pmodels / Mpich

not

		MPICH Release %VERSION%

- REQUIRED: This tar file mpich-%VERSION%.tar.gz

- REQUIRED: A C compiler (C99 support is required. See
  https://wiki.mpich.org/mpich/index.php/Shifting_toward_C99)

- 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 MPICH is described in step 1(d)
  below).

- OPTIONAL: A Fortran compiler, if Fortran applications are to be
  used (gfortran, ifort, etc.). If you do not require support for
  Fortran applications, you can disable this support using
  --disable-fortran (configuring MPICH 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.

  tar xzf mpich-%VERSION%.tar.gz
  cd mpich-%VERSION%

If your tar doesn't accept the z option, use

  gunzip mpich-%VERSION%.tar.gz
  tar xf mpich-%VERSION%.tar
  cd mpich-%VERSION%

for csh and tcsh:

  ./configure --prefix=/home/<USERNAME>/mpich-install |& tee c.txt

for bash and sh:

  ./configure --prefix=/home/<USERNAME>/mpich-install 2>&1 | tee c.txt

The configure will try to determine the best device (the internal
network modules) based on system environment. It will abort when it
can't decide which is the best choice. Supply the device option to
proceed. E.g.

  ./configure --prefix=... --with-device=ch4:ofi |...

or:

  ./configure --prefix=... --with-device=ch4:ucx |...

Refer to section below -- Alternate Channels and Devices -- for
more details.

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 compiler found. If you don't need to build any
    Fortran programs, you can disable Fortran support using
    --disable-fortran. 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 MPICH.

If you are unable to understand what went wrong, please go to step
(2) below, for reporting the issue to the MPICH developers and
other users.

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 (2) below, for reporting the issue to the MPICH
developers and other users.

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.

for csh and tcsh:

  setenv PATH /home/<USERNAME>/mpich-install/bin:$PATH

for bash and sh:

  PATH=/home/<USERNAME>/mpich-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 MPICH 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.

Now we will run an MPI job, using the mpiexec command as specified
in the MPI standard. There are some examples in the install
directory, which you have already put in your path, as well as in
the directory mpich-%VERSION%/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 <number> ./examples/cpi

Test that you can run an 'n' process CPI job on multiple nodes:

  mpiexec -f machinefile -n <number> ./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.mpich.org/mpich/index.php/Using_the_Hydra_Process_Manager

mpich-%VERSION%/c.txt (generated in step 1(d) above)
mpich-%VERSION%/m.txt (generated in step 1(e) above)
mpich-%VERSION%/mi.txt (generated in step 1(f) above)
mpich-%VERSION%/config.log (generated in step 1(d) above)
mpich-%VERSION%/src/mpl/config.log (generated in step 1(d) above)
mpich-%VERSION%/src/pm/hydra/config.log (generated in step 1(d) above)
mpich-%VERSION%/src/pm/hydra/tools/topo/hwloc/hwloc/config.log (generated in step 1(d) above)

DID WE MENTION? DO NOT FORGET TO COMPRESS THESE FILES!

mpiexec -info

               *************************************

The ofi netmod provides support for the OFI network programming interface.
To enable, configure with the following option:

  --with-device=ch3:nemesis:ofi

If the OFI include files and libraries are not in the normal search paths,
you can specify them with the following options:

  --with-ofi-include= and --with-ofi-lib=

... or the if lib/ and include/ are in the same directory, you can use
the following option:

  --with-ofi=

If the OFI 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
environment. 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.

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

ch4 device
**********
The ch4 device contains different network and shared memory modules
for communication. We currently support the ofi and ucx network
modules, and posix shared memory module.

ofi network module

The ucx netmod provides support for the Unified Communication X
library. It can be built with the following configure option:

  --with-device=ch4:ucx

If the UCX include files and libraries are not in the normal search paths,
you can specify them with the following options:

  --with-ucx-include= and --with-ucx-lib=

... or the if lib/ and include/ are in the same directory, you can use
the following option:

  --with-ucx=

By default, the UCX library throws warnings when the system does not
enable certain features that might hurt performance.  These are
important warnings that might cause performance degradation on your
system.  But you might need root privileges to fix some of them.  If
you would like to disable such warnings, you can set the UCX log level
to "error" instead of the default "warn" by using:

  UCX_LOG_LEVEL=error
  export UCX_LOG_LEVEL

-------------------------------------------------------------------------

5. 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.mpich.org/mpich/index.php/Using_the_Hydra_Process_Manager

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
MPICH. MPICH's default process manager, hydra, has native support
for Slurm and you can directly use it in Slurm environments (it will
automatically detect Slurm and use Slurm capabilities). However, if
you want to use the Slurm-provided "srun" process manager, you can use
the "--with-pmi=slurm --with-pm=no" option with configure. Note that
the "srun" process manager that comes with Slurm uses an older PMI
standard which does not have some of the performance enhancements that
hydra provides in Slurm environments.

