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matlab_remote.html
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<html>
<head>
<title>
MATLAB_REMOTE - Remote Computing with MATLAB
</title>
</head>
<body bgcolor="#EEEEEE" link="#CC0000" alink="#FF3300" vlink="#000055">
<h1 align = "center">
MATLAB_REMOTE <br>
Remote Computing with MATLAB
</h1>
<hr>
<p>
<b>MATLAB_REMOTE</b>
is a directory of information which
discusses the use of remote computing with MATLAB.
</p>
<p>
The latest versions of MATLAB include a facility for preparing jobs and data
on a desktop machine, and then submitting them for execution on a remote machine.
The local copy of MATLAB is responsible for communicating with the remote machine,
transferring files and data to the remote machine,
setting up the appropriate job control language and submitting a job there,
and then retrieving the results when the job is completed. In the meantime,
the user can do other work, or turn off MATLAB, or in fact turn off the
desktop computer and go home for a while!
</p>
<p>
There are a number of steps that must be taken to ensure that this remote
job submission process works correctly. These steps are outlined in the
document "Notes on Enabling Remote Submission of MATLAB Jobs".
</p>
<p>
In outline, these steps involve:
<ol>
<li>
Setting up passwordless remote access to Ithaca from your machine.
</li>
<li>
Copying some necessary files into the <b>toolbox/local</b> subdirectory
of your copy of MATLAB.
</li>
<li>
Copying a parallel configuration file <i>ithaca_2009b.mat</i> to
your machine, installing it into MATLAB, and modifying it appropriately
for your environment.
</li>
</ol>
</p>
<p>
Once these steps are completed, you should try first to validate the
ithaca_2009b configuration. Then you could go to the directory
<a href = "../../m_src/matlab_distcomp/matlab_distcomp.html">MATLAB_DISTCOMP</a>
and download the set of tests there. Then by typing the single command <b>test_all</b>,
your local copy of MATLAB can send commands and data to ITHACA for processing
there.
</p>
<p>
One issue is that certain MATLAB utility functions must be copied into
the <b>toolbox/local</b> directory on the user's desktop machine. These
scripts may be found lower down on this page.
</p>
<h3 align = "center">
Licensing:
</h3>
<p>
The computer code and data files described and made available on this web page
are distributed under
<a href = "../../txt/gnu_lgpl.txt">the GNU LGPL license.</a>
</p>
<h3 align = "center">
Related Data and Programs:
</h3>
<p>
<a href = "../../m_src/birthday_remote/birthday_remote.html">
BIRTHDAY_REMOTE</a>,
a MATLAB program which
runs a Monte Carlo simulation of the birthday paradox, and includes
instructions on how to run the job, via MATLAB's BATCH facility,
on a remote system such as Virginia Tech's ITHACA cluster.
</p>
<p>
<a href = "../../m_src/cell_detection_tasks/cell_detection_tasks.html">
CELL_DETECTION_TASKS</a>,
a MATLAB program which
creates modified versions of a sequence of gray-scale TIF files containing
images of cells; the process of each file is carried out independently,
using the "task" feature of MATLAB's parallel computing toolbox.
</p>
<p>
<a href = "../../m_src/cg_distributed/cg_distributed.html">
CG_DISTRIBUTED</a>,
a MATLAB program which
implements a version of the NAS CG conjugate gradient benchmark,
using distributed memory.
</p>
<p>
<a href = "../../m_src/color_remote/color_remote.html">
COLOR_REMOTE</a>,
a MATLAB program which
carries out the color segmentation of an image in parallel,
via SPMD commands; this includes instructions on how to run the job,
via MATLAB's BATCH facility,
on a remote system such as Virginia Tech's ITHACA cluster.
</p>
<p>
<a href = "../../m_src/contrast_spmd/contrast_spmd.html">
CONTRAST_SPMD</a>,
a MATLAB program which
demonstrates the SPMD parallel programming feature for image operations;
the client reads an image, the workers increase contrast over separate portions, and
the client assembles and displays the results.
</p>
<p>
<a href = "../../m_src/contrast2_spmd/contrast2_spmd.html">
CONTRAST2_SPMD</a>,
a MATLAB program which
demonstrates the SPMD parallel programming feature for image operations;
this improves the contrast_spmd program by allowing the workers to share some
data; this makes it possible to eliminate artificial "seams" in the processed
image.
</p>
<p>
<a href = "../../m_src/fd2d_heat_explicit_spmd/fd2d_heat_explicit_spmd.html">
FD2D_HEAT_EXPLICIT_SPMD</a>
a MATLAB program which
uses the finite difference method and explicit time stepping
to solve the time dependent heat equation in 2D. A black and white image
is used as the "initial condition". MATLAB's SPMD facility is used to
carry out the computation in parallel.
</p>
<p>
<a href = "../../m_src/fmincon_parallel/fmincon_parallel.html">
FMINCON_PARALLEL</a>,
a MATLAB program which
demonstrates the use of MATLAB's FMINCON constrained minimization
function, taking advantage of MATLAB's Parallel Computing Toolbox
for faster execution.
</p>
<p>
<a href = "../../m_src/image_denoise_spmd/image_denoise_spmd.html">
IMAGE_DENOISE_SPMD</a>,
a MATLAB program which
demonstrates the SPMD parallel programming feature for image operations;
the client reads an image, the workers process portions of it, and
the client assembles and displays the results.
