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--- doku:matlab-save [2015/05/12 10:18] – ir
+++ doku:matlab-save [2017/08/31 13:57] – removed ir
@@ Line 1: / Line 1: @@
-====== Matlab Jobs ======
-==== Run Matlab Task from command line ====
-Generate a matlab package called //test.m//,
-<code>
-add(2,3.4)
-</code>
-and a function //add.m//,
-<code>function z=add(x,y)
-z=x+y</code>
-There are two ways to run this from the command line
-option 1:<code>
-/opt/sw/matlab-80/bin/matlab -nodisplay < test.m</code>
-option 2:<code>
-/opt/sw/matlab-80/bin/matlab -nodisplay -r  "add(2,3.4)"</code>
-===== Batch Matlab job on VSC-2 =====
-==== Example: Serial Matlab Task ====
-Create a new directory
-<code>
-[username@l01 ~]$ mkdir TestMatlab
-[username@l01 ~]$ cd TestMatlab
-</code>
-Create an example file called ''myplot.m'' or download it from {{doku:myplot.m|here}} and put it in this directory:
-<code>
-[username@l01 TestMatlab]$ cat myplot.m
-h = figure;
-t = 0:pi/20:2*pi;
-plot('v6',t,sin(t).*2)
-saveas(h,'myFigFile','jpg')
-</code>
-Then create a new file called ''matlab.sh'' as your job script, with the following basic contents:
-<code>
-#$ -N matlab
-#$ -l h_rt=00:10:00
-/opt/sw/matlab-80/bin/matlab < myplot.m
-</code>
-The contents of your directory should now be:
-<code>
-[username@l01 TestMatlab]$ ls
-matlab.sh  myplot.m
-</code>
-Submit your job:
-<code>
-[username@l01 TestMatlab]$ qsub matlab.sh
-</code>
-When the job has finished you will see a "myFigFile.jpg" image file created.
-==== Example: Local Matlabpool ====
-For using all cores on a machine effetively, a so-called matlabpool can be started:
-<code>
-#$ -N matlab
-#$ -pe mpich 8
-#$ -V
-#$ -cwd
-#$ -l h_rt=00:10:00
-/opt/matlab-tu/bin/matlab < main.m
-</code>
-<code>
-matlabpool %open local 8	% local profile is default setting, at most 8 workers are allowed with the local scheduler
-matlabpool size
-n = 500; K = 50; L = 10; T = zeros(1,L);
-% serial inner loop
-for l = 1:L
-tic
-for k = 1:K
-    eig(rand(n));
-end
-T(l) = toc;
-end
-disp(['serial: ',num2str(mean(T))])
-% parallel inner loop
-for l = 1:L
-tic
-parfor k = 1:K
-    eig(rand(n));
-end
-T(l) = toc;
-end
-disp(['parallel: ',num2str(mean(T))])
-matlabpool close
-</code>
-==== Currently not available on VSC: Matlab Parallel Jobs using Matlab distributed computed environment (MDCE) ====
-In November 2012 a test installation of the MDCE enviroment was available for one month. For running Matlab in
-parallel it has to connect to so called matlab workers. The job script below starts the MDCE processes, sets up
-a MJS environment and connects a number of worker to it. Start up of the workers takes some minutes.
-__Currenlty this software is not installed. From VSC Administration point of view most task can be handled with
-the already existing campus workstation licences. If you are in need of this feature please **[[doku:contact|contact system administration]]**.__
-The job script and a sample parallel matlab job can be downloaded here:  {{:doku:matlab:matlab_mjs.tar.gz}}
-Job script:
-<code>
-#$ -N matlab_test
-#$ -pe mpich 32
-#$ -V
-#$ -cwd
-MATLAB_SCRIPT=calc_mjs.m
-MATLAB=/opt/sw/matlab-80/bin/matlab
-MDCE=/opt/sw/matlab-dcs_R2012b/toolbox/distcomp/bin/mdce
-DIST_DIR=/opt/sw/matlab-80/toolbox/distcomp/bin
-NSLOTS_PER_NODE_AVAILABLE=8
-NSLOTS_PER_NODE_USED=2
-NSLOTS_REDUCED=`echo "$NSLOTS / $NSLOTS_PER_NODE_AVAILABLE * $NSLOTS_PER_NODE_USED" | bc  `
-echo "starting run with $NSLOTS_REDUCED processes; $NSLOTS_PER_NODE_USED per node"
-uniq $TMPDIR/machines  > $TMPDIR/machines_uniq
-JOBMANAGER_HOST=`head -n 1 $TMPDIR/machines_uniq`
-JOBMANAGER=matlab_`whoami`
-#Kill all old matlab processes
-for node in `cat $TMPDIR/machines_uniq`
-do
-	ssh $node 'for i in `ps axu |grep matlab| tr -s " "|grep -v grep | cut -d " " -f 2`;do echo $i; kill -9 $i; done; rm -rf /tmp/matlab ;'
-done
-$MDCE start -clean
-${DIST_DIR}/startjobmanager -name $JOBMANAGER -remotehost $JOBMANAGER_HOST  -v
-${DIST_DIR}/nodestatus -remotehost $JOBMANAGER_HOST
-#pdsh is too fast for the license server ...
-for worker in `cat $TMPDIR/machines_uniq`
-do
-	echo starting workers on host $worker
-	ssh $worker $MDCE start -clean
-	for i in `seq 1 $NSLOTS_PER_NODE_USED`
-	do
-		${DIST_DIR}/startworker -remotehost $worker -name ${worker}_worker$i -jobmanager $JOBMANAGER -jobmanagerhost $JOBMANAGER_HOST
-	done
-done
-#What we actually want to do:
-$MATLAB -nodisplay < $MATLAB_SCRIPT
-#Clean up:
-${DIST_DIR}/stopjobmanager -name $JOBMANAGER -remotehost $JOBMANAGER_HOST  -v
-for worker in `cat $TMPDIR/machines_uniq`
-do
-	echo stopping worker on $worker
-	for i in `seq 1 $NSLOTS_PER_NODE_USED`
-	do
-		${DIST_DIR}/stopworker -remotehost $worker -name ${worker}_worker$i
-	done
-	ssh $worker $MDCE stop -clean
-done
-echo done
-</code>
-===== Batch Matlab job on VSC-3 =====
-In order to be able to use matlab, you have to load the program with the 'module load xyz' command
-<code>
-[username@l32]$ module avail  # select a matlab version
-[username@l32]$ module load Matlab/v8.5_R2015a # load selected version
-[username@l32]$ module list   # check loaded modules
-Currently Loaded Modulefiles:
-) Matlab/v8.5_R2015a
-</code>
-(See also the introduction to the [[https://wiki.vsc.ac.at/doku.php?id=doku:slurm|module command.]])
-Now, Matlab can be called by
-<code>
-[username@l32]$ matlab
-</code>
-==== Example: Serial Matlab Task ====
-Analogously to VSC-2, we use the matlab m-file {{doku:myplot.m|myplot.m}} and create a file called ''matlab.sh'' as your job script, with the following basic contents:
-<code>
-#!/bin/bash
-#
-#SBATCH -J test
-#SBATCH -N 1
-#SBATCH --ntasks-per-node=1
-#SBATCH --ntasks-per-core=1
-#SBATCH --threads-per-core=1
-#SBATCH --time=10                   # run time unit=minutes
-export OMP_NUM_THREADS=1
-time matlab < myplot.m
-</code>