Re: [Condor-users] Using Freesurfer with Condor

["Shi, Bo" <bo.shi@xxxxxxxxxxxxxxxxxxxxx>]

Hi Ben,

That's great to hear;  do you have a sample .condor file that I might
look at?


Bo


On Mon, Dec 18, 2006 at 02:59:29PM -0600, Rogers, Benjamin P wrote:
> Hello Bo,
> 
> Condor does work for running Freesurfer jobs. We have run several
> thousand jobs and are using our condor pool regularly for this. That
> said we do not allow condor to transfer the job files. Instead we are
> using NFS as our data storage mechanism.
> 
> Our set up is Red Hat Enterprise Linux 4 with OpenLDAP authentication
> and all of the systems mounting NFS.
> 
> If your systems are homogenously configured you should be able to get
> this to work. If they are heterogeneous it may be more difficult.
> 
> Ben Rogers
> Systems Administrator
> Dept. of Psychiatry
> University of Iowa
> 
> 
> -----Original Message-----
> From: condor-users-bounces@xxxxxxxxxxx
> [mailto:condor-users-bounces@xxxxxxxxxxx] On Behalf Of Shi, Bo
> Sent: Monday, December 18, 2006 2:15 PM
> To: condor-users@xxxxxxxxxxx
> Subject: [Condor-users] Using Freesurfer with Condor
> 
> Hi All - 
> 
> I'm exploring the possibility of using Condor to manage Freesurfer
> (https://surfer.nmr.mgh.harvard.edu/fswiki) processes.  Installation of
> Condor went smoothly on a RHEL4 system, but I've come across a possible
> issue with how Freesurfer handles data files.
> 
> Freesurfer processes data located in a subject directory (2 levels deep)
> 
> In section 2.5.4.4,
> > Therefore, the executing program must access input files without
> paths.
> > Because all transferred files are placed into a single, flat
> directory,
> > input files must be uniquely named to avoid collision when
> transferred.
> > A collision causes the last file in the list to overwrite the earlier
> > one.
> 
> Can Condor handle such a usage case?  Can I specify a whole directory as
> program input?
> 
> Or even better, has anyone every used Freesurfer with Condor?
> 
> 
> Thanks,
> Bo
> 
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