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@ -4,8 +4,8 @@ HDF5 version 1.10.2-snap0 currently under development
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INTRODUCTION
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This document describes the differences between HDF5-1.10.0-patch1 and
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HDF5 1.10.1, and contains information on the platforms tested and known problems in HDF5-1.10.1.
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This document describes the differences between HDF5-1.11.x and
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HDF5 1.10.1, and contains information on the platforms tested and known problems in HDF5-1.11.x.
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For more details check the HISTORY*.txt files in the HDF5 source.
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@ -28,8 +28,8 @@ in 1.10.1?" document:
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https://support.hdfgroup.org/HDF5/doc/ADGuide/WhatsNew1101.html
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All new and modified APIs are listed in detail in the "HDF5 Software Changes
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from Release to Release" document, in the section "Release 1.8.19 (current
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release) versus Release 1.10.1
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from Release to Release" document, in the section "Release 1.10.1 (current
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release) versus Release 1.11.x
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https://support.hdfgroup.org/HDF5/doc1.10/ADGuide/Changes.html
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@ -42,7 +42,7 @@ CONTENTS
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- New Features
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- Support for new platforms and languages
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- Bug Fixes since HDF5-1.10.0-patch1
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- Bug Fixes since HDF5-1.10.1
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- Supported Platforms
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- Tested Configuration Features Summary
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- More Tested Platforms
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@ -54,13 +54,7 @@ New Features
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Configuration:
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-------------
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- CMake minimum is now 3.2.2.
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(ADB 2017/01/10)
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- Tools folder is separated into source and test folders. This
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allows autotools to skip the make command and just execute
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the make check command.
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(HDFFV-9719 ADB 2016/10/27)
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-
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Library:
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--------
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@ -166,6 +160,7 @@ New Features
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High-Level APIs:
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---------------
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-
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C Packet Table API
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------------------
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@ -182,13 +177,12 @@ Support for new platforms, languages and compilers.
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=======================================
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-
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Bug Fixes since HDF5-1.10.0-patch1 release
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Bug Fixes since HDF5-1.10.1 release
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==================================
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Library
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-------
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- Changed the plugins dlopen option from RTLD_NOW to RTLD_LAZY
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(PR 201 ADB 2016/12/12)
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-
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- Fix error when copying dataset with attribute which is a compound datatype
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consisting of a variable length string.
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@ -208,18 +202,7 @@ Bug Fixes since HDF5-1.10.0-patch1 release
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Configuration
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-------------
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- Configuration will check for the strtoll and strtoull functions
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before using alternatives
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(PR 340 ADB 2017/03/17)
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- CMake uses a Windows pdb directory variable if available and
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will generate both static and shared pdb files.
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(HDFFV-9875 ADB 2017/02/06)
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- CMake now builds shared versions of tools.
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(HDFFV-10123 ADB 2017/02/01)
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Performance
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-
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-------------
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-
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@ -229,11 +212,7 @@ Bug Fixes since HDF5-1.10.0-patch1 release
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Tools
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-----
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- h5diff correctly ignores strpad in comparing strings.
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(HDFFV-10128 ADB 2017/03/03)
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- h5repack now correctly parses the command line filter options.
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(HDFFV-10046 ADB 2017/01/24)
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-
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High-Level APIs:
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------
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@ -285,6 +264,7 @@ Bug Fixes since HDF5-1.10.0-patch1 release
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detail and should not affect applications. (HDFFV-9725) -BMR, 2016/04/25
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Testing
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-------
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-
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@ -437,249 +417,4 @@ The following platforms are not supported but have been tested for this release.
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Known Problems
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==============
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* "make check" fails on CYGWIN when building shared lib files is enabled. The
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default on Cygwin has been changed to disable shared. It can be enabled with
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the --enable-shared configure option but is likely to fail "make check"
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with GCC compilers. (LK -2015/04/16)
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* CLANG compiler with the options -fcatch-undefined-behavior and -ftrapv
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catches some undefined behavior in the alignment algorithm of the macro DETECT_I
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in H5detect.c (Issue 8147). Since the algorithm is trying to detect the alignment
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of integers, ideally the flag -fcatch-undefined-behavior shouldn't to be used for
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H5detect.c. In the future, we can separate flags for H5detect.c from the rest of
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the library. (SLU - 2013/10/16)
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* The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It
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complains with this message:
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"/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined.
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The reason is that __func__ is a predefined identifier in C99 standard. The
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HDF5 C library uses it in H5private.h. The test ttypes.cpp includes
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H5private.h (H5Tpkg.h<-H5Fprivate.h<-H5Vprivate.h<-H5private.h). Sun's 5.9
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C++ compiler doesn't support __func__, thus fails to compile the C++ test.
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But 5.11 C++ compiler does. To check whether your Sun C++ compiler knows this
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identifier, try to compile the following simple C++ program:
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#include<stdio.h>
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int main(void)
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{
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printf("%s\n", __func__);
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return 0;
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}
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(SLU - 2012/11/5)
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* The C++ and FORTRAN bindings are not currently working on FreeBSD with the
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native release 8.2 compilers (4.2.1), but are working with gcc 4.6 from the
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ports (and probably gcc releases after that).
