diff options
Diffstat (limited to 'release_docs')
| -rw-r--r-- | release_docs/HISTORY-1_10.txt | 367 | ||||
| -rw-r--r--[-rwxr-xr-x] | release_docs/INSTALL | 0 | ||||
| -rw-r--r-- | release_docs/INSTALL_CMake.txt | 2 | ||||
| -rw-r--r--[-rwxr-xr-x] | release_docs/INSTALL_Cygwin.txt | 0 | ||||
| -rw-r--r--[-rwxr-xr-x] | release_docs/INSTALL_parallel | 10 | ||||
| -rw-r--r-- | release_docs/README_HDF5_CMake | 23 | ||||
| -rw-r--r-- | release_docs/README_HPC | 206 | ||||
| -rw-r--r--[-rwxr-xr-x] | release_docs/RELEASE.txt | 553 |
8 files changed, 1049 insertions, 112 deletions
diff --git a/release_docs/HISTORY-1_10.txt b/release_docs/HISTORY-1_10.txt index 4344482..ad8beb2 100644 --- a/release_docs/HISTORY-1_10.txt +++ b/release_docs/HISTORY-1_10.txt @@ -3,6 +3,7 @@ HDF5 History This file contains development history of the HDF5 1.10 branch +06. Release Information for hdf5-1.10.4 05. Release Information for hdf5-1.10.3 04. Release Information for hdf5-1.10.2 03. Release Information for hdf5-1.10.1 @@ -11,6 +12,372 @@ This file contains development history of the HDF5 1.10 branch [Search on the string '%%%%' for section breaks of each release.] +%%%%1.10.4%%%% + +HDF5 version 1.10.4 released on 2018-10-05 +================================================================================ + + +INTRODUCTION + +This document describes the differences between this release and the previous +HDF5 release. It contains information on the platforms tested and known +problems in this release. For more details check the HISTORY*.txt files in the +HDF5 source. + +Note that documentation in the links below will be updated at the time of each +final release. + +Links to HDF5 documentation can be found on The HDF5 web page: + + https://portal.hdfgroup.org/display/HDF5/HDF5 + +The official HDF5 releases can be obtained from: + + https://www.hdfgroup.org/downloads/hdf5/ + +Changes from Release to Release and New Features in the HDF5-1.10.x release series +can be found at: + + https://portal.hdfgroup.org/display/HDF5/HDF5+Application+Developer%27s+Guide + +If you have any questions or comments, please send them to the HDF Help Desk: + + help@hdfgroup.org + + +CONTENTS + +- Bug Fixes since HDF5-1.10.3 +- Supported Platforms +- Tested Configuration Features Summary +- More Tested Platforms +- Known Problems +- CMake vs. Autotools installations + + +New Features +============ + + Configuration: + ------------- + - Add toolchain and cross-compile support + + Added info on using a toolchain file to INSTALL_CMAKE.txt. A + toolchain file is also used in cross-compiling, which requires + CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling + the fortran configure process, the HDF5UseFortran.cmake file macros + were improved. Fixed a Fortran configure file issue that incorrectly + used #cmakedefine instead of #define. + + (ADB - 2018/10/04, HDFFV-10594) + + - Add warning flags for Intel compilers + + Identified Intel compiler specific warnings flags that should be used + instead of GNU flags. + + (ADB - 2018/10/04, TRILABS-21) + + - Add default rpath to targets + + Default rpaths should be set in shared executables and + libraries to allow the use of loading dependent libraries + without requiring LD_LIBRARY_PATH to be set. The default + path should be relative using @rpath on osx and $ORIGIN + on linux. Windows is not affected. + + (ADB - 2018/09/26, HDFFV-10594) + + Library: + -------- + - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. + + Rather than always running H5detect and generating H5Tinit.c and + H5make_libsettings.c, supply a location for those files. + + (ADB - 2018/09/18, HDFFV-10332) + + +Bug Fixes since HDF5-1.10.3 release +================================== + + Library + ------- + - Allow H5detect and H5make_libsettings to take a file as an argument. + + Rather than only writing to stdout, add a command argument to name + the file that H5detect and H5make_libsettings will use for output. + Without an argument, stdout is still used, so backwards compatibility + is maintained. + + (ADB - 2018/09/05, HDFFV-9059) + + - A bug was discovered in the parallel library where an application + would hang if a collective read/write of a chunked dataset occurred + when collective metadata reads were enabled and some of the ranks + had no selection in the dataset's dataspace. The ranks which had no + selection in the dataset's dataspace called H5D__chunk_addrmap() to + retrieve the lowest chunk address in the dataset. This is because we + require reads/writes to be performed in strictly non-decreasing order + of chunk address in the file. + + When the chunk index used was a version 1 or 2 B-tree, these + non-participating ranks would issue a collective MPI_Bcast() call + that the participating ranks would not issue, causing the hang. Since + the non-participating ranks are not actually reading/writing anything, + the H5D__chunk_addrmap() call can be safely removed and the address used + for the read/write can be set to an arbitrary number (0 was chosen). + + (JTH - 2018/08/25, HDFFV-10501) + + Java Library: + ---------------- + - JNI native library dependencies + + The build for the hdf5_java native library used the wrong + hdf5 target library for CMake builds. Correcting the hdf5_java + library to build with the shared hdf5 library required testing + paths to change also. + + (ADB - 2018/08/31, HDFFV-10568) + + - Java iterator callbacks + + Change global callback object to a small stack structure in order + to fix a runtime crash. This crash was discovered when iterating + through a file with nested group members. The global variable + visit_callback is overwritten when recursion starts. When recursion + completes, visit_callback will be pointing to the wrong callback method. + + (ADB - 2018/08/15, HDFFV-10536) + + - Java HDFLibraryException class + + Change parent class from Exception to RuntimeException. + + (ADB - 2018/07/30, HDFFV-10534) + + - JNI Read and Write + + Refactored variable-length functions, H5DreadVL and H5AreadVL, + to correct dataset and attribute reads. New write functions, + H5DwriteVL and H5AwriteVL, are under construction. + + (ADB - 2018/06/02, HDFFV-10519) + + +Supported Platforms +=================== + + Linux 2.6.32-696.16.1.el6.ppc64 gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + #1 SMP