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Introduction to Matlab

High Performance Computing (HPC) team

W.K. Kwan (hcxckwk@hku.hk)

Asst. IT Director

Phone: 2857 8631

Lilian Y.L. Chan (lilianyl@hku.hk)

IT Manager

Phone: 2859 2485

Tony W.K. Cheung (tonycwk@hku.hk)

IT Officer

Phone: 2241 5185

mailto:kwk@cc.hku.hkmailto:lilianyl@hku.hkmailto:tonycwk@hku.hkmailto:tonycwk@hku.hkmailto:lilianyl@hku.hkmailto:kwk@cc.hku.hk

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HPC computers

hpcpower (32-bit cluster) (128-node dual PIV 2.8 GHz RHL cluster)

+

( 50-node dual PIV 3.06 GHz from Physics)

Will be obsolete

hpcpower2 (64-bit cluster)

smpserve

Machines running in parallel operating environment Your program has been parallelized?? Need special account and requires application

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Agenda

1. Introduction

2. What is Matlab

3. Where and how to access Matlab inHKU CC

4. Elementary operations in Matlab

5. More matrix manipulations in Matlab

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Agenda(cont.)

1. Polynomials operations

2. Graph plotting

3. What is Matlab programming

4. What is m files

5. More beyond

Compiled to binary code

Massively executed in hpcpower2 Massively executed in lab. PCs via CONDOR

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Matlab in CC

Installation of Matlab license server

20+ license + some toolkits

SMPSERVE System Every smpserve account holder can run

matlab in the system, but required accountapplication (but we dont have PC versionof matlab)

HPCPOWER2 Can also run Matlab, but you need special

account on HPCPOWER2

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Other sources of Matlab

Matlab in your dept. laboratory

Can be PC / linux based

Toolkits ??

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History

A high-level language and a problem-

solving environment for mathematical

and scientific calculation

Originated in later 1970s by Cleve

Moler

Aimed at to provide interactive access

to the Fortran linear algebra packages

EISPACK and LINPACK

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History (cont.)

Programming language environment

developed, many m-files circulating

around

More graphical commands and tool-

boxes offered

Go commercial, with the company

MathWorks Inc. formed in 1984 by

Moler and John Little

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Matlab

Text mode operation, very fast

Graphics mode

Require X-Windows facilities

Very slow !!!

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Mechanism for X-display

Local X windows Display

(UNIX workstation

PC Linux

MS-Wins, with emulator s/w)

HOST

Computer

(smpserve)xhost +

setenv DISPLAY

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Steps in running smpserveMatlab under eXcursion X-

Windows emulation

environment

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Excursion setup (PC side)

When power on your DELL PC, boot

from WINME partition

(eXcursion not available in XP, sorry!)

Open a command prompt window

(run->command)

Check the IP address of your current

session (ipconfig)

Call up eXcursion by clicking the

eXcursion icon in Programs

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eXcursion setup (host side)

Click Simpterm icon, telnet and logon hkusua

Type echo $DISPLAY to see where your displaygoes

Type setenv DISPLAY 147.8.xxx.xxx:0.0

Check echo $DISPLAY again to confirm yourmatlab display indeed goes to your PC terminal

To switch back to text-only Matlab (much faster) exit from Matlab

type setenv DISPLAY Check echo $DISPLAY again

Restart Matlab

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Seminar material

HKUCC slide on Matlab

UD200 - Using Matlab 6.5 in the Unix Environ

(http://www.hku.hk/cc/home/documentations/userdoc.htm)

Selected reprint from other Univs.

http://www.hku.hk/local/cc/training/matlab2001.ppthttp://www.hku.hk/local/cc/training/matlab2001.ppt

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Course Materials

Too too many over the Internet

http://www.hku.hk/cc/home/documentatio(hkuccs version)

http://www.math.utah.edu/lab/ms/matlab/m(very good short introductory)

http://www.indiana.edu/~statmath/math/m

(comprehensive yet easy to read)

http://www.hku.hk/cc/home/documentations/training.htmhttp://www.math.utah.edu/lab/ms/matlab/matlab.htmlhttp://www.indiana.edu/~statmath/math/matlab/gettingstarted/index.htmlhttp://www.indiana.edu/~statmath/math/matlab/gettingstarted/index.htmlhttp://www.math.utah.edu/lab/ms/matlab/matlab.htmlhttp://www.hku.hk/cc/home/documentations/training.htm

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Links (cont.)

http://www.math.mtu.edu/~msgocken/intro

(comprehensive and advanced)

http://ist.uwaterloo.ca/ec/scientific/Matlab/

(some very useful tips, easy read)

http://math.ucsd.edu/~driver/21d-s99/matl

(most classical matlab tutorial, updated

version only available in book)

http://www.math.mtu.edu/~msgocken/intro/intro.htmlhttp://ist.uwaterloo.ca/ec/scientific/Matlab/matlab.htmhttp://math.ucsd.edu/~driver/21d-s99/matlab-primer.htmlhttp://math.ucsd.edu/~driver/21d-s99/matlab-primer.htmlhttp://ist.uwaterloo.ca/ec/scientific/Matlab/matlab.htmhttp://www.math.mtu.edu/~msgocken/intro/intro.html

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Links (cont.)