-------------------------------------------------------------------------

6. Alternate Configure Options
==============================

MPICH has a number of other features. If you are exploring MPICH as
part of a development project, you might want to tweak the MPICH
build with the following configure options. A complete list of
configuration options can be found using:

   ./configure --help

-------------------------------------------------------------------------

7. Testing the MPICH installation
==================================

To test MPICH, we package the MPICH test suite in the MPICH
distribution. You can run the test suite using:

     make testing

The results summary will be placed in test/summary.xml

-------------------------------------------------------------------------

8. Fault Tolerance
==================

MPICH 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 MPICH are not fatal
   errors.  This means that if the user sets the error handler to
   MPI_ERRORS_RETURN, MPICH 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 MPICH library.  Users can
   query the list of failed processes using MPIX_Comm_group_failed().
   This functions returns a group consisting of the failed processes
   in the communicator.  The function MPIX_Comm_remote_group_failed()
   is provided for querying failed processes in the remote processes
   of an intercommunicator.

   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 MPICH 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.

Checkpoint and Restart
----------------------

MPICH 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, you don't
need to do anything.

If BLCR is not installed in the default system location, you'll need
to tell MPICH'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:

  --with-blcr=<BLCR_INSTALL_DIR> 
  LD_LIBRARY_PATH=<BLCR_INSTALL_DIR>/lib

where <BLCR_INSTALL_DIR> 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 MPICH 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 <N>

where <N> is the checkpoint number you want to restart from.

These instructions can also be found on the MPICH wiki:

  http://wiki.mpich.org/mpich/index.php/Checkpointing

-------------------------------------------------------------------------

9. Developer Builds
===================
For MPICH developers who want to directly work on the primary version
control system, 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.mpich.org/mpich/index.php/Getting_And_Building_MPICH

-------------------------------------------------------------------------

10. Multiple Fortran compiler support
=====================================

If the C compiler that is used to build MPICH libraries supports both
multiple weak symbols and multiple aliases of common symbols, the
Fortran binding can support multiple Fortran compilers. The
multiple weak symbols support allow MPICH to provide different name
mangling scheme (of subroutine names) required by different Fortran
compilers. The multiple aliases of common symbols support enables
MPICH 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 MPICH 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 compilers
include GNU Fortran compilers (gfortan), Intel Fortran compiler
(ifort), Portland Group Fortran compilers (pgfortran), Absoft Fortran
compilers (af90), and IBM XL fortran compiler (xlf).  What this means
is that if mpich is built by gcc/gfortran, the resulting mpich library
can be used to link a Fortran program compiled/linked by another
fortran compiler, say pgf90, say through mpifort -fc=pgf90.  As long
as the Fortran program is linked without any errors by one of these
compilers, the program shall be running fine.

-------------------------------------------------------------------------

11. ABI Compatibility
=====================

The MPICH ABI compatibility initiative was announced at SC 2014
(http://www.mpich.org/abi).  As a part of this initiative, Argonne,
Intel, IBM and Cray have committed to maintaining ABI compatibility
with each other.

As a first step in this initiative, starting with version 3.1, MPICH
is binary (ABI) compatible with Intel MPI 5.0.  This means you can
build your program with one MPI implementation and run with the other.
Specifically, binary-only applications that were built and distributed
with one of these MPI implementations can now be executed with the
other MPI implementation.

Some setup is required to achieve this.  Suppose you have MPICH
installed in /path/to/mpich and Intel MPI installed in /path/to/impi.

You can run your application with mpich using:

   % export LD_LIBRARY_PATH=/path/to/mpich/lib:$LD_LIBRARY_PATH
   % mpiexec -np 100 ./foo

or using Intel MPI using:

   % export LD_LIBRARY_PATH=/path/to/impi/lib:$LD_LIBRARY_PATH
   % mpiexec -np 100 ./foo

This works irrespective of which MPI implementation your application
was compiled with, as long as you use one of the MPI implementations
in the ABI compatibility initiative.

-------------------------------------------------------------------------

12. Capability Sets
=====================

The CH4 device contains a feature called "capability sets" to simplify
configuration of MPICH on systems using the OFI netmod. This feature
configures MPICH to use a predetermined set of OFI features based on the
provider being used. Capability sets can be configured at compile time or
runtime. Compile time configuration provides better performance by
reducing unnecessary code branches, but at the cost of flexibility.

To configure at compile time, the device string should be amended to include
the OFI provider with the following option:

    --with-device=ch4:ofi:sockets

This will setup the OFI netmod to use the optimal configuration for the
sockets provider, and will set various compile time constants. These settings
cannot be changed at runtime.

If runtime configuration is needed, continue to use the device string as before
(without the OFI provider extension) and set various environment variables to
achieve a similar configuration. To select the desired provider:

    % export MPIR_CVAR_OFI_USE_PROVIDER=sockets

This will select the OFI provider and the associated MPICH capability set. To
change the preset configuration, there exists an extended set of environment
variables. As an example, the immediate data fields can be disabled by using
the environment variable:

    % export MPIR_CVAR_OFI_ENABLE_TAGGED=0

For some configuration options (in particular, MPIR_CVAR_OFI_ENABLE_TAGGED and
MPIR_CVAR_OFI_ENABLE_RMA), a default build of MPICH using the CH4 OFI netmod
will fail if these options are not enabled. This is so that, for performance,
MPICH can assume that some commonly available features are enabled by the OFI
provider.

A full list of capability set configuration variables can be found in the
environment variables README.envvar.

-------------------------------------------------------------------------

13. Threads
===========

MPICH supports multiple threading packages.  The default is posix
threads (pthreads), but solaris threads, windows threads and argobots
are also supported.

To configure mpich to work with argobots threads, use the following
configure options:

    --with-thread-package=argobots \
        CFLAGS="-I<path_to_argobots/include>" \
        LDFLAGS="-L<path_to_argobots/lib>"

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