29:08.749125801 -0700
+++ hdf5-1.8.16/configure.ac 2015-11-13 09:47:02.705174991 -0700
@@ -2278,6 +2278,13 @@ else
unsigned char s2[8];
int ret = 1;
+#if defined __powerpc64__ && defined _LITTLE_ENDIAN
+ /* Don't bother checking on ppc64le, we know it'll work, and
+ * that what hdf5 calls 'special algorithm' simply is
+ * IBM ldouble 128 (i.e. two seperately scaled doubles).
+ * The check below assumes big endian. */
+ ret = 0;
+#endif
if(sizeof(long double) == 16 && sizeof(long) == 8) {
/*make sure the long double type has 16 bytes in size and
* 11 bits of exponent. If it is,
@@ -2355,6 +2362,13 @@ else
unsigned char s[16];
int flag=0, ret=1;
+#if defined __powerpc64__ && defined _LITTLE_ENDIAN
+ /* Don't bother checking on ppc64le, we know it'll work, and
+ * that what hdf5 calls 'special algorithm' simply is
+ * IBM ldouble 128 (i.e. two seperately scaled doubles).
+ * The check below assumes big endian. */
+ ret = 0;
+#endif
/*Determine if long double has 16 byte in size, 11 bit exponent, and
*the bias is 0x3ff */
if(sizeof(long double) == 16) {
diff -up hdf5-1.8.16/configure.ldouble-ppc64le hdf5-1.8.16/configure
diff -up hdf5-1.8.16/test/dt_arith.c.ldouble-ppc64le hdf5-1.8.16/test/dt_arith.c
--- hdf5-1.8.16/test/dt_arith.c.ldouble-ppc64le 2015-10-23 23:13:43.000000000 -0600
+++ hdf5-1.8.16/test/dt_arith.c 2015-11-13 09:29:08.765125707 -0700
@@ -3010,7 +3010,18 @@ test_conv_flt_1 (const char *name, int r
buf, saved, nelmts);
#if H5_SIZEOF_LONG_DOUBLE!=H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE!=0
} else if(src_type == FLT_LDOUBLE) {
- INIT_FP_SPECIAL(src_size, src_nbits, sendian, LDBL_MANT_DIG, dst_size,
+ size_t mant_dig = LDBL_MANT_DIG;
+ if (mant_dig >= src_nbits) {
+ /* This happens for IBM long double in little endian.
+ The macro LDBL_MANT_DIG says 106 mantissa bits, but the
+ HDF5 detection code actually represents it as a normal 64bit
+ double (52 bit mantissa) with the upper double being
+ unspec bits (which is sort of okay as the testsuite
+ wouldn't deal with that format correctly anyway). So
+ override the mantissa size. */
+ mant_dig = 52;
+ }
+ INIT_FP_SPECIAL(src_size, src_nbits, sendian, mant_dig, dst_size,
buf, saved, nelmts);
#endif
} else
@@ -3663,7 +3674,18 @@ test_conv_int_fp(const char *name, int r
INIT_FP_DENORM(long double, LDBL_MANT_DIG, src_size, src_nbits, sendian, dst_size,
buf, saved, nelmts);
} else {
- INIT_FP_SPECIAL(src_size, src_nbits, sendian, LDBL_MANT_DIG, dst_size, buf, saved, nelmts);
+ size_t mant_dig = LDBL_MANT_DIG;
+ if (mant_dig >= src_nbits) {
+ /* This happens for IBM long double in little endian.