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(QAK - 2012/10/19)
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* The data conversion test dt_arith.c has failures (segmentation fault) from
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"long double" to other datatypes during hard conversion when the library
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is built with the default GCC 4.2.1 on Mac Lion system. It only happens
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with optimization (-O3, -O2, and -O1). Some newer versions of GCC do not
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have this problem. Users should disable optimization or try newer version
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of GCC. (Issue 8017. SLU - 2012/6/12)
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* The data conversion test dt_arith.c fails in "long double" to integer
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conversion on Ubuntu 11.10 (3.0.0.13 kernal) with GCC 4.6.1 if the library
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is built with optimization -O3 or -O2. The older GCC (4.5) or newer kernal
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(3.2.2 on Fedora) doesn't have the problem. Users should lower down the
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optimization level (-O1 or -O0) by defining CFLAGS in the command line of
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"configure" like:
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CFLAGS=-O1 ./configure
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It will overwrite the library's default optimization level. (Issue 7829.
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SLU - 2012/2/7)
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* --with-mpe configure option does not work with Mpich2. AKC - 2011/03/10)
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* While working on the 1.8.6 release of HDF5, a bug was discovered that can
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occur when reading from a dataset in parallel shortly after it has been
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written to collectively. The issue was exposed by a new test in the parallel
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HDF5 test suite, but had existed before that. We believe the problem lies with
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certain MPI implementations and/or filesystems.
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We have provided a pure MPI test program, as well as a standalone HDF5
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program, that can be used to determine if this is an issue on your system.
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They should be run across multiple nodes with a varying number of processes.
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These programs can be found at:
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http://www.hdfgroup.org/ftp/HDF5/examples/known_problems/
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* Parallel mode in AIX will fail some of the testcheck_version.sh tests where
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it treats "exit(134) the same as if process 0 had received an abort signal.
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This is fixed and will be available in the next release. AKC - 2009/11/3
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* The PathScale MPI implementation, accessing a Panasas file system, would
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cause H5Fcreate() with H5F_ACC_EXCL to fail even when the file is not
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existing. This is due to the MPI_File_open() call failing if the amode has
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the MPI_MODE_EXCL bit set. (See bug 1468 for details.) AKC - 2009/8/11
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* Parallel tests failed with 16 processes with data inconsistency at testphdf5
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/ dataset_readAll. Parallel tests also failed with 32 and 64 processes with
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collective abort of all ranks at t_posix_compliant / allwrite_allread_blocks
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with MPI IO. (CMC - 2009/04/28)
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* For SNL, spirit/liberty/thunderbird: The serial tests pass but parallel
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tests failed with MPI-IO file locking message. AKC - 2007/6/25.
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* On Intel 64 Linux cluster (RH 4, Linux 2.6.9) with Intel 10.0 compilers use
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-mp -O1 compilation flags to build the libraries. Higher level of optimization
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causes failures in several HDF5 library tests.
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* For HPUX 11.23 many tools tests failed for 64-bit version when linked to the
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shared libraries (tested for 1.8.0-beta2)
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* For SNL, Red Storm: only paralle HDF5 is supported. The serial tests pass
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and the parallel tests also pass with lots of non-fatal error messages.
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* on SUN 5.10 C++ test fails in the "Testing Shared Datatypes with Attributes" test
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* configuring with --enable-debug=all produces compiler errors on most
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platforms. Users who want to run HDF5 in debug mode should use
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--enable-debug rather than --enable-debug=all to enable debugging
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information on most modules.
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* On Mac OS 10.4, test/dt_arith.c has some errors in conversion from long
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double to (unsigned) long long and from (unsigned)long long to long double.
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* On Altix SGI with Intel 9.0 testmeta.c would not compile with -O3
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optimization flag.
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* On VAX, Scaleoffset filter isn't supported. The filter cannot be applied to
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HDF5 data generated on VAX. Scaleoffset filter only supports IEEE standard
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for floating-point data.
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* On Cray X1, a lone colon on the command line of h5dump --xml (as in
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the testh5dumpxml.sh script) is misinterpereted by the operating system
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and causes an error.
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* On mpich 1.2.5 and 1.2.6, we found that if more than two processes
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contribute no IO and the application asks to do IO with collective, we found
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that when using 4 processors, a simple collective write will be hung
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sometimes. This can be verified with t_mpi test under testpar.
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* The dataset created or rewritten with the v1.6.3 library or after can't
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be read with the v1.6.2 library or before when Fletcher32 EDC(filter) is
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enabled. There was a bug in the calculating code of the Fletcher32
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checksum in the library before v1.6.3. The checksum value wasn't consistent
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between big-endian and little-endian systems. This bug was fixed in
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Release 1.6.3. However, after fixing the bug, the checksum value is no
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longer the same as before on little-endian system. The library release
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after 1.6.4 can still read the dataset created or rewritten with the library
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of v1.6.2 or before. SLU - 2005/6/30
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* For the version 6(6.02 and 6.04) of Portland Group compiler on AMD Opteron
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processor, there's a bug in the compiler for optimization(-O2). The library
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failed in several tests but all related to multi driver. The problem has
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been reported to the vendor.
