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462 lines
20 KiB
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462 lines
20 KiB
Plaintext
HDF5 version 1.9.0 currently under development
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================================================================================
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INTRODUCTION
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This document describes the differences between HDF5-1.9.0 and
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HDF5 1.9.x snapshot, and contains information on the platforms
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tested and known problems in HDF5-1.9.x.
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For more details check the HISTORY*.txt files in the HDF5 source.
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Links to HDF5 1.9.x source code can be found on THG's development
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FTP server at the following location:
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ftp://ftp.hdfgroup.uiuc.edu/pub/outgoing/hdf5/snapshots
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User documentation for the snapshot can be accessed directly at this location:
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http://www.hdfgroup.uiuc.edu/HDF5/doc_dev_snapshot/H5_dev/
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For more information, see the HDF5 home page:
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http://www.hdfgroup.org/HDF5/
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If you have any questions or comments, please send them to the HDF Help Desk:
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help@hdfgroup.org
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CONTENTS
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- New Features
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- Support for new platforms and languages
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- Bug Fixes since HDF5-1.8.0
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- Platforms Tested
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- Known Problems
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New Features
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============
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Configuration:
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-------------
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Library:
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--------
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Parallel Library:
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-----------------
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Fortran Library:
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----------------
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C++ Library:
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----------------
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Tools:
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------
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High-Level APIs:
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------
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Documentation
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-------------
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Support for new platforms, languages and compilers.
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=======================================
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Bug Fixes since HDF5-1.8.0 release
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==================================
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Library
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-------
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Configuration
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-------------
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Performance
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-------------
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Tools
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-----
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- Fixed bug in h5diff that prevented datasets & attributes with
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variable-length string elements from comparing correctly.
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(QAK - 2008/02/28)
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- h5import bug on Windows w/binary datasets. fread in windows needs a
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binary file to be open with 'rb' instead of 'r' otherwise it
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terminates execution if an end of file character is found on the
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input file. Besides that the binary file generated needs to be open
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with 'wb' , otherwise an end of line character is read twice.
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(PVN - 2008/02/19)
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Documentation
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-------------
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F90 APIs
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--------
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Platforms Tested
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================
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AIX 5.2 (32/64 bit) xlc 8.0.0.11
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xlC 8.0
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xlf 10.01.0000.0
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mpcc_r 6.0.0.8
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mpxlf_r 8.1.1.7
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FreeBSD 6.2-STABLE i386 gcc 3.4.6 [FreeBSD] 20060305
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(duty) g++ 3.4.6 [FreeBSD] 20060305
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gcc 4.2.1 20080123
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g++ 4.2.1 20080123
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gfortran 4.2.1 20070620
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FreeBSD 6.2-STABLE amd64 gcc 3.4.6 [FreeBSD] 20060305
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(liberty) g++ 3.4.6 [FreeBSD] 20060305
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gcc 4.2.1 20080123
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g++ 4.2.1 20080123
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gfortran 4.2.1 20080123
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IRIX64 6.5 (64 & n32) MIPSpro cc 7.4.4m
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F90 MIPSpro 7.4.4m
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C++ MIPSpro cc 7.4.4m
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Linux 2.6.9 (RHEL4) Intel 10.0 compilers
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(abe.ncsa.uiuc.edu)
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Linux 2.4.21-47 gcc 3.2.3 20030502
