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Jeff Squyres 3e1107262f - Add note about MX fragment sizes 
- Add note that we don't yet support hardware matching (full
  disclosure is best)

This commit was SVN r7928.
2005-10-28 21:49:25 +00:00

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Copyright (c) 2004-2005 The Trustees of Indiana University.
All rights reserved.
Copyright (c) 2004-2005 The Trustees of the University of Tennessee.
All rights reserved.
Copyright (c) 2004-2005 High Performance Computing Center Stuttgart,
University of Stuttgart. All rights reserved.
Copyright (c) 2004-2005 The Regents of the University of California.
All rights reserved.
$COPYRIGHT$
Additional copyrights may follow
$HEADER$
===========================================================================
This is a preliminary README file. It will be scrubbed formally
before release.
===========================================================================
The best way to report bugs, send comments, or ask questions is to
sign up on the user's and/or developer's mailing list (for user-level
and developer-level questions; when in doubt, send to the user's
list):
users@open-mpi.org
devel@open-mpi.org
Because of spam, only subscribers are allowed to post to these lists
(ensure that you subscribe with and post from exactly the same e-mail
address -- joe@example.com is considered different than
joe@mycomputer.example.com!). Visit these pages to subscribe to the
lists:
http://www.open-mpi.org/mailman/listinfo.cgi/users
http://www.open-mpi.org/mailman/listinfo.cgi/devel
Thanks for your time.
===========================================================================
The following abbreviated list of release notes applies to this code
base as of this writing (26 Aug 2005):
- Open MPI includes support for a wide variety of supplemental
hardware and software package. When configuring Open MPI, you may
need to supply additional flags to the "configure" script in order
to tell Open MPI where the header files, libraries, and any other
required files are located. As such, running "configure" by itself
may include support for all the devices (etc.) that you expect,
especially if their support headers / libraries are installed in
non-standard locations. Network interconnects are an easy example
to discuss -- Myrinet and Infiniband, for example, both have
supplemental headers and libraries that must be found before Open
MPI can build support for them. You must specify where these files
are with the appropriate options to configure. See the listing of
configure command-line switches, below, for more details.
- The Open MPI installation must be in your PATH on all nodes (and
potentially LD_LIBRARY_PATH, if libmpi is a shared library).
- LAM/MPI-like mpirun notation of "C" and "N" is not yet supported.
- Striping MPI messages across multiple networks is supported (and
happens automatically when multiple networks are available), but
needs performance tuning.
- The run-time systems that are currently supported are:
- rsh / ssh
- Recent versions of BProc (e.g., Clustermatic)
- PBS Pro, Open PBS, Torque (i.e., anything who supports the TM
interface)
- SLURM
- POE
- XGrid
- Yod
- The majority of Open MPI's documentation is here in this file and on
the web site FAQ (http://www.open-mpi.org/). This will eventually
be supplemented with cohesive installation and user documentation
files.
- MPI-2 one-sided functionality will not be included in the first few
releases of Open MPI.
- Systems that have been tested are:
- Linux, 32 bit, with gcc
- Linux, 64 bit (x86), with gcc
- OS X (10.3), 32 bit, with gcc
- OS X (10.4), 32 bit, with gcc
- Other systems have been lightly (but not fully tested):
- Other compilers on Linux, 32 and 64 bit
- Other 64 bit platforms (Linux and AIX on PPC64, Sparc)
- Building shared libraries on AIX with the xlc compilers is only
supported if you supply the following command line option to
configure: LDFLAGS=-Wl,-brtl.
- At least some versions of the Intel 8.1 compiler seg fault while
compiling certain Open MPI source code files. As such, it is not
supported.
- Early versions of the Portland Group 6.0 compiler have problems
creating the C++ MPI bindings as a shared library (e.g., v6.0-1).
Tests with later versions show that this has been fixed (e.g.,
v6.0-5).
- The Portland Group Fortran compilers use -1 as the default value for
.TRUE. Open MPI does not currently handle this correctly. As such,
the "-Munixlogical" option must be used with the Portland Fortran
compiler to force it to use 1 as the value for .TRUE.