+ The macro LDBL_MANT_DIG says 106 mantissa bits, but the
+ HDF5 detection code actually represents it as a normal 64bit
+ double (52 bit mantissa) with the upper double being
+ unspec bits (which is sort of okay as the testsuite
+ wouldn't deal with that format correctly anyway). So
+ override the mantissa size. */
+ mant_dig = 52;
+ }
+ INIT_FP_SPECIAL(src_size, src_nbits, sendian, mant_dig, dst_size, buf, saved, nelmts);
}
#endif
} else

@ -0,0 +1,76 @@
diff -up hdf5-1.10.4/testpar/t_cache.c.warning hdf5-1.10.4/testpar/t_cache.c
--- hdf5-1.10.4/testpar/t_cache.c.warning 2018-09-10 08:43:41.000000000 -0600
+++ hdf5-1.10.4/testpar/t_cache.c 2018-11-24 08:08:37.333832898 -0700
@@ -79,8 +79,8 @@ long local_pins = 0;
/* the following fields are used by the server process only */
-int total_reads = 0;
-int total_writes = 0;
+unsigned total_reads = 0;
+unsigned total_writes = 0;
/*****************************************************************************
@@ -175,8 +175,8 @@ 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;
};
@@ -2197,7 +2197,7 @@ serve_entry_reads_request(struct mssg_t
reply.base_addr = target_addr;
reply.len = 0;
reply.ver = 0;
- reply.count = (long)(data[target_index].reads);
+ reply.count = data[target_index].reads;
reply.magic = MSSG_MAGIC;
}
}
@@ -2446,12 +2446,12 @@ static herr_t
datum_image_len(const void *thing, size_t *image_len)
{
int idx;
- 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);
@@ -4615,7 +4615,7 @@ verify_entry_reads(haddr_t addr,
int expected_entry_reads)
{
hbool_t success = TRUE;
- int reported_entry_reads;
+ unsigned reported_entry_reads = 0;
struct mssg_t mssg;
if ( success ) {
@@ -4722,7 +4722,7 @@ verify_entry_writes(haddr_t addr,
int expected_entry_writes)
{
hbool_t success = TRUE;
- int reported_entry_writes;
+ unsigned reported_entry_writes = 0;
struct mssg_t mssg;
if ( success ) {
@@ -4827,7 +4827,7 @@ 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 ) {

@ -6,24 +6,21 @@
# NOTE: Try not to release new versions to released versions of Fedora # NOTE: Try not to release new versions to released versions of Fedora
# You need to recompile all users of HDF5 for each version change # You need to recompile all users of HDF5 for each version change
Name: hdf5 Name: hdf5
Version: 1.8.20 Version: 1.10.5
Release: 6%{?dist} Release: 1%{?dist}
Summary: A general purpose library and file format for storing scientific data Summary: A general purpose library and file format for storing scientific data
License: BSD License: BSD
URL: https://portal.hdfgroup.org/display/HDF5/HDF5 URL: https://portal.hdfgroup.org/display/HDF5/HDF5
Source0: https://support.hdfgroup.org/ftp/HDF5/current18/src/hdf5-%{version}%{?snaprel}.tar.bz2 Source0: https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-%{version}/src/hdf5-%{version}.tar.bz2
Source1: h5comp Source1: h5comp
# For man pages # For man pages
Source2: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.8.16+docs-8.debian.tar.xz Source2: http://ftp.us.debian.org/debian/pool/main/h/hdf5/hdf5_1.10.4+repack-1.debian.tar.xz
Patch0: hdf5-LD_LIBRARY_PATH.patch Patch0: hdf5-LD_LIBRARY_PATH.patch
