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<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>Dear all,<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>I've been to a Mathworks
workshop yesterday and they talked about their new distributed computing
toolbox (version 3.1). What they say is that if one has a computer cluster it
is possible to install a slave Matlab engine on each machine and declare a
variable that will be distributed among all the machines and thereby utilize all
their memory even without parallelizing any of the computations. Of course
things will run rather slowly that way. Moreover, it should also be possible to
run several instances of this engine on the same machine and make use of multiple
core processors (if the code is parallelized) but also address more than 2Gb of
memory on a 32-bit machine given that every instance of the engine stores less
than 2Gb. <o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>I have not tried any of
this, but if you try and it works for you I'd be very interested to hear about
it.<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>Best,<o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal dir=LTR><st1:City w:st="on"><st1:place w:st="on"><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Vladimir</span></font></st1:place></st1:City><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> <o:p></o:p></span></font></p>
<p class=MsoNormal dir=LTR><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<p class=MsoNormal dir=LTR><b><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma;font-weight:bold'>From:</span></font></b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> FieldTrip
discussion list [mailto:<st1:PersonName w:st="on">FIELDTRIP@NIC.SURFNET.NL</st1:PersonName>]
<b><span style='font-weight:bold'>On Behalf Of </span></b>Jared Van Snellenberg<br>
<b><span style='font-weight:bold'>Sent:</span></b> Friday, June 29, 2007 3:58
AM<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">FIELDTRIP@NIC.SURFNET.NL</st1:PersonName><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [FIELDTRIP] out of
memory - window machine</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Hi Virginie,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>There are a couple of other things you can do.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>First, make certain that you are not growing any
variables inside a loop. For example, if you have any code like:<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>for i=1:size(data,1)<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>for j=1:size(data,2)<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>newvar(i,j)=data(i,j); <o:p></o:p></span></font></p>
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<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>end<o:p></o:p></span></font></p>
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<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>end<o:p></o:p></span></font></p>
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<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>make sure that you precede this code with:<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>newvar=zeros(size(data));<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>This will not only speed up the execution of your code
but can prevent memory errors in matlab.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Second, use the clear function to remove any variables
that are no longer necessary.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Third, type 'pack' at the command line prior to
executing the part of your code that generates the memory error.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>If none of this works, there are two more options that
I'm aware of for avoiding a memory error.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>First, you can run your analysis on a computer with a
64-bit architecture and a 64-bit operating system. The reason that you are
still encountering memory errors despite having virtual memory maximized is
that 32-bit systems are incapable of addressing more than approximately 4 GB of
memory, regardless of how much is available. This limitation is effectively
removed on 64 bit systems (or rather, the limitation is several orders of
magnitude higher). <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Finally, you can run your analysis in steps, saving
the results of each step and clearing all the data. I've certainly had to do
this before when working in fieldtrip. For example, if you're attempting to
timelock analyses, load each subject individually and grandaverage their
trials, saving the results to a new variable. Then clear their data, load the