ppc64 GNU/Linux g++ (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + (ostrich) GNU Fortran (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18) + 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) + Version 4.9.3, Version 5.2.0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.0.098 Build 20160721 + 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 2015 w/ Intel Fortran 16 (cmake) + + 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) + Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) + Visual Studio 2015 w/ MSMPI 8 (cmake) + + Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + + Windows 10 x64 Visual Studio 2015 w/ Intel Fortran 18 (cmake) + Visual Studio 2017 w/ Intel Fortran 18 (cmake) + + Mac OS X Yosemite 10.10.5 Apple clang/clang++ version 6.1 from Xcode 7.0 + 64-bit gfortran GNU Fortran (GCC) 4.9.2 + (osx1010dev/osx1010test) Intel icc/icpc/ifort version 15.0.3 + + Mac OS X El Capitan 10.11.6 Apple clang/clang++ version 7.3.0 from Xcode 7.3 + 64-bit gfortran GNU Fortran (GCC) 5.2.0 + (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 + + Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42) + 64-bit gfortran GNU Fortran (GCC) 7.1.0 + (kite) Intel icc/icpc/ifort version 17.0.2 + + +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 +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/y n y y y +Windows 7 x64 y y/y y y y y +Windows 7 Cygwin n y/n n y y y +Windows 7 x64 Cygwin n y/n n y y y +Windows 10 y y/y n y y y +Windows 10 x64 y 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 +Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y +Mac OS Sierra 10.12.6 64-bit n y/y n y y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y +Linux 2.6.32-573.18.1.el6.ppc64 n y/y n y y y + + +Platform Shared Shared Shared Thread- + C libs F90 libs C++ libs safe +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 +Windows 7 Cygwin n n n y +Windows 7 x64 Cygwin n n n y +Windows 10 y y y y +Windows 10 x64 y y 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 +Mac OS X El Capitan 10.11.6 64-bit y n y y +Mac OS Sierra 10.12.6 64-bit y n y y +CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n +CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y +CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n +Linux 2.6.32-573.18.1.el6.ppc64 y y y n + +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 GNU C (gcc), Fortran (gfortran), C++ (g++) + #1 SMP x86_64 GNU/Linux compilers: + (mayll/platypus) Version 4.4.7 20120313 + Version 4.9.3, 5.3.0, 6.2.0 + PGI C, Fortran, C++ for 64-bit target on + x86-64; + Version 17.10-0 + Intel(R) C (icc), C++ (icpc), Fortran (icc) + compilers: + Version 17.0.4.196 Build 20170411 + MPICH 3.1.4 compiled with GCC 4.9.3 + + Linux 3.10.0-327.18.2.el7 GNU C (gcc) and C++ (g++) compilers + #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) + (jelly) with NAG Fortran Compiler Release 6.1(Tozai) + GCC Version 7.1.0 + OpenMPI 3.0.0-GCC-7.2.0-2.29, + 3.1.0-GCC-7.2.0-2.29 + Intel(R) C (icc) and C++ (icpc) compilers + Version 17.0.0.098 Build 20160721 + with NAG Fortran Compiler Release 6.1(Tozai) + + Linux 3.10.0-327.10.1.el7 MPICH 3.2 compiled with GCC 5.3.0 + #1 SMP x86_64 GNU/Linux + (moohan) + + Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with + #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 + (ostrich) and IBM XL Fortran for Linux, V15.1 + + Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux + gcc, g++ (Debian 4.9.2-10) 4.9.2 + GNU Fortran (Debian 4.9.2-10) 4.9.2 + (cmake and autotools) + + Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc, g++ (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) + + Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux + gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) + 5.4.0 20160609 + (cmake and autotools) + + +Known Problems +============== + + At present, metadata cache images may not be generated by parallel + applications. Parallel applications can read files with metadata cache + images, but since this is a collective operation, a deadlock is possible + if one or more processes do not participate. + + Three tests fail with OpenMPI 3.0.0/GCC-7.2.0-2.29: + testphdf5 (ecdsetw, selnone, cchunk1, cchunk3, cchunk4, and actualio) + t_shapesame (sscontig2) + t_pflush1/fails on exit + The first two tests fail attempting collective writes. + + Known problems in previous releases can be found in the HISTORY*.txt files + in the HDF5 source. Please report any new problems found to + help@hdfgroup.org. + + +CMake vs. Autotools installations +================================= +While both build systems produce similar results, there are differences. +Each system produces the same set of folders on linux (only CMake works +on standard Windows); bin, include, lib and share. Autotools places the +COPYING and RELEASE.txt file in the root folder, CMake places them in +the share folder. + +The bin folder contains the tools and the build scripts. Additionally, CMake +creates dynamic versions of the tools with the suffix "-shared". Autotools +installs one set of tools depending on the "--enable-shared" configuration +option. + build scripts + ------------- + Autotools: h5c++, h5cc, h5fc + CMake: h5c++, h5cc, h5hlc++, h5hlcc + +The include folder holds the header files and the fortran mod files. CMake +places the fortran mod files into separate shared and static subfolders, +while Autotools places one set of mod files into the include folder. Because +CMake produces a tools library, the header files for tools will appear in +the include folder. + +The lib folder contains the library files, and CMake adds the pkgconfig +subfolder with the hdf5*.pc files used by the bin/build scripts created by +the CMake build. CMake separates the C interface code from the fortran code by +creating C-stub libraries for each Fortran library. In addition, only CMake +installs the tools library. The names of the szip libraries are different +between the build systems. + +The share folder will have the most differences because CMake builds include +a number of CMake specific files for support of CMake's find_package and support +for the HDF5 Examples CMake project. + %%%%1.10.3%%%% HDF5 version 1.10.3 released on 2018-08-21 diff --git a/release_docs/INSTALL b/release_docs/INSTALL index 5c54698..5c54698 