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author | Vailin Choi <vchoi@hdfgroup.org> | 2013-04-19 17:24:43 (GMT) |
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committer | Vailin Choi <vchoi@hdfgroup.org> | 2013-04-19 17:24:43 (GMT) |
commit | 0e1e79f0e02606364018806d465d48eed8ffd153 (patch) | |
tree | c7bffe852a3f284a397638536558b2a198a8bfdb /release_docs | |
parent | 14d8e1c2b5ecaf2e298984f269094dd5f2bd735f (diff) | |
download | hdf5-0e1e79f0e02606364018806d465d48eed8ffd153.zip hdf5-0e1e79f0e02606364018806d465d48eed8ffd153.tar.gz hdf5-0e1e79f0e02606364018806d465d48eed8ffd153.tar.bz2 |
[svn-r23601] Bring revisions #23341 - 23597 from trunk to revise_chunks.
h5committtested.
Diffstat (limited to 'release_docs')
-rw-r--r-- | release_docs/INSTALL_parallel | 67 | ||||
-rw-r--r-- | release_docs/RELEASE.txt | 65 |
2 files changed, 104 insertions, 28 deletions
diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel index eacaf68..03b3ecf 100644 --- a/release_docs/INSTALL_parallel +++ b/release_docs/INSTALL_parallel @@ -186,6 +186,73 @@ TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5 ======== end of bypass ======== +2.5. Hopper (Cray XE6) (for v1.8 and later) +------------------------- + +2.5.1 Building HDF5 for Hopper +------------------------------------------ +The following steps are for building HDF5 for the Hopper compute +nodes. They would probably work for other Cray XE6 systems but have +not been verified. + +Obtain a copy from the HDF ftp server: +http://www.hdfgroup.org/ftp/HDF5/current/src/ +(link might change, so always double check the HDF group website). + +$ wget http://www.hdfgroup.org/ftp/HDF5/current/src/hdf5-x.x.x.tar.gz + +unpack the tarball + +$ cd hdf5-x.x.x/ +$ CC=cc FC=ftn ./configure \ +--prefix=/project/hdf5/hdf5 --enable-parallel --enable-fortran \ +--disable-shared --disable-production +$ make + +Run make check. make check should be run on the compute nodes, not the +front end nodes. So using a PBS batch script, allocate 4 or more +cores. Always consult with the machine's website on how to create PBS +scripts and allocate nodes for your job. For Hopper, all the +information can be found on: +http://www.nersc.gov/systems/hopper-cray-xe6/ + +save the PBS script into your HDF5 build directory. The PBS script +should contain (besides the PBS node allocation requests)the +following: + +-------------------------------------------------------------- +cd $PBS_O_WORKDIR + +##set RUNSERIAL and RUNPARALLEL like this in the PBS script: +export RUNPARALLEL="aprun -n 6" +export RUNSERIAL="aprun -n 1" + +##execute make check: +make check +-------------------------------------------------------------- + +Once the job runs and all is well, install the binary: +$ make install + +2.5.2 Hopper known issues +------------------------------ +Sometimes when building the library with make, you might get this problem: + +LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | \ +sed -e 's/-L/:/g' -e 's/ +//g'`" \ +./H5make_libsettings > H5lib_settings.c +|| \ +(test $HDF5_Make_Ignore && echo "*** Error ignored") +|| \ +(rm -f H5lib_settings.c ; exit 1) +/bin/sh: line 4: 9644 Segmentation fault +LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo | sed -e 's/-L/:/g' -e 's/ +//g'`" ./H5make_libsettings > H5lib_settings.c + +If that happens, you are probable running with make -j <x>. In that +case, you need to cleanup everything and start again as detailed above +but use serial make (do not use -j <x>). 3. Detail explanation --------------------- diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index d2901ab..08420d0 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1,4 +1,4 @@ -HDF5 version 1.9.148-FA_a5 currently under development +HDF5 version 1.9.149-FA_a5 currently under development INTRODUCTION @@ -105,6 +105,9 @@ New Features Library: -------- + - The library can load filter libraries dynamically during runtime. Users + can set the search path through environment variable HDF5_PLUGIN_PATH + and call H5Pset_filter to enable a dynamic filter. (SLU - 2013/04/08) - Added new API functions H5Dscatter and H5Dgather to scatter data to and and gather data from a selection within a memory buffer. (NAF - 2013/02/05) @@ -275,6 +278,10 @@ New Features Tools: ------ + - h5dump: Fixed displaying comporession ratio for unknown or user-defined + filters. HDFFV-8344 (XCAO 2013/03/19) + - h5dump: Changed UNKNOWN_FILTER to USER_DEFINED_FILTER for user defined filter. + HDFFV-8346 (XCAO 2013/03/19) - h5dump: Added capability for "-a" option to show attributes containing "/" by using an escape character. For example, for a dataset "/dset" containing attribute "speed(m/h)", use "h5dump -a "/dset/speed(\/h)" @@ -402,6 +409,8 @@ Support for new platforms, languages and compilers. - Intel V11.1 uses now -O3 optimization in production mode (EIP - 2010/10/08) - PathScale compilers are