Re: [Condor-users] Using Freesurfer with Condor

["Rogers, Benjamin P" <ben-rogers@xxxxxxxxx>]

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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