path: root/release_docs/INSTALL_parallel

	    Installation instructions for Parallel HDF5
	    -------------------------------------------


1. Overview
-----------

This file contains instructions for the installation of parallel HDF5 (PHDF5).
PHDF5 requires an MPI compiler with MPI-IO support and a parallel file system. 
If you don't know yet, you should first consult with your system support staff
of information how to compile an MPI program, how to run an MPI application,
and how to access the parallel file system.  There are sample MPI-IO C and
Fortran programs in the section of "Sample programs".  You can use them to
run simple tests of your MPI compilers and the parallel file system.

If you still have difficulties installing PHDF5 in your system, please
send mail to
	hdfhelp@ncsa.uiuc.edu

In your mail, please include the output of "uname -a". If you have run the
"configure" command, attach the output of the command and the content of
the file "config.log".


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 several 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=<install-directory>
    $ make
    $ make check
    $ make install


-------
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 MP_PROCS     1
    setenv MP_NODES     1
    setenv MP_LABELIO   no
    setenv MP_RMPOOL    0
    setenv LLNL_COMPILE_SINGLE_THREADED TRUE    # for LLNL site only

The shared library configuration for this version is broken. So, only
static library is supported.

Then do the following steps:

    $ ./configure --disable-shared --prefix=<install-directory>
    $ make		# build the library
    $ make check	# verify the correctness
    $ make install


We also suggest that you add "-qxlf90=autodealloc" to FFLAGS when 
building parallel with fortran enabled.  This can be done by invoking:

    setenv FFLAGS -qxlf90=autodealloc		# 32 bit build

or

    setenv FFLAGS "-q64 -qxlf90=autodealloc"	# 64 bit build

prior to running configure.  Recall that the "-q64" is necessary
for 64 bit builds.

---------------
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.


------------------
Red Storm (Cray XT3)
------------------

The following steps are for building the Parallel HDF5 for the Red Storm
compute nodes.  They would probably work for other Cray XT3 systems but have
not been verified.

# Assume you alrady have a copy of HDF5 source code in directory `hdf5' and
# want to install the binary in directory `/project/hdf5/phdf5'.  You also
# have done the proper setup to have mpicc and mpif90 as the compiler commands.

$ cd hdf5
$ bin/yodconfigure configure
$ env RUNSERIAL="yod -sz 1" RUNPARALLEL="yod -sz 3" \
    CC="mpicc -DRED_STORM" F9X=mpif90 \
    ./configure --disable-hl --without-zlib --disable-stream-vfd \
    --enable-parallel --prefix=/project/hdf5/phdf5
$ make
$ make check

# if all is well, install the binary.
# make install


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 messages 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 because HDF5 can use other file-drivers such
as families of files to by pass the file size limit.

By default, the parallel tests use the current directory as the test directory.
This can be changed 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.)


5. Sample programs
------------------

Here are sample MPI-IO C and Fortran programs.  You may use them to run simple
tests of your MPI compilers and the parallel file system.  The MPI commands
used here are mpicc, mpif90 and mpirun.  Replace them with the commands of
your system.  

The programs assume they run in the parallel file system. Thus they create
the test data file in the current directory.  If the parallel file system
is somewhere else, you need to run the sample programs there or edit the
programs to use a different file name.

Example compiling and running:

% mpicc Sample_mpio.c -o c.out
% mpirun -np 4 c.out

% mpif90 Sample_mpio.f90 -o f.out
% mpirun -np 4 f.out


==> Sample_mpio.c <==
/* Simple MPI-IO program testing if a parallel file can be created.
 * Default filename can be specified via first program argument.
 * Each process writes something, then reads all data back.
 */

#include <mpi.h>
#ifndef MPI_FILE_NULL           /*MPIO may be defined in mpi.h already       */
#   include <mpio.h>
#endif

#define DIMSIZE	10		/* dimension size, avoid powers of 2. */
#define PRINTID printf("Proc %d: ", mpi_rank)

main(int ac, char **av)
{
    char hostname[128];
    int  mpi_size, mpi_rank;
    MPI_File fh;
    char *filename = "./mpitest.data";
    char mpi_err_str[MPI_MAX_ERROR_STRING];
    int  mpi_err_strlen;
    int  mpi_err;
    char writedata[DIMSIZE], readdata[DIMSIZE];
    char expect_val;
    int  i, irank; 
    int  nerrors = 0;		/* number of errors */
    MPI_Offset  mpi_off;
    MPI_Status  mpi_stat;