recognized and can build the HDF5 library properly. AKC - 2009/7/28 - + - SunOS 5.11 (emu) 32-bit and 64-bit with Sun C/C++ 5.12 compiler and + Sun Fortran 95 8.6 compiler. (SLU - 2013/04/15) Bug Fixes since HDF5-1.8.0 release ================================== @@ -750,6 +759,8 @@ Bug Fixes since HDF5-1.8.0 release Tools ----- + - h5repack: Fixed failure for converting a layout of small chunked dataset + (size < 1K) to contiguous layout. HDFFV-8214 (JKM 2013/03/18) - h5diff: Fixed to return correct exit code 1 when detect unique extra attribute. Prior to this fix, h5diff returned exit code 0 indicating two files are identical. HDFFV-7643 (JKM 2013/02/15) @@ -1119,10 +1130,11 @@ Supported Platforms MPICH mpich2-1.4.1p1 compiled with gcc 4.1.2 and gfortran 4.1.2 - Linux 2.6.32-220.7.1.el6.ppc64 gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) - #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) - (ostrich) GNU Fortran (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) - + Linux 2.6.32-358.2.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-3) + IBM XL C/C++ V11.1 + IBM XL Fortran V13.1 Linux 2.6.32-220.23.1.1chaos Intel C, C++, Fortran Compilers ch5.x86_64 GNU/Linux Version 12.1.5.339 (LLNL Aztec) @@ -1131,12 +1143,9 @@ Supported Platforms (LLNL uDawn) XL C++ for Blue Gene/P, bgxlC V9.0 XL Fortran for Blue Gene/P, bgxlf90 V11.1 - SunOS 5.10 32- and 64-bit Sun C 5.9 Sun OS_sparc Patch 124867-16 - (linew) Sun Fortran 95 8.3 Sun OS_sparc Patch 127000-13 - Sun C++ 5.9 Sun OS_sparc Patch 124863-26 - Sun C 5.11 SunOS_sparc - Sun Fortran 95 8.5 SunOS_sparc - Sun C++ 5.11 SunOS_sparc + 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 XP Visual Studio 2008 w/ Intel Fortran 10.1 (project files) @@ -1154,15 +1163,9 @@ Supported Platforms Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - (fred) gfortran GNU Fortran (GCC) 4.6.2 - Intel C (icc), Fortran (ifort), C++ (icpc) - 12.1.0.038 Build 20110811 - - Mac OS X Snow Leopard 10.6.8 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - Darwin Kernel Version 10.8.0 g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 3.2.6 - Intel 32-bit gfortran GNU Fortran (GCC) 4.6.1 - (tejeda) Intel C (icc), Fortran (ifort), C++ (icpc) - 12.1.0.038 Build 20110811 + 64-bit gfortran GNU Fortran (GCC) 4.6.2 + (fred) Intel C (icc), Fortran (ifort), C++ (icpc) + 12.1 Build 20120928 Mac OS X Lion 10.7.3 gcc i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 from Xcode 4.2.1 32- and 64-bit g++ i686-apple-darwin11-llvm-g++-4.2 (GCC) 4.2.1 from Xcode 4.2.1 @@ -1190,11 +1193,10 @@ Tested Configuration Features Summary Platform C F90/ F90 C++ zlib SZIP parallel F2003 parallel -Solaris2.10 32-bit n y/y n y y y -Solaris2.10 64-bit n y/n n y y y +Solaris2.11 32-bit n y/y n y y y +Solaris2.11 64-bit n y/n n y y y Windows 7 y y/n n y y y Windows 7 x64 y y/n n y y y -Mac OS X Snow Leopard 10.6.8 32-bit n y/y n y y n Mac OS X Snow Leopard 10.6.8 64-bit n y/y n y y y Mac OS X Lion 10.7.3 32-bit n y/y n y y n Mac OS X Lion 10.7.3 64-bit n y/y n y y y @@ -1206,16 +1208,15 @@ CentOS 5.5 Linux 2.6.18-308 i686 PGI n y/y n y y y CentOS 5.5 Linux 2.6.18 x86_64 GNU y y/y y y y y CentOS 5.5 Linux 2.6.18 x86_64 Intel n y/y n y y y CentOS 5.5 Linux 2.6.18 x86_64 PGI n y/y n y y y -Linux 2.6.32-220.7.1.el6.ppc64 n y/n n y y y +Linux 2.6.32-358.2.1.el6.ppc64 n y/n n y y y Platform Shared Shared Shared Thread- C libs F90 libs C++ libs safe -Solaris2.10 32-bit y y y y -Solaris2.10 64-bit n n n n +Solaris2.11 32-bit y y y y +Solaris2.11 64-bit y y y y Windows 7 y y y y Windows 7 x64 y y y y -Mac OS X Snow Leopard 10.6.8 32-bit y n y n Mac OS X Snow Leopard 10.6.8 64-bit y n y n Mac OS X Lion 10.7.3 32-bit y n y y Mac OS X Lion 10.7.3 64-bit y n y y @@ -1227,7 +1228,7 @@ CentOS 5.5 Linux 2.6.18-308 i686 PGI y y y n CentOS 5.5 Linux 2.6.18 x86_64 GNU y y y y CentOS 5.5 Linux 2.6.18 x86_64 Intel y y y n CentOS 5.5 Linux 2.6.18 x86_64 PGI y y y n -Linux 2.6.32-220.7.1.el6.ppc64 y y y n +Linux 2.6.32-358.2.1.el6.ppc64 y y y n Compiler versions for each platform are listed in the preceding "Supported Platforms" table. @@ -1296,6 +1297,14 @@ The following platforms are not supported but have been tested for this release. Known Problems ============== +* The h5dump and h5diff utilities occasionally produce different output + between Linux and Windows systems. This is caused by lower-level library + routines that fail to write fill values to the user's buffer when reading + unallocated chunks from datasets that have a fill value set to + H5D_FILL_VALUE_DEFAULT. Due to platform differences the return of + spurious data values have only been encountered on Windows 32-bit systems. + (Issue HDFFV-8247; JP - 2013/03/27) + * The 5.9 C++ compiler on Sun failed to compile a C++ test ttypes.cpp. It complains with this message: "/home/hdf5/src/H5Vprivate.h", line 130: Error: __func__ is not defined. |