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Accepting request 356581 from home:rudi_m:branches:science

Browse Source 
- update to 1.8.16, changes documented here: 
  https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.16/src/hdf5-1.8.16-RELEASE.txt
- rebase hdf5-ldouble-ppc64le.patch
- remove hdf5-cpp-compilation-errors.patch
- prepare independent so versions and add TODO

!!! see TODO in spec file !!!
I'm not the right persion to split packages and care for deps and baselibs etc.
Don't forward to Factory before this TODO is fixed!

OBS-URL: https://build.opensuse.org/request/show/356581
OBS-URL: https://build.opensuse.org/package/show/science/hdf5?expand=0&rev=17
This commit is contained in:
Todd R 2016-01-29 10:06:01 +00:00 committed by Git OBS Bridge
parent 49a03eafb5
commit bbed69ec6c
9 changed files with 201 additions and 101 deletions
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24
baselibs.conf
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@ -1,18 +1,18 @@
libhdf5-10 libhdf5-11
hdf5-devel hdf5-devel
requires -<targettype> requires -<targettype>
requires "libhdf5-10-<targettype> = <version>" requires "libhdf5-11-<targettype> = <version>"
requires "libhdf5_hl10-<targettype> = <version>" requires "libhdf5_hl11-<targettype> = <version>"
libhdf5-10-openmpi libhdf5-11-openmpi
hdf5-openmpi-devel hdf5-openmpi-devel
requires -openmpi-<targettype> requires -openmpi-<targettype>
requires "libhdf5-10-openmpi-<targettype> = <version>" requires "libhdf5-11-openmpi-<targettype> = <version>"
requires "libhdf5_hl10-openmpi-<targettype> = <version>" requires "libhdf5_hl11-openmpi-<targettype> = <version>"
libhdf5-10-mvapich2 libhdf5-11-mvapich2
libhdf5_hl10 libhdf5_hl11
libhdf5_hl10-mvapich2 libhdf5_hl11-mvapich2
libhdf5_hl10-openmpi libhdf5_hl11-openmpi
hdf5-mvapich2-devel hdf5-mvapich2-devel
requires -openmpi-<targettype> requires -openmpi-<targettype>
requires "libhdf5-10-mvapich2-<targettype> = <version>" requires "libhdf5-11-mvapich2-<targettype> = <version>"
requires "libhdf5_hl10-mvapich2-<targettype> = <version>" requires "libhdf5_hl11-mvapich2-<targettype> = <version>"

18
baselibs.conf.in Normal file
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@ -0,0 +1,18 @@
libhdf5-@sonum@
hdf5-devel
requires -<targettype>
requires "libhdf5-@sonum@-<targettype> = <version>"
requires "libhdf5_hl@sonum@-<targettype> = <version>"
libhdf5-@sonum@-openmpi
hdf5-openmpi-devel
requires -openmpi-<targettype>
requires "libhdf5-@sonum@-openmpi-<targettype> = <version>"
requires "libhdf5_hl@sonum@-openmpi-<targettype> = <version>"
libhdf5-@sonum@-mvapich2
libhdf5_hl@sonum@
libhdf5_hl@sonum@-mvapich2
libhdf5_hl@sonum@-openmpi
hdf5-mvapich2-devel
requires -openmpi-<targettype>
requires "libhdf5-@sonum@-mvapich2-<targettype> = <version>"
requires "libhdf5_hl@sonum@-mvapich2-<targettype> = <version>"

3
hdf5-1.8.15.tar.bz2
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@ -1,3 +0,0 @@
version https://git-lfs.github.com/spec/v1
oid sha256:0003ac76314b9c3dd819f595eb33890f02f6bf000414013a89f9907ac09e3920
size 10002545

3
hdf5-1.8.16.tar.bz2 Normal file
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@ -0,0 +1,3 @@
version https://git-lfs.github.com/spec/v1
oid sha256:13aaae5ba10b70749ee1718816a4b4bfead897c2fcb72c24176e759aec4598c6
size 10047405

