diff options
| -rw-r--r-- | config/cmake/scripts/HPC/par-HDF5options.cmake | 117 | ||||
| -rw-r--r-- | config/cmake/scripts/HPC/ser-HDF5options.cmake | 117 | ||||
| -rw-r--r-- | release_docs/README_HPC | 79 |
3 files changed, 313 insertions, 0 deletions
diff --git a/config/cmake/scripts/HPC/par-HDF5options.cmake b/config/cmake/scripts/HPC/par-HDF5options.cmake new file mode 100644 index 0000000..0527995 --- /dev/null +++ b/config/cmake/scripts/HPC/par-HDF5options.cmake @@ -0,0 +1,117 @@ +# +# Copyright by The HDF Group. +# All rights reserved. +# +# This file is part of HDF5. The full HDF5 copyright notice, including +# terms governing use, modification, and redistribution, is contained in +# the COPYING file, which can be found at the root of the source code +# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# If you do not have access to either file, you may request a copy from +# help@hdfgroup.org. +# +############################################################################################# +#### Change default configuration of options in config/cmake/cacheinit.cmake file ### +#### format: set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ") ### +############################################################################################# + +### uncomment/comment and change the following lines for other configuration options + +############################################################################################# +#### maximum parallel processor count for build and test #### +set (MAX_PROC_COUNT 8) + +############################################################################################# +#### alternate toolsets #### +#set (CMAKE_GENERATOR_TOOLSET "Intel C++ Compiler 17.0") + +############################################################################################# +#### Only build static libraries #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=OFF") +#### Add PICC option on linux/mac #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_ANSI_CFLAGS:STRING=-fPIC") + +############################################################################################# +#### fortran enabled #### +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=ON") + ### enable Fortran 2003 depends on HDF5_BUILD_FORTRAN +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=ON") +#### fortran disabled #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF") + ### enable Fortran 2003 depends on HDF5_BUILD_FORTRAN +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=OFF") + +############################################################################################# +#### java enabled #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON") +#### java disabled #### +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF") + +############################################################################################# +### change install prefix (default use INSTALLDIR value) +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_INSTALL_PREFIX:PATH=${INSTALLDIR}") + +############################################################################################# +#### ext libraries #### + +### ext libs from tgz +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=TGZ -DTGZPATH:PATH=${CTEST_SCRIPT_DIRECTORY}") +### ext libs from git +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=GIT") +### ext libs on system +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include") + +### disable using ext zlib +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF") +### disable using ext szip +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF") + +#### package examples #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACK_EXAMPLES:BOOL=ON -DHDF5_EXAMPLES_COMPRESSED:STRING=HDF5Examples-1.10.9-Source.tar.gz -DHDF5_EXAMPLES_COMPRESSED_DIR:PATH=${CTEST_SCRIPT_DIRECTORY}") + +############################################################################################# +### enable parallel builds + +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=ON") +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF") +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF") +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=OFF") + +############################################################################################# +### enable thread-safety builds + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=ON") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_HL_LIB:BOOL=OFF") + +############################################################################################# +### disable test program builds + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_TESTING:BOOL=OFF") + +############################################################################################# +### disable packaging + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_NO_PACKAGES:BOOL=ON") +### Create install package with external libraries (szip, zlib) +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_EXTLIBS:BOOL=ON") + +############################################################################################# +### use a toolchain file + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/craype.cmake") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/intel.cmake") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/GCC.cmake") + +#options to run test scripts in batch commands +set (LOCAL_BATCH_TEST ON) +set (LOCAL_BATCH_SCRIPT_COMMAND "sbatch") +set (LOCAL_BATCH_SCRIPT_NAME "knl_ctestS.sl") +set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "knl_ctestP.sl") +set(MPIEXEC_EXECUTABLE "srun") + +############################################################################################# diff --git a/config/cmake/scripts/HPC/ser-HDF5options.cmake b/config/cmake/scripts/HPC/ser-HDF5options.cmake new file mode 100644 index 0000000..71266ec --- /dev/null +++ b/config/cmake/scripts/HPC/ser-HDF5options.cmake @@ -0,0 +1,117 @@ +# +# Copyright by The HDF Group. +# All rights reserved. +# +# This file is part of HDF5. The full HDF5 copyright notice, including +# terms governing use, modification, and redistribution, is contained in +# the COPYING file, which can be found at the root of the source code +# distribution tree, or in https://support.hdfgroup.org/ftp/HDF5/releases. +# If you do not have access to either file, you may request a copy from +# help@hdfgroup.org. +# +############################################################################################# +#### Change default configuration of options in config/cmake/cacheinit.cmake file ### +#### format: set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DXXX:YY=ZZZZ") ### +############################################################################################# + +### uncomment/comment and change the following lines for other configuration options + +############################################################################################# +#### maximum parallel processor count for build and test #### +#set (MAX_PROC_COUNT 8) + +############################################################################################# +#### alternate toolsets #### +#set (CMAKE_GENERATOR_TOOLSET "Intel C++ Compiler 17.0") + +############################################################################################# +#### Only build static libraries #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_SHARED_LIBS:BOOL=OFF") +#### Add PICC option on linux/mac #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_ANSI_CFLAGS:STRING=-fPIC") + +############################################################################################# +#### fortran