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CVS commit: pkgsrc/devel/hdf5
Module Name: pkgsrc
Committed By: alnsn
Date: Sat Dec 3 18:56:36 UTC 2016
Modified Files:
pkgsrc/devel/hdf5: Makefile.common distinfo
Log Message:
Update devel/hdf5 and devel/hdf5-c++ to version 1.8.18.
New Features
============
Configuration
-------------
- CMake: Added NAMESPACE hdf5:: to package configuration files to allow
projects using installed HDF5 binaries built with CMake to link with
them without specifying the HDF5 library location via IMPORTED_LOCATION.
(ADB, 2016/10/17, HDFFV-10003)
- CMake: Changed the CTEST_BUILD_CONFIGURATION option to
CTEST_CONFIGURATION_TYPE as recommended by the CMake documentation.
(ADB, 2016/10/17, HDFFV-9971)
- CMake: Added support for GIT
(ADB, 2016/07/12)
Bug Fixes since HDF5-1.8.17
===========================
Configuration
-------------
- Fixed a problem preventing HDF5 to be built on 32-bit CYGWIN by
condensing cygwin configuration files into a single file and
removing outdated compiler settings.
(ABD, 2016/07/12, HDFFV-9946)
- CMake: Fixed a command length overflow error by converting custom
commands inside CMakeTest.cmake files into regular dependencies and
targets.
(ABD, 2016/07/12, HDFFV-9939)
- CMake: Fixed a timeout error that would occasionally occur when running
the virtual file driver tests simultaneously due to test directory and file
name collisions.
(ABD, 2016/09/19, HDFFV-9431)
Library
-------
- Fixed a memory leak that would occur when the library allocated memory
for an external file prefix (H5Pset_efile_prefix) and failed to free it.
(DER, 2016/04/29)
- Fixed an error that would occur when calling H5Adelete on an attribute
which is attached to an externally linked object in the target file and
whose datatype is a committed datatype in the main file.
(VC, 2016-07-04, HDFFV-9940)
- Fixed a problem where a plugin compiled into a DLL in the default plugin
directory could not be found by the HDF5 library at runtime on Windows
when the HDF5_PLUGIN_PATH environment variable was not set.
(ABD, 2016/08/01, HDFFV-9706)
- Fixed an issue where H5Pset_alignment could result in misaligned blocks
with some input combinations, causing an assertion failure in debug mode.
(NAF, 2016/08/11, HDFFV-9948)
- A number of issues were fixed when reading/writing from/to corrupted
files to ensure that the library fails gracefully in these cases:
* Writing to a corrupted file that has an object message which is
incorrectly marked as sharable on disk results in a buffer overflow /
invalid write instead of a clean error message.
* Decoding data from a corrupted file with a dataset encoded with the
H5Z_NBIT decoding can result in a code execution vulnerability under
the context of the application using the HDF5 library.
* When decoding an array datatype from a corrupted file, the HDF5 library
fails to return an error in production if the number of dimensions
decoded is greater than the maximum rank.
* When decoding an "old style" array datatype from a corrupted file, the
HDF5 library fails to return an error in production if the number of
dimensions decoded is greater than the maximum rank.
(NAF, 2016/10/06, HDFFV-9950, HDFFV-9951, HDFFV-9992, HDFFV-9993)
- Fixed an error that would occur when copying an object with an attribute
which is a compound datatype consisting of a variable length string.
(VC, 2016-10-17, HDFFV-7991)
Parallel Library
----------------
- Fixed a bug that could occur when allocating a chunked dataset in parallel
with an alignment set and an alignment threshold greater than the chunk
size but less than or equal to the raw data aggregator size.
(NAF, 2016/08/11, HDFFV-9969)
Performance
-------------
- None
Tools
-----
- Fixed an error in the compiler wrapper scripts (h5cc, h5fc, et al.)
in which they would erroneously drop the file argument specified via
the -o flag when the -o flag was specified before the -c flag on the
command line, resulting in a failure to compile.
(LRK, 2016/06/08, HDFFV-9938, HDFFV-9530)
- h5repack User Defined (UD) filter parameters were not parsed correctly.
The UD filter parameters were not being parsed correctly. Reworked coding
section to parse the correct values and verify number of parameters.