******************************************************************
*** NOTE: It is also necessary to compile all MPI applications ***
*** with these flags! ***
******************************************************************
The Open MPI team recommends using setting FFLAGS and FCFLAGS as
well as using the --with-wrapper-fflags and --with-wrapper-fcflags
arguments to configure. This both compiles Open MPI and all MPI
applications (that are compiled with mpif77 or mpif90) with the
appropriate compiler flags. For example:
shell$ ./configure \
FFLAGS=-Munixlogical \
FCFLAGS=-Munixlogical \
--with-wrapper-fflags=-Munixlogical \
--with-wrapper-fcflags=-Munixlogical ...
This will be fixed in a future version of Open MPI.
- For any version of the Intel compiler >= 8.0, the default value for
.TRUE. is -1. Open MPI does not currently handle this correctly.
As such, the "-fpscomp logicals" option must be used with the Intel
Fortran compiler in to force it to use 1 as the value for .TRUE.
This can be added to the FFLAGS environment variable when running
configure:
The Open MPI team recommends using setting FFLAGS and FCFLAGS as
well as using the --with-wrapper-fflags and --with-wrapper-fcflags
arguments to configure. This both compiles Open MPI and all MPI
applications (that are compiled with mpif77 or mpif90) with the
appropriate compiler flags. For example:
shell$ ./configure \
"FFLAGS=-fpscomp logicals" \
"FCLAGS=-fpscomp logicals" \
"--with-wrapper-fflags=-fpscomp logicals" \
"--with-wrapper-fcflags=-fpscomp logicals"
This will be fixed in a future version of Open MPI.
- The MPI and run-time layers do not free all used memory properly
during MPI_FINALIZE.
- Running on nodes with different endian and/or different datatype
sizes within a single parallel application is not supported in this
release.
- MPI_THREAD_MULTIPLE support is included, but is only lightly tested.
- Asynchronous message passing progress support is not included in
this release.
- Due to limitations in the Libtool 1.5 series, Fortran 90 MPI
bindings support can only be built as a static library. It is
expected that Libtool 2.0 will be able to support shared libraries
for the Fortran 90 bindings.
- On Linux, if either the malloc_hooks or malloc_interpose memory
hooks are enabled, it will not be possible to link against a static
libc.a. libmpi can still be built statically - it is only the final
application link step that can not be static. If applications must be
statically linked, it is recommended you compile Open MPI with the
--without-memory-manager configure option.
- The XGrid support is experimental - see the Open MPI FAQ for more
information.
- The MX library limits the maximum message fragment size for both
on-node and off-node messages. As of MX v1.0.3, the inter-node
maximum fragment size is 32k, and the intra-node maximum fragment
size is 16k -- fragments sent larger than these sizes will fail.
Open MPI automatically fragments large messages; it currently limits
its first fragment size on MX networks to the lower of these two
values -- 16k. As such, increasing the value of the MCA parameter
named "btl_mx_first_frag_size" larger than 16k may cause failures in
some cases (i.e., when using MX to send large messages to processes
on the same node); it will cause failures in all cases if it is set
above 32k. Note that this only affects the *first* fragment of
messages; latter fragments do not have this size restriction. The
MCA parameter btl_mx_max_send_size can be used to vary the maximum
size of subsequent fragments.
- The current version of the Open MPI point-to-point engine does not
yet support hardware-level MPI message matching. As such, MPI
message matching must be performed in software, artifically
increasing latency for short messages on certain networks (such as
MX and hardware-supported Portals). Future versions of Open MPI
will support hardware matching on networks that provide it, and will
eliminate the extra overhead of software MPI message matching where
possible.
===========================================================================
Building Open MPI
-----------------
Open MPI uses a traditional configure script paired with "make" to
build. Typical installs can be of the pattern:
---------------------------------------------------------------------------
shell$ ./configure [...options...]
shell$ make all install
---------------------------------------------------------------------------
There are many available configure options (see "./configure --help"
for a full list); a summary of the more important ones follows:
--prefix=<directory>
Install Open MPI into the base directory named <directory>. Hence,
Open MPI will place its executables in <directory>/bin, its header
files in <directory>/include, its libraries in <directory>/lib, etc.
