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资源说明：Raspberry Pi - MPICH2 for parallel processing, including .deb build and Python installation scripts
# MPICH2 Release 1.4.1p1
MPICH2 is a high-performance and widely portable implementation of the
MPI-2.2 standard from the Argonne National Laboratory. This release
has all MPI 2.2 functions and features required by the standard with
the exception of support for the "external32" portable I/O format and
user-defined data representations for I/O.
The distribution has been tested by us on a variety of machines in our
environments as well as our partner institutes. If you have problems
with the installation or usage of MPICH2, please send an email to
mpich-discuss@mcs.anl.gov (you need to subscribe to this list
(https://lists.mcs.anl.gov/mailman/listinfo/mpich-discuss) before
sending an email). If you have found a bug in MPICH2, we request that
you report it at our bug tracking system:
(https://trac.mcs.anl.gov/projects/mpich2/newticket).
This README file should contain enough information to get you started
with MPICH2. More extensive installation and user guides can be found
in the doc/installguide/install.pdf and doc/userguide/user.pdf files
respectively. Additional information regarding the contents of the
release can be found in the CHANGES file in the top-level directory,
and in the RELEASE_NOTES file, where certain restrictions are
detailed. Finally, the MPICH2 web site,
http://www.mcs.anl.gov/research/projects/mpich2, contains information
on bug fixes and new releases.
1. Getting Started
2. Compiler Flags
3. Alternate Channels and Devices
4. Alternate Process Managers
5. Alternate Configure Options
6. Testing the MPICH2 installation
7. Fault Tolerance
8. Environment Variables
9. Developer Builds
10. Installing MPICH2 on windows
11. Multiple Fortran compiler support
-------------------------------------------------------------------------
1. Getting Started
==================
The following instructions take you through a sequence of steps to get
the default configuration (ch3 device, nemesis channel (with TCP and
shared memory), Hydra process management) of MPICH2 up and running.
(a) You will need the following prerequisites.
- REQUIRED: This tar file mpich2-1.4.1p1.tar.gz
- REQUIRED: A C compiler (gcc is sufficient)
- OPTIONAL: A C++ compiler, if C++ applications are to be used
(g++, etc.). If you do not require support for C++ applications,
you can disable this support using the configure option
--disable-cxx (configuring MPICH2 is described in step 1(d)
below).
- OPTIONAL: A Fortran 77 compiler, if Fortran 77 applications are
to be used (gfortran, ifort, etc.). If you do not require
support for Fortran 77 applications, you can disable this
support using --disable-f77 (configuring MPICH2 is described in
step 1(d) below).
- OPTIONAL: A Fortran 90 compiler, if Fortran 90 applications are
to be used (gfortran, ifort, etc.). If you do not require
support for Fortran 90 applications, you can disable this
support using --disable-fc. Note that Fortran 77 support is a
prerequisite for Fortran 90 support (configuring MPICH2 is
described in step 1(d) below).
Also, you need to know what shell you are using since different shell
has different command syntax. Command "echo $SHELL" prints out the
current shell used by your terminal program.
(b) Unpack the tar file and go to the top level directory:
tar xzf mpich2-1.4.1p1.tar.gz
cd mpich2-1.4.1p1
If your tar doesn't accept the z option, use
gunzip mpich2-1.4.1p1.tar.gz
tar xf mpich2-1.4.1p1.tar
cd mpich2-1.4.1p1
(c) Choose an installation directory, say
/home//mpich2-install, which is assumed to non-existent
or empty. It will be most convenient if this directory is shared
by all of the machines where you intend to run processes. If not,
you will have to duplicate it on the other machines after
installation.
(d) Configure MPICH2 specifying the installation directory:
for csh and tcsh:
./configure --prefix=/home//mpich2-install |& tee c.txt
for bash and sh:
./configure --prefix=/home//mpich2-install 2>&1 | tee c.txt
Bourne-like shells, sh and bash, accept "2>&1 |". Csh-like shell,
csh and tcsh, accept "|&". If a failure occurs, the configure
command will display the error. Most errors are straight-forward
to follow. For example, if the configure command fails with:
"No Fortran 77 compiler found. If you don't need to build any
Fortran programs, you can disable Fortran support using
--disable-f77 and --disable-fc. If you do want to build
Fortran programs, you need to install a Fortran compiler such
as gfortran or ifort before you can proceed."
... it means that you don't have a Fortran compiler :-). You will
need to either install one, or disable Fortran support in MPICH2.
