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Subject:

Re: Avoid disk access when running a first-level model

From:

"Bruno L. Giordano" <[log in to unmask]>

Reply-To:

Bruno L. Giordano

Date:

Tue, 28 Jan 2014 18:04:59 +0000

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (78 lines)

Thank you Pierre for these useful suggestions: with all of these inputs 
I have the feeling you guys almost ran my analysis ;-)

	Bruno

On 28/01/2014 17:57, Pierre Bellec wrote:
> Hi Bruno,
>
> Looks like Donald got you covered. For future reference, if you can't
> avoid using files for a simulation and want to be as efficient as
> possible, the simplest hack is to store those files on a virtual
> partition in memory instead of a hard drive. If you are using a
> high-performance computing infrastructure, chances are this is available
> to you or can be arranged with the staff. You would have to make sure
> that the intermediate outputs fit in the virtual partition, but if we
> are talking about one parameter map at a time this will be no problem.
>
> Also, if you are writing all files in the local drive of your compute
> node (the tmp), you won't be clogging the grid (because you don't put
> any load on the shared file system).
>
> Finally, the computation time you will save by not using the disk may
> not actually be that large. You may want to start doing a bit of
> profiling (with the profile command) on a small simulation to check how
> big the overhead of using files actually is, rather than assume it will
> be large. Matlab is a weird beast, and computational bottlenecks are not
> necessarily where you would expect them to be.
>
> I hope this helps,
>
> Pierre Bellec, PhD
> Researcher / Chercheur, Research Centre of the Montreal Geriatric Institute
> Professeur adjoint sous octroi, Department of Computer Science and
> Operations Research
> University of Montreal, Québec, Canada
> 1 514 340 3540 #3367
> http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
>
>
> 2014-01-28 Bruno L. Giordano <[log in to unmask] <mailto:[log in to unmask]>>
>
>     Hello,
>
>     I am planning to run some permutation analysis by permuting
>     condition labels in the first-level model.
>
>     I wonder whether someone managed to hack the first-level model
>     routines so that they take in input and give in output variables
>     stored in the workspace rather than stored on the disk (I would
>     actually need only the parameter estimates, and not the stats, which
>     should make things much easier). I suspect that in the case of a
>     permutation analysis disk access is going to be a considerable
>     limiting factor for the speed of the computations, and I wouldn't
>     like to overload the parallel grid with unnecessary overheads.
>
>     Thank you for any tip.
>
>              Bruno
>
>     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~__~~
>     Bruno L. Giordano, PhD
>     Institute of Neuroscience and Psychology
>     58 Hillhead Street, University of Glasgow
>     Glasgow, G12 8QB, Scotland
>     T +44 (0) 141 330 5484 <tel:%2B44%20%280%29%20141%20330%205484>
>     Www: http://www.brunolgiordano.net
>
>

-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Bruno L. Giordano, PhD
Institute of Neuroscience and Psychology
58 Hillhead Street, University of Glasgow
Glasgow, G12 8QB, Scotland
T +44 (0) 141 330 5484
Www: http://www.brunolgiordano.net

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