--with-gm=<directory>
Specify the directory where the GM libraries and header files are
located. This enables GM support in Open MPI.
--with-mx=<directory>
Specify the directory where the MX libraries and header files are
located. This enables MX support in Open MPI.
--with-mvapi=<directory>
Specify the directory where the mVAPI libraries and header files are
located. This enables mVAPI support in Open MPI.
--with-openib=<directory>
Specify the directory where the Open IB libraries and header files are
located. This enables mVAPI support in Open MPI.
--with-tm=<directory>
Specify the directory where the TM libraries and header files are
located. This enables PBS / Torque support in Open MPI.
--with-mpi-param_check(=value)
"value" can be one of: always, never, runtime. If no value is
specified, or this option is not used, "always" is the default.
Using --without-mpi-param-check is equivalent to "never".
- always: the parameters of MPI functions are always checked for
errors
- never: the parameters of MPI functions are never checked for
errors
- runtime: whether the parameters of MPI functions are checked
depends on the value of the MCA parameter mpi_param_check
(default: yes).
--with-threads=value
Since thread support (both support for MPI_THREAD_MULTIPLE and
asynchronous progress) is only partially tested, it is disabled by
default. To enable threading, use "--with-threads=posix". This is
most useful when combined with --enable-mpi-threads and/or
--enable-progress-threads.
--enable-mpi-threads
Allows the MPI thread level MPI_THREAD_MULTIPLE. See
--with-threads; this is currently disabled by default.
--enable-progress-threads
Allows asynchronous progress in some transports. See
--with-threads; this is currently disabled by default.
--disable-mpi-cxx
Disable building the C++ MPI bindings. Note that this does *not*
disable the C++ checks during configure; some of Open MPI's tools
are written in C++ and therefore require a C++ compiler to be built.
--disable-mpi-f77
Disable building the Fortran 77 MPI bindings.
--disable-mpi-f90
Disable building the Fortran 90 MPI bindings. Also related to the
--with-f90-max-array-dim option.
--with-f90-max-array-dim=<DIM>
The F90 MPI bindings are stictly typed, even including the number of
dimensions for arrays for MPI choice buffer parameters. Open MPI
generates these bindings at compile time with a maximum number of
dimensions as specified by this parameter. The default value is 4.
--disable-shared
By default, libmpi is built as a shared library, and all components
are built as dynamic shared objects (DSOs). This switch disables
this default; it is really only useful when used with
--enable-static.
--enable-static
Build libmpi as a static library, and statically link in all
components.
There are several other options available -- see "./configure --help".
Open MPI supports all the "make" targets that are provided by GNU
Automake, such as:
all - build the entire Open MPI package
install - install Open MPI
uninstall - remove all traces of Open MPI from the $prefix
clean - clean out the build tree
Once Open MPI has been built and installed, it is safe to run "make
clean" and/or remove the entire build tree.
VPATH builds are fully supported.
Generally speaking, the only thing that users need to do to use Open
MPI is ensure that <prefix>/bin is in their PATH and <prefix>/lib is
in their LD_LIBRARY_PATH. Users may need to ensure to set the PATH
and LD_LIBRARY_PATH in their shell setup files (e.g., .bashrc, .cshrc)
so that rsh/ssh-based logins will be able to find the Open MPI
executables.
===========================================================================
Checking Your Open MPI Installation
-----------------------------------
The "ompi_info" command can be used to check the status of your Open
MPI installation (located in <prefix>/bin/ompi_info). Running it with
no arguments provides a summary of information about your Open MPI
installation.
Note that the ompi_info command is extremely helpful in determining
which components are installed as well as listing all the run-time
settable parameters that are available in each component (as well as
their default values).
The following options may be helpful:
--all Show a *lot* of information about your Open MPI
installation.
--parsable Display all the information in an easily
grep/cut/awk/sed-able format.
