Okay. We don't use AFP for a number of reasons even where server and
client are both MacOS. Worst problem, I seem to recall, was that your
client couldn't be used "multiuser" as all the files on a share look
like they belong to the user who initiated the mount! That made it
impossible for this to be used in our cluster environment. All our
clients, incl. Macs, are accessing shares via NFS.
The reason shared libs are soft linked in this fashion is to allow for
multiple versions to coexist, i.e., foo could be using the latest
libBlah while bar can be using one a minor version older for
compatability reasons. This mechanism is not currently used by FSL so
your work-around should be okay for now.
Dave Flitney, IT Manager
University of Oxford, FMRIB Centre
JR Hospital, Oxford OX3 9DU
T: 01865 222713 F: 01865 222717
On 20 Feb 2010, at 05:39, Robert Welsh <[log in to unmask]> wrote:
> Hi Dave,
>
>
> I think it is an interaction between mac os and the nas device. the
> nas
> device is linux based and so the file system is gonna be ext2 (or 3
> due
> to journaling), but the mac's connect to it via afp instead of nfs. i
> think the issue is coming with the afp mount interaction. i see this
> issue if i try to build a softlink explicitly without regard to fsl,
> initially the softlink works but if another mac attaches to the device
> (using the same uid/gid) the softlink fails. i could do a nfs mount i
> guess. this same device model works fine in a pure linux environment
> (i.e. nfs) with softlinks.
>
>
> anyway, i'm going though and making the shared libraries explicit
> copies
> of the specific versions. hopefully that will clear it up.
>
>
> thanks,
>
>
> robert
>
>
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> Robert C. Welsh, PhD
> Research Assistant Professor
> Departments of Radiology and Psychiatry
> University of Michigan
> (734) - 764 - 8541 (fax)
> (734) - 647 - 6781 (Ofc)
> rcwelsh @ med.umich.edu
>>>> Dave Flitney 02/19/10 2:35 PM >>>
> Yes, your storage device needs to be compatible with soft links. That
> said I'm very suprised this isn't working. What filesystem's are you
> using? As far as I can remember only fslview, atlastool and possibly
> some first components are likely to depend on shared libs in this way.
>
> Dave
> Sent using BlackBerry® from Orange
>
> -----Original Message-----
> From: Robert Welsh
> Date: Fri, 19 Feb 2010 13:43:40
> To:
> Subject: [FSL] Issue with installing 4.1.5 on Mac cluster on netgear
> server, problem with soft links.
>
> Hi,
>
>
> I downloaded the lastest - 4.1.5 for Max OS X. I can successfully
> get it
> to run when installed locally to /usr/local/fsl. However, if I drop it
> on a netgear readynas NAS device and do all appropriate
> .bashrc/.bash_profile changes, then executables like fslview fail.
>
>
> Here is my session:
>
>
> bash-3.2$ printenv FSLDIR
> /Volumes/ALS/Software/fsl
> bash-3.2$ fslview
> dyld: Library not loaded:
> @executable_path/../Frameworks/libqt-mt.3.dylib
> Referenced from:
> /Volumes/ALS/Software/fsl/bin/fslview.app/Contents/MacOS/fslview
> Reason: no suitable image found. Did find:
>
> /Volumes/ALS/Software/fsl/bin/fslview.app/Contents/Frameworks/libqt-
> mt.3.dylib:
> unknown file type, first eight bytes: 0x6C 0x69 0x62 0x71 0x74 0x2D
> 0x6D
> 0x74
>
> /Volumes/ALS/Software/fsl/bin/fslview.app/Contents/MacOS/../
> Frameworks/libqt-mt.3.dylib:
> unknown file type, first eight bytes: 0x6C 0x69 0x62 0x71 0x74 0x2D
> 0x6D
> 0x74
>
> /Volumes/ALS/Software/fsl/bin/fslview.app/Contents/MacOS/../
> Frameworks/libqt-mt.3.dylib:
> unknown file type, first eight bytes: 0x6C 0x69 0x62 0x71 0x74 0x2D
> 0x6D
> 0x74
> /Volumes/ALS/Software/fsl/bin/fslview: line 7: 14158 Trace/BPT trap
> ${FSLDIR}/bin/fslview.app/Contents/MacOS/fslview $@
>
>
> I've tracked this down to an interaction between soft links and the
> netgear device. So yes, this is not explicitly the responsibility of
> the
> fsl programming group etc. As a work around I think if I just remove
> the
> softlinks and explicitly rename the dynamic libraries to what is being
> accessed then this should work.
>
>
> Given that, any possibly way to get a list of the soft link commands
> that are processed during the make of the distribution.
>
>
> This was not an issue with version 4.0.x
>
>
> Thanks,
>
>
> Robert Welsh
>
>
>
> -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
> Robert C. Welsh, PhD
> Research Assistant Professor
> Departments of Radiology and Psychiatry
> University of Michigan
> (734) - 764 - 8541 (fax)
> (734) - 647 - 6781 (Ofc)
> rcwelsh @ med.umich.edu
>>>> Reza Salimi 02/19/10 8:13 AM >>>
> Hi Marisa,
> the cluster inference in feat in cluster-based or cluster-size-based
> inference (using the parametric random-field-theory-based test of
> significance).
> Feat does not do a cluster-mass inference, so that you can use
> randomise
> (the other tool in FSL, which is capable of nonparametric tests) in
> case
> you
> need that test.
> There are also new parametric methods for
> cluster-massinference
> that you might like to look at, but unfortunately, they are not
> part of FSL (yet).
> Best, Reza
>
> On Fri, Feb 19, 2010 at 11:39 AM, Marisa Loitfelder <
> [log in to unmask]> wrote:
>
>> Hi,
>>
>> I have a short question concerning Feat/Post-stats:
>> The default setting for analyses is"clusterwise", and I was wandering
>> whether it is
>> "cluster size" or "cluster mass", because I found the difference on
> the
>> homepage.
>> Further, is there a possibility to switch between these two options
>> in
> the
>> GUI?
>>
>> Regards,
>> Marisa
>>
>
>
>
> --
> Reza Salimi-Khorshidi,
> DPhil Candidate, Dept. of Clinical Neurology, University of Oxford
> (Linacre
> College).
> [log in to unmask]
> FMRIB Centre, John Radcliffe Hospital, Oxford OX3 9DU
> Tel: +44 (0) 1865 222466 Fax: +44 (0)1865 222717
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should
> not
> be used for urgent or sensitive issues
>
>
>
>
> **********************************************************
> Electronic Mail is not secure, may not be read every day, and should
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