If you are unable to understand what went wrong, please go to step
1(i) below, for reporting the issue to the MPICH2 developers and
other users.
(e) Build MPICH2:
for csh and tcsh:
make |& tee m.txt
for bash and sh:
make 2>&1 | tee m.txt
This step should succeed if there were no problems with the
preceding step. Check file m.txt. If there were problems, do a
"make clean" and then run make again with V=1.
make V=1 |& tee m.txt (for csh and tcsh)
OR
make V=1 2>&1 | tee m.txt (for bash and sh)
Then go to step 1(i) below, for reporting the issue to the MPICH2
developers and other users.
(f) Install the MPICH2 commands:
for csh and tcsh:
make install |& tee mi.txt
for bash and sh:
make install 2>&1 | tee mi.txt
This step collects all required executables and scripts in the bin
subdirectory of the directory specified by the prefix argument to
configure.
(g) Add the bin subdirectory of the installation directory to your
path in your startup script (.bashrc for bash, .cshrc for csh,
etc.):
for csh and tcsh:
setenv PATH /home//mpich2-install/bin:$PATH
for bash and sh:
PATH=/home//mpich2-install/bin:$PATH ; export PATH
Check that everything is in order at this point by doing:
which mpicc
which mpiexec
These commands should display the path to your bin subdirectory of
your install directory.
IMPORTANT NOTE: The install directory has to be visible at exactly
the same path on all machines you want to run your applications
on. This is typically achieved by installing MPICH2 on a shared
NFS file-system. If you do not have a shared NFS directory, you
will need to manually copy the install directory to all machines
at exactly the same location.
(h) MPICH2 uses a process manager for starting MPI applications. The
process manager provides the "mpiexec" executable, together with
other utility executables. MPICH2 comes packaged with multiple
process managers; the default is called Hydra.
Now we will run an MPI job, using the mpiexec command as specified
in the MPI-2 standard. There are some examples in the install
directory, which you have already put in your path, as well as in
the directory mpich2-1.4.1p1/examples. One of them is the
classic CPI example, which computes the value of pi by numerical
integration in parallel.
To run the CPI example with 'n' processes on your local machine,
you can use:
mpiexec -n ./examples/cpi
Test that you can run an 'n' process CPI job on multiple nodes:
mpiexec -f machinefile -n ./examples/cpi
The 'machinefile' is of the form:
host1
host2:2
host3:4 # Random comments
host4:1
'host1', 'host2', 'host3' and 'host4' are the hostnames of the
machines you want to run the job on. The ':2', ':4', ':1' segments
depict the number of processes you want to run on each node. If
nothing is specified, ':1' is assumed.
More details on interacting with Hydra can be found at
http://wiki.mcs.anl.gov/mpich2/index.php/Using_the_Hydra_Process_Manager
If you have completed all of the above steps, you have successfully
installed MPICH2 and run an MPI example.
(i) If you run into any errors configuring, building or running
MPICH2, please send the below files to mpich-discuss@mcs.anl.gov.
PLEASE COMPRESS BEFORE SENDING, AS THE FILES CAN BE LARGE. Note that,
depending on which step the build failed, some of the files might not
exist.
mpich2-1.4.1p1/c.txt (generated in step 1(d) above)
mpich2-1.4.1p1/m.txt (generated in step 1(e) above)
mpich2-1.4.1p1/mi.txt (generated in step 1(f) above)
mpich2-1.4.1p1/config.log (generated in step 1(d) above)
mpich2-1.4.1p1/src/openpa/config.log (generated in step 1(d) above)
More details on arguments to mpiexec are given in the User's Guide in
the doc subdirectory.
-------------------------------------------------------------------------
2. Compiler Flags
=================
MPICH2 allows several sets of compiler flags to be used. The first
three sets are configure-time options for MPICH2, while the fourth is
only relevant when compiling applications with mpicc and friends.
(a) CFLAGS, CPPFLAGS, CXXFLAGS, FFLAGS, FCFLAGS, LDFLAGS and LIBS
(abbreviated as xFLAGS): Setting these flags would result in the
MPICH2 library being compiled/linked with these flags and the flags
internally being used in mpicc and friends.
(b) MPICH2LIB_CFLAGS, MPICH2LIB_CPPFLAGS, MPICH2LIB_CXXFLAGS,
MPICH2LIB_FFLAGS, MPICH2LIB_FCFLAGS, MPICH2LIB_LDFLAGS and
MPICH2LIB_LIBS (abbreviated as MPICH2LIB_xFLAGS): Setting these flags
would result in the MPICH2 library being compiled/linked with these
flags. However, these flags will *not* be used by mpicc and friends.