--param <framework> <component>
A <framework> of "all" and a <component> of "all" will
show all parameters to all components. Otherwise, the
parameters of all the components in a specific framework,
or just the parameters of a specific component can be
displayed by using an appropriate <framework> and/or
<component> name.
Changing the values of these parameters is explained in the "The
Modular Component Architecture (MCA)" section, below.
===========================================================================
Compiling Open MPI Applications
-------------------------------
Open MPI provides "wrapper" compilers that should be used for
compiling MPI applications:
C: mpicc
C++: mpiCC (or mpic++ if your filesystem is case-insensitive)
Fortran 77: mpif77
Fortran 90: mpif90
For example:
shell$ mpicc hello_world_mpi.c -o hello_world_mpi -g
shell$
All the wrapper compilers do is add a variety of compiler and linker
flags to the command line and then invoke a back-end compiler. To be
specific: the wrapper compilers do not parse source code at all; they
are solely command-line manipulators, and have nothing to do with the
actual compilation or linking of programs. The end result is an MPI
executable that is properly linked to all the relevant libraries.
===========================================================================
Running Open MPI Applications
-----------------------------
Open MPI supports both mpirun and mpiexec (they are actually the
same). For example:
shell$ mpirun -np 2 hello_world_mpi
or
shell$ mpiexec -np 1 hello_world_mpi : -np 1 hello_world_mpi
are equivalent. Many of mpiexec's switches (such as -host and -arch)
are not yet functional, although they will not error if you try to use
them.
The rsh starter accepts a -hostfile parameter (the option
"-machinefile" is equivalent); you can specify a -hostfile parameter
indicating an standard mpirun-style hostfile (one hostname per line):
shell$ mpirun -hostfile my_hostfile -np 2 hello_world_mpi
If you intend to run more than one process on a node, the hostfile can
use the "slots" attribute. If "slots" is not specified, a count of 1
is assumed. For example, using the following hostfile:
---------------------------------------------------------------------------
node1.example.com
node2.example.com
node3.example.com slots=2
node4.example.com slots=4
---------------------------------------------------------------------------
shell$ mpirun -hostfile my_hostfile -np 8 hello_world_mpi
will launch MPI_COMM_WORLD rank 0 on node1, rank 1 on node2, ranks 2
and 3 on node3, and ranks 4 through 7 on node4.
Other starters, such as the batch scheduling environments, do not
require hostfiles (and will ignore the hostfile if it is supplied).
Note that the values of component parameters can be changed on the
mpirun / mpiexec command line. This is explained in the section
below, "The Modular Component Architecture (MCA)".
===========================================================================
The Modular Component Architecture (MCA)
The MCA is the backbone of Open MPI -- most services and functionality
are implemented through MCA components. Here is a list of all the
component frameworks in Open MPI:
---------------------------------------------------------------------------
MPI component frameworks:
-------------------------
allocator - Memory allocator
bml - BTL management layer
btl - MPI point-to-point byte transfer layer
coll - MPI collective algorithms
io - MPI-2 I/O
mpool - Memory pooling
pml - MPI point-to-point management layer
ptl - (Outdated / deprecated) MPI point-to-point transport layer
rcache - Memory registration cache
topo - MPI topology routines
Back-end run-time environment component frameworks:
---------------------------------------------------
errmgr - RTE error manager
gpr - General purpose registry
iof - I/O forwarding
ns - Name server
oob - Out of band messaging
pls - Process launch system
ras - Resource allocation system
rds - Resource discovery system
rmaps - Resource mapping system
rmgr - Resource manager
rml - RTE message layer
schema - Name schemas
sds - Startup / discovery service
soh - State of health monitor
Miscellaneous frameworks:
-------------------------
maffinity - Memory affinity
memory - Memory subsystem hooks
paffinity - Processor affinity
timer - High-resolution timers
---------------------------------------------------------------------------
Each framework typically has one or more components that are used at
run-time. For example, the btl framework is used by MPI to send bytes
across underlying networks. The tcp btl, for example, sends messages
across TCP-based networks; the gm btl sends messages across GM
Myrinet-based networks.