# Properly run MPI_Finalize() in t_pflush1 # Properly run MPI_Finalize() in t_pflush1
Patch1: hdf5-mpi.patch Patch1: hdf5-mpi.patch
# Fix compilation with -Werror=implicit-function-declaration # Fix some warnings
Patch2: hdf5-implicit.patch Patch2: hdf5-warning.patch
# Fix long double conversions on ppc64le
# https://bugzilla.redhat.com/show_bug.cgi?id=1078173
Patch3: hdf5-ldouble-ppc64le.patch
BuildRequires: krb5-devel, openssl-devel, zlib-devel, gcc-gfortran, time BuildRequires: krb5-devel, openssl-devel, zlib-devel, gcc-gfortran, time
# For patches/rpath # For patches/rpath
@ -152,9 +149,8 @@ HDF5 parallel openmpi static libraries
%prep %prep
%setup -q -a 2 -n %{name}-%{version}%{?snaprel} %setup -q -a 2 -n %{name}-%{version}%{?snaprel}
%patch0 -p1 -b .LD_LIBRARY_PATH %patch0 -p1 -b .LD_LIBRARY_PATH
%patch1 -p1 -b .mpi #patch1 -p1 -b .mpi
%patch2 -p1 -b .implicit %patch2 -p1 -b .warning
%patch3 -p1 -b .ldouble-ppc64le
# Force shared by default for compiler wrappers (bug #1266645) # Force shared by default for compiler wrappers (bug #1266645)
sed -i -e '/^STATIC_AVAILABLE=/s/=.*/=no/' */*/h5[cf]*.in sed -i -e '/^STATIC_AVAILABLE=/s/=.*/=no/' */*/h5[cf]*.in
@ -225,69 +221,65 @@ done
%install %install
%make_install -C build %make_install -C build
rm $RPM_BUILD_ROOT%{_libdir}/*.la rm %{buildroot}%{_libdir}/*.la
#Fortran modules #Fortran modules
mkdir -p ${RPM_BUILD_ROOT}%{_fmoddir} mkdir -p %{buildroot}%{_fmoddir}
mv ${RPM_BUILD_ROOT}%{_includedir}/*.mod ${RPM_BUILD_ROOT}%{_fmoddir} mv %{buildroot}%{_includedir}/*.mod %{buildroot}%{_fmoddir}
for mpi in %{?mpi_list} for mpi in %{?mpi_list}
do do
module load mpi/$mpi-%{_arch} module load mpi/$mpi-%{_arch}
make -C $mpi install DESTDIR=${RPM_BUILD_ROOT} make -C $mpi install DESTDIR=%{buildroot}
rm $RPM_BUILD_ROOT/%{_libdir}/$mpi/lib/*.la rm %{buildroot}/%{_libdir}/$mpi/lib/*.la
#Fortran modules #Fortran modules
mkdir -p ${RPM_BUILD_ROOT}${MPI_FORTRAN_MOD_DIR} mkdir -p %{buildroot}${MPI_FORTRAN_MOD_DIR}
mv ${RPM_BUILD_ROOT}%{_includedir}/${mpi}-%{_arch}/*.mod ${RPM_BUILD_ROOT}${MPI_FORTRAN_MOD_DIR}/ mv %{buildroot}%{_includedir}/${mpi}-%{_arch}/*.mod %{buildroot}${MPI_FORTRAN_MOD_DIR}/
module purge module purge
done done
#Fixup example permissions #Fixup example permissions
find ${RPM_BUILD_ROOT}%{_datadir} \( -name '*.[ch]*' -o -name '*.f90' \) -exec chmod -x {} + find %{buildroot}%{_datadir} \( -name '*.[ch]*' -o -name '*.f90' \) -exec chmod -x {} +
#Fixup headers and scripts for multiarch #Fixup headers and scripts for multiarch
%ifarch x86_64 ppc64 ia64 s390x sparc64 alpha %ifarch x86_64 ppc64 ia64 s390x sparc64 alpha
sed -i -e s/H5pubconf.h/H5pubconf-64.h/ ${RPM_BUILD_ROOT}%{_includedir}/H5public.h sed -i -e s/H5pubconf.h/H5pubconf-64.h/ %{buildroot}%{_includedir}/H5public.h
mv ${RPM_BUILD_ROOT}%{_includedir}/H5pubconf.h \ mv %{buildroot}%{_includedir}/H5pubconf.h \
${RPM_BUILD_ROOT}%{_includedir}/H5pubconf-64.h %{buildroot}%{_includedir}/H5pubconf-64.h
for x in h5c++ h5cc h5fc for x in h5c++ h5cc h5fc
do do
mv ${RPM_BUILD_ROOT}%{_bindir}/${x} \ mv %{buildroot}%{_bindir}/${x} \
${RPM_BUILD_ROOT}%{_bindir}/${x}-64 %{buildroot}%{_bindir}/${x}-64
