Accepting request 318150 from science

- update to 1.8.15

fixed baselibs.conf compared to previous version

OBS-URL: https://build.opensuse.org/request/show/318150
OBS-URL: https://build.opensuse.org/package/show/openSUSE:Factory/hdf5?expand=0&rev=23

baselibs.conf

@@ -1,18 +1,18 @@
-libhdf5-9
+libhdf5-10
 hdf5-devel
   requires -<targettype>
-  requires "libhdf5-9-<targettype> = <version>"
+  requires "libhdf5-10-<targettype> = <version>"
-  requires "libhdf5_hl9-<targettype> = <version>"
+  requires "libhdf5_hl10-<targettype> = <version>"
-libhdf5-9-openmpi
+libhdf5-10-openmpi
 hdf5-openmpi-devel
   requires -openmpi-<targettype>
-  requires "libhdf5-9-openmpi-<targettype> = <version>"
+  requires "libhdf5-10-openmpi-<targettype> = <version>"
-  requires "libhdf5_hl9-openmpi-<targettype> = <version>"
+  requires "libhdf5_hl10-openmpi-<targettype> = <version>"
-libhdf5-9-mvapich2
+libhdf5-10-mvapich2
-libhdf5_hl9
+libhdf5_hl10
-libhdf5_hl9-mvapich2
+libhdf5_hl10-mvapich2
-libhdf5_hl9-openmpi
+libhdf5_hl10-openmpi
 hdf5-mvapich2-devel
   requires -openmpi-<targettype>
-  requires "libhdf5-9-mvapich2-<targettype> = <version>"
+  requires "libhdf5-10-mvapich2-<targettype> = <version>"
-  requires "libhdf5_hl9-mvapich2-<targettype> = <version>"
+  requires "libhdf5_hl10-mvapich2-<targettype> = <version>"

hdf5-1.8.14.tar.bz2

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:53722cb9f5977af2908f92fc1a3f8c597800a5cb448cfe5c75060d6335bb9bab
-size 9503743

hdf5-1.8.15.tar.bz2

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

hdf5-configure-long-double.patch

@@ -1,66 +0,0 @@
-Index: hdf5-1.8.14/configure
-===================================================================
---- hdf5-1.8.14.orig/configure
-+++ hdf5-1.8.14/configure
-@@ -30288,7 +30288,7 @@ else
-             /* Test if the last 2 bytes of mantissa are lost.  Mainly for FreeBSD on Intel
-              * architecture(sleipnir) where it happens. */
-             /*if(endian==0 && c2[0]==0 && c2[1]==0)*/ /*little endian*/
--            if(endian==0 && c2[0]==0) { /*little endian*/
-+            if(endian==0 && size == 12 && c2[0]==0) { /*little endian*/
-                 ret = 1;
-                 goto done;
-             }
-@@ -30307,16 +30307,16 @@ else
-              * instead of 0x0000403effffffffffffffff, 0x0000403efffffffffffffffe, ...,
-              * 0x0000403efffffffffffff000 ...
-              */
--            if(endian==0 && c2_cyg[0]==0 && c2_cyg[1]==0 && c2_cyg[2]==0 && c2_cyg[3]==0)
-+            if(endian==0 && size == 12 && c2_cyg[0]==0 && c2_cyg[1]==0 && c2_cyg[2]==0 && c2_cyg[3]==0)
-                 ret = 1;
- 
-+            if(c2_cyg)
-+                free(c2_cyg);
-     done:
-             if(c1)
-                 free(c1);
-             if(c2)
-                 free(c2);
--            if(c2_cyg)
--                free(c2_cyg);
-             exit(ret);
-         }
- 
-Index: hdf5-1.8.14/configure.ac
-===================================================================
---- hdf5-1.8.14.orig/configure.ac
-+++ hdf5-1.8.14/configure.ac
-@@ -3625,7 +3625,7 @@ else
-             /* Test if the last 2 bytes of mantissa are lost.  Mainly for FreeBSD on Intel
-              * architecture(sleipnir) where it happens. */        
-             /*if(endian==0 && c2[0]==0 && c2[1]==0)*/ /*little endian*/
--            if(endian==0 && c2[0]==0) { /*little endian*/
-+            if(endian==0 && size == 12 && c2[0]==0) { /*little endian*/
-                 ret = 1;
-                 goto done;
-             }
-@@ -3644,16 +3644,16 @@ else
-              * instead of 0x0000403effffffffffffffff, 0x0000403efffffffffffffffe, ..., 
-              * 0x0000403efffffffffffff000 ...
-              */    
--            if(endian==0 && c2_cyg[0]==0 && c2_cyg[1]==0 && c2_cyg[2]==0 && c2_cyg[3]==0)
-+            if(endian==0 && size == 12 && c2_cyg[0]==0 && c2_cyg[1]==0 && c2_cyg[2]==0 && c2_cyg[3]==0)
-                 ret = 1;
- 
-+            if(c2_cyg)
-+                free(c2_cyg);
-     done:
-             if(c1)
-                 free(c1);
-             if(c2)
-                 free(c2);
--            if(c2_cyg)
--                free(c2_cyg);
-             exit(ret);
-         }
-         ], [hdf5_cv_ullong_to_ldouble_precision=yes], [hdf5_cv_ullong_to_ldouble_precision=no],)])