18
hdf5-cpp-compilation-errors.patch
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@ -1,18 +0,0 @@
Index: src/H5api_adpt.h
===================================================================
--- src/H5api_adpt.h (revision 26991)
+++ src/H5api_adpt.h (revision 27474)
@@ -21,13 +21,6 @@
#ifndef H5API_ADPT_H
#define H5API_ADPT_H
-#ifdef __cplusplus
-#define __attribute__(X) /*void*/
-#endif /* __cplusplus */
-#ifndef H5_HAVE_ATTRIBUTE
-#define __attribute__(X) /*void*/
-#endif /* H5_HAVE_ATTRIBUTE */
-
/* This will only be defined if HDF5 was built with CMake */
#ifdef H5_BUILT_AS_DYNAMIC_LIB

129
hdf5-ldouble-ppc64le.patch
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@ -1,72 +1,75 @@
Index: hdf5-1.8.14/configure diff -rupN hdf5-1.8.16.orig/configure hdf5-1.8.16/configure
=================================================================== --- hdf5-1.8.16.orig/configure 2015-11-10 15:01:10.000000000 +0100
--- hdf5-1.8.14.orig/configure +++ hdf5-1.8.16/configure 2016-01-28 13:44:58.136709651 +0100
+++ hdf5-1.8.14/configure @@ -27347,6 +27347,14 @@ main ()
@@ -30438,6 +30438,13 @@ else unsigned char s2[8];
unsigned char s2[8]; int ret = 1;
int ret = 1;
+#if defined __powerpc64__ && defined _LITTLE_ENDIAN +#if defined __powerpc64__ && defined _LITTLE_ENDIAN
+ /* Don't bother checking on ppc64le, we know it'll work, and + /* Don't bother checking on ppc64le, we know it'll work, and
+ that what hdf5 calls 'special algorithm' simply is + that what hdf5 calls 'special algorithm' simply is
+ IBM ldouble 128 (i.e. two seperately scaled doubles). + IBM ldouble 128 (i.e. two seperately scaled doubles).
+ The check below assumes big endian. */ + The check below assumes big endian. */
+ ret = 0; + ret = 0;
+#endif +#endif
if(sizeof(long double) == 16 && sizeof(long) == 8) { +
/*make sure the long double type has 16 bytes in size and if(sizeof(long double) == 16 && sizeof(long) == 8) {
* 11 bits of exponent. If it is, /*make sure the long double type has 16 bytes in size and
@@ -30542,6 +30549,13 @@ else * 11 bits of exponent. If it is,
unsigned char s[16]; @@ -27464,6 +27472,14 @@ main ()
int flag=0, ret=1; unsigned char s[16];
int flag=0, ret=1;
+#if defined __powerpc64__ && defined _LITTLE_ENDIAN +#if defined __powerpc64__ && defined _LITTLE_ENDIAN
+ /* Don't bother checking on ppc64le, we know it'll work, and + /* Don't bother checking on ppc64le, we know it'll work, and
+ that what hdf5 calls 'special algorithm' simply is + that what hdf5 calls 'special algorithm' simply is
+ IBM ldouble 128 (i.e. two seperately scaled doubles). + IBM ldouble 128 (i.e. two seperately scaled doubles).
+ The check below assumes big endian. */ + The check below assumes big endian. */
+ ret = 0; + 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 -rupN hdf5-1.8.16.orig/configure.ac hdf5-1.8.16/configure.ac
--- hdf5-1.8.16.orig/configure.ac 2015-11-04 23:29:55.000000000 +0100
+++ hdf5-1.8.16/configure.ac 2016-01-28 13:44:58.144709750 +0100
@@ -2277,7 +2277,15 @@ else
unsigned char s[16];
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,
@@ -2354,6 +2362,14 @@ else
unsigned long ull;
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 +#endif
/*Determine if long double has 16 byte in size, 11 bit exponent, and
*the bias is 0x3ff */
if(sizeof(long double) == 16) {
Index: hdf5-1.8.14/configure.ac
===================================================================
--- hdf5-1.8.14.orig/configure.ac
+++ hdf5-1.8.14/configure.ac
@@ -3723,6 +3723,13 @@ else
unsigned char s2[8];
int ret = 1;
+#if defined __powerpc64__ && defined _LITTLE_ENDIAN /*Determine if long double has 16 byte in size, 11 bit exponent, and
+ /* Don't bother checking on ppc64le, we know it'll work, and *the bias is 0x3ff */
+ that what hdf5 calls 'special algorithm' simply is diff -rupN hdf5-1.8.16.orig/test/dt_arith.c hdf5-1.8.16/test/dt_arith.c
+ IBM ldouble 128 (i.e. two seperately scaled doubles). --- hdf5-1.8.16.orig/test/dt_arith.c 2015-10-24 07:13:43.000000000 +0200
+ The check below assumes big endian. */ +++ hdf5-1.8.16/test/dt_arith.c 2016-01-28 13:44:58.153709861 +0100
+ ret = 0; @@ -3010,7 +3010,18 @@ test_conv_flt_1 (const char *name, int r
+#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,
@@ -3801,6 +3808,13 @@ 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) {
Index: hdf5-1.8.14/test/dt_arith.c
===================================================================
--- hdf5-1.8.14.orig/test/dt_arith.c
+++ hdf5-1.8.14/test/dt_arith.c
@@ -3088,7 +3088,18 @@ test_conv_flt_1 (const char *name, int r
buf, saved, nelmts); buf, saved, nelmts);
#if H5_SIZEOF_LONG_DOUBLE!=H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE!=0 #if H5_SIZEOF_LONG_DOUBLE!=H5_SIZEOF_DOUBLE && H5_SIZEOF_LONG_DOUBLE!=0
} else if(src_type == FLT_LDOUBLE) { } else if(src_type == FLT_LDOUBLE) {
@ -86,7 +89,7 @@ Index: hdf5-1.8.14/test/dt_arith.c
buf, saved, nelmts); buf, saved, nelmts);
#endif #endif
} else } else
@@ -3824,7 +3835,18 @@ test_conv_int_fp(const char *name, int r @@ -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, INIT_FP_DENORM(long double, LDBL_MANT_DIG, src_size, src_nbits, sendian, dst_size,
buf, saved, nelmts); buf, saved, nelmts);
} else { } else {

