Ok sorry, new to this mailing lark, will post to mailing list :-)
Thanks
________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 21 March 2014 15:56 To: Charnjit Sidhu; Freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] localgi make_outer_surface
Hi Charnjit, that script is Maria's code I think (which is why it is a good idea to post to the list and not to us personally :-) doug
On 03/21/2014 07:28 AM, Charnjit Sidhu wrote:
Hi Doug,
I think the problem is similar to the following post on the mailing lists:
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg29476.html
I think the error "denied: host hostname is no submit host" is being caused when matlab is requested in the make_outer_surface process, if you can tell me where and how matlab is requested in the process I can then add code to run our script that enables matlab to run on our cluster.
Thanks
Charnjit
From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve@nmr.mgh.harvard.edu] Sent: 19 March 2014 15:14 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] (no subject)
Hi, I have not idea what is going wrong. I would try goggling that error msg to see what it means and how it might be fixed
doug
On 03/19/2014 06:32 AM, Charnjit Sidhu wrote:
Dear freesurfers,
This is the first time I am posting so hope the following makes sense, I don't use freesurfer but manage the installation of freesurfer on our cluster.
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
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 changed to the script allowing us to run the above script when matlab is called? Or are we missing something from our script?
I have attached the relevant scripts and output sent to me by the user.
Can you help me.
Thanks
Charnjit
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