(c) MPICH2_MAKE_CFLAGS: Setting these flags would result in MPICH2's
configure tests to not use these flags, but the makefile's to use
them. This is a temporary hack for certain cases that advanced
developers might be interested in, but which break existing configure
tests (e.g., -Werror). These are NOT recommended for regular users.
(d) MPICH2_MPICC_FLAGS, MPICH2_MPICPP_FLAGS, MPICH2_MPICXX_FLAGS,
MPICH2_MPIF77_FLAGS, MPICH2_MPIFC_FLAGS, MPICH2_LDFLAGS and
MPICH2_LIBS (abbreviated as MPICH2_MPIX_FLAGS): These flags do *not*
affect the compilation of the MPICH2 library itself, but will be
internally used by mpicc and friends.
+--------------------------------------------------------------------+
| | | |
| | MPICH2 library | mpicc and friends |
| | | |
+--------------------+----------------------+------------------------+
| | | |
| xFLAGS | Yes | Yes |
| | | |
+--------------------+----------------------+------------------------+
| | | |
| MPICH2LIB_xFLAGS | Yes | No |
| | | |
+--------------------+----------------------+------------------------+
| | | |
| MPICH2_MAKE_xFLAGS | Yes | No |
| | | |
+--------------------+----------------------+------------------------+
| | | |
| MPICH2_MPIX_FLAGS | No | Yes |
| | | |
+--------------------+----------------------+------------------------+
All these flags can be set as part of configure command or through
environment variables.
Default flags
--------------
By default, MPICH2 automatically adds certain compiler optimizations
to MPICH2LIB_CFLAGS. The currently used optimization level is -O2.
** IMPORTANT NOTE: Remember that this only affects the compilation of
the MPICH2 library and is not used in the wrappers (mpicc and friends)
that are used to compile your applications or other libraries.
This optimization level can be changed with the --enable-fast option
passed to configure. For example, to build an MPICH2 environment with
-O3 for all language bindings, one can simply do:
./configure --enable-fast=O3
Or to disable all compiler optimizations, one can do:
./configure --disable-fast
For more details of --enable-fast, see the output of "configure
--help".
Examples
--------
Example 1:
./configure --disable-fast MPICH2LIB_CFLAGS=-O3 MPICH2LIB_FFLAGS=-O3 \
MPICH2LIB_CXXFLAGS=-O3 MPICH2LIB_FCFLAGS=-O3
This will cause the MPICH2 libraries to be built with -O3, and -O3
will *not* be included in the mpicc and other MPI wrapper script.
Example 2:
./configure --disable-fast CFLAGS=-O3 FFLAGS=-O3 CXXFLAGS=-O3 FCFLAGS=-O3
This will cause the MPICH2 libraries to be built with -O3, and -O3
will be included in the mpicc and other MPI wrapper script.
Example 3:
There are certain compiler flags that should not be used with MPICH2's
configure, e.g. gcc's -Werror, which would confuse configure and cause
certain configure tests to fail to detect the correct system features.
To use -Werror in building MPICH2 libraries, you can pass the compiler
flags during the make step through the Makefile variable
MPICH2_MAKE_CFLAGS as follows:
make MPICH2_MAKE_CFLAGS="-Wall -Werror"
The content of MPICH2_MAKE_CFLAGS is appended to the CFLAGS in all
relevant Makefiles.
-------------------------------------------------------------------------
3. Alternate Channels and Devices
=================================
The communication mechanisms in MPICH2 are called "devices". MPICH2
supports several internal devices including ch3 (default), dcmfd (for
Blue Gene/P) and globus (for Globus), as well as many third-party
devices that are released and maintained by other institutes such as
osu_ch3 (from Ohio State University for InfiniBand and iWARP), ch_mx
(from Myricom for Myrinet MX), etc.
