Matlab MPI

Shuxia Zhang
Supercomputing Institute
e-mail: szhang@msi.umn.edu
help@msi.umn.edu
Tel: 612-624-8858 (direct)
612-626-0802(help)
Outline:

Introduction
MatlabMPI functions/syntax
Matlab functions
How to write MatlabMPI program
How to run MatlabMPI jobs
Hands-on
 INTRODUCTION

Message Passing Interface (MPI)

-- C, C++ and Fortran standard functions defined
for communication.
-- widely used in large scale of computations.

Matlab – High level intuitive language for numerical computations,

algorithm development, simulation, data reduction, testing
and evaluation.
-- needs an efficient mechanism for running Matlab programs
in parallel to achieve high performance
-- Memory limitation of 32-bit memory addressing
 INTRODUCTION

MatlabMPI
-- developed at Lincoln Laboratory, MIT
-- implements a subset of MPI
-- allows any Matlab programs to run in parallel,
speeding up calculations and addressing memory > 2 GB
on both SMP and DMP systems
-- implements the widely used MPI "look and feel" on top
of standard Matlab file i/o, resulting in a "pure" Matlab
implementation of MPI
-- is exceedingly small (~300 lines of code).
-- runs on any combination of computers that Matlab supports.
 Requirements
- Matlab license
A single Matlab license on SMP
Floating license on DMP
- File system visible to all processors
uses file I/O for communication,
there must be a directory that is visible to every machine
where the program is launched. The directory can be
changed within the MatlabMPI program.
- Data-transfer or communication strongly depends on the network,
which can be slow .
MatlabMPI is suitable for coarse granularity applications
 MPI functions

function MPI_Init()
% Called at the beginning of an MPI program.
function size = MPI_Comm_size(comm)
% MPI_Comm_size - returns the number of processors
% in the communicator
% comm is an MPI Communicator, typically
% a copy of MPI_COMM_WORLD
function rank = MPI_Comm_rank(comm)
% MPI_Comm_rank - returns the rank of the current processor.
%
% rank = MPI_Comm_rank(comm)
 MPI functions

function MPI_Send( dest, tag, comm, varargin )

% MPI_Send - Sends variables to dest.
% Send message containing variables to dest with a given tag
% dest can be an integer from 0 to comm_size-1
% tag can be any integer
% comm is an MPI Communicator
% MPI_Send( dest, tag, comm, sdata1, sdata2, … )
 MPI functions

function varargout = MPI_Recv( source, tag, comm )

% MPI_Recv - Receives message from source.

% [var1, var2, ...] = MPI_Recv( source, tag, comm )
% Receives message from source with a given tag
% and returns the variables in the message.
% Source can be an integer from 0 to comm_size-1
% tag can be any integer
 MPI functions

function MPI_Abort()
% MPI_Abort - Aborts any currently running MatlabMPI sessions.
% It will abort any currently running MatlabMPI sessions.
% by looking for leftover Matlab jobs and killing them.
% Cannot be used after MatMPI_Delete_all.

function MPI_Finalize()
% MPI_Finalize
% Called at the end of a MatlabMPI program.
 MPI functions
MPI_Run( m_file, n_proc, machines )

% MPI_Run - Run m_file on multiple processors.

% Runs n_proc copies of m_file on machines,
% where machines = {}, run on a local processor.
% machines = {'machine1' 'machine2'}, run on a
% multi processors: nb01, nb02, …, nb12

MatMPI_Delete_all
% MatMPI_Delete_all - Deletes leftover MatlabMPI files

More MPI related functions and example can be found:

/usr/local/MatlabMPI/src

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 Matlab functions

EVAL: execute string with MATLAB expression

DISP(X) displays the array, without printing the array name..

If X is a string, the text is displayed.

Examples:

eval( MPI_Run('basic',2,{'machine1' 'machine2'}))

disp(['Hello World from rank: ',num2str(my_rank)]);

For rank 0, the output appears on the screen.

For rank 1, 2, …, the output goes to a file.
 How to write
MatlabMPI code?
(1) Setup the path
addpath /usr/local/MatlabMPI/src
(2) Initialize MPI.
MPI_Init;
(3) Create communicator.
comm = MPI_COMM_WORLD;
(4) Get size and rank.
size = MPI_Comm_size(comm);
my_rank = MPI_Comm_rank(comm);
(5) Do computation using matlab
(6) Do communication using MPI for exchanging data
(7) Finalize MPI application
 Examples
“Hello World”
addpath /usr/local/MatlabMPI/src
MPI_Init;
comm = MPI_COMM_WORLD;
% Get size and rank
size = MPI_Comm_size(comm);
my_rank = MPI_Comm_rank(comm);
disp(['Hello World from rank: ',num2str(my_rank)]);
% Finalize Matlab MPI.
MPI_Finalize;
disp('SUCCESS');
quit

