Hi Charnjit,
I'm sorry I can't really help you on that, I'm not really familiar with matlab installation on a cluster. And given that lGI calls matlab repeatedly, if you want to split the process you may have to do it at several stages. But maybe someone else has an idea for the cluster and can jump in the discussion?
Sorry not to be of more help,
Marie
On Apr 2, 2014, at 1:58 PM, Charnjit Sidhu c.sidhu@bham.ac.uk wrote:
Hi Maria,
The following are details of the problems we are having which I posted earlier:
We have a user who is trying run a script that submits a recon-all job to our cluster using the -localGI flag:
recon-all -subjid $i -localGI
I know this requires matlab which we have installed on the cluster however we cannot submit matlab within a working node which the submitted node is trying to do, we get the following error:
denied: host "hostname" is no submit host
I know what is causing the error, I just don't know how to fix it, as Matlab cannot be run directly on this computer.
this message is given when the make_outer_surface script matlab script is submitted within the submitted job.
We have a script that allows matlab to run from within the cluster and have tried to add this as an environment variable to the script:
matlab=matlab_cluster ; export matlab source $matlab
But when we add this it still fails with the same error,
Do you know how I can make changes to the script allowing us to run the above script when matlab is called? Or are we missing something from our script? Or should we split the process into a further script?
I have attached the relevant scripts and output.
Can you help me.
Thanks
Charnjit
From: Marie Schaer [Marie.Schaer@unige.ch] Sent: 02 April 2014 12:45 To: Freesurfer support list Cc: Charnjit Sidhu Subject: Re: [Freesurfer] localgi make_outer_circle
Hi Charnjit,
Can you copy / paste the error message? Otherwise I can't help you.
Best,
Marie
On Apr 2, 2014, at 12:54 PM, Charnjit Sidhu c.sidhu@bham.ac.uk wrote:
Hi,
Does anyone know how matlab is called in the localgi process.
My script fails during the make_outer_circle process, I need to export some variables before Matlab is called to enable it to work on our cluster (i.e different matlab path, userid) . How can I change the way matlab is called?
Thanks
Charnjit
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