hdf5-non_void_return.patch

@@ -49,19 +49,6 @@ Index: tools/h5copy/h5copy.c
  leave(int ret)
  {
      if (fname_src)
-Index: tools/h5repack/h5repack_main.c
-===================================================================
---- tools/h5repack/h5repack_main.c.orig
-+++ tools/h5repack/h5repack_main.c
-@@ -21,7 +21,7 @@
- #define PROGRAMNAME "h5repack"
- 
- static int parse_command_line(int argc, const char **argv, pack_opt_t* options);
--static void leave(int ret);
-+static void leave(int ret) __attribute__((__noreturn__));
- 
- 
- /* module-scoped variables */
 Index: tools/misc/h5mkgrp.c
 ===================================================================
 --- tools/misc/h5mkgrp.c.orig

hdf5.changes

@@ -1,3 +1,97 @@
+-------------------------------------------------------------------
+Thu Jul 23 11:30:56 UTC 2015 - toddrme2178@gmail.com
+
+- Fix baselibs.conf
+
+-------------------------------------------------------------------
+Wed Jul 22 11:23:14 UTC 2015 - toddrme2178@gmail.com
+
+- update to 1.8.15
+  * New Features
+    + Library
+      - Added Memory Allocation Functions that Use the Library's Allocator
+      - H5Pset_istore_k and H5Pset_sym_k added validation of "ik" to not 
+        exceed the max v1 btree entries (2 bytes) to these two routines.
+      - Added Functions to Control the Value of H5PL_no_plugin_g without 
+        Using an Environment Variable
+    + Parallel Library
+      - Attached an attribute destroy callback to MPI_COMM_SELF that
+        shuts down the HDF5 library when MPI_COMM_SELF is destroyed,
+        in other words, on MPI_Finalize. This should fix several issues 
+        that users see when they forget to close HDF5 objects before 
+    + Fortran API
+      - Added Global Variables. These new global variables are equivalent to 
+        the C definitions  without the '_F':
+        o H5G_UDLINK_F  
+        o H5G_SAME_LOC_F
+        o H5O_TYPE_UNKNOWN_F
+        o H5O_TYPE_GROUP_F
+        o H5O_TYPE_DATASET_F
+        o H5O_NAMED_DATATYPE_F
+        o H5O_TYPE_NTYPES_F
+    + C++ API
+      - New Wrappers for C Functions H5P[s/g]et_libver_bounds
+      - New Wrappers to Get the Object Header's Version
+      - New DataType Constructor
+    + Support for New Platforms, Languages, and Compilers
+      - Support for Linux 3.10.0-123.20.1.el7 added (LK - 2015/04/01) 
+  * Bug Fixes since HDF5-1.8.14
+    + Library
+      - Addition of Error Tracing Functionality to Several C API Calls
+      - H5Rdereference Now Checks for HADDR_UNDEF or Uninitialized References
+      - Fixed Bugs in H5Sextent_copy
+    + Parallel Library
+      - Fixed a Potential Memory Error
+      - Parallel Test Problem Fixed
+      - MPE Support
+    + Tools
+      - h5repack crashed on enumerated 8-bit type.
+      - h52gif crashed non-8bit images.
+      - perform/benchpar.c retired.
+      - Source perform/ directory moved to tools/perform.
+    + Fortran API
+      - Fortran Fails with --enable-fortran2003 and Intel 15.x Compilers
+      - h5tenum_insert_f Does Not Work with Default 8 Byte Integers 
+        (xlf compiler)
+      - Some Fortran APIs Never Returned the Error State
+      - Fixed h5pget_class_f 
+    + C++ API
+      - Combined Two H5File::getObjCount Overloaded Methods
+        The following two methods   
+        o ssize_t getObjCount(unsigned types) const;
+        o ssize_t getObjCount() const;
+        were combined into one:
+        o ssize_t getObjCount(unsigned types = H5F_OBJ_ALL) const;
+      - Many Warnings Were Removed
+      - Functionality Deprecation
+         The following two constructors of classes AbstractDs, IdComponent,
+        H5Location, and H5Object are no longer appropriate after the data member
+        "id" had been moved from IdComponent to the sub-classes in previous
+        releases.
+        o <Classname>(const hid_t h5_id);
+        o <Classname>(const <Classname>& original);
+        The copy constructors were no-op and removed in 1.8.15.  The other
+        constructors will be removed from 1.10 release, and then from 1.8.17
+        if their removal does not cause any problems.
+    + High-Level APIs:
+      - Suppress Warnings from Flex/Bison-generated Code
+      - Changed hdf5_hl.h to Include the HDF5 Main Library "hdf5.h"
+      - H5PTcreate_fl Does Not Convert to Memory Datatype
+      - Fix for H5LT Attribute Functions
+    + Fortran High-Level APIs:
+      - Internal Library Fix for Missing Argument Declaration
+- Build in thread-safe mode to allow parallel reads
+  * These are only unsupported to avoid confusing casual users.  
+    The fotran and C++ libraries don't support thread-safe mode, 
+    while the C library does.  So you have to explicitly allow
+    building the thread-safe C library and the non-thread-safe C++
+    and fortran libraries in order to make sure only people who 
+    have done their research do so.  Since users are going to be
+    accessing this through other programs, this doesn't matter.
+- Build fortran 2003 libraries
+- Rebase hdf5-non_void_return.patch
+- Remove irrelevant hdf5-configure-long-double.patch
+
 -------------------------------------------------------------------
 Mon May 11 13:37:50 UTC 2015 - dmueller@suse.com
 

