openmpi/README

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===========================================================================

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:

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Thanks for your time.

===========================================================================

The following abbreviated list of release notes applies to this code
base as of this writing (27 Feb 2006):

- 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
  - 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.

- 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)

- Some MCA parameters can be set in a way that renders Open MPI
  inoperable (see notes about MCA parameters later in this file).  In
  particular, some parameters have required options that must be
  included.
  - The "btl" parameter must include the "self" component, or Open MPI
    will not be able to deliver messages to the same rank as the
    sender.
  - The "btl_tcp_if_exclude" paramater must include "lo", or Open MPI
    will not be able to route MPI messages using the TCP BTL.

- 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 compilers require the "-Msignextend" compiler
  flag to extend the sign bit when converting from a shorter to longer
  integer.  This is is different than other compilers (such as GNU).
  When compiling Open MPI with the Portland compiler suite, the
  following flags should be passed to Open MPI's configure script:

  shell$ ./configure CFLAGS=-Msignextend CXXFLAGS=-signextent \
	--with-wrapper-cflags=-Msignextend \
	--with-wrapper-cxxflags=-Msignextend ...

  This will both compile Open MPI with the proper compile flags and
  also automatically add "-Msignextend" when the C and C++ MPI wrapper
  compilers are used to compile user MPI applications.

- Open MPI will build bindings suitable for all common forms of
  Fortran 77 compiler symbol mangling on platforms that support it
  (e.g., Linux).  On platforms that do not support weak symbols (e.g.,
  OS X), Open MPI will build Fortran 77 bindings just for the compiler
  that Open MPI was configured with.  

  Hence, on platforms that support it, if you configure Open MPI with
  a Fortran 77 compiler that uses one symbol mangling scheme, you can
  successfully compile and link MPI Fortran 77 applications with a
  Fortran 77 compiler that uses a different symbol mangling scheme.

  NOTE: For platforms that support the multi-Fortran-compiler bindings
  (i.e., weak symbols are supported), due to limitations in the MPI
  standard and in Fortran compilers, it is not possible to hide these
  differences in all cases.  Specifically, the following two cases may
  not be portable between different Fortran compilers:

  1. The C constants MPI_F_STATUS_IGNORE and MPI_F_STATUSES_IGNORE
     will only compare properly to Fortran applications that were
     created with Fortran compilers that that use the same
     name-mangling scheme as the Fortran compiler that Open MPI was
     configured with.

  2. Fortran compilers may have different values for the logical
     .TRUE. constant.  As such, any MPI function that uses the Fortran
     LOGICAL type may only get .TRUE. values back that correspond to
     the the .TRUE. value of the Fortran compiler that Open MPI was
     configured with.  Note that some Fortran compilers allow forcing
     .TRUE. to be 1 and .FALSE. to be 0.  For example, the Portland
     Group compilers provide the "-Munixlogical" option, and Intel
     compilers (version >= 8.) provide the "-fpscomp logicals" option.

  You can use the ompi_info command to see the Fortran compiler that
  Open MPI was configured with.

- 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 (and therefore future releases of Open
  MPI) 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 and this
  post on the Open MPI user's mailing list for more information:

  http://www.open-mpi.org/community/lists/users/2006/01/0539.php

- 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, artificially
  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.

- The Fortran 90 MPI bindings can now be built in one of four sizes
  using --with-mpi-f90-size=SIZE (see description below).  These sizes
  reflect the number of MPI functions included in the "mpi" Fortran 90
  module and therefore which functions will be subject to strict type
  checking.  All functions not included in the Fortran 90 module can
  still be invoked from F90 applications, but will fall back to
  Fortran-77 style checking (i.e., little/none).

  - trivial: Only includes F90-specific functions from MPI-2.  This
    means overloaded versions of MPI_SIZEOF for all the MPI-supported
    F90 intrinsic types.

  - small (default): All the functions in "trivial" plus all MPI
    functions that take no choice buffers (meaning buffers that are
    specified by the user and are of type (void*) in the C bindings --
    generally buffers specified for message passing).  Hence,
    functions like MPI_COMM_RANK are included, but functions like
    MPI_SEND are not.

  - medium: All the functions in "small" plus all MPI functions that
    take one choice buffer (e.g., MPI_SEND, MPI_RECV, ...).  All
    one-choice-buffer functions have overloaded variants for each of
    the MPI-supported Fortran intrinsic types up to the number of
    dimensions specified by --with-f90-max-array-dim (default value is
    4).

  - large: All MPI functions (i.e., all the functions in "medium" plus
    all MPI functions that take two choice buffers, such as
    MPI_SCATTER, MPI_GATHER, etc.).  All the two-choice-buffer
    functions will have variants for each of the MPI-supported Fortran
    intrinsic types up to the number of dimensions specified by
    --with-f90-max-array-dim, but both buffers will be of the same
    type.

  Increasing the size of the F90 module (in order from trivial, small,
  medium, and large) will generally increase the length of time
  required to compile user MPI applications.  Specifically, "trivial"-
  and "small"-sized F90 modules generally allow user MPI applications
  to be compiled fairly quickly but lose type safety for all MPI
  functions with choice buffers.  "medium"- and "large"-sized F90
  modules generally take longer to compile user applications but
  provide greater type safety for MPI functions.

===========================================================================

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 commonly used 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 --with-mpi-param
  is not specified, "runtime" is the default.  If --with-mpi-param
  is specified with no value, "always" is used.  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 and --with-mpi-f90-size options.

--with-mpi-f90-size=<SIZE>
  Four sizes of the MPI F90 module can be built: trivial (only a
  handful of MPI-2 F90-specific  functions are included in the F90
  module), small (trivial + all MPI functions that take no choice
  buffers), medium (small + all MPI functions that take 1 choice
  buffer), and large (medium + all MPI functions that take 2 choice
  buffers, but only where the types of both choice buffers are the
  same).  This parameter is only used if the F90 bindings are
  enabled.

--with-f90-max-array-dim=<DIM>
  The F90 MPI bindings are strictly 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".

Changing the compilers that Open MPI uses to build itself uses the
standard Autoconf mechanism of setting special environment variables
either before invoking configure or on the configure command line.
The following environment variables are recognized by configure:

CC          - C compiler to use
CFLAGS      - Compile flags to pass to the C compiler
CPPFLAGS    - Preprocessor flags to pass to the C compiler

CXX         - C++ compiler to use
CXXFLAGS    - Compile flags to pass to the C++ compiler
CXXCPPFLAGS - Preprocessor flags to pass to the C++ compiler

F77         - Fortran 77 compiler to use
FFLAGS      - Compile flags to pass to the Fortran 77 compiler

FC          - Fortran 90 compiler to use
FCFLAGS     - Compile flags to pass to the Fortran 90 compiler

LDFLAGS     - Linker flags to pass to all compilers
LIBS        - Libraries to pass to all compilers (it is rarely
              necessary for users to need to specify additional LIBS)

For example:

shell$ ./configure CC=mycc CXX=myc++ F77=myf77 F90=myf90 ...

It is required that the compilers specified be compile and link
compatible, meaning that object files created by one compiler must be
able to be linked with object files from the other compilers and
produce correctly functioning executables.

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 exactly
equivalent).  For example:

shell$ mpirun -np 2 hello_world_mpi

or

shell$ mpiexec -np 1 hello_world_mpi : -np 1 hello_world_mpi

are equivalent.  Some 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.