hdf5/release_docs/README_HPC

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*    Using CMake to build and test HDF5 source on HPC machines         *
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                    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

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========================================================================
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.