Save it into a file named ‘hello.m’ and run it

 Examples
Send - Recv
MatlabMPI program using 2 processors
source =1; % Matlab Program
dest = 0; % Set who is source and who is destination
tag = 1; % Create a unique tag id for this message
A=ones(10,40);
if(comm_size == 2) % Make sure exactly two processors B=rand(40);
if (my_rank == source) C=A * B;
D=rand(40); save out C -ascii
MPI_Send( dest, tag, comm, D);
end
if (my_rank == dest)
A=ones(10,40);
B = MPI_Recv( source, tag, comm );
C = A*B
save out C -ascii
end
else
disp(‘No data sent’);
end
MPI_Finalize;
disp('SUCCESS');
quit
 More Examples
/usr/local/MatlabMPI/examples

basi.m Simple MatlabMPI program that sends data from processor 1

to processor 0.
multi_basic.m Simple MatlabMPI program that sends data from processor 1
to processor 0 a few times.
probe.m Simple MatlabMPI program that demonstrates the using
MPI_Probe to check for incoming messages.
broadcast.m Tests MatlabMPI broadcast command.
basic_app.m Examples of the most common usages of MatlabMPI.
 More Examples
/usr/local/MatlabMPI/examples

basic_app2.m Examples of the most common usages of MatlabMPI.

basic_app3.m Examples of the most common usages of MatlabMPI.
basic_app4.m Examples of the most common usages of MatlabMPI.
blurimage.m MatlabMPI test parallel image processing application.
speedtest.m Times MatlabMPI for a variety of messages.
 More Examples
/usr/local/MatlabMPI/examples

synch_start.m Function for synchronizing

starts.machines.m Example script for creating a machine
description.
unit_test.m Wrapper for using an example as a unit
test.
unit_test_all.m Calls all of the examples as way of
testing the entire library.
unit_test_mcc.m Wrapper for using an example as a mcc
unit test.
 How to run matlabMPI job
interactively?

(1) Login to Netfinity:

ssh -l temp01 nf.msi.umn.edu
rsh nb01, rsh nb02, …, rsh nb12
(2) Load the module MatlabMPI
module load matlabMPI

%For across node runs, please add it to the .cshrc file

(3) Start Matlab

matlab –nojvm –nodisplay
 How to run matlabMPI job
interactively?

>> addpath /usr/local/MatlabMPI/src

>> help MatlabMPI
>> machines = {};
>> eval( MPI_Run(‘Mycode', 2,machines) )
% Mycode is a matlabMPI application code, which
% needs to exist in the same working directory
>> MatMPI_Delete_all;
% Deletes leftover MatlabMPI files.
>> quit
 How to run matlabMPI job
across nodes?

>> addpath /usr/local/MatlabMPI/src

>> machines = {‘nb0x’ ‘nb02’ ‘nb03’};
% nb0x is the login node. For each user, nb0x may be
% different, e.g., nb05 for you, nb08 for him.
>> eval( MPI_Run(‘hello', 3,machines) )
% hello.m is a matlabMPI application code, which
% exists in the same working directory
>> MatMPI_Delete_all;
% Deletes leftover MatlabMPI files.
>> quit
 Examples
“Hello World”
To run the job on the login node, type:
>> addpath /usr/local/MatlabMPI/src
>> eval(MPI_Run(‘hello’, 4, {}))

To run the job across nodes, type

>> eval(MPI_Run(‘hello’, 4, {‘nb0x’ ‘nb03’ ‘nb07’ ‘nb08’ }))
where nb0x is the node you login, e.g., nb02

It will create output in the directory MatMPI:

hello.1.out
hello.2.out
hello.3.out
 Hands on
Exercises:
(1) Write a MatlabMPI program to print ‘hello world’
and run it using 4 processor on the login node ;
(2) Run the above case on different nodes;
(3) Write a MatlabMPI program to solve the following problem
using 2 processes
% Matlab Program
A=ones(10,40);
B=rand(40);
C=A * B;
save out C -ascii
(4) Copy any example from /usr/local/MatlabMPI/examples,
make modifications if necessary and run the job.
References:

http://www.ll.mit.edu/MatlabMPI/
http://www.msi.umn.edu/tutorial/scicomp/general/MPI/
workshop_MPI/
http://www.mathworks.com/products/
http://www.mpi-forum.org/
This room is reserved for a tutorial
On June. 1 from 1:00pm to 4:00pm
Thank you for your cooperation!