Others http://www.engin.umich.edu/group/ctm/basic/ba(handling of polynomials)

http://www-personal.engin.umich.edu/~tilbury/tutorials/ma(Mech. Engin.: automatic control)

http://users.ece.gatech.edu/~bonnie/book/TUTO(Transfer function response)

http://www.mathworks.com/products/education/(collection of Matlab tutorial web-pages

http://www.engin.umich.edu/group/ctm/basic/basic.htmlhttp://www-personal.engin.umich.edu/~tilbury/tutorials/matlab_tutorial.htmlhttp://users.ece.gatech.edu/~bonnie/book/TUTORIAL/tutorial.htmlhttp://www.mathworks.com/products/education/basics.shtmlhttp://www.mathworks.com/products/education/basics.shtmlhttp://users.ece.gatech.edu/~bonnie/book/TUTORIAL/tutorial.htmlhttp://www-personal.engin.umich.edu/~tilbury/tutorials/matlab_tutorial.htmlhttp://www.engin.umich.edu/group/ctm/basic/basic.html

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For Interactive users

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Get familiar with the basic operation on

matlab, in particular related to your

discipline

Find resources over Internet

Study M-files examples(/sua_d1/matlab7/toolbox)

Programming keeps to the minimum

Ask

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For HEAVY numbercrunching users

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Interfacing with C/Fortran

programs Working in Matlab but calling C/Fortran

modules to handle the complicatednumerical calculation Main advantage: to take advantage of the graphics

plotting and build-in matrix operation facilities inMatlab

C/Fortran routines (sayprog1.exe) compiled asindependent executable programs

Matlab results wrote to disk files Execute C/Fortran programs by specifying !

prog1.exe (i.e. treatingprog1.exe as a standardUNIX command like ls or cd )

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Working in C/Fortran but calling Matlab to

handle the matrix operation Main advantage: build-in matrix operation facilities

in Matlab

C/Fortran results wrote to disk files

Prepare the Matlab instructions and storing in am-file (say ml-bat1.m)

Execute Matlab in batch mode, within the mainprogram by specifying

call system ( matlab < ml-bat1.m > ml-bat1.out, ierr) !

Fortranierr = system (matlab < ml-bat1.m > ml-bat1.out) ! C

where the Matlab output will be captured in file ml-bat1.outfor further processing in the Fortran/Cprogram

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Compiled Matlab M-files

Program(s) will be linked and convertedinto a single executable file

Executable program much compact in size

When actual running, Matlab system (theinterpreter) will not longer be required Much faster running

Much memory available for program use NO License count problem

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Compiled Matlab M-files (cont.)

Better program security (executable programcant be viewed)

Need extra software license, Matlab compiler Different licenses required for Linux and

Microsoft Windows versions (BUT, both notavailable yet in HKUCC)

During actual program execution, many run-timevendor-provided libraries have to be pre-

installed (shared libraries under Linux dlls (Dynamic-link libraries) under MSFT Windows

environment )

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Direct running of Matlab

matlab < myprog.m >

Slow, as the instructions in myprog.m will

have to be interpreted at statement by

statement (take care of your loops!)

matlab software itself will eat your big

chunk of memory

We have only 20 licenses

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Matlab compiler (mcr)

Matlab M-files compiled and stored in

exe files

For program security and faster operation

Dont need matlab when in actual running

No license count concern

(Of course the matlab compiler needs

independent license)

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mcr procedure

1. Create a separate directory and place all your relatedm files there

(a sample: mysquare.m)

function magicsquare(n)%MAGICSQUARE generates a magic square matrix of the

size

% specified by the input parameter n.

% Copyright 2003 The MathWorks, Inc.

if (ischar(n))

n=str2num(n);

end

magic(n)

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mcr procedure (cont.)

2. Test run your m file(s) within matlabmatlab>> pwd

>> ls>> magicsquare(3)

ans =

8 1 63 5 74 9 2

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mcr procedure (cont.)

3. Compile your file(s) within matlab

>> mcc m magicsquare.m

>> ls

(many files include the executable magicsquare will be produced)

4. Open a new windows,

run this magicsquare OUTSIDE matlab

./magicsquare 3

ans =8 1 6

3 5 7

4 9 2

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Running Matlab in aparallel computing

environment

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MultiMatlab

Parallelized Matlab, still academic R&Dprojects with little real general-purposeproducts available, very expensive

Not all mathematical algorithms can beparallelized

For one single task, trying to split theintense calculation for using multiple

CPUs/cores (But if you have many independent

tasks .)

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Running Matlab in parallel computing

environment

Analysis your program flow

split the serial execution into separate independenttasks that can be executed asynchronously byspecifying 1 (or 2) parameters

Write a mpi driving program (Fortran/C) to call uprequired no. of CPUs (available)

Drive different CPUs/cores to work on differentserial tasks

Consolidate the result, either through disk files orMatlab memory files

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Other Scientific computing software

packages in CC

Mathematica

2 licenses on smpserve platform only

Symbolic math. software

PV-WAVE Visual data analysis development environment

Very powerful, file I/O, 2D, 3D analysis, animated

show, programming interface

Many licenses on PCs platform, and HPCPOWER