(ADB, 2016/10/19, HDFFV-9996, HDFFV-9974, HDFFV-9515, HDFFV-9039)
Fortran API
-----------
- Fortran library fails to compile and fails tests with NAG compiler.
* Removed the non-standard assumption that KIND=SIZEOF, in the HDF5
configure programs.
* Removed Fortran 66 character/integer conversions from tests.
* Removed the use of C_SIZEOF in the test programs
* Changed to using STORAGE_SIZE in the test programs if available. Otherwise,
uses C_SIZEOF or SIZEOF.
(MSB, 2016/9/22, HDFFV-9973)
- Fortran segfaults for F03 tests with NAG compiler
* Removed INTENT(OUT) from 'fillvalue' in F2003 interface
for H5Pget_fill_value_f.
(MSB, 2016/9/22, HDFFV-9980)
C++ API
-------
- The macro H5_NO_NAMESPACE is deprecated from the HDF5 C++ API library.
In future releases, the macros H5_NO_STD and OLD_HEADER_FILENAME may
also be removed.
(BMR, 2016/10/27, HDFFV-9532)
High-Level APIs:
---------------
- The high-level API Packet Table (PT) did not write data correctly when
the datatype is a compound type that has string type as one of the
members. This problem started in 1.8.15, after the fix of HDFFV-9042
was applied, which caused the Packet Table to use native type to access
the data. It should be up to the application to specify whether the
buffer to be read into memory in the machine’s native architecture.
Thus, the PT is fixed to not use native type but to make a copy of the
user's provided datatype during creation or the packet table's datatype
during opening. If an application wishes to use native type to read the
data, then the application will request that. However, the Packet Table
doesn't provide a way to specify memory datatype in this release. This
feature will be available in future releases, HDFFV-10023.
(BMR, 2016/10/27, HDFFV-9758)
Fortran High-Level APIs:
------------------------
- None
Testing
-------
- None
Supported Platforms
===================
The following platforms are supported and have been tested for this release.
They are built with the configure process unless specified otherwise.
Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(platypus/mayll) Version 4.4.7 20120313
Versions 4.8.4, 4.9.3, 5.2.0
PGI C, Fortran, C++ for 64-bit target on
x86-64;
Version 15.7-0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 15.0.3.187 Build 20150407
MPICH 3.1.4 compiled with GCC 4.9.3
Linux 2.6.32-573.18.1.el6 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
#1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
(ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-16)
IBM XL C/C++ V13.1
IBM XL Fortran V15.1
Linux 3.10.0-327.10.1.el7 GNU C (gcc), Fortran (gfortran), C++ (g++)
#1 SMP x86_64 GNU/Linux compilers:
(kituo/moohan) Version 4.8.5 20150623 (Red Hat 4.8.5-4)
Versions 4.9.3, 5.2.0
Intel(R) C (icc), C++ (icpc), Fortran (icc)
compilers:
Version 15.0.3.187 Build 20150407
MPICH 3.1.4 compiled with GCC 4.9.3
SunOS 5.11 32- and 64-bit Sun C 5.12 SunOS_sparc
(emu) Sun Fortran 95 8.6 SunOS_sparc
Sun C++ 5.12 SunOS_sparc
Windows 7 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Cygwin(CYGWIN_NT-6.1 2.2.1(0.289/5/3) gcc(4.9.3) compiler and gfortran)
(cmake and autotools)
Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake)
Visual Studio 2013 w/ Intel Fortran 15 (cmake)
Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Windows 10 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 16 (cmake)
Mac OS X Mt. Lion 10.8.5 Apple LLVM version 5.1 (clang-503.0.40)
64-bit gfortran GNU Fortran (GCC) 4.8.2
(swallow/kite) Intel icc/icpc/ifort version 15.0.3
Mac OS X Mavericks 10.9.5 Apple LLVM version 6.0 (clang-600.0.57)
64-bit gfortran GNU Fortran (GCC) 4.9.2
(wren/quail) Intel icc/icpc/ifort version 15.0.3
Mac OS X Yosemite 10.10.5 Apple LLVM version 6.1 (clang-602.0.53)
64-bit gfortran GNU Fortran (GCC) 4.9.2
(osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3
