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FSL  August 2009

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Subject:

Re: Grid processing in snow leopard

From:

Cinly Ooi <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Wed, 26 Aug 2009 16:03:52 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (87 lines)

PPSS (http://code.google.com/p/ppss) can be useful if you plan to use
one computer only. It detects the number of processors and use them
all up.

Catch: you cannot run two ppss.sh instances. The processing will not
be affected, but both instances cannot quit when the job is completed.
The reason is it counts the number of ppss.sh instances running in the
computer using 'ps' and decides that processing is done if the number
of ppss.sh processes drops below 2. With two instances of ppss.sh,
that can never be true.

HTH
Cinly

2009/8/26 Evi Vanoost <[log in to unmask]>:
> You can also use XGrid if you want an integrated solution. Technically you
> can modify the script that submits it to SGE and make it so it starts
> multiple processes locally.
>
> Evi Vanoost
> [log in to unmask]
> (585) 275-4549
>
>
>
> On Aug 26, 2009, at 5:59 AM, Ajay Garg wrote:
>
>> Dear Dave,
>>
>> Thanks a lot.
>> So  I have to learn about SGE installation.
>>
>> Regards,
>> -Ajay
>> On 26-Aug-09, at 10:35 AM, Dave Flitney wrote:
>>
>>> Dear Ajay,
>>>
>>> On 26 Aug 2009, at 01:38, Ajay Garg wrote:
>>>
>>>> Dear FSL users
>>>>
>>>> The snow leopard is coming this Friday. They say it can make use of
>>>> multiple processors. I
>>>> have 8-core Mac Pro? What could be advantage in the processing time of
>>>> TBSS? Will there
>>>> be any need for SGE grid engine installation?
>>>>
>>>> Regards.
>>>> Ajay
>>>>
>>>
>>> As far as I'm aware all versions of MacOS X have been able to use
>>> multiple processors where available, however, FSL scripts and programs are
>>> not inherently able to use multiple processors, i.e., "threaded". Instead
>>> these scripts use scheduling software, SGE, and divide the tasks into
>>> smaller, independent parallelisable sections. This form of parallel
>>> processing has the advantage that it is compatible with using both multiple
>>> processors and multiple hosts and doesn't need any complex thread code to
>>> achieve parallelism.
>>>
>>> So the short answer is that any of Snow Leopard's new multiple processor
>>> capabilities are not  going to make any difference to TBSS or any other FSL
>>> software. You still need SGE or similar installed to take advantage of your
>>> Mac's multiple cores.
>>>
>>> Regards, Dave
>>>
>>> --
>>> Dave Flitney, IT Manager
>>> Oxford Centre for Functional MRI of the Brain
>>> E:[log in to unmask] W:+44-1865-222713 F:+44-1865-222717
>>> URL: http://www.fmrib.ox.ac.uk/~flitney
>>
>



-- 
Best Regards,
Cinly

*****
I promise to take all due care and respect for you email, BUT will not
agree to abide to any T&C you care attached to the email. This applies
especially if this is a reply to your  email  containing one.

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