9
hdf5.changes
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@ -1,3 +1,12 @@
-------------------------------------------------------------------
Thu Jan 28 00:08:01 UTC 2016 - sweet_f_a@gmx.de
- update to 1.8.16, changes documented here:
https://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.16/src/hdf5-1.8.16-RELEASE.txt
- rebase hdf5-ldouble-ppc64le.patch
- remove hdf5-cpp-compilation-errors.patch
- prepare independent so versions and add TODO
------------------------------------------------------------------- -------------------------------------------------------------------
Fri Aug 21 09:45:05 UTC 2015 - toddrme2178@gmail.com Fri Aug 21 09:45:05 UTC 2015 - toddrme2178@gmail.com

18
hdf5.spec
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@ -25,11 +25,22 @@
%define _mpi %{?_openmpi:openmpi} %{?_mvapich2:mvapich2} %define _mpi %{?_openmpi:openmpi} %{?_mvapich2:mvapich2}
# TODO: since 1.8.16 we have independent so versions, see config/lt_vers.am.
# We already have added a script "update_so_version.sh" to update all the
# defines below and baselibs.conf. But we still need to split certain
# subpackages to be able to use these versions.
%define sonum 11
%define sonum_CXX 11
%define sonum_F 10
%define sonum_HL 10
%define sonum_HL_CXX 11
%define sonum_HL_F 10
%define sonum_TOOLS 10
Name: hdf5 Name: hdf5
%define libname libhdf5 %define libname libhdf5
Version: 1.8.15 Version: 1.8.16
Release: 0 Release: 0
%define sonum 10
Summary: Command-line programs for the HDF5 scientific data format Summary: Command-line programs for the HDF5 scientific data format
License: BSD-3-Clause License: BSD-3-Clause
Group: Productivity/Scientific/Other Group: Productivity/Scientific/Other
@ -44,8 +55,6 @@ Patch2: hdf5-1.8.11-abort_unknown_host_config.patch
Patch4: hdf5-1.8.10-tests-arm.patch Patch4: hdf5-1.8.10-tests-arm.patch
%endif %endif
Patch5: hdf5-ldouble-ppc64le.patch Patch5: hdf5-ldouble-ppc64le.patch
# PATCH-FIX-UPSTREAM hdf5-cpp-compilation-errors.patch badshah400@gmail.com -- Reverted a change to the H5api_adpt.h that caused compilation errors for the C++ HDF5 applications; patch taken from upstream svn
Patch6: hdf5-cpp-compilation-errors.patch
BuildRoot: %{_tmppath}/%{name}-%{version}-build BuildRoot: %{_tmppath}/%{name}-%{version}-build
BuildRequires: gcc-c++ BuildRequires: gcc-c++
%if 0%{?suse_version} > 1140 %if 0%{?suse_version} > 1140
@ -532,7 +541,6 @@ test "%{sonum}" = "${LT_VERS_INTERFACE}" || exit 1
%patch4 -p0 -b .tests-arm %patch4 -p0 -b .tests-arm
%endif %endif
%patch5 -p1 %patch5 -p1
%patch6 -p0
echo "prepare parallel builds: %_mpi" echo "prepare parallel builds: %_mpi"
for build_dir in build %_mpi; do for build_dir in build %_mpi; do