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(osage)
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Linux 2.6.9-42.0.10 gcc 3.4.6 20060404
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(kagiso) PGI 7.0-7 (pgcc, pgf90, pgCC)
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Intel 9.1 (icc, ifort, icpc)
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Linux 2.6.16.27 x86_64 AMD gcc 4.1.0 (SuSE Linux), g++ 4.1.0, g95 (GCC 4.0.3)
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(smirom) PGI 6.2-5 (pgcc, pgf90, pgCC)
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Intel 9.1 (icc, iort, icpc)
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Linux 2.6.5-7.252.1-rtgfx #1
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SMP ia64 Intel(R) C++ Version 9.0
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(cobalt) Intel(R) Fortran Itanium(R) Version 9.0
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SGI MPI
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SunOS 5.8 32,46 Sun WorkShop 6 update 2 C 5.3
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(Solaris 2.8) Sun WorkShop 6 update 2 Fortran 95 6.2
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Sun WorkShop 6 update 2 C++ 5.3
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SunOS 5.10 cc: Sun C 5.8
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(linew) f90: Sun Fortran 95 8.2
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CC: Sun C++ 5.8
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Xeon Linux 2.4.21-32.0.1.ELsmp-perfctr-lustre
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(tungsten) gcc 3.2.2 20030222
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Intel(R) C++ Version 9.0
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Intel(R) Fortran Compiler Version 9.0
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IA-64 Linux 2.4.21.SuSE_292.til1 ia64
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(NCSA tg-login) gcc 3.2.2
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Intel(R) C++ Version 8.1
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Intel(R) Fortran Compiler Version 8.1
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mpich-gm-1.2.5..10-intel-r2
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Windows XP
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Visual Studio .NET
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Visual Studio 2005 w/ Intel Fortran 9.1
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Cygwin(native gcc compiler and g95)
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MinGW(native gcc compiler and g95)
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Windows XP x64
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Visual Studio 2005 w/ Intel Fortran 9.1
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Windows Vista
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Visual Studio 2005
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MAC OS 10.4 (Intel) gcc i686-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1
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G95 (GCC 4.0.3 (g95 0.91!) Nov 21 2006)
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Alpha Open VMS 7.3
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Supported Configuration Features Summary
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========================================
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In the tables below
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y = tested and supported
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n = not supported or not tested in this release
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x = not working in this release
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( ) = footnote appears below second table
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<blank> = testing incomplete on this feature or platform
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W or C indicates workstation or cluster, respectively.
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Platform C F90 F90 C++ zlib SZIP
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parallel parallel
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SunOS5.8 64-bit n y n y y y
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SunOS5.8 32-bit n y n y y y
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SunOS5.10 64-bit n y n y y y
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SunOS5.10 32-bit n y n y y y
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IRIX64_6.5 64-bit n y y y y y
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IRIX64_6.5 32-bit n n n n y y
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AIX-5.2 32-bit y y y y y y
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AIX-5.2 64-bit y y y y y y
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Cray XT3 (not tested
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for this release) n n n n n n
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Windows XP n y(3) n(3) y y y
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Windows XP x64 n y(3) n(3) y y y
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Windows Vista n n n y y y
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Mac OS X 10.4 PowerPC n n
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Mac OS X 10.4 Intel n y n y y y
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FreeBSD 6.2 32-bit n n n y y y
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FreeBSD 6.2 64-bit
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RedHat EL4 2.6.9 i686 GNU W y(2) y(4) y(2) y y y
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RedHat EL4 2.6.9 i686 Intel W n y n y y n
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RedHat EL4 2.6.9 i686 PGI W n y n y y n
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SuSe Linux 2.6.16 x86_64 GNU (5) W y(2) y n y y y
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SuSe Linux 2.6.16 x86_64 Int (5) W n y n y n n
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SuSe Linux 2.6.16 x86_64 PGI (5) W n y n y n n
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RHL9 Linux 2.4 Xeon Lustre Intel C n y n y y n
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RHEL3 Linux 2.4 Xeon Intel W n y n n y n
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RHEL4 Linux 2.6 Xeon Lustre Int C n y n y y n
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SuSE Linux 2.4 ia64 Intel C y(1) y y y y y
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SuSe Linux 2.6.5
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SGI Altix ia64 Intel C n y n y n y
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Alpha OpenVMS 7.3.2 n y n y n n
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Platform Shared Shared Shared static- Thread-
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C libs F90 libs C++ libs exec safe
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SunOS 5.8 32-bit y y y x y
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SunOS 5.8 64-bit y y y x y
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SunOS 5.10 32-bit y y y x y
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SunOS 5.10 64-bit y y y x y
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IRIX64_6.5 32-bit y n y x y