100755..100644 --- a/release_docs/INSTALL +++ b/release_docs/INSTALL diff --git a/release_docs/INSTALL_CMake.txt b/release_docs/INSTALL_CMake.txt index edd876a..5d76b58 100644 --- a/release_docs/INSTALL_CMake.txt +++ b/release_docs/INSTALL_CMake.txt @@ -635,13 +635,13 @@ HDF5_ENABLE_DIRECT_VFD "Build the Direct I/O Virtual File Driver" HDF5_ENABLE_EMBEDDED_LIBINFO "embed library info into executables" ON HDF5_ENABLE_HSIZET "Enable datasets larger than memory" ON HDF5_ENABLE_PARALLEL "Enable parallel build (requires MPI)" OFF +HDF5_ENABLE_PREADWRITE "Use pread/pwrite in sec2/log/core VFDs in place of read/write (when available)" ON HDF5_ENABLE_TRACE "Enable API tracing capability" OFF HDF5_ENABLE_USING_MEMCHECKER "Indicate that a memory checker is used" OFF HDF5_GENERATE_HEADERS "Rebuild Generated Files" ON HDF5_BUILD_GENERATORS "Build Test Generators" OFF HDF5_JAVA_PACK_JRE "Package a JRE installer directory" OFF HDF5_MEMORY_ALLOC_SANITY_CHECK "Indicate that internal memory allocation sanity checks are enabled" OFF -HDF5_METADATA_TRACE_FILE "Enable metadata trace file collection" OFF HDF5_NO_PACKAGES "Do not include CPack Packaging" OFF HDF5_PACK_EXAMPLES "Package the HDF5 Library Examples Compressed File" OFF HDF5_PACK_MACOSX_FRAMEWORK "Package the HDF5 Library in a Frameworks" OFF diff --git a/release_docs/INSTALL_Cygwin.txt b/release_docs/INSTALL_Cygwin.txt index 74f494c..74f494c 100755..100644 --- a/release_docs/INSTALL_Cygwin.txt +++ b/release_docs/INSTALL_Cygwin.txt diff --git a/release_docs/INSTALL_parallel b/release_docs/INSTALL_parallel index f32fffc..d3d7830 100755..100644 --- a/release_docs/INSTALL_parallel +++ b/release_docs/INSTALL_parallel @@ -102,7 +102,7 @@ qsub -I -q debug -l mppwidth=8 - configure HDF5: RUNSERIAL="aprun -q -n 1" RUNPARALLEL="aprun -q -n 6" FC=ftn CC=cc /path/to/source/configure --enable-fortran --enable-parallel --disable-shared - RUNSERIAL and RUNPARALLEL tells the library how it should launch programs that are part of the build procedure. + RUNSERIAL and RUNPARALLEL tell the library how it should launch programs that are part of the build procedure. - Compile HDF5: gmake @@ -155,12 +155,16 @@ to run a parallel application on one processor and on many processors. If the compiler is `mpicc' and the user hasn't specified values for RUNSERIAL and RUNPARALLEL then configure chooses `mpiexec' from the same directory as `mpicc': - RUNSERIAL: /usr/local/mpi/bin/mpiexec -np 1 - RUNPARALLEL: /usr/local/mpi/bin/mpiexec -np $${NPROCS:=6} + RUNSERIAL: mpiexec -n 1 + RUNPARALLEL: mpiexec -n $${NPROCS:=6} The `$${NPROCS:=6}' will be substituted with the value of the NPROCS environment variable at the time `make check' is run (or the value 6). +Note that some MPI implementations (e.g. OpenMPI 4.0) disallow oversubscribing +nodes by default so you'll have to either set NPROCS equal to the number of +processors available (or fewer) or redefine RUNPARALLEL with appropriate +flag(s) (--oversubscribe in OpenMPI). 4. Parallel test suite ---------------------- diff --git a/release_docs/README_HDF5_CMake b/release_docs/README_HDF5_CMake new file mode 100644 index 0000000..484710d --- /dev/null +++ b/release_docs/README_HDF5_CMake @@ -0,0 +1,23 @@ +This tar file contains + + build-unix.sh script to build HDF5 with CMake on unix machines + build-unix-hpc.sh script to build HDF5 with CMake on unix machines and run + tests with batch scripts (sbatch). + CTestScript.cmake + HDF5config.cmake CMake scripts for building HDF5 + HDF5options.cmake + hdf5-1.10.5-pre1 HDF5 1.10.5-pre1 source + SZip.tar.gz source for building SZIP + ZLib.tar.gz source for building ZLIB + +For more information about building HDF5 with CMake, see USING_HDF5_CMake.txt in +hdf5-1.10.5-pre1/release_docs, or +https://portal.hdfgroup.org/display/support/Building+HDF5+with+CMake. + +For more information about building HDF5 with CMake on HPC machines, including +cross compiling on Cray XC40, see README_HPC in hdf5-1.10.5-pre1/release_docs. + + + + + diff --git a/release_docs/README_HPC b/release_docs/README_HPC new file mode 100644 index 0000000..67a5d6c --- /dev/null +++ b/release_docs/README_HPC @@ -0,0 +1,206 @@ +************************************************************************ +* Using CMake to build and test HDF5 source on HPC machines * +************************************************************************ + + Contents + +Section I: Prerequisites +Section II: Obtain HDF5 source +Section III: Using ctest command to build and test +Section IV: Cross compiling +Section V: Manual alternatives +Section VI: Other cross compiling options + +************************************************************************ + +======================================================================== +I. Prerequisites +======================================================================== + 1. Create a working directory that is accessible from the compute nodes for + running tests; the working directory should be in a scratch space or a + parallel file system space since testing will use this space. Building + from HDF5 source in a 'home' directory typically results in test + failures and should be avoided. + + 2. Load modules for desired compilers, module for cmake version 3.10 or greater, + and set any needed environment variables for compilers (i.e., CC, FC, CXX). + Unload any problematic modules (i.e., craype-hugepages2M). + +======================================================================== +II. Obtain HDF5 source +======================================================================== +Obtain HDF5 source code from the HDF5 repository using a git command or +from a release tar file in a working directory: + + git clone https://git@bitbucket.hdfgroup.org/scm/hdffv/hdf5.git + [-b branch] [source directory] + +If no branch is specified, then the 'develop' version will be checked out. +If no source directory is specified, then the source will be located in the +'hdf5' directory. The Cmake scripts expect the source to be in a directory +named hdf5-<version string>, where 'version string' uses the format '1.xx.xx'. +For example, for the current 'develop' version, the "hdf5" directory should +be renamed "hdf5-1.11.4", or for the first hdf5_1_10_5 pre-release version, +it should be renamed "hdf5-1.10.5-pre1". + +If the version