Re: [Condor-users] Using Freesurfer with Condor

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

Bo,

First let me say that while I was involved in getting Freesurfer to run on condor, I was far from being the primary developer and as such don't know the exact details. 

What I do know is that it is not as simple as a single condor file. We have a 2000 line shell script that is responsible for the steps necessary in the analysis which generates a condor DAG and then submits the DAG to condor for processing.

As it stands there are a lot of assumptions in the main script that make it relatively site specific as well as specific to the way that we have configured condor (in a very trusting manner because we directly manage all of the systems).

If you are still interested please email me directly and I?ll see if the main developer of the script would have any time to discuss it with you.

Ben
ben-rogers*_at_*uiowa.edu



-----Original Message-----
From: condor-users-bounces@xxxxxxxxxxx on behalf of Shi, Bo
Sent: Mon 12/18/2006 3:08 PM
To: Condor-Users Mail List
Subject: Re: [Condor-users] Using Freesurfer with Condor
 
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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