*************************************
ch3 device
**********
The ch3 device contains different internal communication options
called "channels". We currently support nemesis (default) and sock
channels, and experimentally provide a dllchan channel within the ch3
device.
nemesis channel
---------------
Nemesis provides communication using different networks (tcp, mx) as
well as various shared-memory optimizations. To configure MPICH2 with
nemesis, you can use the following configure option:
--with-device=ch3:nemesis
The TCP network module gets configured in by default. To specify a
different network module such as MX, you can use:
--with-device=ch3:nemesis:mx
If the MX include files and libraries are not in the normal search
paths, you can specify them with the following options:
--with-mx-include= and --with-mx-lib=
... or the if lib/ and include/ are in the same directory, you can use
the following option:
--with-mx=
If the MX libraries are shared libraries, they need to be in the
shared library search path. This can be done by adding the path to
/etc/ld.so.conf, or by setting the LD_LIBRARY_PATH variable in your
.bashrc (or .tcshrc) file. It's also possible to set the shared
library search path in the binary. If you're using gcc, you can do
this by adding
LD_LIBRARY_PATH=/path/to/lib
(and)
LDFLAGS="-Wl,-rpath -Wl,/path/to/lib"
... as arguments to configure.
By default, MX allows for only eight endpoints per node causing
ch3:nemesis:mx to give initialization errors with greater than 8
processes on the same node (this is an MX error and not an inherent
limitation in the MPICH2/Nemesis design). If needed, this can be set
to a higher number when MX is loaded. We recommend the user to contact
help@myri.com for details on how to do this.
Shared-memory optimizations are enabled by default to improve
performance for multi-processor/multi-core platforms. They can be
disabled (at the cost of performance) either by setting the
environment variable MPICH_NO_LOCAL to 1, or using the following
configure option:
--enable-nemesis-dbg-nolocal
The --with-shared-memory= configure option allows you to choose how
Nemesis allocates shared memory. The options are "auto", "sysv", and
"mmap". Using "sysv" will allocate shared memory using the System V
shmget(), shmat(), etc. functions. Using "mmap" will allocate shared
memory by creating a file (in /dev/shm if it exists, otherwise /tmp),
then mmap() the file. The default is "auto". Note that System V
shared memory has limits on the size of shared memory segments so
using this for Nemesis may limit the number of processes that can be
started on a single node.
sock channel
------------
sock is the traditional TCP sockets based communication channel. It
uses TCP/IP sockets for all communication including intra-node
communication. So, though the performance of this channel is worse
than that of nemesis, it should work on almost every platform. This
channel can be configured using the following option:
--with-device=ch3:sock
sctp channel
------------
The SCTP channel is a new channel using the Stream Control
Transmission Protocol (SCTP). This channel supports regular MPI-1
operations as well as dynamic processes and RMA from MPI-2; it
currently does not offer support for multiple threads.
Configure the sctp channel by using the following option:
--with-device=ch3:sctp
If the SCTP include files and libraries are not in the normal search
paths, you can specify them with the --with-sctp-include= and
--with-sctp-lib= options, or the --with-sctp= option if lib/ and
include/ are in the same directory.
SCTP stack specific instructions:
For FreeBSD 7 and onward, SCTP comes with CURRENT and is enabled with
the "option SCTP" in the kernel configuration file. The sctp_xxx()
calls are contained within libc so to compile ch3:sctp, make a soft-link
named libsctp.a to the target libc.a, then pass the path of the
libsctp.a soft-link to --with-sctp-lib.
For FreeBSD 6.x, kernel patches and instructions can be downloaded at
http://www.sctp.org/download.html . These kernels place libsctp and
headers in /usr, so nothing needs to be specified for --with-sctp
since /usr is often in the default search path.
For Mac OS X, the SCTP Network Kernel Extension (NKE) can be
downloaded at http://sctp.fh-muenster.de/sctp-nke.html . This places
the lib and include in /usr, so nothing needs to be specified for
--with-sctp since /usr is often in the default search path.
For Linux, SCTP comes with the default kernel from 2.4.23 and later as
a module. This module can be loaded as root using "modprobe sctp".
After this is loaded, you can verify it is loaded using "lsmod".
Once loaded, the SCTP socket lib and include files must be downloaded
and installed from http://lksctp.sourceforge.net/ . The prefix
location must then be passed into --with-sctp. This bundle is called
lksctp-tools and is available for download off their website.
For Solaris, SCTP comes with the default Solaris 10 kernel; the lib
and include in /usr, so nothing needs to be specified for --with-sctp
since /usr is often in the default search path. In order to compile
under Solaris, MPICH2LIB_CFLAGS must have
-DMPICH_SCTP_CONCATENATES_IOVS set when running MPICH2's configure
script.
*************************************
IBM Blue Gene/P device
**********************
MPICH2 also supports the IBM Blue Gene/P systems. Since BG/P's
front-end uses a different architecture than the actual compute nodes,
MPICH2 has to be cross-compiled for this platform. The configuration
of MPICH2 on BG/P relies on the availability of the DCMF driver stack
and cross compiler binaries on the system. These are packaged by IBM
in their driver releases (default installation path is
/bgsys/drivers/ppcfloor) and are not released with MPICH2.
