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:

IntroductionMatlabMPI functions/syntaxMatlab functionsHow to write MatlabMPI programHow to run MatlabMPI jobsHands-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 GBon both SMP and DMP systems

-- implements the widely used MPI "look and feel" on topof standard Matlab file i/o, resulting in a "pure" Matlabimplementation 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 processorsuses 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_WORLDfunction 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

Matlab functions

Bioinformatics ToolboxCommunications ToolboxControl System ToolboxCurve Fitting ToolboxData Acquisition ToolboxDatabase ToolboxDatafeed ToolboxExcel LinkFilter Design ToolboxFinancial ToolboxFinancial Derivatives ToolboxFinancial Time Series ToolboxFixed-Income ToolboxFuzzy Logic ToolboxGARCH ToolboxGenetic Algorithm ToolboxImage Acquisition ToolboxImage Processing ToolboxInstrument Control Toolbox

LMI Control ToolboxMapping ToolboxModel-Based Calibration ToolboxModel Predictive Control ToolboxMu-Analysis and Synthesis ToolboxNeural Network ToolboxOptimization ToolboxPartial Differential Equation (PDE) ToolboxRobust Control ToolboxSignal Processing ToolboxSpline ToolboxStatistics ToolboxSymbolic Math ToolboxSystem Identification ToolboxVirtual Reality ToolboxWavelet Toolbox

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 writeMatlabMPI 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/srcMPI_Init;comm = MPI_COMM_WORLD; % Get size and ranksize = 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

ExamplesSend - Recv

MatlabMPI program using 2 processors

source =1;dest = 0; % Set who is source and who is destinationtag = 1; % Create a unique tag id for this message if(comm_size == 2) % Make sure exactly two processors

if (my_rank == source)D=rand(40);MPI_Send( dest, tag, comm, D);

endif (my_rank == dest)

A=ones(10,40);B = MPI_Recv( source, tag, comm );C = A*Bsave out C -ascii

endelse

disp(‘No data sent’);end MPI_Finalize;disp('SUCCESS');quit

% Matlab ProgramA=ones(10,40);B=rand(40);C=A * B;save out C -ascii

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 jobinteractively?

(1) Login to Netfinity:

ssh -l temp01 nf.msi.umn.edursh 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 Matlabmatlab –nojvm –nodisplay

How to run matlabMPI jobinteractively?

>> 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 jobacross 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 ProgramA=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 4:00pmThank you for your cooperation!