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Diffstat (limited to 'release_docs/README_HPC')
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1 files changed, 206 insertions, 79 deletions
diff --git a/release_docs/README_HPC b/release_docs/README_HPC index bdeab67..67a5d6c 100644 --- a/release_docs/README_HPC +++ b/release_docs/README_HPC @@ -1,79 +1,206 @@ -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. -- +************************************************************************ +* 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. |