next subject, and continue. In addition, with the datasets I've used in
FIELDTRIP I've noticed that for most functions specifying cfg.keeptrials='yes'
is likely to generate memory errors, and for frequency analyses specifying
cfg.parameter='powandcsd' and using a large number of pairings in
cfg.channelcmb (or leaving it at default) is pretty well guarenteed to generate
a memory error. <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Good luck!<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>-Jared<br>
<br>
<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal dir=LTR><span class=gmailquote><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>On 6/28/07, <b><span
style='font-weight:bold'>Virginie van Wassenhove</span></b> <<a
href="mailto:vvw@caltech.edu">vvw@caltech.edu</a>> wrote:</span></font></span>
<o:p></o:p></p>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'>Hi fieldtrippers,<br>
<br>
would anyone have a trick to share for optimizing memory in matlab...?<br>
<br>
What I have tried so far (insufficient still): <br>
- let windows manage memory<br>
- boost virtual memory to maximum (on 2 drives!)<br>
- clear all unnecessary variables in mat space<br>
- disable java<br>
- turned off graphic hardware acceleration<br>
- shut off unused processes <br>
<br>
I am running out of options...Would using a mac solve these issues?<br>
<br>
Thanks in advance,<br>
-vv<br>
<br>
<br>
Virginie van Wassenhove, PhD<br>
<br>
:::::::::::: contact info :::::::::::::<br>
Caltech - Division of Biology <br>
<st1:Street w:st="on"><st1:address w:st="on">1200 E. California Blvd</st1:address></st1:Street>
M/C 139-74<br>
<st1:place w:st="on"><st1:City w:st="on">Pasadena</st1:City> <st1:State w:st="on">CA</st1:State>
<st1:PostalCode w:st="on">91125</st1:PostalCode> <st1:country-region w:st="on">USA</st1:country-region></st1:place><br>
:::::::::::::::::::::::::::::::::::::::::::::::::<br>
<a href="mailto:vvw@caltech.edu">vvw@caltech.edu</a><br>
<a href="mailto:Virginie.van.Wassenhove@gmail.com">Virginie.van.Wassenhove@gmail.com</a><br>
W: 626.395.8959<br>
<a href="http://www.its.caltech.edu/~vvw">http://www.its.caltech.edu/~vvw</a><br>
<br>
:::::::::::::::::: extras ::::::::::::::::::::<br>
<a href="http://www.kiva.org">http://www.kiva.org</a><br>
<a href="http://www.thehungersite.com/">http://www.thehungersite.com/</a><br>
<a href="http://www.agloco.com/r/BBBS1539">http://www.agloco.com/r/BBBS1539</a><br>
::::::::::::::::::::::::::::::::::::::::::::::::: <br>
<br>
----------------------------------<br>
The aim of this list is to facilitate the discussion between users of the
FieldTrip toolbox, to share experiences and to discuss new ideas for
MEG and EEG analysis. See also <a
href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a>
and <a href="http://www.ru.nl/fcdonders/fieldtrip">http://www.ru.nl/fcdonders/fieldtrip</a>.<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal dir=LTR><font size=3 face="Times New Roman"><span
style='font-size:12.0pt'><br>
<br clear=all>
<br>
-- <br>
Jared Van Snellenberg<br>
Social Cognitive Affective Neuroscience Unit<br>
<a href="http://scan.psych.columbia.edu">http://scan.psych.columbia.edu</a><br>
(212) 854-7858 p<br>
(212) 854-3609 f <br>
Department of Psychology, <st1:place w:st="on"><st1:PlaceName w:st="on">Columbia</st1:PlaceName>
<st1:PlaceType w:st="on">University</st1:PlaceType></st1:place><br>
406 Schermerhorn Hall<br>
<st1:Street w:st="on"><st1:address w:st="on">1190 Amsterdam Avenue</st1:address></st1:Street>,
Mail Code 5501<br>
<st1:place w:st="on"><st1:City w:st="on">New York</st1:City>, <st1:State w:st="on">NY</st1:State>
<st1:PostalCode w:st="on">10027</st1:PostalCode></st1:place><br>
_______________________________<br>
"Luck is the residue of design"<br>
-Attributed to Branch Rickey, former US Baseball Administrator, and also to
John Milton. Go figure. <o:p></o:p></span></font></p>
<p dir=LTR><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>----------------------------------<o:p></o:p></span></font></p>
<p dir=LTR><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>The
aim of this list is to facilitate the discussion between users of the FieldTrip
toolbox, to share experiences and to discuss new ideas for MEG and EEG
analysis.<o:p></o:p></span></font></p>
<p dir=LTR><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>http://listserv.surfnet.nl/archives/fieldtrip.html<o:p></o:p></span></font></p>
<p dir=LTR><font size=3 face="Times New Roman"><span style='font-size:12.0pt'>http://www.ru.nl/fcdonders/fieldtrip/<o:p></o:p></span></font></p>
</div>
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<p>----------------------------------</p>
<p>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>