number is not known a priori, the version string +can be obtained by running bin/h5vers in the top level directory of the source clone, and +the source directory renamed 'hdf5-<version string>'. + +Release or snapshot tar files may also be extracted and used. + +======================================================================== +III. Using ctest command to build and test +======================================================================== + +The ctest command [1]: + + ctest -S HDF5config.cmake,BUILD_GENERATOR=Unix -C Release -V -O hdf5.log + +will configure, build, test and package HDF5 from the downloaded source +after the setup steps outlined below are followed. + +CMake option variables are available to allow running test programs in batch +scripts on compute nodes and to cross-compile for compute node hardware using +a cross-compiling emulator. The setup steps will make default settings for +parallel or serial only builds available to the CMake command. + + 1. For the current 'develop' version the "hdf5" directory should be renamed + "hdf5-1.11.4". + + 2. Three cmake script files need to be copied to the working directory, or + have symbolic links to them, created in the working directory: + + hdf5-1.11.4/config/cmake/scripts/HDF5config.cmake + hdf5-1.11.4/config/cmake/scripts/CTestScript.cmake + hdf5-1.11.4/config/cmake/scripts/HDF5options.cmake + + should be copied to the working directory. + + 3. The resulting contents of the working directory are then: + + CTestScript.cmake + HDF5config.cmake + HDF5options.cmake + hdf5-1.11.4 + + Additionally, when the ctest command runs [1], it will add a build directory + in the working directory. + + 4. The following options (among others) can be added to the ctest + command [1], following '-S HDF5config.cmake,' and separated by ',': + + HPC=sbatch (or 'bsub' or 'raybsub') indicates which type of batch + files to use for running tests. If omitted, test + will run on the local machine or login node. + + KNL=true to cross-compile for KNL compute nodes on CrayXC40 + (see section IV) + + MPI=true enables parallel, disables c++, java, and threadsafe + + LOCAL_BATCH_SCRIPT_ARGS="--account=<account#>" to supply user account + information for batch jobs + + The HPC options will add BUILD_GENERATOR=Unix for the three HPC options. + An example ctest command for a parallel build on a system using sbatch is + + ctest -S HDF5config.cmake,HPC=sbatch,MPI=true -C Release -V -O hdf5.log + + Adding the option 'KNL=true' to the above list will compile for KNL nodes, + for example, on 'mutrino' and other CrayXC40 machines. + + Changing -V to -VV will produce more logging information in HDF5.log. + + More detailed CMake information can be found in the HDF5 source in + release_docs/INSTALL_CMake.txt. + +======================================================================== +IV. Cross-compiling +======================================================================== +For cross-compiling on Cray, set environment variables CC=cc, FC=ftn +and CXX=CC (for c++) after all compiler modules are loaded since switching +compiler modules may unset or reset these variables. + +CMake provides options for cross-compiling. To cross-compile for KNL hardware +on mutrino and other CrayXC40 machines, add HPC=sbatch,KNL=true to the +ctest command line. This will set the following options from the +config/cmake/scripts/HPC/sbatch-HDF5options.cmake file: + + set (COMPILENODE_HWCOMPILE_MODULE "craype-haswell") + set (COMPUTENODE_HWCOMPILE_MODULE "craype-mic-knl") + set (LOCAL_BATCH_SCRIPT_NAME "knl_ctestS.sl") + set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "knl_ctestP.sl") + set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/crayle.cmake") + +On the Cray XC40 the craype-haswell module is needed for configuring, and the +craype-mic-knl module is needed for building to run on the KNL nodes. CMake +with the above options will swap modules after configuring is complete, +but before compiling programs for KNL. + +The sbatch script arguments for running jobs on KNL nodes may differ on CrayXC40 +machines other than mutrino. The batch scripts knl_ctestS.sl and knl_ctestP.sl +have the correct arguments for mutrino: "#SBATCH -p knl -C quad,cache". For +cori, another CrayXC40, that line is replaced by "#SBATCH -C knl,quad,cache". +For cori (and other machines), the values in LOCAL_BATCH_SCRIPT_NAME and +LOCAL_BATCH_SCRIPT_PARALLEL_NAME in the config/cmake/scripts/HPC/sbatch-HDF5options.cmake +file can be replaced by cori_knl_ctestS.sl and cori_knl_ctestS.sl, or the lines +can be edited in the batch files in hdf5-1.11.4/bin/batch. + +======================================================================== +V. Manual alternatives +======================================================================== +If using ctest is undesirable, one can create a build directory and run the cmake +configure command, for example + +"/projects/Mutrino/hpcsoft/cle6.0/common/cmake/3.10.2/bin/cmake" +-C "<working directory>/hdf5-1.11.4/config/cmake/cacheinit.cmake" +-DCMAKE_BUILD_TYPE:STRING=Release -DHDF5_BUILD_FORTRAN:BOOL=ON +-DHDF5_BUILD_JAVA:BOOL=OFF +-DCMAKE_INSTALL_PREFIX:PATH=<working directory>/HDF_Group/HDF5/1.11.4 +-DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF +-DHDF5_ENABLE_PARALLEL:BOOL=ON -DHDF5_BUILD_CPP_LIB:BOOL=OFF +-DHDF5_BUILD_JAVA:BOOL=OFF -DHDF5_ENABLE_THREADSAFE:BOOL=OFF +-DHDF5_PACKAGE_EXTLIBS:BOOL=ON -DLOCAL_BATCH_TEST:BOOL=ON +-DMPIEXEC_EXECUTABLE:STRING=srun -DMPIEXEC_NUMPROC_FLAG:STRING=-n +-DMPIEXEC_MAX_NUMPROCS:STRING=6 +-DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/crayle.cmake +-DLOCAL_BATCH_SCRIPT_NAME:STRING=knl_ctestS.sl +-DLOCAL_BATCH_SCRIPT_PARALLEL_NAME:STRING=knl_ctestP.sl -DSITE:STRING=mutrino +-DBUILDNAME:STRING=par-knl_GCC493-SHARED-Linux-4.4.156-94.61.1.16335.0.PTF.1107299-default-x86_64 +"-GUnix Makefiles" "" "<working directory>/hdf5-1.11.4" + +followed by make and batch jobs to run tests. + +To cross-compile on CrayXC40, run the configure command with the craype-haswell +module loaded, then switch to the craype-mic-knl module for the build process. + +Tests on machines using slurm can be run with + +"sbatch -p knl -C quad,cache ctestS.sl" + +or + +"sbatch -p knl -C quad,cache ctestP.sl" + +for parallel builds. + +Tests on machines using LSF will