Hi,
I ran 40 process and all finished with
/b/03/netfi01/freesurfer/subjects/rodiguespierinam/scripts/recon-all.log:mri s_volmask.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory
But in /usr/lib there is a libXmu.so.6
My questions are:
1) Anybody know why it failed?
2) If I fix this how can I run recon-all from this point?
Thanks
PPJ
Hi Pedro,
What do you see if you run the following command:
ldd /usr/lib/libXmu.so.6
Once you fix the problem, if you are running FreeSurfer 4, I *think* you can re-run recon-all with the -make flag and it will just do the processing that got missed.
mjp
On Mar 22, 2008, at 9:51 PM, Pedro Paulo Oliveira Jr wrote:
Hi,
I ran 40 process and all finished with
/b/03/netfi01/freesurfer/subjects/rodiguespierinam/scripts/recon- all.log:mris_volmask.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory
But in /usr/lib there is a libXmu.so.6
My questions are:
Anybody know why it failed?If I fix this how can I run recon-all from this point?Thanks
PPJ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Pedro,
You have encountered the achilles heel of freesurfer running on a cluster. clusters often don't have the X-Windows libs (like libXmu) installed, because they dont need them. But mris_volmask is the one binary in the recon-all stream that is built against VTK, and VTK builds against X-Windows (at least on Linux, and our default distribution). I'd like to eliminate this dependency, but haven't had the time.
You have three options:
1) copy the necessary X libs to your cluster (run ldd mris_volmask.bin to see them).
2) or use the -nocortribbon flag to skip that step (no downstream steps depend on the ?h.ribbon.mgz files)
3) or build freesurfer from source, based on a VTK which is built without an X Windows dependency.
Nick
On Sat, 2008-03-22 at 22:51 -0300, Pedro Paulo Oliveira Jr wrote:
Hi,
I ran 40 process and all finished with
/b/03/netfi01/freesurfer/subjects/rodiguespierinam/scripts/recon- all.log:mris_volmask.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory
But in /usr/lib there is a libXmu.so.6
My questions are:
Anybody know why it failed?If I fix this how can I run recon-all from this point?Thanks
PPJ
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Nick,
Thanks for the hint. I already solved the problem.
We are testing a Cluster-on demand, pay-per-hour-used service in US and seems pretty good. I ran 100 recon-all in 33 hours!!!
When I finish my tests I'll send a message to the list indicating this service.
PPJ
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: segunda-feira, 24 de março de 2008 12:53 To: Pedro Paulo Oliveira Jr Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] libXmu error on cluster
Pedro,
You have encountered the achilles heel of freesurfer running on a cluster. clusters often don't have the X-Windows libs (like libXmu) installed, because they dont need them. But mris_volmask is the one binary in the recon-all stream that is built against VTK, and VTK builds against X-Windows (at least on Linux, and our default distribution). I'd like to eliminate this dependency, but haven't had the time.
You have three options:
1) copy the necessary X libs to your cluster (run ldd mris_volmask.bin to see them).
2) or use the -nocortribbon flag to skip that step (no downstream steps depend on the ?h.ribbon.mgz files)
3) or build freesurfer from source, based on a VTK which is built without an X Windows dependency.
Nick
On Sat, 2008-03-22 at 22:51 -0300, Pedro Paulo Oliveira Jr wrote:
Hi,
I ran 40 process and all finished with
/b/03/netfi01/freesurfer/subjects/rodiguespierinam/scripts/recon- all.log:mris_volmask.bin: error while loading shared libraries: libXmu.so.6: cannot open shared object file: No such file or directory
But in /usr/lib there is a libXmu.so.6
My questions are:
Anybody know why it failed?If I fix this how can I run recon-all from this point?Thanks
PPJ
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Mark J. Pearrow -
Nick Schmansky -
Pedro Paulo Oliveira Jr