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author | Allen Byrne <byrn@hdfgroup.org> | 2019-09-23 20:30:07 (GMT) |
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committer | Allen Byrne <byrn@hdfgroup.org> | 2019-09-23 20:30:07 (GMT) |
commit | a4d6a270783d69c663357c31fcd6196b98706dfb (patch) | |
tree | ce4cd3ff16aa0a3918c4e999d3b6ba63a35a41fe /release_docs | |
parent | a0947d808fb3b0af98032beb1a4f5353443c8aa3 (diff) | |
download | hdf5-a4d6a270783d69c663357c31fcd6196b98706dfb.zip hdf5-a4d6a270783d69c663357c31fcd6196b98706dfb.tar.gz hdf5-a4d6a270783d69c663357c31fcd6196b98706dfb.tar.bz2 |
HDFFV-10903 merge S3 from dev
Diffstat (limited to 'release_docs')
-rw-r--r-- | release_docs/README_HDF5_CMake | 23 | ||||
-rw-r--r-- | release_docs/README_HPC | 206 | ||||
-rw-r--r-- | release_docs/RELEASE.txt | 25 | ||||
-rw-r--r-- | release_docs/USING_CMake_Examples.txt | 5 |
4 files changed, 257 insertions, 2 deletions
diff --git a/release_docs/README_HDF5_CMake b/release_docs/README_HDF5_CMake new file mode 100644 index 0000000..9580fc7 --- /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 + hdf5-1.8.22 HDF5 1.8.22 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 +hdf5-1.8.22/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 hdf5-1.8.22/release_docs. + + + + + diff --git a/release_docs/README_HPC b/release_docs/README_HPC new file mode 100644 index 0000000..97f088c --- /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 "hdf5-1.8.22", or for the first hdf5_1_8_22 pre-release version, +it should be renamed "hdf5-1.8.22-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 + "hdf5-1.8.22". + + 2. Three cmake script files need to be copied to the working directory, or + have symbolic links to them, created in the working directory: + + hdf5-1.8.22/config/cmake/scripts/HDF5config.cmake + hdf5-1.8.22/config/cmake/scripts/CTestScript.cmake + hdf5-1.8.22/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 + hdf5-1.8.22 + + 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 hdf5-1.8.22/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>/hdf5-1.8.22/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/HDF5/1.8.22 +-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_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>/hdf5-1.8.22" + +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 05fe857..23f3652 100644 --- a/release_docs/RELEASE.txt +++ b/release_docs/RELEASE.txt @@ -148,6 +148,31 @@ New Features Library ------- + - Add S3 and HDFS VFDs to HDF5 maintenance + + Fix windows requirements and java tests. Windows requires CMake 3.13. + Install openssl library (with dev files); + from "Shining Light Productions". msi package preferred. + + PATH should have been updated with the installation dir. + set ENV variable OPENSSL_ROOT_DIR to the installation dir. + set ENV variable OPENSSL_CONF to the cfg file, likely %OPENSSL_ROOT_DIR%\bin\openssl.cfg + Install libcurl library (with dev files); + download the latest released version using git: https://github.com/curl/curl.git + + Open a Visual Studio Command prompt + change to the libcurl root folder + run the "buildconf.bat" batch file + change to the winbuild directory + nmake /f Makefile.vc mode=dll MACHINE=x64 + copy libcurl-vc-x64-release-dll-ipv6-sspi-winssl dir to C:\curl (installation dir) + set ENV variable CURL_ROOT to C:\curl (installation dir) + update PATH ENV variable to %CURL_ROOT%\bin (installation bin dir). + the aws credentials file should be in %USERPROFILE%\.aws folder + set the ENV variable "HDF5_ROS3_TEST_BUCKET_URL=https://s3.us-east-2.amazonaws.com/hdf5ros3" + + (ADB - 2019/09/12, HDFFV-10854) + - Allow pre-generated H5Tinit.c and H5make_libsettings.c to be used. Rather than always running H5detect and generating H5Tinit.c and diff --git a/release_docs/USING_CMake_Examples.txt b/release_docs/USING_CMake_Examples.txt index f98b39e..a5ababa 100644 --- a/release_docs/USING_CMake_Examples.txt +++ b/release_docs/USING_CMake_Examples.txt @@ -58,8 +58,9 @@ Default installation process: with the CTEST_CONFIGURATION_TYPE script option. Note that this must be the same as the value used with the -C command line option. The default build configuration is defined to build and use static libraries. - Shared libraries can be used with the STATIC_ONLY script option set to "NO". - Other options can be changed by editing the HDF518_Examples.cmake file. + + Shared libraries and other options can be changed by editing the + HDF5_Examples_options.cmake file. If the defaults are okay, execute from this directory: ctest -S HDF518_Examples.cmake -C Release -V -O test.log |