Mac OS X El Capitan 10.11.4 Apple LLVM version 7.3.0 (clang-703.0.29)
64-bit gfortran GNU Fortran (GCC) 5.2.0
(VM osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2
Tested Configuration Features Summary
=====================================
In the tables below
y = tested
n = not tested in this release
C = Cluster
W = Workstation
x = not working in this release
dna = does not apply
( ) = footnote appears below second table
<blank> = testing incomplete on this feature or platform
Platform C F90/ F90 C++ zlib SZIP
parallel F2003 parallel
SunOS 5.11 32-bit n y/y n y y y
SunOS 5.11 64-bit n y/y n y y y
Windows 7 y y/y n y y y
Windows 7 x64 y y/y n y y y
Windows 7 Cygwin n y/y n y y n
Windows 10 n y/y n y y y
Windows 10 x64 n y/y n y y y
Mac OS X Mountain Lion 10.8.5 64-bit n y/y n y y y
Mac OS X Mavericks 10.9.5 64-bit n y/y n y y y
Mac OS X Yosemite 10.10.5 64-bit n y/y n y y y
AIX 6.1 32- and 64-bit n y/n n y y y
CentOS 6.7 Linux 2.6.32 x86_64 GNU y y/y y y y y
CentOS 6.7 Linux 2.6.32 x86_64 Intel n y/y n y y y
CentOS 6.7 Linux 2.6.32 x86_64 PGI n y/y n y y y
CentOS 7.1 Linux 3.10.0 x86_64 GNU y y/y y y y y
CentOS 7.1 Linux 3.10.0 x86_64 Intel n y/y n y y y
Linux 2.6.32-431.11.2.el6.ppc64 n y/n n y y y
Platform Shared Shared Shared Thread-
C libs F90 libs C++ libs safe
SunOS 5.11 32-bit y y y y
SunOS 5.11 64-bit y y y y
Windows 7 y y y y
Windows 7 x64 y y y y
Windows 7 Cygwin n n n y
Windows 10 y y y y
Windows 10 x64 y y y y
Mac OS X Mountain Lion 10.8.5 64-bit y n y y
Mac OS X Mavericks 10.9.5 64-bit y n y y
Mac OS X Yosemite 10.10.5 64-bit y n y y
AIX 6.1 32- and 64-bit y n n y
CentOS 6.7 Linux 2.6.32 x86_64 GNU y y y y
CentOS 6.7 Linux 2.6.32 x86_64 Intel y y y y
CentOS 6.7 Linux 2.6.32 x86_64 PGI y y y y
CentOS 7.1 Linux 3.10.0 x86_64 GNU y y y y
CentOS 7.1 Linux 3.10.0 x86_64 Intel y y y y
Linux 2.6.32-431.11.2.el6.ppc64 y y y y
Compiler versions for each platform are listed in the preceding
"Supported Platforms" table.
More Tested Platforms
=====================
The following platforms are not supported but have been tested for this release.
Linux 2.6.32-573.22.1.el6 g95 (GCC 4.0.3 (g95 0.94!)
#1 SMP x86_64 GNU/Linux
(platypus)
Debian8.4.0 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux
gcc (Debian 4.9.2-10) 4.9.2
GNU Fortran (Debian 4.9.2-10) 4.9.2
(cmake and autotools)
Fedora24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
gcc (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
GNU Fortran (GCC) 6.1.1 20160621 (Red Hat 6.1.1-3)
(cmake and autotools)
CentOS 7.2 3.10.0-327.28.2.el7.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux
gcc (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
GNU Fortran (GCC) 4.8.5 20150623 (Red Hat 4.8.5-4)
(cmake and autotools)
Ubuntu 16.04 4.4.0-38-generic #62-Ubuntu SMP x86_64 GNU/Linux
gcc (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) 5.4.0
(cmake and autotools)
Known Problems
==============
* On windows platforms in debug configurations, the VFD flush1 tests will fail
with the split and multi VFD drivers. These tests will display a modal debug
dialog which must be answered or wait for the test timeout to expire.
(ADB - 2014/06/23 - HDFFV-8851)
* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
catches some undefined behavior in the alignment algorithm of the macro DETECT_I
in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment
of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for
H5detect.c. In the future, we can separate flags for H5detect.c from the rest of
the library. (SLU - 2013/10/16)
* Make provided by Solaris fails in "make check". Solaris users should use
gmake to build and install the HDF5 software. (AKC - 2013/10/08 - HDFFV-8534)
* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
ports (and probably gcc releases after that).