typically use "bsub ctestS.lsf", etc. + +======================================================================== +VI. Other cross compiling options +======================================================================== +Settings for two other cross-compiling options are also in the config/toolchain +files which do not seem to be necessary with the Cray PrgEnv-* modules + +1. HDF5_USE_PREGEN. This option, along with the HDF5_USE_PREGEN_DIR CMake + variable would allow the use of an appropriate H5Tinit.c file with type + information generated on a compute node to be used when cross compiling + for those compute nodes. The use of the variables in lines 110 and 111 + of HDF5options.cmake file seem to preclude needing this option with the + available Cray modules and CMake option. + +2. HDF5_BATCH_H5DETECT and associated CMake variables. This option when + properly configured will run H5detect in a batch job on a compute node + at the beginning of the CMake build process. It was also found to be + unnecessary with the available Cray modules and CMake options. diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt index 7def78e..2192811 100755..100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -1,4 +1,4 @@ -HDF5 version 1.10.4 released on 2018-10-05 +HDF5 version 1.10.5 released on 2019-02-25 ================================================================================ @@ -32,7 +32,9 @@ If you have any questions or comments, please send them to the HDF Help Desk: CONTENTS -- Bug Fixes since HDF5-1.10.3 +- New Features +- Support for new platforms and languages +- Bug Fixes since HDF5-1.10.4 - Supported Platforms - Tested Configuration Features Summary - More Tested Platforms @@ -45,110 +47,441 @@ New Features Configuration: ------------- - - Add toolchain and cross-compile support + - Cross compile on mutrino and other Cray XC40 systems. - Added info on using a toolchain file to INSTALL_CMAKE.txt. A - toolchain file is also used in cross-compiling, which requires - CMAKE_CROSSCOMPILING_EMULATOR to be set. To help with cross-compiling - the fortran configure process, the HDF5UseFortran.cmake file macros - were improved. Fixed a Fortran configure file issue that incorrectly - used #cmakedefine instead of #define. + Added support for CMake options to use CrayLinuxEnvironment, craype-mic-knl + module for building with craype-haswell module for configuration, and + batch scripts in bin/batch for use with sbatch or bsub to run tests in + batch jobs on compute nodes. An instruction file README_HPC describing + the use of these options was added in release_docs. - (ADB - 2018/10/04, HDFFV-10594) + (LRK - 2019/02/18, TRILABS-34) - - Add warning flags for Intel compilers + - Rework CMake command files to fix MPI testing. - Identified Intel compiler specific warnings flags that should be used - instead of GNU flags. + Added setup fixture to remove any test generated files and added DEPENDS + to test properties to execute tests in order expected. - (ADB - 2018/10/04, TRILABS-21) + (ADB - 2019/02/14, TRILABS-111) - - Add default rpath to targets + - Disable SZIP or ZLIB options if TGZ files are not available. - Default rpaths should be set in shared executables and - libraries to allow the use of loading dependent libraries - without requiring LD_LIBRARY_PATH to be set. The default - path should be relative using @rpath on osx and $ORIGIN - on linux. Windows is not affected. + Changed the TGZ option for SZip and ZLib to disable the options + if the source tar.gz files are not found. + + (ADB - 2019/02/05, HDFFV-10697) + + - Added a new option to enable/disable using pread/pwrite instead of + read/write in the sec2, log, and core VFDs. + + This option is enabled by default when pread/pwrite are detected. + + Autotools: --enable-preadwrite + CMake: HDF5_ENABLE_PREADWRITE + + (DER - 2019/02/03, HDFFV-10696) + + - Rework CMake versioning for OSX platforms. + + Changed the current_version and compatibility_version flags from optional + with HDF5_BUILD_WITH_INSTALL_NAME to always setting the flags for OSX. + + (ADB - 2019/01/22, HDFFV-10685) + + - Rework CMake command files to eliminate developer CMP005 warning + + Use variables without quotes in if () statements. + + (ADB - 2019/01/18, TILABS-105) + + - Rework CMake configure files to eliminate developer CMP0075 warning + + Renamed varname to HDF5_REQUIRED_LIBRARIES as the contents were not + required for configuration. Also moved check includes calls to top of + files. + + (ADB - 2019/01/03, HDFFV-10546) + + - Keep stderr and stdout separate in tests + + Changed test handling of output capture. Tests now keep the stderr + output separate from the stdout output. It is up to the test to decide + which output to check against a reference. Also added the option + to grep for a string in either output. + + (ADB - 2018/12/12, HDFFV-10632) + + - Incorrectly installed private header files were removed from + CMake installs. + + The CMake build files incorrectly flagged the following header files + as public and installed them. They are private and will no longer be + installed. + + HDF5 library private package files (H5Xpkg.h) + H5Edefin.h + H5Einit.h + H5Eterm.h + H5LTparse.h + h5diff.h + h5tools_dump.h + h5tools.h + h5tools_ref.h + h5tools_str.h + h5tools_utils.h + h5trav.h + + (DER - 2018/10/26, HDFFV-10614, 10609) + + - Autotools installs now install H5FDwindows.h + + This is simply to align the installed header files between the + autotools and CMake. H5FDwindows.h has no functionality on + non-Windows systems. + + (DER - 2018/10/26, HDFFV-10614) - (ADB - 2018/09/26, HDFFV-10594) Library: -------- - - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. + - The sec2, log, and core VFDs can now use pread/pwrite instead of + read/write. + + pread and pwrite do not change the file offset, a feature that was + requested by a user working with a multi-threaded application. + + The option to configure this feature is described above. + + (DER - 2019/02/03, HDFFV-10696) + + - Add ability to minimze dataset object headers. + + Creation of many, very small datasets resulted in extensive file bloat + due to extra space in the dataset object headers -- this space is + allocated by default to allow for the insertion of a small number of + attributes within the object header and