    MPI_Init(&ac, &av);
    MPI_Comm_size(MPI_COMM_WORLD, &mpi_size);
    MPI_Comm_rank(MPI_COMM_WORLD, &mpi_rank);

    /* get file name if provided */
    if (ac > 1){
	filename = *++av;
    }
    if (mpi_rank==0){
	printf("Testing simple MPIO program with %d processes accessing file %s\n",
	    mpi_size, filename);
        printf("    (Filename can be specified via program argument)\n");
    }

    /* show the hostname so that we can tell where the processes are running */
    if (gethostname(hostname, 128) < 0){
	PRINTID;
	printf("gethostname failed\n");
	return 1;
    }
    PRINTID;
    printf("hostname=%s\n", hostname);

    if ((mpi_err = MPI_File_open(MPI_COMM_WORLD, filename,
	    MPI_MODE_RDWR | MPI_MODE_CREATE | MPI_MODE_DELETE_ON_CLOSE,
	    MPI_INFO_NULL, &fh))
	    != MPI_SUCCESS){
	MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
	PRINTID;
	printf("MPI_File_open failed (%s)\n", mpi_err_str);
	return 1;
    }

    /* each process writes some data */
    for (i=0; i < DIMSIZE; i++)
	writedata[i] = mpi_rank*DIMSIZE + i;
    mpi_off = mpi_rank*DIMSIZE;
    if ((mpi_err = MPI_File_write_at(fh, mpi_off, writedata, DIMSIZE, MPI_BYTE,
	    &mpi_stat))
	    != MPI_SUCCESS){
	MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
	PRINTID;
	printf("MPI_File_write_at offset(%ld), bytes (%d), failed (%s)\n",
		(long) mpi_off, (int) DIMSIZE, mpi_err_str);
	return 1;
    };

    /* make sure all processes has done writing. */
    MPI_Barrier(MPI_COMM_WORLD);

    /* each process reads all data and verify. */
    for (irank=0; irank < mpi_size; irank++){
	mpi_off = irank*DIMSIZE;
	if ((mpi_err = MPI_File_read_at(fh, mpi_off, readdata, DIMSIZE, MPI_BYTE,
		&mpi_stat))
		!= MPI_SUCCESS){
	    MPI_Error_string(mpi_err, mpi_err_str, &mpi_err_strlen);
	    PRINTID;
	    printf("MPI_File_read_at offset(%ld), bytes (%d), failed (%s)\n",
		    (long) mpi_off, (int) DIMSIZE, mpi_err_str);
	    return 1;
	};
	for (i=0; i < DIMSIZE; i++){
	    expect_val = irank*DIMSIZE + i;
	    if (readdata[i] != expect_val){
		PRINTID;
		printf("read data[%d:%d] got %d, expect %d\n", irank, i,
			readdata[i], expect_val);
		nerrors++;
	    }
	}
    }
    if (nerrors)
	return 1;

    MPI_File_close(&fh);

    PRINTID;
    printf("all tests passed\n");

    MPI_Finalize();
    return 0;
}

==> Sample_mpio.f90 <==
!
! The following example demonstrates how to create and close a parallel
! file using MPI-IO calls.
!
! USE MPI is the proper way to bring in MPI definitions but many
! MPI Fortran compiler supports the pseudo standard of INCLUDE.
! So, HDF5 uses the INCLUDE statement instead.
! 

     PROGRAM MPIOEXAMPLE

     ! USE MPI

     IMPLICIT NONE

     INCLUDE 'mpif.h'
        
     CHARACTER(LEN=80), PARAMETER :: filename = "filef.h5" ! File name
     INTEGER     ::   ierror  ! Error flag
     INTEGER     ::   fh      ! File handle
     INTEGER     ::   amode   ! File access mode
     
     call MPI_INIT(ierror)
     amode = MPI_MODE_RDWR + MPI_MODE_CREATE + MPI_MODE_DELETE_ON_CLOSE
     call MPI_FILE_OPEN(MPI_COMM_WORLD, filename, amode, MPI_INFO_NULL, fh, ierror)
     print *, "Trying to create ", filename
     if ( ierror .eq. MPI_SUCCESS ) then
        print *, "MPI_FILE_OPEN succeeded"
        call MPI_FILE_CLOSE(fh, ierror)
     else
        print *, "MPI_FILE_OPEN failed"
     endif

     call MPI_FINALIZE(ierror);
     END PROGRAM