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Diffstat (limited to 'release_docs/README_HPC')
| -rw-r--r-- | release_docs/README_HPC | 156 |
1 files changed, 78 insertions, 78 deletions
diff --git a/release_docs/README_HPC b/release_docs/README_HPC index 67a5d6c..513064c 100644 --- a/release_docs/README_HPC +++ b/release_docs/README_HPC @@ -1,6 +1,6 @@ ************************************************************************ * Using CMake to build and test HDF5 source on HPC machines * -************************************************************************ +************************************************************************ Contents @@ -16,34 +16,34 @@ Section VI: Other cross compiling options ======================================================================== I. Prerequisites ======================================================================== - 1. Create a working directory that is accessible from the compute nodes for + 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 + 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, + + 2. Load modules for desired compilers, module for cmake version 3.12 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 +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 + 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 +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". +For example, for the current 'develop' version, the "hdf5" directory should +be renamed "hdf5-1.13.0", or for the first hdf5_1_12_0 pre-release version, +it should be renamed "hdf5-1.12.0-5". -If the version number is not known a priori, the version string +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>'. @@ -57,23 +57,23 @@ 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 +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 +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. +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". + 1. For the current 'develop' version the "hdf5" directory should be renamed + "hdf5-1.13.0". 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 + + hdf5-1.13.0/config/cmake/scripts/HDF5config.cmake + hdf5-1.13.0/config/cmake/scripts/CTestScript.cmake + hdf5-1.13.0/config/cmake/scripts/HDF5options.cmake should be copied to the working directory. @@ -82,16 +82,16 @@ parallel or serial only builds available to the CMake command. CTestScript.cmake HDF5config.cmake HDF5options.cmake - hdf5-1.11.4 + hdf5-1.13.0 - Additionally, when the ctest command runs [1], it will add a build directory + 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 + 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 @@ -104,27 +104,27 @@ parallel or serial only builds available to the CMake command. 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, + 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. + Changing -V to -VV will produce more logging information in HDF5.log. - More detailed CMake information can be found in the HDF5 source in + 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 +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 +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") @@ -133,74 +133,74 @@ config/cmake/scripts/HPC/sbatch-HDF5options.cmake file: 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 +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, +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. +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 hdf5-1.13.0/bin/batch. ======================================================================== V. Manual alternatives ======================================================================== -If using ctest is undesirable, one can create a build directory and run the cmake +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" +"/projects/Mutrino/hpcsoft/cle6.0/common/cmake/3.12/bin/cmake" +-C "<working directory>/hdf5-1.13.0/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/HDF5/1.13.0 +-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>/hdf5-1.13.0" followed by make and batch jobs to run tests. -To cross-compile on CrayXC40, run the configure command with the craype-haswell +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 +Tests on machines using slurm can be run with -"sbatch -p knl -C quad,cache ctestS.sl" +"sbatch -p knl -C quad,cache ctestS.sl" -or +or -"sbatch -p knl -C quad,cache ctestP.sl" +"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 +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. +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. |