enabled #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=ON") + ### enable Fortran 2003 depends on HDF5_BUILD_FORTRAN +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=ON") +#### fortran disabled #### +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF") + ### enable Fortran 2003 depends on HDF5_BUILD_FORTRAN +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_F2003:BOOL=OFF") + +############################################################################################# +#### java enabled #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=ON") +#### java disabled #### +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF") + +############################################################################################# +### change install prefix (default use INSTALLDIR value) +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_INSTALL_PREFIX:PATH=${INSTALLDIR}") + +############################################################################################# +#### ext libraries #### + +### ext libs from tgz +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=TGZ -DTGZPATH:PATH=${CTEST_SCRIPT_DIRECTORY}") +### ext libs from git +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=GIT") +### ext libs on system +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ALLOW_EXTERNAL_SUPPORT:STRING=NO") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DZLIB_LIBRARY:FILEPATH=some_location/lib/zlib.lib -DZLIB_INCLUDE_DIR:PATH=some_location/include") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DSZIP_LIBRARY:FILEPATH=some_location/lib/szlib.lib -DSZIP_INCLUDE_DIR:PATH=some_location/include") + +### disable using ext zlib +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=OFF") +### disable using ext szip +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_SZIP_ENCODING:BOOL=OFF") + +#### package examples #### +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACK_EXAMPLES:BOOL=ON -DHDF5_EXAMPLES_COMPRESSED:STRING=HDF5Examples-1.10.9-Source.tar.gz -DHDF5_EXAMPLES_COMPRESSED_DIR:PATH=${CTEST_SCRIPT_DIRECTORY}") + +############################################################################################# +### enable parallel builds + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=ON") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_JAVA:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=OFF") + +############################################################################################# +### enable thread-safety builds + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_THREADSAFE:BOOL=ON") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_ENABLE_PARALLEL:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_CPP_LIB:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_FORTRAN:BOOL=OFF") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_BUILD_HL_LIB:BOOL=OFF") + +############################################################################################# +### disable test program builds + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DBUILD_TESTING:BOOL=OFF") + +############################################################################################# +### disable packaging + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_NO_PACKAGES:BOOL=ON") +### Create install package with external libraries (szip, zlib) +set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF5_PACKAGE_EXTLIBS:BOOL=ON") + +############################################################################################# +### use a toolchain file + +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/intel.cmake") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/crayle.cmake") +#set (ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DCMAKE_TOOLCHAIN_FILE:STRING=config/toolchain/GCC.cmake") + +#options to run test scripts in batch commands +set (LOCAL_BATCH_TEST ON) +set (LOCAL_BATCH_SCRIPT_COMMAND "sbatch") +set (LOCAL_BATCH_SCRIPT_NAME "knl_ctestS.sl") +set (LOCAL_BATCH_SCRIPT_PARALLEL_NAME "knl_ctestP.sl") +set(MPIEXEC_EXECUTABLE "srun") + +############################################################################################# diff --git a/release_docs/README_HPC b/release_docs/README_HPC new file mode 100644 index 0000000..bdeab67 --- /dev/null +++ b/release_docs/README_HPC @@ -0,0 +1,79 @@ +HDF5 version 1.11.4 currently under development + +HDF5 source tar files with the HPC prefix are intended for use on clusters where +configuration and build steps will be done on a login node and executable and +lib files that are built will be run on compute nodes. + +Note these differences from the regular CMake tar and zip files: + - Test programs produced by this tar file will be run using batch scripts. + - Serial and parallel HDF5options.cmake files, using parallel options by default. + +Note also that options are now available in HDF5 source to facilitate use of +toolchain files for using cross compilers available on login nodes to compile +HDF5 for compute nodes. + +Instructions to configure build and test HDF5 using CMake: + +1. The cmake version must be 3.10 or later (cmake --version). +2. Load or switch modules and set CC, FC, CXX for compilers desired. +3. run build-unix.sh to configure, build, test and package HDF5 with CMake. + +Contents: + +build-unix.sh Simple script for running CMake to configure, build, + test, and package HDF5. +CTestScript.cmake CMake script to configure, build, test and package + HDF5. +hdf5-<version> HDF5 source for <version>. +HDF5config.cmake CMake script to configure, build, test and package + HDF5. +HDF5Examples Source for HDF5 Examples. +HDF5options.cmake symlink to parallel or serial HDF5options.cmake files. + Default is parallel file, which builds and tests both + serial and parallel C and Fortran wrappers. + To build serial only, C Fortran and C++ wrappers, delete + The HDF5options.cmake link and run + 'ln -s ser-HDF5options.cmake HDF5options.cmake' to switch. +par-HDF5options.cmake Options file for HDF5 serial and parallel build and test. +ser-HDF5options.cmake Options file for HDF5 serial only build and test. +SZip.tar.gz Source for building SZip. +ZLib.tar.gz Source for buildng Zlib. + + +To cross compile with this HPC-CMake tar.gz HDF5 source file: +On Cray XC40 haswell login node for knl compute nodes using CMake and Cray modules: + 1. Uncomment line in HDF5options.txt to use a toolchain file - line 106 for + config/toolchain/crayle.cmake. + 2. Uncomment lines 110, 111, and 115 - 122 of HDF5options.cmake. + Line 110 allows configuring to complete on the haswell node. + Line 111 switches the compiler to build files for knl nodes. + Lines 115 - 122 set up test files to use sbatch to run build tests + in batch jobs on a knl compute node with 6 processes. + 3. Compiler module may be the default PrgEnv-intel/6.0.4 to use + intel/18.0.2 or other intel, PrgEnv-cray/6.0.4 to use cce/8.7.4, + or PrgEnv-gnu/6.0.4 for GCC compilers. PrgEnv-pgi/6.0.4 is also + available but has not been tested with this tar file. + 4. These CMake options are set in config/toolchain/crayle.cmake: + set(CMAKE_SYSTEM_NAME Linux) + set(CMAKE_COMPILER_VENDOR "CrayLinuxEnvironment") + set(CMAKE_C_COMPILER cc) + set(CMAKE_CXX_COMPILER c++) + set(CMAKE_Fortran_COMPILER ftn) + set(CMAKE_CROSSCOMPILING_EMULATOR "") + + 5. 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 + a. 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 options. + b. 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. +- |