Assuming DRIVER_PATH points to the driver installation path (e.g.,
/bgsys/drivers/ppcfloor), the following is an example configure
command-line for MPICH2:
GCC=${DRIVER_PATH}/gnu-linux/bin/powerpc-bgp-linux-gcc \
CC=${DRIVER_PATH}/gnu-linux/bin/powerpc-bgp-linux-gcc \
CXX=${DRIVER_PATH}/gnu-linux/bin/powerpc-bgp-linux-g++ \
F77=${DRIVER_PATH}/gnu-linux/bin/powerpc-bgp-linux-gfortran \
FC=${DRIVER_PATH}/gnu-linux/bin/powerpc-bgp-linux-gfortran \
CFLAGS="-mcpu=450fp2" \
CXXFLAGS="-mcpu=450fp2" \
FFLAGS="-mcpu=450fp2" \
FCFLAGS="-mcpu=450fp2" \
AR=${DRIVER_PATH}/gnu-linux/bin/powerpc-bgp-linux-ar \
LD=${DRIVER_PATH}/gnu-linux/bin/powerpc-bgp-linux-ld \
MSGLAYER_INCLUDE="-I${DRIVER_PATH}/comm/include" \
MSGLAYER_LIB="-L${DRIVER_PATH}/comm/lib -ldcmfcoll.cnk -ldcmf.cnk -lpthread -lrt \
-L$DRIVER_PATH/runtime/SPI -lSPI.cna" \
./configure --with-device=dcmfd:BGP --with-pmi=no --with-pm=no --with-file-system=bgl \
--enable-timer-type=device --with-cross=src/mpid/dcmfd/cross \
--host=powerpc-bgp-linux --target=powerpc-bgp-linux --build=powerpc64-linux-gnu
-------------------------------------------------------------------------
4. Alternate Process Managers
=============================
hydra
-----
Hydra is the default process management framework that uses existing
daemons on nodes (e.g., ssh, pbs, slurm, sge) to start MPI
processes. More information on Hydra can be found at
http://wiki.mcs.anl.gov/mpich2/index.php/Using_the_Hydra_Process_Manager
mpd
---
MPD was the traditional process manager in MPICH2. The file
mpich2-1.4.1p1/src/pm/mpd/README has more information about
interactive commands for managing the ring of MPDs. The MPD process
manager is now deprecated.
smpd
----
SMPD is a process manager for interoperability between Microsoft
Windows and UNIX, where some processes are running on Windows and
others are running on a variant of UNIX. For more information, please
see mpich2-1.4.1p1/src/pm/smpd/README.
gforker
-------
gforker is a process manager that creates processes on a single
machine, by having mpiexec directly fork and exec them. gforker is
mostly meant as a research platform and for debugging purposes, as it
is only meant for single-node systems.
slurm
-----
SLURM is an external process manager not distributed with
MPICH2. However, we provide configure options that allow integration
with SLURM. To enable this support, use "--with-pmi=slurm
--with-pm=no" option with configure.
-------------------------------------------------------------------------
5. Alternate Configure Options
==============================
MPICH2 has a number of other features. If you are exploring MPICH2 as
part of a development project, you might want to tweak the MPICH2
build with the following configure options. A complete list of
configuration options can be found using:
./configure --help
However, for your convenience, we list a few important options here:
Performance Options:
--enable-fast - Turns off error checking and collection of internal
timing information
--enable-timing=no - Turns off just the collection of internal timing
information
--enable-ndebug - Turns on NDEBUG, which disables asserts. This is a
subset of the optimizations provided by
enable-fast, but is useful in environments where
the user wishes to retain the debug symbols, e.g.,
this can be combined with the --enable-g option.
MPI Features:
--enable-romio - Build the ROMIO implementation of MPI-IO (enabled
by default).
--with-file-system - When used with --enable-romio, specifies
filesystems ROMIO should support. They can be
specified by passing them in a '+'-delimited
list: (e.g.,
--with-file-system="pvfs+nfs+ufs").
If you have installed version 2 of the PVFS
file system, you can use the
'--with-pvfs2=' configure option to
specify where libraries, headers, and utilities
have been installed. If you have added the pvfs
utilities to your PATH, then ROMIO will detect
this and build support for PVFS automatically.