not require a continuation + block, an unnecessary provision in the target use case. + + Inform the library to expect no attributes on created datasets, and to + allocate the least space possible for the object headers. + NOTE: A continuation block is created if attributes are added to a + 'minimized' dataset, which can reduce performance. + NOTE: Some extra space is allocated for attributes essential to the + correct behavior of the object header (store creation times, e.g.). This + does not violate the design principle, as the space is calculated and + allocated as needed at the time of dataset object header creation -- + unused space is not generated. + New API calls: + H5Fget_dset_no_attrs_hint + H5Fset_dset_no_attrs_hint + H5Pget_dset_no_attrs_hint + H5Pset_dset_no_attrs_hint + + (JOS - 2019/01/04, TRILAB-45) + + - Added new chunk query functions + + The following public functions were added to discover information about + the chunks in an HDF5 file. + herr_t H5Dget_num_chunks(dset_id, fspace_id, *nchunks) + herr_t H5Dget_chunk_info_by_coord(dset_id, *coord, *filter_mask, *addr, *size) + herr_t H5Dget_chunk_info(dset_id, fspace_id, index, *coord, *filter_mask, *addr, *size) + + (BMR - 2018/11/07, HDFFV-10615) + + - Several empty public header files where removed from the distribution + + The following files were empty placeholders. They are for internal + packages that are unlikely to ever have public functionality and have + thus been removed. + + H5Bpublic.h + H5B2public.h + H5FSpublic.h + H5HFpublic.h + H5HGpublic.h + H5HLpublic.h + + They were only installed in CMake builds. + + (DER - 2018/10/26, HDFFV-10614) + + + Parallel Library: + ----------------- + - Changed the default behavior in parallel when reading the same dataset in its entirety + (i.e. H5S_ALL dataset selection) which is being read by all the processes collectively. + The dataset must be contiguous, less than 2GB, and of an atomic datatype. + The new behavior is the HDF5 library will use an MPI_Bcast to pass the data read from + the disk by the root process to the remain processes in the MPI communicator associated + with the HDF5 file. + + (MSB - 2019/01/02, HDFFV-10652) + + - All MPI-1 API calls have been replaced with MPI-2 equivalents. + + This was done to better support OpenMPI, as default builds no longer + include MPI-1 support (as of OpenMPI 4.0). + + (DER - 2018/12/30, HDFFV-10566) + + Fortran Library: + ---------------- + - Added wrappers for dataset object header minimization calls. + (see the note for TRILAB-45, above) + + New API calls: + + h5fget_dset_no_attrs_hint_f + h5fset_dset_no_attrs_hint_f + h5pget_dset_no_attrs_hint_f + h5pset_dset_no_attrs_hint_f + + (DER - 2019/01/09, TRILAB-45) + + - Added new Fortran derived type, c_h5o_info_t, which is interoperable with + C's h5o_info_t. This is needed for callback functions which + pass C's h5o_info_t data type definition. + + (MSB, 2019/01/08, HDFFV-10443) + + - Added new Fortran API, H5gmtime, which converts (C) 'time_t' structure + to Fortran DATE AND TIME storage format. + + (MSB, 2019/01/08, HDFFV-10443) + + - Added new Fortran 'fields' optional parameter to: h5ovisit_f, h5oget_info_by_name_f, + h5oget_info, h5oget_info_by_idx and h5ovisit_by_name_f. + + (MSB, 2019/01/08, HDFFV-10443) + + C++ Library: + ------------ + - Added new function to the C++ interface + + Added wrapper for H5Ovisit2: + H5Object::visit() + + (BMR - 2019/02/14, HDFFV-10532) + + + Java Library: + ---------------- + - Rewrote the JNI error handling to be much cleaner - Rather than always running H5detect and generating H5Tinit.c and - H5make_libsettings.c, supply a location for those files. + (JTH - 2019/02/12) - (ADB - 2018/09/18, HDFFV-10332) + - Add new functions to java interface + Added wrappers for: + H5Fset_libver_bounds + H5Fget_dset_no_attrs_hint/H5Fset_dset_no_attrs_hint + H5Pget_dset_no_attrs_hint/H5Pset_dset_no_attrs_hint -Bug Fixes since HDF5-1.10.3 release + (ADB - 2019/01/07, HDFFV-10664) + + - Fix java unit tests when Time is a natural number + + Time substitution in java/test/junit.sh.in doesn't + handle the case when Time is a natural number. Fixed + the regular expression. + + (ADB - 2019/01/07, HDFFV-10674) + + - Duplicate the data read/write functions of Datasets for Attributes. + + Region references could not be displayed for attributes as they could + for datasets. Datasets had overloaded read and write functions for different + datatypes that were not available for attributes. After adding similar + functions, attribute region references work normally. + + (ADB - 2018/12/12, HDFVIEW-4) + + + Tools: + ------ + - The h5repart -family-to-sec2 argument was changed to -family-to-single + + In order to better support other single-file VFDs which could work with + h5repart, the -family-to-sec2 argument was renamed to -family-to-single. + This is just a name change and the functionality of the argument has not + changed. + + The -family-to-sec2 argument has been kept for backwards-compatibility. + This argument should be considered deprecated. + + (DER - 2018/11/14, HDFFV-10633) + + +Bug Fixes since HDF5-1.10.4 release ================================== Library ------- - - Allow H5detect and H5make_libsettings to take a file as an argument. + - Fix hangs with collective metadata reads during chunked dataset I/O + + In the parallel library, it was discovered that when a particular + sequence of operations following a pattern of: + + "write to chunked dataset" -> "flush file" -> "read from dataset" + + occurred with collective metadata reads enabled, hangs could be + observed due to certain MPI ranks not participating in the collective + metadata reads. + + To fix the issue, collective metadata reads are now disabled during + chunked dataset raw data I/O. + + (JTH - 2019/02/11, HDFFV-10563, HDFFV-10688) + + - Performance issue when closing an object + + The slow down is due to the search of the "tag_list" to find + out the "corked" status of an object and "uncork" it if so. + + Improve performance by skipping the search of the "tag_list" + if there are no "corked" objects when closing an object. + + (VC - 2019/02/06) + + - Uninitialized bytes from a type conversion buffer could be written + to disk in H5Dwrite calls where type conversion takes place + and the type conversion buffer was