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Installation instructions for Parallel HDF5
-------------------------------------------
1. Overview
-----------
This file contains instructions for the installation of parallel HDF5 (PHDF5).
It is assumed that you are familiar with the general installation steps as
described in the INSATLL file. Get familiar with that file before trying
the parallel HDF5 installation.
The remaining of this section explains the requirements to run PHDF5.
Section 2 shows quick instructions for some well know systems. Section 3
explains the details of the installation steps. Section 4 shows some details
of running the parallel test suites.
1.1. Requirements
-----------------
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 appendix section of "Sample programs". You can use
them to run simple tests of your MPI compilers and the parallel file system.
1.2. Further Help
-----------------
If you still have difficulties installing PHDF5 in your system, please send
mail to
help@hdfgroup.org
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.
2.1. 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 # build the library
$ make check # verify the correctness
# Read the Details section about parallel tests.
$ make install
2.2. IBM SP
-----------
During the build stage, the H5detect is compiled and executed to generate
the source file H5Tinit.c which is compiled as part of the HDF5 library. In
parallel mode, make sure your environment variables are set correctly to
execute a single process mpi application. Otherwise, multiple processes
attempt to write to the same H5Tinit.c file, resulting in a scrambled
source file. Unfortunately, the setting varies from machine to machine.
E.g., the following works for the IBM SP machine at 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 is problematic. 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
# Read the Details section about parallel tests.
$ 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.
2.3. 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.
2.4. Red Storm (Cray XT3) (for v1.8 and later)
-------------------------
Both serial and parallel HDF5 are supported in Red Storm.
2.4.1 Building serial HDF5 for Red Storm
------------------------------------------
The following steps are for building the serial HDF5 for the Red Storm
compute nodes. They would probably work for other Cray XT3 systems but have
not been verified.
# Assume you already have a copy of HDF5 source code in directory `hdf5' and
# want to install the binary in directory `/project/hdf5/hdf5'.
$ cd hdf5
$ bin/yodconfigure configure
$ env RUNSERIAL="yod -sz 1" \
CC=cc FC=ftn CXX=CC \
./configure --prefix=/project/hdf5/hdf5
$ make
$ make check
# if all is well, install the binary.
$ make install
2.4.2 Building parallel HDF5 for Red Storm
------------------------------------------
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 already 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=cc FC=ftn \
./configure --enable-parallel --prefix=/project/hdf5/phdf5
$ make
$ make check
# if all is well, install the binary.
$ make install
2.4.3 Red Storm known problems
------------------------------
For Red Storm, a Cray XT3 system, the yod command sometimes gives the
message, "yod allocation delayed for node recovery". This interferes with
test suites that do not expect seeing this message. To bypass this problem,
I launch the executables with a command shell script called "myyod" which
consists of the following lines. (You should set $RUNSERIAL and $RUNPARALLEL
to use myyod instead of yod.)
==== myyod =======
#!/bin/sh
# sleep 2 seconds to allow time for the node recovery else it pops the
# message,
# yod allocation delayed for node recovery
sleep 2
yod $*
==== end of myyod =======
For Red Storm, a Cray XT3 system, the tools/h5ls/testh5ls.sh will fail on
the test "Testing h5ls -w80 -r -g tgroup.h5" fails. This test is
expected to fail and exit with a non-zero code but the yod command does
not propagate the exit code of the executables. Yod always returns 0 if it
can launch the executable. The test suite shell expects a non-zero for
this particular test, therefore it concludes the test has failed when it
receives 0 from yod. To bypass this problem for now, change the following
lines in the tools/h5ls/testh5ls.sh.
======== Original =========
# The following combination of arguments is expected to return an error message
# and return value 1
TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== Skip the test =========
echo SKIP TOOLTEST tgroup-1.ls 1 -w80 -r -g tgroup.h5
======== end of bypass ========
3. Detail explanation
---------------------
3.1. Installation steps (Uni/Multiple processes modes)
-----------------------
During the step of configure, you must be running in the uni-process mode.
If multiple processes are doing the configure simultaneously, they will
incur errors.
In the build step (make), it depends on your make command whether it can
run correctly in multiple processes mode. If you are not sure, you should
try running it in uni-process mode.
In the test step (make check), if your system can control number of processes
running in the MPI application, you can just use "make check". But if your
system (e.g., IBM SP) has a fixed number of processes for each batch run,
you need to do the serial tests by "make check-s", requesting 1 process and
then do the parallel tests by "make check-p", requesting n processes.
Lastly, "make install" should be run in the uni-process mode.
3.2. Configure details
----------------------
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 the compiler name as the value of the CC environment variable.
For examples,
$ CC=mpcc_r ./configure
$ CC=/usr/local/mpi/bin/mpicc ./configure
If no such a compiler command is available then you must use your normal
C compiler along with the location(s) of MPI/MPI-IO files to be used.
For example,
$ 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 `mpiexec' from the same directory as `mpicc':
RUNSERIAL: /usr/local/mpi/bin/mpiexec -np 1
RUNPARALLEL: /usr/local/mpi/bin/mpiexec -np $${NPROCS:=6}
The `$${NPROCS:=6}' will be substituted with the value of the NPROCS
environment variable at the time `make check' is run (or the value 6).
4. Parallel test suite
----------------------
The testpar/ directory contains tests for Parallel HDF5 and MPI-IO. Here are
some notes about some of the tests.
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 underlying 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 bypass the file size limit.
The t_posix_compliant tests if the file system is POSIX compliant when POSIX
and MPI IO APIs are used. This is for information only and it always exits
with 0 even when non-compliance errors have occurred. This is to prevent
the test from aborting the remaining parallel HDF5 tests unnecessarily.
The t_cache does many small sized I/O requests and may not run well in a
slow file system such as NFS disk. If it takes a long time to run it, try
set the environment variable $HDF5_PARAPREFIX to a file system more suitable
for MPI-IO requests before running t_cache.
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.)
Appendix A. 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 mpiexec. 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
% mpiexec -np 4 c.out
% mpif90 Sample_mpio.f90 -o f.out
% mpiexec -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
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