--enable-threads - Build MPICH2 with support for multi-threaded
applications. Only the sock and nemesis channels
support MPI_THREAD_MULTIPLE.
--with-thread-package - When used with --enable-threads, this option
specifies the thread package to use. This
option defaults to "posix". At the moment,
only POSIX threads are supported on UNIX
platforms. We plan to support Solaris
threads in the future.
Language bindings:
--enable-f77 - Build the Fortran 77 bindings (enabled by default).
--enable-fc - Build the Fortran 90 bindings (enabled by default).
--enable-cxx - Build the C++ bindings (enabled by default).
Shared library support:
--enable-shared - Enable shared library support. Shared libraries
are currently only supported for gcc (and gcc-like
compilers) on Linux and Mac and for cc on
Solaris. To have shared libraries created when
MPICH2 is built, specify the following when MPICH2
is configured:
For users who wish to manually control the linker parameters, this
can be done using:
--enable-sharedlibs=gcc (on Linux)
--enable-sharedlibs=osx-gcc (on Mac OS X)
--enable-sharedlibs=solaris-cc (on Solaris)
Cross compilation:
--with-cross=filename - Provide values for the tests that required
running a program, such as the tests that
configure uses to determine the sizes of the
basic types. This should be a fine in
Bourne shell format containing variable
assignment of the form
CROSS_SIZEOF_INT=2
for all of the CROSS_xxx variables.
Error checking and reporting:
--enable-error-checking=level - Control the amount of error
checking. Currently, only "no" and
"all" is supported; all is the
default.
--enable-error-messages=level - Control the aount of detail in error
messages. By default, MPICH2
provides instance-specific error
messages; but, with this option,
MPICH2 can be configured to provide
less detailed messages. This may be
desirable on small systems, such as
clusters built from game consoles or
high-density massively parallel
systems. This is still under active
development.
Compilation options for development:
--enable-g=value - Controls the amount of debugging information
collected by the code. The most useful choice
here is dbg, which compiles with -g.
--enable-coverage - An experimental option that enables GNU coverage
analysis.
--with-logging=name - Select a logging library for recording the
timings of the internal routines. We have
used this to understand the performance of the
internals of MPICH2. More information on the
logging options, capabilities and usage can be
found in doc/logging/logging.pdf.
--enable-timer-type=name - Select the timer to use for MPI_Wtime and
internal timestamps. name may be one of:
gethrtime - Solaris timer (Solaris systems
only)
clock_gettime - Posix timer (where available)
gettimeofday - Most Unix systems
linux86_cycle - Linux x86; returns cycle
counts, not time in seconds*
linuxalpha_cycle - Like linux86_cycle, but for
Linux Alpha*
gcc_ia64_cycle - IPF ar.itc timer*
device - The timer is provided by the device
*Note that the cycle timers are intended to be used by
MPICH2 developers for internal low-level timing.
Normal users should not use these as they are not
guaranteed to be accurate in certain situations.
-------------------------------------------------------------------------
6. Testing the MPICH2 installation
==================================
To test MPICH2, we package the MPICH2 test suite in the MPICH2
distribution. You can run the test suite using:
make testing
The results summary will be placed in test/summary.xml
-------------------------------------------------------------------------
7. Fault Tolerance
==================
MPICH2 has some tolerance to process failures, and supports
checkpointing and restart.
Tolerance to Process Failures
-----------------------------
The features described in this section should be considered
experimental. Which means that they have not been fully tested, and
the behavior may change in future releases. The below notes are some
guidelines on what can be expected in this feature:
- ERROR RETURNS: Communication failures in MPICH2 are not fatal
errors. This means that if the user sets the error handler to
MPI_ERRORS_RETURN, MPICH2 will return an appropriate error code in
the event of a communication failure. When a process detects a
failure when communicating with another process, it will consider
the other process as having failed and will no longer attempt to
communicate with that process. The user can, however, continue
making communication calls to other processes. Any outstanding
send or receive operations to a failed process, or wildcard
receives (i.e., with MPI_ANY_SOURCE) posted to communicators with a
failed process, will be immediately completed with an appropriate
error code.
- COLLECTIVES: For collective operations performed on communicators
with a failed process, the collective would return an error on
some, but not necessarily all processes. A collective call
returning MPI_SUCCESS on a given process means that the part of the
collective performed by that process has been successful.
- PROCESS MANAGER: If used with the hydra process manager, hydra will
detect failed processes and notify the MPICH2 library. Users can
query the list of failed processes using the
MPICH_ATTR_FAILED_PROCESSES predefined attribute on MPI_COMM_WORLD.
