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Subject:

Re: ?Problems with swap space?

From:

Vince Calhoun <[log in to unmask]>

Reply-To:

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

Date:

Fri, 15 Oct 2004 09:00:59 -0400

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (298 lines)

Hi,
        XP definitely has a 2GB process limit (although this can, on some
machines, be raised to 3GB...but be careful).  See, e.g.
http://support.microsoft.com/default.aspx?scid=kb;en-us;328269.

Cheers,

VDC

> -----Original Message-----
> From: FSL - FMRIB's Software Library
> [mailto:[log in to unmask]] On Behalf Of Stephen Smith
> Sent: Friday, October 15, 2004 8:29 AM
> To: [log in to unmask]
> Subject: Re: [FSL] ?Problems with swap space?
>
> Also - did you look into the 2GB process limit - is that
> applying on your
> linux machine? XP is almost certainly worse....
>
> Cheers.
>
>
>
> On Fri, 15 Oct 2004, Christian F. Beckmann wrote:
>
> > Hi
> >
> > there is no limitation build into FSL - are you sure that you don't
> > have NANs or something similar stored in the file?
> > Can you please send us the output from fslerrorreport (a new script
> > which compiles plenty of information about the machine and
> your setup).
> > Also, if you send us a link for downloading an example file
> we can have
> > a look at it in detail.
> > cheers
> > christian
> >
> >
> >
> > On 15 Oct 2004, at 00:08, Axel Thielscher wrote:
> >
> > > 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
> > >
> > >
> > --
> >   Christian F. Beckmann
> >   Oxford University Centre for Functional
> >   Magnetic Resonance Imaging of the Brain,
> >   John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
> >   Email: [log in to unmask] -
> http://www.fmrib.ox.ac.uk/~beckmann/
> >   Phone: +44(0)1865 222782 Fax: +44(0)1865 222717
> >
>
> --
>  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
>

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