80
update_so_version.sh Normal file
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@ -0,0 +1,80 @@
#!/bin/bash
exit_error()
{
echo "$0: $@" >&2
exit 1
}
dbg()
{
echo "dbg: $@" >&2
}
cleanup()
{
rm -f lt_vers.sh sonum_spec.sed sonum_baselibs.sed
rm -f hdf5.spec.tmp baselibs.conf.tmp
}
## We are going to parse these variables from tarball:
# LT_VERS_INTERFACE
# LT_CXX_VERS_INTERFACE
# LT_F_VERS_INTERFACE
# LT_HL_VERS_INTERFACE
# LT_HL_CXX_VERS_INTERFACE
# LT_HL_F_VERS_INTERFACE
# LT_TOOLS_VERS_INTERFACE
cleanup
VER="$(grep -m1 "^Version:" hdf5.spec)" || exit_error "can't grep version"
read x VER <<<$VER
SRC="$(grep -m1 "^Source0:" hdf5.spec)" || exit_error "can't grep source"
read x SRC <<<$SRC
SRC=$(basename "$SRC" | sed "s/%{version}/$VER/")
test -f "$SRC" || exit_error "tarball '$SRC' does not exist"
dbg "inspecting $SRC"
tar --wildcards -x -O -f "$SRC" "*/config/lt_vers.am" \
| tr -d ' \t' \
| grep "^LT_.*INTERFACE=" \
> lt_vers.sh \
|| exit_error "can't grep interface versions"
# we expect exactly 7 variables
. lt_vers.sh || exit_error "can't source lt_vers.sh"
test $(wc -l < lt_vers.sh) -le "7" \
|| exit_error "more than 7 vars found, update this script!"
for infix in "" _CXX _F _HL _HL_CXX _HL_F _TOOLS; do
var="LT${infix}_VERS_INTERFACE"
test "${!var}" -gt 0 || exit_error "$var='${!var}' bad or undefined"
dbg "update $var=${!var}"
def_sonum="sonum${infix}"
# create sed scripts for spec file and baselibs
echo "s/^%define $def_sonum .*/%define $def_sonum ${!var}/" >> sonum_spec.sed
echo "s/@${def_sonum}@/${!var}/g" >> sonum_baselibs.sed
done
# update spec file if needed
sed -f sonum_spec.sed hdf5.spec > hdf5.spec.tmp
if diff -q hdf5.spec.tmp hdf5.spec &>/dev/null; then
dbg "hdf5.spec was up-to-date"
else
mv hdf5.spec.tmp hdf5.spec
echo "hdf5.spec updated" >&2
fi
# update baselibs if needed
sed -f sonum_baselibs.sed baselibs.conf.in > baselibs.conf.tmp
if diff -q baselibs.conf.tmp baselibs.conf &>/dev/null; then
dbg "baselibs.conf was up-to-date"
else
mv baselibs.conf.tmp baselibs.conf
echo "baselibs.conf updated" >&2
fi
cleanup