Each component typically has some tunable parameters that can be
changed at run-time. Use the ompi_info command to check a component
to see what its tunable parameters are. For example:
shell$ ompi_info --param btl tcp
shows all the parameters (and default values) for the tcp btl
component.
These values can be overridden at run-time in several ways. At
run-time, the following locations are examined (in order) for new
values of parameters:
1. <prefix>/etc/openmpi-mca-params.conf
This file is intended to set any system-wide default MCA parameter
values -- it will apply, by default, to all users who use this Open
MPI installation. The default file that is installed contains many
comments explaining its format.
2. $HOME/.openmpi/mca-params.conf
If this file exists, it should be in the same format as
<prefix>/etc/openmpi-mca-params.conf. It is intended to provide
per-user default parameter values.
3. environment variables of the form OMPI_MCA_<name> set equal to a
<value>
Where <name> is the name of the parameter. For example, set the
variable named OMPI_MCA_btl_tcp_frag_size to the value 65536
(Bourne-style shells):
shell$ OMPI_MCA_btl_tcp_frag_size=65536
shell$ export OMPI_MCA_btl_tcp_frag_size
4. the mpirun command line: --mca <name> <value>
Where <name> is the name of the parameter. For example:
shell$ mpirun --mca btl_tcp_frag_size 65536 -np 2 hello_world_mpi
These locations are checked in order. For example, a parameter value
passed on the mpirun command line will override an environment
variable; an environment variable will override the system-wide
defaults.
===========================================================================
Common Questions
----------------
Many common questions about building and using Open MPI are answered
on the FAQ:
http://www.open-mpi.org/faq/
===========================================================================
Got more questions?
-------------------
Found a bug? Got a question? Want to make a suggestion? Want to
contribute to Open MPI? Please let us know!
User-level questions and comments should generally be sent to the
user's mailing list (users@open-mpi.org). Because of spam, only
subscribers are allowed to post to this list (ensure that you
subscribe with and post from *exactly* the same e-mail address --
joe@example.com is considered different than
joe@mycomputer.example.com!). Visit this page to subscribe to the
user's list:
http://www.open-mpi.org/mailman/listinfo.cgi/users
Developer-level bug reports, questions, and comments should generally
be sent to the developer's mailing list (devel@open-mpi.org). Please
do not post the same question to both lists. As with the user's list,
only subscribers are allowed to post to the developer's list. Visit
the following web page to subscribe:
http://www.open-mpi.org/mailman/listinfo.cgi/devel
When submitting bug reports to either list, be sure to include the
following information in your mail (please compress!):
- the stdout and stderr from Open MPI's configure
- the top-level config.log file
- the stdout and stderr from building Open MPI
- the output from "ompi_info --all" (if possible)
For Bourne-type shells, here's one way to capture this information:
shell$ ./configure ... 2>&1 | tee config.out
[...lots of configure output...]
shell$ make 2>&1 | tee make.out
[...lots of make output...]
shell$ mkdir ompi-output
shell$ cp config.out config.log make.out ompi-output
shell$ ompi_info --all |& tee ompi-output/ompi-info.out
shell$ tar cvf ompi-output.tar ompi-output
[...output from tar...]
shell$ gzip ompi-output.tar
For C shell-type shells, the procedure is only slightly different:
shell% ./configure ... |& tee config.out
[...lots of configure output...]
shell% make |& tee make.out
[...lots of make output...]
shell% mkdir ompi-output
shell% cp config.out config.log make.out ompi-output
shell% ompi_info --all |& tee ompi-output/ompi-info.out
shell% tar cvf ompi-output.tar ompi-output
[...output from tar...]
shell% gzip ompi-output.tar
In either case, attach the resulting ompi-output.tar.gz file to your
mail. This provides the Open MPI developers with a lot of information
about your installation and can greatly assist us in helping with your
problem.
Be sure to also include any other useful files (in the
ompi-output.tar.gz tarball), such as output showing specific errors.
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