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