We just solved the same problem by upgrading the driver of video card on the cluster.  An early massage in the freesurfer archive gives more details.

 

Xin 

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From: Siddharth Srivastava [mailto:siddys@gmail.com]
Sent: Wed 11/19/2008 1:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tksurfer display problems

Hi mjp,
           Thanks for an account of a working solution to the problem. I just wanted to
know if this intervention has to done on the client machine (from where i am
viewing the results), or on the server side (on which i am processing the data)? Further,
in case of a 64 bit machine, would the source and the destination directories change
accordingly?
best regards,
sid.

On Wed, Nov 19, 2008 at 8:50 AM, Mark J. Pearrow <mjp@mit.edu> wrote:

Hi all,

This is a bug that has baffled me for almost a year now, so today I decided to just attend to it exclusively. I have never understood why, exactly, the anecdotal and illogical fix for the sliver-of-the-brain issue seems to be to install an NVidia graphics card in the afflicted server.

I found this posting:
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007558.html

Which seemed to indicate that it was not the card itself that made the difference, but rather some software component that made things work. There is an extension to X11, called GLX, which allows the remote side (the "client", in X11 speak) to bypass the processing of OpenGL commands and to send them to the server.

So, following the advice in the posting above, I downloaded the latest NVidia.run package and unpacked it by using the "-x" flag - then I copied all of the usr/lib/ and usr/lib32/ difrectories in the (freshly unpacked) NVIDIA-linux directory into /usr/lib and /usr/lib32, respectively. Then I ran "ldconfig -v" to update the ld cache.

And voila, I can run tksurfer over X11, VNC and NX now on a server that has no NVidia card, without any problems.

I still don't understand what exactly is being provided by NVidia's version of the libraries, but I suspect it has to do with "TLS" (in the context of OpenGL, not in the crypto sense). This appeared in the output of `ldd tksurfer.bin` on my systems with nvidia cards, and on my previously-broken system after I installed those files:

libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1

mjp

On Nov 18, 2008, at 9:35 PM, Bruce Fischl wrote:

Hi Sid,

this is a known problem. It actually used to work and we broke it. The current workaround is to use VNC.

cheers,
Bruce


On Tue, 18 Nov 2008, Siddharth Srivastava wrote:

Hi !
  I am a relatively new user of freesurfer, and currently i have 2
instances
of the same -stable 64bit Linux versions installed, one on my local machine,
and the
other on a cluster, accessible over the network. I have been able to get
freesurfer
running without any problems on my local machine, but after i installed the
same version on the remote machine, the tksurfer window did not display
what i expectd to see, but only a small part of the data (%tksurfer bert lh
inflated).
This small patch responds to all commands from the GIU, but that is all
that i see.
  I have trawled through the archives, both old and new, and there have
been
references to similar problems, without any definitive way to solve it. What
exact
aspect of the system configuration has to be examined/re-worked to solve it?
Does anyone have any experience with this kind of problem?
  with regards,
  sid.

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