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IRIX64_6.5 64-bit y y n x y
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AIX-5.2 32-bit n n n x n
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AIX-5.2 64-bit n n n x n
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Cray XT3 (not tested
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for this release) n n n x n
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Windows XP y y(3) y y y
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Windows XP x64 y y(3) y y y
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Windows Vista y n n y y
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Mac OS X 10.4 Intel Duo y y y x n
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FreeBSD 6.2 32-bit y y y x n
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FreeBSD 6.2 64-bit y y y x n
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RHEL4 2.6.9 i686 GNU W y y(4) y x y
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RHEL4 2.6.9 i686 Intel W y y y x n
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RHEL4 2.6.9 i686 PGI W y y y x n
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SuSE Linux 2.6.16 x86_64 GNU (5) W y y y x y
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SuSE Linux 2.6.16 x86_64 Intel(5) W y y y x n
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SuSE Linux 2.6.16 x86_64 PGI(5) W y y y x n
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RHL9 Linux 2.4 Xeon Lustre Intel C y y y x n
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RHEL3 Linux 2.4 Xeon Intel W y n n x n
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RHEL4 Linux 2.6 Xeon Lustre Intel C y y y x n
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SuSE Linux 2.4 ia64 Intel C y y y x n
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SuSe Linux 2.6.5
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SGI Altix ia64 Intel C n n n x n
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Notes: (1) Using mpich 1.2.6.
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(2) Using mpich2 1.0.6.
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(3) Using Visual Studio 2005 or Cygwin
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(4) With PGI and Absoft compilers.
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(5) AMD Opteron x86_64
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Compiler versions for each platform are listed in the preceding
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"Platforms Tested" table.
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Known Problems
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==============
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* We discovered two problems when running collective IO parallel HDF5 tests
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with chunking storage on ChaMPIon MPI compiler on tungsten, a linux
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cluster at NCSA.
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Under some complex selection cases,
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1) MPI_Get_element returns the wrong value.
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2) MPI_Type_struct also generates wrong derived data type and corrupt data
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may be generated.
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This only happens when turning on collective IO with chunking storage
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with some complex selections. We haven't found these problems on other
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MPI-IO compilers. If you encounter these problems, you may use Independent IO
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instead.
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Change the following line in your code:
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H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_COLLECTIVE);
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to
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H5Pset_dxpl_mpio(xfer_plist, H5FD_MPIO_INDEPENDENT);
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KY - 2007/08/24
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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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* For LLNL, uP: both serial and parallel pass. Zeus: serial passes but
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parallel fails with a known proglem in MPI. ubgl: serial passes but
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parallel fails.
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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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* On IRIX6.5, when C compiler version >7.4, the complicate MPI derived data type
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code will work. However, the user should be aware to enlarge MPI_TYPE_MAX environment
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variable to some certian value in order to use collective irregular selection code.
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For example, the current parallel HDF5 test needs to enlarge MPI_TYPE_MAX to
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200,000 to make the test pass.
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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 fails to compile for Solaris
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platforms. This is due to the fact that not all of the system
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libraries on Solaris are available in a static format.
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The --enable-static-exec configure flag also fails to correctly compile
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on IBM SP2 platform for the serial mode. The parallel mode works fine
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with this option.
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It is suggested that you don't use this option on these platforms
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during configuration.
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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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* The Stream VFD was not tested yet under Windows. It is not supported
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in the TFLOPS machine.
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* The ./dsets tests failed in the TFLOPS machine if the test program,
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dsets.c, is compiled with the -O option. The hdf5 library still works
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correctly with the -O option. The test program works fine if it is
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compiled with -O1 or -O0. Only -O (same as -O2) causes the test
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program to fail.
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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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