install -m 0755 %SOURCE1 ${RPM_BUILD_ROOT}%{_bindir}/${x} install -m 0755 %SOURCE1 %{buildroot}%{_bindir}/${x}
done done
%else %else
sed -i -e s/H5pubconf.h/H5pubconf-32.h/ ${RPM_BUILD_ROOT}%{_includedir}/H5public.h sed -i -e s/H5pubconf.h/H5pubconf-32.h/ %{buildroot}%{_includedir}/H5public.h
mv ${RPM_BUILD_ROOT}%{_includedir}/H5pubconf.h \ mv %{buildroot}%{_includedir}/H5pubconf.h \
${RPM_BUILD_ROOT}%{_includedir}/H5pubconf-32.h %{buildroot}%{_includedir}/H5pubconf-32.h
for x in h5c++ h5cc h5fc for x in h5c++ h5cc h5fc
do do
mv ${RPM_BUILD_ROOT}%{_bindir}/${x} \ mv %{buildroot}%{_bindir}/${x} \
${RPM_BUILD_ROOT}%{_bindir}/${x}-32 %{buildroot}%{_bindir}/${x}-32
install -m 0755 %SOURCE1 ${RPM_BUILD_ROOT}%{_bindir}/${x} install -m 0755 %SOURCE1 %{buildroot}%{_bindir}/${x}
done done
%endif %endif
# rpm macro for version checking # rpm macro for version checking
mkdir -p ${RPM_BUILD_ROOT}%{macrosdir} mkdir -p %{buildroot}%{macrosdir}
cat > ${RPM_BUILD_ROOT}%{macrosdir}/macros.hdf5 <<EOF cat > %{buildroot}%{macrosdir}/macros.hdf5 <<EOF
# HDF5 version is # HDF5 version is
%%_hdf5_version %{version} %%_hdf5_version %{version}
EOF EOF
# Install man pages from debian # Install man pages from debian
mkdir -p ${RPM_BUILD_ROOT}%{_mandir}/man1 mkdir -p %{buildroot}%{_mandir}/man1
cp -p debian/man/*.1 ${RPM_BUILD_ROOT}%{_mandir}/man1/ cp -p debian/man/*.1 %{buildroot}%{_mandir}/man1/
for mpi in %{?mpi_list} for mpi in %{?mpi_list}
do do
mkdir -p ${RPM_BUILD_ROOT}%{_libdir}/$mpi/share/man/man1 mkdir -p %{buildroot}%{_libdir}/$mpi/share/man/man1
cp -p debian/man/h5p[cf]c.1 ${RPM_BUILD_ROOT}%{_libdir}/$mpi/share/man/man1/ cp -p debian/man/h5p[cf]c.1 %{buildroot}%{_libdir}/$mpi/share/man/man1/
done done
rm ${RPM_BUILD_ROOT}%{_mandir}/man1/h5p[cf]c.1 rm %{buildroot}%{_mandir}/man1/h5p[cf]c*.1
%check %check
make -C build 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
# testphdf5 is hanging on arm with openmpi
%ifnarch s390 s390x %{arm}
export HDF5_Make_Ignore=yes export HDF5_Make_Ignore=yes
for mpi in %{?mpi_list} for mpi in %{?mpi_list}
do do
@ -295,20 +287,23 @@ do
make -C $mpi check make -C $mpi check
module purge module purge
done done
%endif
%ldconfig_scriptlets %ldconfig_scriptlets
%files %files
%license COPYING %license COPYING
%doc MANIFEST README.txt release_docs/RELEASE.txt %doc MANIFEST README.txt release_docs/RELEASE.txt
%doc release_docs/HISTORY*.txt %doc release_docs/HISTORY*.txt
%{_bindir}/gif2h5 %{_bindir}/gif2h5
%{_bindir}/h52gif %{_bindir}/h52gif
%{_bindir}/h5clear
%{_bindir}/h5copy %{_bindir}/h5copy
%{_bindir}/h5debug %{_bindir}/h5debug
%{_bindir}/h5diff %{_bindir}/h5diff
%{_bindir}/h5dump %{_bindir}/h5dump
%{_bindir}/h5format_convert
%{_bindir}/h5import %{_bindir}/h5import
%{_bindir}/h5jam %{_bindir}/h5jam
%{_bindir}/h5ls %{_bindir}/h5ls
@ -318,9 +313,13 @@ done
%{_bindir}/h5repart %{_bindir}/h5repart
%{_bindir}/h5stat %{_bindir}/h5stat
%{_bindir}/h5unjam %{_bindir}/h5unjam
%{_libdir}/*.so.10* %{_bindir}/h5watch
%{_libdir}/libhdf5_cpp.so.15* %{_libdir}/libhdf5.so.103*
%{_libdir}/libhdf5_hl_cpp.so.11* %{_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*
%{_mandir}/man1/gif2h5.1* %{_mandir}/man1/gif2h5.1*
%{_mandir}/man1/h52gif.1* %{_mandir}/man1/h52gif.1*