created by the HDF5 library. + + When H5Dwrite is called and datatype conversion must be performed, + the library will create a temporary buffer for type conversion if + one is not provided by the user via H5Pset_buffer. This internal + buffer is allocated via malloc and contains uninitialized data. In + some datatype conversions (float to long double, possibly others), + some of this uninitialized data could be written to disk. + + This was flagged by valgrind in the dtransform test and does not + appear to be a common occurrence (it is flagged in one test out + of the entire HDF5 test suite). + + Switching to calloc fixed the problem. + + (DER - 2019/02/03, HDFFV-10694) + + - There was missing protection against division by zero reported to + The HDF Group as issue #CVE-2018-17434. + + Protection against division by zero was added to address the issue + #CVE-2018-17434. + + (BMR - 2019/01/29, HDFFV-10586) + + - The issue CVE-2018-17437 was reported to The HDF Group - Rather than only writing to stdout, add a command argument to name - the file that H5detect and H5make_libsettings will use for output. - Without an argument, stdout is still used, so backwards compatibility - is maintained. + Although CVE-2018-17437 reported a memory leak, the actual issue + was invalid read. It was found that the attribute name length + in an attribute message was corrupted, which caused the buffer + pointer to be advanced too far and later caused an invalid read. - (ADB - 2018/09/05, HDFFV-9059) + A check was added to detect when the attribute name or its length + was corrupted and report the potential of data corruption. + + (BMR - 2019/01/29, HDFFV-10588) + + - H5Ewalk did not stop when it was supposed to + + H5Ewalk was supposed to stop when the callback function stopped + even though the errors in the stack were not all visited, but it + did not. This problem is now fixed. + + (BMR - 2019/01/29, HDFFV-10684) + + - Revert H5Oget_info* and H5Ovisit* functions + + In 1.10.3 new H5Oget_info*2 and H5Ovisit*2 functions were + added for performance. Inadvertently, the original functions; + H5Oget_info, + H5Oget_info_by_name, + H5Oget_info_by_idx, + H5Ovisit, + H5Ovisit_by_name + were versioned to H5Oget_info*1 and H5Ovisit*1. This + broke the API compatibility for a maintenance release. The + original functions have been restored. + + (ADB - 2019/01/24, HDFFV-10686) + + - Fixed a potential invalid memory access and failure that could occur when + decoding an unknown object header message (from a future version of the + library). + + (NAF - 2019/01/07) + + - Deleting attributes in dense storage + + The library aborts with "infinite loop closing library" after + attributes in dense storage are created and then deleted. + + When deleting the attribute nodes from the name index v2 B-tree, + if an attribute is found in the intermediate B-tree nodes, + which may be merged/redistributed in the process, we need to + free the dynamically allocated spaces for the intermediate + decoded attribute. + + (VC - 2018/12/26, HDFFV-10659) + + - There was missing protection against division by zero reported to + The HDF Group as issue #CVE-2018-17233. + + Protection against division by zero was added to address the issue + #CVE-2018-17233. In addition, several similar occurrences in the same + file were fixed as well. + + (BMR - 2018/12/23, HDFFV-10577) + + - Fixed an issue where the parallel filters tests would fail + if zlib was not available on the system. Until support can + be added in the tests for filters beyond gzip/zlib, the tests + will be skipped if zlib is not available. + + (JTH - 2018/12/05) - A bug was discovered in the parallel library where an application - would hang if a collective read/write of a chunked dataset occurred - when collective metadata reads were enabled and some of the ranks - had no selection in the dataset's dataspace. The ranks which had no - selection in the dataset's dataspace called H5D__chunk_addrmap() to - retrieve the lowest chunk address in the dataset. This is because we - require reads/writes to be performed in strictly non-decreasing order - of chunk address in the file. - - When the chunk index used was a version 1 or 2 B-tree, these - non-participating ranks would issue a collective MPI_Bcast() call - that the participating ranks would not issue, causing the hang. Since - the non-participating ranks are not actually reading/writing anything, - the H5D__chunk_addrmap() call can be safely removed and the address used - for the read/write can be set to an arbitrary number (0 was chosen). - - (JTH - 2018/08/25, HDFFV-10501) + would eventually consume all of the available MPI communicators + when continually writing to a compressed dataset in parallel. This + was due to internal copies of an HDF5 File Access Property List, + which each contained a copy of the MPI communicator, not being + closed at the end of each write operation. This problem was + exacerbated by larger numbers of processors. + + (JTH - 2018/12/05, HDFFV-10629) - Java Library: - ---------------- - - JNI native library dependencies - - The build for the hdf5_java native library used the wrong - hdf5 target library for CMake builds. Correcting the hdf5_java - library to build with the shared hdf5 library required testing - paths to change also. - (ADB - 2018/08/31, HDFFV-10568) + Fortran + -------- + - Fixed issue with Fortran not returning h5o_info_t field values + meta_size%attr%index_size and meta_size%attr%heap_size. - - Java iterator callbacks + (MSB, 2019/01/08, HDFFV-10443) - Change global callback object to a small stack structure in order - to fix a runtime crash. This crash was discovered when iterating - through a file with nested group members. The global variable - visit_callback is overwritten when recursion starts. When recursion - completes, visit_callback will be pointing to the wrong callback method. + - Added symbolic links libhdf5_hl_fortran.so to libhdf5hl_fortran.so and + libhdf5_hl_fortran.a to libhdf5hl_fortran.a in hdf5/lib directory for + autotools installs. These were added to match the name of the files + installed by cmake and the general pattern of hl lib files. We will + change the names of the installed lib files to the matching name in + the next major release. - (ADB - 2018/08/15, HDFFV-10536) + (LRK - 