(QAK - 2012/10/19)
* The following h5dump test case fails in BG/P machines (and potentially other
machines that use a command script to launch executables):
h5dump --no-compact-subset -d "AHFINDERDIRECT::ah_centroid_t[0] it=0 tl=0"
tno-subset.h5
This is due to the embedded spaces in the dataset name being interpreted
by the command script launcher as meta-characters, thus passing three
arguments to h5dump's -d flag. The command passes if run by hand, just
not via the test script.
(AKC - 2012/05/03)
* The STDIO VFD does not work on some architectures, possibly due to 32/64
bit or large file issues. The basic STDIO VFD test is known to fail on
64-bit SunOS 5.10 on SPARC when built with -m64 and 32-bit OS X/Darwin
10.7.0. The STDIO VFD test has been disabled while we investigate and
a fix should appear in a future release.
(DER - 2011/10/14 - HDFFV-8235)
* h5diff can report inconsistent results when comparing datasets of enum type
that contain invalid values. This is due to how enum types are handled in
the library and will be addressed in a future release.
(DER - 2011/10/14 - HDFFV-7527)
* The links test can fail under the stdio VFD due to some issues with external
links. This will be investigated and fixed in a future release.
(DER - 2011/10/14 - HDFFV-7768)
* After the shared library support was fixed for some bugs, it was discovered
that "make prefix=XXX install" no longer works for shared libraries. It
still works correctly for static libraries. Therefore, if you want to
install the HDF5 shared libraries in a location such as /usr/local/hdf5,
you need to specify the location via the --prefix option during configure
time. E.g, ./configure --prefix=/usr/local/hdf5 ...
(AKC - 2011/05/07 - HDFFV-7583)
* The parallel test, t_shapesame, in testpar/, may run for a long time and may
be terminated by the alarm signal. If that happens, one can increase the
alarm seconds (default is 1200 seconds = 20 minutes) by setting the
environment variable, $HDF5_ALARM_SECONDS, to a larger value such as 3600
(60 minutes). Note that the t_shapesame test may fail in some systems
(see the "While working on the 1.8.6 release..." problem below). If
it does, it will waste more time if $HDF5_ALARM_SECONDS is set
to a larger value.
(AKC - 2011/05/07)
* Shared Fortran libraries are not quite working on AIX. While they are
generated when --enable-shared is specified, the fortran and hl/fortran
tests fail. the issue. HL and C++ shared libraries should now be
working as intended, however.
(MAM - 2011/04/20)
* While working on the 1.8.6 release of HDF5, a bug was discovered that can
occur when reading from a dataset in parallel shortly after it has been
written to collectively. The issue was exposed by a new test in the parallel
HDF5 test suite, but had existed before that. We believe the problem lies with
certain MPI implementations and/or file systems.
We have provided a pure MPI test program, as well as a standalone HDF5
program, that can be used to determine if this is an issue on your system.
They should be run across multiple nodes with a varying number of processes.
These programs can be found at:
http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
(NAF - 2011/01/19)
* All the VFL drivers aren't backward compatible. In H5FDpublic.h, the
structure H5FD_class_t changed in 1.8. There is new parameter added to
get_eoa and set_eoa callback functions. A new callback function
get_type_map was added in. The public function H5FDrealloc was taken
out in 1.8. The problem only happens when users define their own driver
for 1.6 and try to plug in 1.8 library. Because there's only one user
complaining about it, we (Elena, Quincey, and I) decided to leave it as
it is (see bug report #1279). Quincey will make a plan for 1.10.
(SLU - 2010/02/02)
* The --enable-static-exec configure flag will only statically link libraries
if the static version of that library is present. If only the shared version
of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
for example, only have shared versions), the flag should still result in a
successful compilation, but note that the installed executables will not be
fully static. Thus, the only guarantee on these systems is that the
executable is statically linked with just the HDF5 library.
(MAM - 2009/11/04)
* A dataset created or rewritten with a v1.6.3 library or after cannot be read
with the v1.6.2 library or before when the Fletcher32 EDC filter is enabled.
