Installation instructions for Parallel HDF5 ------------------------------------------- 1. Overview ----------- This file contains instructions for the installation of parallel HDF5. Platforms supported by this release are SGI Origin 2000, IBM SP2, Intel TFLOPs, and Linux version 2.2 and greater. The steps are kind of unnatural and will be more automized in the next release. If you have difficulties installing the software in your system, please send mail to hdfparallel@ncsa.uiuc.edu In your mail, please include the output of "uname -a". Also attach the content of "config.log" if you ran the "configure" command. First, you must obtain and unpack the HDF5 source as described in the INSTALL file. You also need to obtain the information of the include and library paths of MPI and MPIO software installed in your system since the parallel HDF5 library uses them for parallel I/O access. 2. Quick Instruction for known systems -------------------------------------- The following shows particular steps to run the parallel HDF5 configure for a few machines we've tested. If your particular platform is not shown or somehow the steps do not work for yours, please go to the next section for more detailed explanations. ------ Know parallel compilers ------ HDF5 knows serveral parallel compilers: mpicc, hcc, mpcc, mpcc_r. To build parallel HDF5 with one of the above, just set CC as it and configure. The "--enable-parallel" is optional in this case. $ CC=/usr/local/mpi/bin/mpicc ./configure --prefix= $ make $ make check $ make install ------ TFLOPS ------ Follow the instuctions in INSTALL_TFLOPS. ------- IBM SP ------- First of all, make sure your environment variables are set correctly to compile and execute a single process mpi applications for the SP machine. Unfortunately, the setting varies from machine to machine. E.g., the following works for the Blue machine of LLNL. setenv CC mpcc_r setenv F9X mpxlf_r # if parallel Fortran API is wanted setenv MP_PROCS 1 setenv MP_NODES 1 setenv MP_LABELIO no setenv MP_RMPOOL 0 setenv RUNPARALLEL "MP_PROCS=2 MP_TASKS_PER_NODE=2 poe" setenv LLNL_COMPILE_SINGLE_THREADED TRUE The shared library configuration for this version is broken. So, only static library is supported. Then do the following steps: $ ./configure --disable-shared --prefix= $ make # build the library $ make check # verify the correctness $ make install --------------- SGI Origin 2000 Cray T3E (where MPI-IO is part of system MPI library such as the mpt module) --------------- #!/bin/sh RUNPARALLEL="mpirun -np 3" export RUNPARALLEL LIBS="-lmpi" export LIBS ./configure --enable-parallel --prefix=$PWD/installdir make make check make install ***Known problem*** Some O2K system may encounter an error during make. ld32: FATAL 9: I/O error (-lmpi): No such file or directory This is because libtool tries too hard to locate the loader 'ld' but ends up with one that does not know where to find the right version of libmpi.a for the particular ABI requested. The fix is to edit the file 'libtool' at the top of the build directory. Search for a string that looks like the following: LD="/opt/MIPSpro/MIPSpro_default/opt/MIPSpro/bin/ld -n32" Replace it with something that knows how to find the right libmpi.a. E.g., LD="/opt/MIPSpro/MIPSpro_default/opt/MIPSpro/bin/cc -n32" Or you can pre-empt it by setting LD at configure time $ LD="cc" ./configure --enable-parallel ... --------------- SGI Origin 2000 Cray T3E (where MPI-IO is not part of system MPI library or I want to use my own version of MPIO) --------------- mpi1_inc="" #mpi-1 include mpi1_lib="" #mpi-1 library mpio_inc=-I$HOME/ROMIO/include #mpio include mpio_lib="-L$HOME/ROMIO/lib/IRIX64" #mpio library MPI_INC="$mpio_inc $mpi1_inc" MPI_LIB="$mpio_lib $mpi1_lib" #for version 1.1 CPPFLAGS=$MPI_INC export CPPFLAGS LDFLAGS=$MPI_LIB export LDFLAGS RUNPARALLEL="mpirun -np 3" export RUNPARALLEL LIBS="-lmpio -lmpi" export LIBS ./configure --enable-parallel --prefix=$PWD/installdir make make check make install --------------------- Linux 2.4 and greater --------------------- Be sure that your installation of MPICH was configured with the following configuration command-line option: -cflags="-D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_FILE_OFFSET_BITS=64" This allows for >2GB sized files on Linux systems and is only available with Linux kernels 2.4 and greater. ------------------ HP V2500 and N4000 ------------------ Follow the instructions in section 3. 3. Detail explanation --------------------- The HDF5 library can be configured to use MPI and MPI-IO for parallelism on a distributed multi-processor system. The easiest way to do this is to have a properly installed parallel compiler (e.g., MPICH's mpicc or IBM's mpcc_r) and supply that executable as the value of the CC environment variable. For examples, $ CC=mpcc_r ./configure $ CC=/usr/local/mpi/bin/mpicc ./configure If no such wrapper script is available then you must specify your normal C compiler along with the distribution of MPI/MPI-IO which is to be used (values other than `mpich' will be added at a later date): $ ./configure --enable-parallel=mpich If the MPI/MPI-IO include files and/or libraries cannot be found by the compiler then their directories must be given as arguments to CPPFLAGS and/or LDFLAGS: $ CPPFLAGS=-I/usr/local/mpi/include \ LDFLAGS=-L/usr/local/mpi/lib/LINUX/ch_p4 \ ./configure --enable-parallel=mpich If a parallel library is being built then configure attempts to determine how to run a parallel application on one processor and on many processors. If the compiler is `mpicc' and the user hasn't specified values for RUNSERIAL and RUNPARALLEL then configure chooses `mpirun' from the same directory as `mpicc': RUNSERIAL: /usr/local/mpi/bin/mpirun -np 1 RUNPARALLEL: /usr/local/mpi/bin/mpirun -np $${NPROCS:=3} The `$${NPROCS:=3}' will be substituted with the value of the NPROCS environment variable at the time `make check' is run (or the value 3). 4. Parallel tests ----------------- The testpar/ directory contains tests for Parallel HDF5 and MPI-IO. The t_mpi tests the basic functionalities of some MPI-IO features used by Parallel HDF5. It usually exits with non-zero code if a required MPI-IO feature does not succeed as expected. One exception is the testing of accessing files larger than 2GB. If the underlaying filesystem or if the MPI-IO library fails to handle file sizes larger than 2GB, the test will print informational essages stating the failure but will not exit with non-zero code. Failure to support file size greater than 2GB is not a fatal error for HDF5 becuase HDF5 can use other file-drivers such as families of files to by pass the file size limit. By default, the parallel tests use /tmp/$LOGIN as the test directory. This can be override by the environment variable $HDF5_PARAPREFIX. For example, if the tests should use directory /PFS/user/me, do HDF5_PARAPREFIX=/PFS/user/me export HDF5_PARAPREFIX make check (In some batch job system, you many need to hardset HDF5_PARAPREFIX in the shell initial files like .profile, .cshrc, etc.)