2019/01/04, HDFFV-10596) - - Java HDFLibraryException class + - Made Fortran specific subroutines PRIVATE in generic procedures. - Change parent class from Exception to RuntimeException. + Affected generic procedures were functions in H5A, H5D, H5P, H5R and H5T. - (ADB - 2018/07/30, HDFFV-10534) + (MSB, 2018/12/04, HDFFV-10511) - - JNI Read and Write - Refactored variable-length functions, H5DreadVL and H5AreadVL, - to correct dataset and attribute reads. New write functions, - H5DwriteVL and H5AwriteVL, are under construction. + Testing + ------- + - Fixed a test failure in testpar/t_dset.c caused by + the test trying to use the parallel filters feature + on MPI-2 implementations. - (ADB - 2018/06/02, HDFFV-10519) + (JTH, 2019/2/7) Supported Platforms @@ -175,10 +508,9 @@ Supported Platforms Windows 7 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Windows 7 x64 Visual Studio 2012 w/ Intel Fortran 15 (cmake) - Visual Studio 2013 w/ Intel Fortran 15 (cmake) + Windows 7 x64 Visual Studio 2013 Visual Studio 2015 w/ Intel Fortran 16 (cmake) - Visual Studio 2015 w/ Intel C, Fortran 2017 (cmake) + Visual Studio 2015 w/ Intel C, Fortran 2018 (cmake) Visual Studio 2015 w/ MSMPI 8 (cmake) Windows 10 Visual Studio 2015 w/ Intel Fortran 18 (cmake) @@ -194,9 +526,8 @@ Supported Platforms 64-bit gfortran GNU Fortran (GCC) 5.2.0 (osx1011dev/osx1011test) Intel icc/icpc/ifort version 16.0.2 - Mac OS Sierra 10.12.6 Apple LLVM version 8.1.0 (clang/clang++-802.0.42) - 64-bit gfortran GNU Fortran (GCC) 7.1.0 - (kite) Intel icc/icpc/ifort version 17.0.2 + MacOS High Sierra 10.13.6 Apple LLVM version 10.0.0 (clang/clang++-1000.10.44.4) + 64-bit gfortran GNU Fortran (GCC) 8.3.0 Tested Configuration Features Summary @@ -222,10 +553,9 @@ Windows 7 Cygwin n y/n n y y y Windows 7 x64 Cygwin n y/n n y y y Windows 10 y y/y n y y y Windows 10 x64 y 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 Mac OS X El Capitan 10.11.6 64-bit n y/y n y y y -Mac OS Sierra 10.12.6 64-bit n y/y n y y y +MacOS High Sierra 10.13.6 64-bit n y/y n y y y CentOS 7.2 Linux 3.10.0 x86_64 PGI n y/y n y y y CentOS 7.2 Linux 3.10.0 x86_64 GNU y y/y y y y y CentOS 7.2 Linux 3.10.0 x86_64 Intel n y/y n y y y @@ -242,10 +572,9 @@ Windows 7 Cygwin n n n y Windows 7 x64 Cygwin n n n y Windows 10 y y y y Windows 10 x64 y y 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 -Mac OS X El Capitan 10.11.6 64-bit y n y y -Mac OS Sierra 10.12.6 64-bit y n y y +Mac OS X Yosemite 10.10.5 64-bit y y y y +Mac OS X El Capitan 10.11.6 64-bit y y y y +MacOS High Sierra 10.13.6 64-bit y y y y CentOS 7.2 Linux 3.10.0 x86_64 PGI y y y n CentOS 7.2 Linux 3.10.0 x86_64 GNU y y y y CentOS 7.2 Linux 3.10.0 x86_64 Intel y y y n @@ -257,7 +586,7 @@ Compiler versions for each platform are listed in the preceding More Tested Platforms ===================== -The following platforms are not supported but have been tested for this release. +The following configurations are not supported but have been tested for this release. Linux 2.6.32-573.22.1.el6 GNU C (gcc), Fortran (gfortran), C++ (g++) #1 SMP x86_64 GNU/Linux compilers: @@ -275,8 +604,9 @@ The following platforms are not supported but have been tested for this release. #1 SMP x86_64 GNU/Linux Version 4.8.5 20150623 (Red Hat 4.8.5-4) (jelly) with NAG Fortran Compiler Release 6.1(Tozai) GCC Version 7.1.0 - OpenMPI 3.0.0-GCC-7.2.0-2.29, - 3.1.0-GCC-7.2.0-2.29 + MPICH 3.2-GCC-4.9.3 + MPICH 3.2.1-GCC-7.2.0-2.29 + OpenMPI 2.1.5-GCC-7.2.0-2.29 Intel(R) C (icc) and C++ (icpc) compilers Version 17.0.0.098 Build 20160721 with NAG Fortran Compiler Release 6.1(Tozai) @@ -285,29 +615,15 @@ The following platforms are not supported but have been tested for this release. #1 SMP x86_64 GNU/Linux (moohan) - Linux 2.6.32-573.18.1.el6.ppc64 MPICH mpich 3.1.4 compiled with - #1 SMP ppc64 GNU/Linux IBM XL C/C++ for Linux, V13.1 - (ostrich) and IBM XL Fortran for Linux, V15.1 - - Debian 8.4 3.16.0-4-amd64 #1 SMP Debian 3.16.36-1 x86_64 GNU/Linux - gcc, g++ (Debian 4.9.2-10) 4.9.2 - GNU Fortran (Debian 4.9.2-10) 4.9.2 - (cmake and autotools) - - Fedora 24 4.7.2-201.fc24.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux - gcc, g++ (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) - - Ubuntu 16.04.1 4.4.0-38-generic #57-Ubuntu SMP x86_64 GNU/Linux - gcc, g++ (Ubuntu 5.4.0-6ubuntu1~16.04.2) - 5.4.0 20160609 - GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.2) - 5.4.0 20160609 + Fedora 29 4.20.10-200.fc29.x86_64 #1 SMP x86_64 x86_64 x86_64 GNU/Linux + gcc, g++ (GCC) 8.2.1 20181215 + (Red Hat 8.2.1-6) + GNU Fortran (GCC) 8.2.1 20181215 + (Red Hat 8.2.1-6) (cmake and autotools) + Windows 7 x64 Visual Studio 2008 + Known Problems ============== @@ -323,6 +639,27 @@ Known Problems t_pflush1/fails on exit The first two tests fail attempting collective writes. + CPP ptable test fails on VS2017 with Intel compiler, JIRA issue: HDFFV-10628. + This test will pass with VS2015 with Intel compiler. + + Older MPI libraries such as OpenMPI 2.0.1 and MPICH 2.1.5 were tested + while attempting to resolve the Jira issue: HDFFV-10540. + The known problems of reading or writing > 2GBs when using MPI-2 was + partially resolved with the MPICH library. The proposed support recognizes + IO operations > 2GB and if the datatype is not a derived type, the library + breaks the IO into chunks which can be input or output with the existing + MPI 2 limitations, i.e. size reporting and function API size/count + arguments are restricted to be 32 bit integers. For derived types larger + than 2GB, MPICH 2.1.5 fails while attempting to read or write data. + OpenMPI in contrast, implements MPI-3 APIs even in the older releases + and thus does not suffer from the 32 bit size limitation described here. + OpenMPI releases prior to v3.1.3 appear to have other datatype issues however, + e.g. within a single parallel test (testphdf5) the subtests (cdsetr, eidsetr) + report data verfication errors before eventually aborting. + The most recent versions of OpenMPI (v3.1.3 or newer) have evidently + resolved these isses and parallel HDF5 testing does not currently report + errors though occasional hangs have been observed. + Known problems in previous releases can be found in the HISTORY*.txt files in the HDF5 source. Please report any new problems found to help@hdfgroup.org. |