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* On IBM AIX systems, parallel HDF5 mode will fail some tests with error
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messages like "INFO: 0031-XXX ...". This is from the command poe.
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Set the environment variable MP_INFOLEVEL to 0 to minimize the messages
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and run the tests again.
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The tests may fail with messages like "The socket name is already
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in use". HDF5 does not use sockets (except for stream-VFD). This is
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due to problems of the poe command trying to set up the debug socket.
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Check if there are many old /tmp/s.pedb.* staying around. These are
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sockets used by the poe command and left behind due to failed commands.
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Ask your system administrator to clean them out. Lastly, request IBM
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to provide a mean to run poe without the debug socket.
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* The C++ library's tests fails when compiling with PGI C++ compiler. The
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workaround until the problem is correctly handled is to use the
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flag "--instantiate=local" prior to the configure and build steps, as:
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setenv CXX "pgCC --instantiate=local" for pgCC 5.02 and higher
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* The stream-vfd test uses ip port 10007 for testing. If another
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application is already using that port address, the test will hang
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indefinitely and has to be terminated by the kill command. To try the
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test again, change the port address in test/stream_test.c to one not
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being used in the host.
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* The --enable-static-exec configure flag will only statically link libraries
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if the static version of that library is present. If only the shared version
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of a library exists (i.e., most system libraries on Solaris, AIX, and Mac,
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for example, only have shared versions), the flag should still result in a
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successful compilation, but note that the installed executables will not be
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fully static. Thus, the only guarantee on these systems is that the
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executable is statically linked with just the HDF5 library.
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* With the gcc 2.95.2 compiler, HDF 5 uses the `-ansi' flag during
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compilation. The ANSI version of the compiler complains about not being
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able to handle the `long long' datatype with the warning:
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warning: ANSI C does not support `long long'
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This warning is innocuous and can be safely ignored.
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* Certain platforms give false negatives when testing h5ls:
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- Cray J90 and Cray T90IEEE give errors during testing when displaying
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some floating-point values. These are benign differences due to
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the different precision in the values displayed and h5ls appears to
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be dumping floating-point numbers correctly.
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* Not all platforms behave correctly with szip's shared libraries. Szip is
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disabled in these cases, and a message is relayed at configure time. Static
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libraries should be working on all systems that support szip, and should be
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used when shared libraries are unavailable. There is also a configure error
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on Altix machines that incorrectly reports when a version of szip without
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an encoder is being used.
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* On some platforms that use Intel and Absoft compilers to build HDF5 fortran library,
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compilation may fail for fortranlib_test.f90, fflush1.f90 and fflush2.f90
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complaining about exit subroutine. Comment out the line
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IF (total_error .ne. 0) CALL exit (total_error)
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* Information about building with PGI and Intel compilers is available in
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INSTALL file sections 5.7 and 5.8
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* On at least one system, (SDSC DataStar), the scheduler (in this case
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LoadLeveler) sends job status updates to standard error when you run
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any executable that was compiled with the parallel compilers.
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This causes problems when running "make check" on parallel builds, as
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many of the tool tests function by saving the output from test runs,
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and comparing it to an exemplar.
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The best solution is to reconfigure the target system so it no longer
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inserts the extra text. However, this may not be practical.
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In such cases, one solution is to "setenv HDF5_Make_Ignore yes" prior to
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the configure and build. This will cause "make check" to continue after
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detecting errors in the tool tests. However, in the case of SDSC DataStar,
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it also leaves you with some 150 "failed" tests to examine by hand.
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A second solution is to write a script to run serial tests and filter
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out the text added by the scheduler. A sample script used on SDSC
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DataStar is given below, but you will probably have to customize it
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for your installation.
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Observe that the basic idea is to insert the script as the first item
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on the command line which executes the the test. The script then
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executes the test and filters out the offending text before passing
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it on.
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#!/bin/csh
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set STDOUT_FILE=~/bin/serial_filter.stdout
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set STDERR_FILE=~/bin/serial_filter.stderr
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rm -f $STDOUT_FILE $STDERR_FILE
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($* > $STDOUT_FILE) >& $STDERR_FILE
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set RETURN_VALUE=$status
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cat $STDOUT_FILE
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tail +3 $STDERR_FILE
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exit $RETURN_VALUE
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You get the HDF make files and test scipts to execute your filter script
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by setting the environment variable "RUNSERIAL" to the full path of the
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script prior to running configure for parallel builds. Remember to
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"unsetenv RUNSERIAL" before running configure for a serial build.
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Note that the RUNSERIAL environment variable exists so that we can
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can prefix serial runs as necessary on the target system. On DataStar,
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no prefix is necessary. However on an MPICH system, the prefix might
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have to be set to something like "/usr/local/mpi/bin/mpirun -np 1" to
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get the serial tests to run at all.
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In such cases, you will have to include the regular prefix in your
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filter script.
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* H5Ocopy() does not copy reg_ref attributes correctly when shared-message
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is turn on. The value of the reference in the destination attriubte is
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wrong. This H5Ocopy problem will affect h5copy tool
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lrknox