The attribute value is an integer array containing the ranks of the
failed processes. The array is terminated by MPI_PROC_NULL.
MPICH2 release specific note: The user needs to declare the
following extern within the application in order to use the
attribute (this ideally should be added to mpi.h, but has not
been done so, to preserve ABI compatibility in the 1.3.x
release series):
extern int MPICH_ATTR_FAILED_PROCESSES;
MPICH2 release specific note: The MPICH_ATTR_FAILED_PROCESSES
attribute is currently only defined on MPI_COMM_WORLD, but not
on other communicators.
Note that hydra by default will abort the entire application when
any process terminates before calling MPI_Finalize. In order to
allow an application to continue running despite failed processes,
you will need to pass the -disable-auto-cleanup option to mpiexec.
- FAILURE NOTIFICATION: THIS IS AN UNSUPPORTED FEATURE AND WILL
ALMOST CERTAINLY CHANGE IN THE FUTURE!
In the current release, hydra notifies the MPICH2 library of failed
processes by sending a SIGUSR1 signal. The application can catch
this signal to be notified of failed processes. If the application
replaces the library's signal handler with its own, the application
must be sure to call the library's handler from it's own
handler. Note that you cannot call any MPI function from inside a
signal handler.
In future releases, the plan is to provide a call such as
MPIX_Failure_notify that will allow the user to register a callback
function that will be called on process failures. This mechanism
has not been added yet to preserve ABI compatibility in the 1.3.x
release series.
Checkpoint and Restart
----------------------
MPICH2 supports checkpointing and restart fault-tolerance using BLCR.
CONFIGURATION
First, you need to have BLCR version 0.8.2 or later installed on your
machine. If it's installed in the default system location, add the
following two options to your configure command:
--enable-checkpointing
--with-hydra-ckpointlib=blcr
If BLCR is not installed in the default system location, you'll need
to tell MPICH2's configure where to find it. You might also need to
set the LD_LIBRARY_PATH environment variable so that BLCR's shared
libraries can be found. In this case add the following options to
your configure command:
--enable-checkpointing
--with-hydra-ckpointlib=blcr
--with-blcr=
LD_LIBRARY_PATH=/lib
where is the directory where BLCR has been
installed (whatever was specified in --prefix when BLCR was
configured).
After it's configured compile as usual (e.g., make; make install).
Note, checkpointing is only supported with the Hydra process manager.
VERIFYING CHECKPOINTING SUPPORT
Make sure MPICH2 is correctly configured with BLCR. You can do this
using:
mpiexec -info
This should display 'BLCR' under 'Checkpointing libraries available'.
CHECKPOINTING THE APPLICATION
There are two ways to cause the application to checkpoint. You can ask
mpiexec to periodically checkpoint the application using the mpiexec
option -ckpoint-interval (seconds):
mpiexec -ckpointlib blcr -ckpoint-prefix /tmp/app.ckpoint \
-ckpoint-interval 3600 -f hosts -n 4 ./app
Alternatively, you can also manually force checkpointing by sending a
SIGUSR1 signal to mpiexec.
The checkpoint/restart parameters can also be controlled with the
environment variables HYDRA_CKPOINTLIB, HYDRA_CKPOINT_PREFIX and
HYDRA_CKPOINT_INTERVAL.
To restart a process:
mpiexec -ckpointlib blcr -ckpoint-prefix /tmp/app.ckpoint -f hosts -n 4 -ckpoint-num
where is the checkpoint number you want to restart from.
These instructions can also be found on the MPICH2 wiki:
http://wiki.mcs.anl.gov/mpich2/index.php/Checkpointing
-------------------------------------------------------------------------
8. Environment Variables
========================
MPICH2 provides several environment variables that have different
purposes.
Generic Environment Variables
-----------------------------
MPICH_NO_LOCAL - Disable shared-memory communication. With this
option, even communication within a node will use the network
stack.
************************************
MPICH_PORT_RANGE - Port range to use for MPICH2 internal TCP
connections. This is useful when some of the host ports are
blocked by a firewall. For example, setting MPICH_PORT_RANGE
to "2000:3000" will ensure that MPICH2 will internally only
uses ports between 2000 and 3000.
************************************
MPICH_ASYNC_PROGRESS - Initiates a spare thread to provide
asynchronous progress. This improves progress semantics for
all MPI operations including point-to-point, collective,
one-sided operations and I/O. Setting this variable would
increase the thread-safety level to
MPI_THREAD_MULTIPLE. While this improves the progress
semantics, it might cause a small amount of performance
overhead for regular MPI operations.