hdf5.spec

@@ -16,7 +16,7 @@
 #
 
 
-%define hdf5_libver 9
+%define hdf5_libver 10
 %define libname libhdf5
 
 %if 0%{?sles_version}
@@ -29,7 +29,7 @@
 %define _mpi %{?_openmpi:openmpi} %{?_mvapich2:mvapich2}
 
 Name:           hdf5
-Version:        1.8.14
+Version:        1.8.15
 Release:        0
 Summary:        A general purpose library and file format for storing scientific data
 License:        BSD-3-Clause
@@ -44,8 +44,7 @@ Patch2:         hdf5-1.8.11-abort_unknown_host_config.patch
 %ifarch %arm
 Patch4:         hdf5-1.8.10-tests-arm.patch
 %endif
-Patch5:         hdf5-configure-long-double.patch
+Patch5:         hdf5-ldouble-ppc64le.patch
-Patch6:         hdf5-ldouble-ppc64le.patch
 BuildRoot:      %{_tmppath}/%{name}-%{version}-build
 BuildRequires:  gcc-c++
 %if 0%{?suse_version} > 1140
@@ -285,7 +284,6 @@ test "%{hdf5_libver}" = "${LT_VERS_INTERFACE}" || exit 1
 %patch4 -p0 -b .tests-arm
 %endif
 %patch5 -p1
-%patch6 -p1
 
 echo "prepare parallel builds: %_mpi"
 for build_dir in build %_mpi; do
@@ -306,16 +304,29 @@ fi
 test -e config/linux-gnueabi || cp config/linux-gnu config/linux-gnueabi
 %endif
 
+# NOTE: --enable-unsupported is required when --enable-fortran
+# and/or --enable-cxx is enabled along with --enable-threadsafe.
+# Building with thise combination results in thread-safe C 
+# libraries and non-thread-safe fotran and/or C++ libraries. So 
+# you have to explicitly allow building the thread-safe C 
+# library and the non-thread-safe C++ and fortran libraries in 
+# order to make sure people don't assume that their fotran or 
+# C++ code is thread-safe.  Since our users are going to be 
+# accessing this through other programs, this doesn't matter.
+
 pushd build
 %configure \
   --docdir=%{_docdir}/%{name} \
   --disable-dependency-tracking \
 %if 0%{?suse_version} > 1140
   --enable-fortran \
+  --enable-fortran2003 \
 %endif
+  --enable-unsupported \
   --enable-hl \
   --enable-shared \
   --enable-cxx \
+  --enable-threadsafe \
   --with-pthread
 
 make V=1 %{?_smp_mflags}
@@ -339,9 +350,12 @@ export LD_LIBRARY_PATH="%{_libdir}/mpi/gcc/$mpi/%_lib"
   --disable-dependency-tracking \
 %if 0%{?suse_version} > 1140
   --enable-fortran \
+  --enable-fortran2003 \
 %endif
+  --enable-unsupported \
   --enable-hl \
   --enable-shared \
+  --enable-threadsafe \
   --enable-parallel \
   --with-pthread