</p>
<p>
<a href = "../../m_src/lyrics_remote/lyrics_remote.html">
LYRICS_REMOTE</a>,
a MATLAB program which
runs in parallel, using three workers which cooperate "systolically", that is,
as through they were on an assembly line. The output from worker 1 is passed to
worker 2 for further processing, and so on. This includes
instructions on how to run the job, via MATLAB's BATCH facility,
on a remote system such as Virginia Tech's ITHACA cluster.
</p>
<p>
<a href = "../../m_src/matlab_distcomp/matlab_distcomp.html">
MATLAB_DISTCOMP</a>,
a MATLAB program which
remotely runs a set of 5 jobs on the Ithaca cluster.
These jobs are equivalent to the BIRTHDAY_REMOTE, COLOR_REMOTE,
KNAPSACK_REMOTE, LYRICS_REMOTE and MD_PARALLEL jobs.
</p>
<p>
<a href = "../../m_src/md_parfor/md_parfor.html">
MD_PARFOR</a>,
a MATLAB program which
carries out a molecular dynamics simulation,
running in parallel using MATLAB's "PARFOR" feature.
</p>
<p>
<a href = "../../m_src/ode_sweep_parfor/ode_sweep_parfor.html">
ODE_SWEEP_PARFOR</a>,
a MATLAB program which
demonstrates how the PARFOR command can be used to parallelize the computation
of a grid of solutions to a parameterized system of ODE's.
</p>
<p>
<a href = "../../m_src/plot_spmd/plot_spmd.html">
PLOT_SPMD</a>,
a MATLAB library which
demonstrates the SPMD parallel programming feature, by having a number
of labs compute parts of a sine plot, which is then displayed by the
client process.
</p>
<p>
<a href = "../../m_src/prime_parfor/prime_parfor.html">
PRIME_PARFOR</a>,
a MATLAB program which
counts the number of primes between 1 and N;
running in parallel using MATLAB's "PARFOR" feature.
</p>
<p>
<a href = "../../m_src/quad_parfor/quad_parfor.html">
QUAD_PARFOR</a>,
a MATLAB program which
estimates an integral using quadrature;
running in parallel using MATLAB's "PARFOR" feature.
</p>
<p>
<a href = "../../m_src/quad_tasks/quad_tasks.html">
QUAD_TASKS</a>,
a MATLAB program which
estimates an integral using quadrature;
running in parallel using MATLAB's "TASK" feature.
</p>
<p>
<a href = "../../m_src/random_walk_2d_avoid_tasks/random_walk_2d_avoid_tasks.html">
RANDOM_WALK_2D_AVOID_TASKS</a>,
a MATLAB program which
computes many self avoiding random walks in 2D by creating a job which
defines each walk as a task, and then computes these independently
using MATLAB's Parallel Computing Toolbox task computing capability.
</p>
<p>
<a href = "../../m_src/satisfy_parfor/satisfy_parfor.html">
SATISFY_PARFOR</a>,
a MATLAB program which
demonstrates, for a particular circuit, an exhaustive search
for solutions of the circuit satisfiability problem,
running in parallel using MATLAB's "PARFOR" feature.
</p>
<p>
<a href = "../../m_src/subset_sum_tasks/subset_sum_tasks.html">
SUBSET_SUM_TASKS</a>,
a MATLAB program which
solves a subset sum problem by exhaustive search,
subdividing the search range among separate tasks.
</p>
<h3 align = "center">
Reference:
</h3>
<p>
The User's Guide for the Parallel Computing Toolbox is available at
<a href = "http://www.mathworks.com/access/helpdesk/help/pdf_doc/distcomp/distcomp.pdf">
http://www.mathworks.com/access/helpdesk/help/pdf_doc/distcomp/distcomp.pdf</a>
</p>
<p>
<ul>
<li>
Gaurav Sharma, Jos Martin,<br>
MATLAB: A Language for Parallel Computing,<br>
International Journal of Parallel Programming,<br>
Volume 37, Number 1, pages 3-36, February 2009.
</li>
</ul>
</p>
<h3 align = "center">
Source Code:
</h3>
<p>
In order to carry out remote job submission, copies of the following functions
and one shell script must be available on the user's local machine, in
MATLAB's subdirectory <b>toolbox/local</b>.
<ul>
<li>
<a href = "copyDataFromCluster.m">copyDataFromCluster.m</a>
</li>
<li>
<a href = "copyDataToCluster.m">copyDataToCluster.m</a>
</li>
<li>
<a href = "copyJobFilesIfFinished.m">copyJobFilesIfFinished.m</a>
</li>
<li>
<a href = "pbsDestroyJob.m">pbsDestroyJob.m</a>
</li>
<li>
<a href = "pbsGetJobState.m">pbsGetJobState.m</a>
</li>
<li>
<a href = "pbsNonSharedParallelDecodeFcn.m">pbsNonSharedParallelDecodeFcn.m</a>
</li>
<li>
<a href = "pbsNonSharedParallelSubmitFcn.m">pbsNonSharedParallelSubmitFcn.m</a>
</li>
<li>
<a href = "pbsNonSharedSimpleDecodeFcn.m">pbsNonSharedSimpleDecodeFcn.m</a>
</li>
<li>
<a href = "pbsNonSharedSimpleSubmitFcn.m">pbsNonSharedSimpleSubmitFcn.m</a>
</li>
<li>
<a href = "pbsParallelWrapper.sh">pbsParallelWrapper.sh</a>
</li>
<li>
<a href = "runCmdOnCluster.m">runCmdOnCluster.m</a>
</li>
</ul>
</p>
<p>
You can go up one level to <a href = "../m_src.html">
the MATLAB source codes</a>.
</p>
<hr>
<i>
Last revised on 12 December 2009.
</i>
<!-- John Burkardt -->
</body>
</html>