%{_mandir}/man1/h5copy.1* %{_mandir}/man1/h5copy.1*
@ -363,10 +362,12 @@ done
%doc release_docs/HISTORY*.txt %doc release_docs/HISTORY*.txt
%{_libdir}/mpich/bin/gif2h5 %{_libdir}/mpich/bin/gif2h5
%{_libdir}/mpich/bin/h52gif %{_libdir}/mpich/bin/h52gif
%{_libdir}/mpich/bin/h5clear
%{_libdir}/mpich/bin/h5copy %{_libdir}/mpich/bin/h5copy
%{_libdir}/mpich/bin/h5debug %{_libdir}/mpich/bin/h5debug
%{_libdir}/mpich/bin/h5diff %{_libdir}/mpich/bin/h5diff
%{_libdir}/mpich/bin/h5dump %{_libdir}/mpich/bin/h5dump
%{_libdir}/mpich/bin/h5format_convert
%{_libdir}/mpich/bin/h5import %{_libdir}/mpich/bin/h5import
%{_libdir}/mpich/bin/h5jam %{_libdir}/mpich/bin/h5jam
%{_libdir}/mpich/bin/h5ls %{_libdir}/mpich/bin/h5ls
@ -378,6 +379,7 @@ done
%{_libdir}/mpich/bin/h5repart %{_libdir}/mpich/bin/h5repart
%{_libdir}/mpich/bin/h5stat %{_libdir}/mpich/bin/h5stat
%{_libdir}/mpich/bin/h5unjam %{_libdir}/mpich/bin/h5unjam
%{_libdir}/mpich/bin/h5watch
%{_libdir}/mpich/bin/ph5diff %{_libdir}/mpich/bin/ph5diff
%{_libdir}/mpich/lib/*.so.10* %{_libdir}/mpich/lib/*.so.10*
@ -403,10 +405,12 @@ done
%doc release_docs/HISTORY*.txt %doc release_docs/HISTORY*.txt
%{_libdir}/openmpi/bin/gif2h5 %{_libdir}/openmpi/bin/gif2h5
%{_libdir}/openmpi/bin/h52gif %{_libdir}/openmpi/bin/h52gif
%{_libdir}/openmpi/bin/h5clear
%{_libdir}/openmpi/bin/h5copy %{_libdir}/openmpi/bin/h5copy
%{_libdir}/openmpi/bin/h5debug %{_libdir}/openmpi/bin/h5debug
%{_libdir}/openmpi/bin/h5diff %{_libdir}/openmpi/bin/h5diff
%{_libdir}/openmpi/bin/h5dump %{_libdir}/openmpi/bin/h5dump
%{_libdir}/openmpi/bin/h5format_convert
%{_libdir}/openmpi/bin/h5import %{_libdir}/openmpi/bin/h5import
%{_libdir}/openmpi/bin/h5jam %{_libdir}/openmpi/bin/h5jam
%{_libdir}/openmpi/bin/h5ls %{_libdir}/openmpi/bin/h5ls
@ -418,6 +422,7 @@ done
%{_libdir}/openmpi/bin/h5repart %{_libdir}/openmpi/bin/h5repart
%{_libdir}/openmpi/bin/h5stat %{_libdir}/openmpi/bin/h5stat
%{_libdir}/openmpi/bin/h5unjam %{_libdir}/openmpi/bin/h5unjam
%{_libdir}/openmpi/bin/h5watch
%{_libdir}/openmpi/bin/ph5diff %{_libdir}/openmpi/bin/ph5diff
%{_libdir}/openmpi/lib/*.so.10* %{_libdir}/openmpi/lib/*.so.10*
@ -438,6 +443,9 @@ done
%changelog %changelog
* Sat Mar 16 2019 Orion Poplawski <orion@nwra.com> - 1.10.5-1
- Update to 1.10.5
* Thu Feb 14 2019 Orion Poplawski <orion@nwra.com> - 1.8.20-6 * Thu Feb 14 2019 Orion Poplawski <orion@nwra.com> - 1.8.20-6
- Rebuild for openmpi 3.1.3 - Rebuild for openmpi 3.1.3

@ -1,2 +1,2 @@
SHA512 (hdf5-1.8.20.tar.bz2) = 288e4772a946d406de9096843c92dd6874a0753ed6fbe859aaadf565aa0509fc612ebdb00c301b7955bc0dc63e45f3a224c6b2638f480fe6738ee0c96a993c6e SHA512 (hdf5-1.10.5.tar.bz2) = 769e43b8672e26fe24ed68da0228c010d3d9bc950ca09f0bc60707911a2f26f2f8415c8abc8ec06e07667148d8cdb3b0c7b3e7860d9b19739629c5dfd5ce73d4
SHA512 (hdf5_1.8.16+docs-8.debian.tar.xz) = 03a7d08966952e382d4990ef37be3e475e99066b9e12199800fa1c8d5f2665ca64c26d73ef1c712738d6885c3673eac4691c2c0e2682d539fb2bfad21dac4559 SHA512 (hdf5_1.10.4+repack-1.debian.tar.xz) = 7e08a79c8e96b843331e30d027628065ccbe72843a3ac525ad52d506238d328b9ebae57eff772b6215419943fd1804b4879cbdcd612e2f2c160c65a3d44ef965

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