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Subject:

Re: ?Problems with swap space?

From:

Axel Thielscher <[log in to unmask]>

Reply-To:

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

Date:

Fri, 15 Oct 2004 00:08:23 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (181 lines)

Hi,

thanks a lot for the information concerning the swap space.

However, after increasing swap space to 10GB and trying out several
variants (including update to FSL version 3.2, as well as a try using
Windows XP with 4GB swap), FSL still doesn't process the EPI-File. FSLview
accepts it, but film_gls still doesn't read the file.

So my question is:
Does anyone have experience with FSL and EPI-files around the size I try to
use (630MB, 1280 volumes)? Does it work at all, or does FSL have some kind
of internal limitation? Thanks for the help!

Bye,
Axel





On Mon, 11 Oct 2004 13:55:16 +0200, Cornelius Werner <co.werner@FZ-
JUELICH.DE> wrote:

>OK, here some refinements for systems running a kernel 2.6:
>
>- swap files should have the same speed as swap partitions
>- you can have up to 32 swap files/partitions
>- with a current mkswap (in util-linux), each file/partition can have up
>to 64GB. Without that, it's 2GB.
>
>- with kernel 2.6, processes can grow up to any size (physical ram + swap
>is the limit)
>- file sizes on block-oriented devices can be in the terabyte range (32bit)
>
>Hope that helps,
>Cornelius
>
>
>
>
>On Mon, 11 Oct 2004 13:37:06 +0200, Cornelius Werner
><[log in to unmask]> wrote:
>
>> Besides, swap FILES are extremely slow as opposed to true swap
>> PARTITIONS.
>> And multiple swap partitions will be reasonably fast only if placed on
>> different (physical) hard drives (like in a RAID system). Remember to
>> give
>> each swap partition entry in your /etc/fstab the same pri=xx statement.
>>
>> Best regards,
>> Cornelius
>>
>>
>> On Mon, 11 Oct 2004 11:26:30 +0100, Stephen Smith <[log in to unmask]>
>> wrote:
>>
>>> Sure - that all makes sense, thanks. Though note - I was referring not
>>> to
>>> maximum swap size, but there's a separate point, which is that I think
>>> that on some OS's there is a limit to the max size that a single process
>>> can have, which I think may be 2GB on linux - I think there's ways to
>>> change that.
>>>
>>> Cheers.
>>>
>>>
>>>
>>> On Mon, 11 Oct 2004, Denis Brown wrote:
>>>
>>>> For what it's worth...
>>>>
>>>> Bear in mind that you can set up multiple swap partitions or swap files
>>>> (each 2GB in size) and use them.   If I recall reading correctly, up to
>>>> eight partitions/files can be used to give the equivalent of 16GB under
>>>> a
>>>> 2.4 series kernel.   The 2.6 kernel may have expanded that.   I have
>>>> never
>>>> had to set up systems that support more than a single swap partition so
>>>> I
>>>> cannot speak from experience.
>>>>
>>>> Best regards,
>>>> Denis
>>>>
>>>>
>>>> On Mon, 11 Oct 2004, Stephen Smith wrote:
>>>>
>>>> > Hi. This is a very large dataset - you'll need quite a lot more swap
>>>> > probably - try 4GB (though you may have a problem with the 2GB
>>>> process
>>>> > limit on linux if you need more than that - though I think you can
>>>> > change the kernel params to increase that?).
>>>> >
>>>> > Cheers.
>>>> >
>>>> >
>>>> > On Fri, 8 Oct 2004, Axel Thielscher wrote:
>>>> >
>>>> > > Hi - I try to analyze an EP image series created with AFNI using
>>>> the
>>>> > > GLM-module of FSL. I used 3dAFNItoANALYZE provided by AFNI to
>>>> transform the
>>>> > > EP BRIK to an 4D-Analyze-File. The size of this file is either
>>>> around 630 MB
>>>> > > (voxel values stored as integer) or 1.3GB (voxel values stored as
>>>> floating
>>>> > > point) and it contains 1280 volumes of one session.
>>>> > >
>>>> > > The analysis with FEAT doesn't work with either of the two files.
>>>> More
>>>> > > specifically, the command
>>>> > > /usr/local/fsl/bin/film_gls -rn stats -noest filtered_func_data
>>>> design.mat
>>>> > > 11.12 3201
>>>> > > fails and is apparently unable to read to file.
>>>> > >
>>>> > > My computer: Red Hat Linux 9, Intel P-4, 1GB RAM, 2GB swap space
>>>> > >
>>>> > > Does this problem stem from insufficient swap space? The analysis
>>>> with AFNI
>>>> > > works fine, but I would be happy to use the more advanced features
>>>> such as
>>>> > > prewhitening etc. provided by FSL. How much memory do you recommend
>>>> for
>>>> > > input file sizes as quoted above?  Can this failure be caused by a
>>>> different
>>>> > > problem?
>>>> > >
>>>> > > Thanks,
>>>> > > Axel
>>>> > >
>>>> >
>>>> >  Stephen M. Smith  DPhil
>>>> >  Associate Director, FMRIB and Analysis Research Coordinator
>>>> >
>>>> >  Oxford University Centre for Functional MRI of the Brain
>>>> >  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>>>> >  +44 (0) 1865 222726  (fax 222717)
>>>> >
>>>> >  [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve
>>>> >
>>>>
>>>
>>> --
>>>  Stephen M. Smith  DPhil
>>>  Associate Director, FMRIB and Analysis Research Coordinator
>>>
>>>  Oxford University Centre for Functional MRI of the Brain
>>>  John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
>>>  +44 (0) 1865 222726  (fax 222717)
>>>
>>>  [log in to unmask]  http://www.fmrib.ox.ac.uk/~steve
>>>
>>
>>
>>
>> --
>> Cornelius Werner, AiP
>> Institut fuer Medizin (IME)
>> AG Kognitive Neurologie
>> Forschungszentrum Juelich
>> 52425  Juelich
>> Germany
>>
>> Tel. +49-(0)2461-61-8609
>>
>
>
>
>--
>Cornelius Werner
>Institut fuer Medizin (IME)
>AG Kognitive Neurologie
>Forschungszentrum Juelich
>52425  Juelich
>Germany
>
>Tel. +49-(0)2461-61-8609

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