************************************
MPICH_NAMEPUB_DIR - Allows the user to override where the publish
and lookup information is placed for connect/accept based
applications.
-------------------------------------------------------------------------
9. Developer Builds
===================
For MPICH2 developers who want to directly work on the svn, there are
a few additional steps involved (people using the release tarballs do
not have to follow these steps). Details about these steps can be
found here:
http://wiki.mcs.anl.gov/mpich2/index.php/Getting_And_Building_MPICH2
-------------------------------------------------------------------------
10. Installing MPICH2 on Windows
================================
Here are the instructions for setting up MPICH2 on a Windows machine:
(a) Install:
Microsoft Developer Studio 2003 or later
Intel Fortran 8.0 or later
cygwin
choose the dos file format option
install perl and cvs
(b) Checkout mpich2:
Bring up a command prompt.
(replace "yourname" with your MCS login name):
svn co https://svn.mcs.anl.gov/repos/mpi/mpich2/trunk mpich2
(c) Generate *.h.in
Bring up a cygwin bash shell.
cd mpich2
maint/updatefiles
exit
(d) Execute winconfigure.wsf
(e) Open Developer Studio
open mpich2\mpich2.sln
build the ch3sockDebug mpich2 solution
build the ch3sockDebug mpich2s project
build the ch3sockRelease mpich2 solution
build the ch3sockRelease mpich2s project
build the Debug mpich2 solution
build the Release mpich2 solution
build the fortDebug mpich2 solution
build the fortRelease mpich2 solution
build the gfortDebug mpich2 solution
build the gfortRelease mpich2 solution
build the sfortDebug mpich2 solution
build the sfortRelease mpich2 solution
(f) Open a command prompt
cd to mpich2\maint
execute "makegcclibs.bat"
(g) Open another Developer Studio instance
open mpich2\examples\examples.sln
build the Release target of the cpi project
(h) Return to Developer Studio with the mpich2 solution
set the version numbers in the Installer project
build the Installer mpich2 solution
(i) Test and distribute mpich2\maint\ReleaseMSI\mpich2.msi
mpich2.msi can be renamed, eg mpich2-1.1.msi
(j) To install the launcher:
Copy smpd.exe to a local directory on all the nodes.
Log on to each node as an administrator and execute "smpd.exe -install"
(k) Compile and run an MPI application:
Compile an mpi application. Use mpi.h from mpich2\src\include\win32
and mpi.lib in mpich2\lib
Place your executable along with the mpich2 dlls somewhere accessable
to all the machines.
Execute a job by running something like: mpiexec -n 3 myapp.exe
-------------------------------------------------------------------------
11. Multiple Fortran compiler support
=====================================
If the C compiler that is used to build MPICH2 libraries supports both
multiple weak symbols and multiple aliases of common symbols, the
Fortran 77 binding can support multiple Fortran compilers. The
multiple weak symbols support allow MPICH2 to provide different name
mangling scheme (of subroutine names) required by differen Fortran
compilers. The multiple aliases of common symbols support enables
MPICH2 to equal different common block symbols of the MPI Fortran
constant, e.g. MPI_IN_PLACE, MPI_STATUS_IGNORE. So they are understood
by different Fortran compilers.
Since the support of multiple aliases of common symbols is
new/experimental, users can disable the feature by using configure
option --disable-multi-aliases if it causes any undesirable effect,
e.g. linker warnings of different sizes of common symbols, MPIFCMB*
(the warning should be harmless).
We have only tested this support on a limited set of
platforms/compilers. On linux, if the C compiler that builds MPICH2
is either gcc or icc, the above support will be enabled by configure.
At the time of this writing, pgcc does not seem to have this multiple
aliases of common symbols, so configure will detect the deficiency and
disable the feature automatically. The tested Fortran compiler
includes GNU Forran compilers(gfortan, g77), Intel Fortran
compiler(ifort), Portland Group Fortran compilers(pgf77, pgf90),
Absoft Fortran compilers (af77, af90), and IBM XL fortran
compiler(xlf). What this mean is that if mpich2 is built by
gcc/gfortran, the resulting mpich2 library can be used to link a
Fortran program compiled/linked by another fortran compiler, say
pgf77, say through mpif77 -f77=pgf77. As long as the Fortran program
is linked without any errors by one of these compilers, the program
shall be running fine.
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