There was a bug in the calculation of the Fletcher32 checksum in the
library before v1.6.3; the checksum value was not consistent between big-
endian and little-endian systems. This bug was fixed in Release 1.6.3.
However, after fixing the bug, the checksum value was no longer the same as
before on little-endian system. Library releases after 1.6.4 can still read
datasets created or rewritten with an HDF5 library of v1.6.2 or before.
(SLU - 2005/06/30)
To generate a diff of this commit:
cvs rdiff -u -r1.13 -r1.14 pkgsrc/devel/hdf5/Makefile.common
cvs rdiff -u -r1.37 -r1.38 pkgsrc/devel/hdf5/distinfo
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
Modified files:
Index: pkgsrc/devel/hdf5/Makefile.common
diff -u pkgsrc/devel/hdf5/Makefile.common:1.13 pkgsrc/devel/hdf5/Makefile.common:1.14
--- pkgsrc/devel/hdf5/Makefile.common:1.13 Sun Oct 9 18:44:35 2016
+++ pkgsrc/devel/hdf5/Makefile.common Sat Dec 3 18:56:36 2016
@@ -1,10 +1,10 @@
-# $NetBSD: Makefile.common,v 1.13 2016/10/09 18:44:35 alnsn Exp $
+# $NetBSD: Makefile.common,v 1.14 2016/12/03 18:56:36 alnsn Exp $
# used by devel/hdf5/Makefile
# used by devel/hdf5-c++/Makefile
-DISTNAME= hdf5-1.8.17
+DISTNAME= hdf5-1.8.18
CATEGORIES= devel
-MASTER_SITES= ftp://ftp.hdfgroup.org/HDF5/current/src/
+MASTER_SITES= ftp://ftp.hdfgroup.org/HDF5/current18/src/
EXTRACT_SUFX= .tar.bz2
MAINTAINER= pkgsrc-users%NetBSD.org@localhost
Index: pkgsrc/devel/hdf5/distinfo
diff -u pkgsrc/devel/hdf5/distinfo:1.37 pkgsrc/devel/hdf5/distinfo:1.38
--- pkgsrc/devel/hdf5/distinfo:1.37 Sun Oct 9 18:44:35 2016
+++ pkgsrc/devel/hdf5/distinfo Sat Dec 3 18:56:36 2016
@@ -1,9 +1,9 @@
-$NetBSD: distinfo,v 1.37 2016/10/09 18:44:35 alnsn Exp $
+$NetBSD: distinfo,v 1.38 2016/12/03 18:56:36 alnsn Exp $
-SHA1 (hdf5-1.8.17.tar.bz2) = 640f1a46cb1b353339695355b4fca42df05be765
-RMD160 (hdf5-1.8.17.tar.bz2) = a7e45f68896d4ad56faff0b94800904e2f377321
-SHA512 (hdf5-1.8.17.tar.bz2) = b0fe630b98a83470c48443215b7073fd22c4390cc459127a4c9554682ae8aec215017c7f34adb8494da4b31fabe6580e9d1b63eddb949432d595e99705c0bbd1
-Size (hdf5-1.8.17.tar.bz2) = 10030234 bytes
+SHA1 (hdf5-1.8.18.tar.bz2) = d7e008cbfcf5cb6913b5327a81bbcaf34cc9436d
+RMD160 (hdf5-1.8.18.tar.bz2) = a3910b7129f80080c0574bb798f6d40849724005
+SHA512 (hdf5-1.8.18.tar.bz2) = 01f6d14bdd3be2ced9c63cc9e1820cd7ea11db649ff9f3a3055c18c4b0fffe777fd23baad536e3bce31c4d76fe17db64a3972762e1bb4d232927c1ca140e72b2
+Size (hdf5-1.8.18.tar.bz2) = 10081294 bytes
SHA1 (patch-bin_cmakehdf5) = c31107e3f67dd2b58318ebc94e6044c8c76df049
SHA1 (patch-c++_examples_Makefile.in) = 2b62c0b30258fcce5e22b5932bd400ca5897e0c3
SHA1 (patch-c++_examples_run-c++-ex.sh.in) = f0605ce2cf35e72f47a1c848aa637342eab65070
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