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OpenMPI

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Open MPI is a Message Passing Interface (MPI) used in relax for parallalised calculations. == mpi4py OpenMPI ==

This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/2/3 specification and exposes an API which grounds on the standard MPI-2 C++ bindings.

Gary has achieved near perfect scaling efficiency:

~~https://mail.~~{{gna~~.org/public/~~mailing list url|relax-devel/2007-05/msg00000.html}}

=== Dependencies ===

# Python 2.4 to 2.7 or 3.0 to 3.4, or a recent PyPy release.

# A functional MPI 1.x/2.x/3.x implementation like MPICH or Open MPI built with shared/dynamic libraries.

=== How does it work ? ===

If mpirun is started with "np 4", relax will get 4 "rank" processors. <br>

# Simultaneously make 10 Monte-Carlo simulations

=== Install OpenMPI on linux and set environments ===

See https://www10.informatik.uni-erlangen.de/Cluster/

# Show what loading does

module show openmpi-x86_64

# or

module show openmpi-1.10-x86_64

# See if anything is loaded

# Load

module load openmpi-x86_64

# Or

module load openmpi-1.10-x86_64

# See list

module list

# For 64 bit computer.

sudo ln -s /usr/lib64/openmpi/bin/mpicc /usr/bin/mpicc

# or

sudo ln -s /usr/lib64/openmpi-1.10/bin/mpicc /usr/bin/mpicc

</source>

== Install mpi4py ==

=== Linux and Mac ===

Remember to check, if there are newer versions of [https://bitbucket.org/mpi4py/mpi4py/downloads/ mpi4py]. <br>

The [https://bitbucket.org/mpi4py/mpi4py mpi4py] library can be installed on all UNIX systems by typing:

<{{#tag:source ~~lang="bash">~~|

# Change to bash, if in tcsh shell

#bash

v=~~1.3.1~~{{current version mpi4py}}

#tcsh

set v=~~1.3.1~~{{current version mpi4py}}

pip install https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-$v.tar.gz

pip install https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-$v.tar.gz --upgrade

# Or to use another python interpreter than standard

wget https://bitbucket.org/mpi4py/mpi4py/downloads/mpi4py-$v.tar.gz

tar -xzf mpi4py-$v.tar.gz

rm mpi4py-$v.tar.gz

cd mpi4py-$v

# Use the path to the python to build with

python setup.py build

python setup.py install

cd ..

rm -rf mpi4py-$v

|lang="bash"

}}

Then test

python

import mpi4py

mpi4py.__file__

</source>

== Relax In multiprocessor mode ==

'''How many processors should I start?''' <br>

You can continue try this, until a good results

# With shellmpirun -np 4 echo "hello world" # With pythonmpirun -np 4 python -m mpi4py helloworld # If newer version of mpirun, then --report-bindings worksmpirun --report-bindings -np 11 4 echo "hello world"

mpirun --report-bindings -np 12 echo "hello world"

# This is too much

This code runs in the GUI, the script UI and the prompt UI, i.e. everywhere.

=== Helper start scripts ===

If you have several versions or development branches of relax installed, you could probably use some of these scripts, and put them in your PATH.

==== Script for force running relax on server computer ====

This script exemplifies a setup, where the above installation requirements is met on one server computer ''haddock'', and where satellite computers are forced to run on this computer.

</source>

==== Script for running relax with maximum number of processors available ====

This script exemplifies a setup, to test the running relax with maximum number of processors.

# Set number of available CPUs.

set NPROC=`nproc`

set NP=`echo $NPROC + 1 0 | bc `

echo "Running relax with NP=$NP in multi-processor mode"

</source>

==== Script for force running relax on server computer with openmpi ====

#!/bin/tcsh

#set NPROC=`nproc`

set NPROC=10

set NP=`echo $NPROC + 1 0 | bc `

# Run relax in multi processor mode.

</source>

== Setting up relax on super computer Beagle2 == Please see post from Lora Picton [[relax_on_Beagle2]] Message: http://thread.gmane.org/gmane.science.nmr.relax.user/1821 == Commands and FAQ about mpirun ==

See oracles page on mpirun and the manual openmpi:

# https://docs.oracle.com/cd/E19923-01/820-6793-10/ExecutingPrograms.html

</source>

=== Find number of Socket, Cores and Threads ===

See http://blogs.cisco.com/performance/open-mpi-v1-5-processor-affinity-options

</source>

=== Test binding to socket ===

module load openmpi-x86_64

</source>

== Use mpirun with ssh hostfile == ~~'''NOTE:'''~~ {{caution|This is test only. This appears not to function well! ~~<br>~~}}

See

</source>

== Running Parallel Jobs with queue system ==

See:

# https://docs.oracle.com/cd/E19923-01/820-6793-10/ExecutingBatchPrograms.html

=== Running Parallel Jobs in the Sun Grid Engine Environment ===

See

# https://www.open-mpi.org/faq/?category=building#build-rte-sge

</source>

=== Running Parallel Jobs in the PBS/Torque ===

See

# https://www.open-mpi.org/faq/?category=building#build-rte-tm

</source>

=== Running Parallel Jobs in SLURM ===

See

# https://www.open-mpi.org/faq/?category=building#build-rte-sge# https://www.open-mpi.org/faq/?category=slurm

Test if you have it

ompi_info | grep tmslurm

</source>

== Updates ==

=== Update 2013/09/11 ===

See [http://thread.gmane.org/gmane.science.nmr.relax.scm Commit]

'''no clustering''' is defined and the Monte Carlo simulations for error analysis.

=== Test of speed ===

==== Performed tests ====

===== A - Relax_disp systemtest =====

'''Relax_disp_systemtest'''

</source>

===== B - Relax full analysis performed on dataset =========== First initialize data ======

set CPU1=tomat ;

relax_single $TDATA/$CPU2/$MODE2/relax_1_ini.py ;

</source>

====== Relax_full_analysis_performed_on_dataset ======

#!/bin/tcsh -e

cat $LOG ;

</source>

===== C - Relax full analysis performed on dataset with clustering =====

'''Relax_full_analysis_performed_on_dataset_cluster'''

</source>

==== Setup of test ====

===== List of computers - the 'lscpu' command =====

CPU 1

</source>

===== Execution scripts =====

'''relax_single'''

</source>

=== Results ===

{| class="wikitable sortable" border="1"

# MODEL_ALL = ['R2eff', 'No Rex', 'TSMFK01', 'LM63', 'LM63 3-site', 'CR72', 'CR72 full', 'IT99', 'NS CPMG 2-site 3D', 'NS CPMG 2-site expanded', 'NS CPMG 2-site star']

== See also ==

[[Category:Installation]]

[[Category:~~Devel~~Development]]

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