Hello,
I am not able to do a regular recon-all of my data on seychelles-- I am doing the same thing I used to do. We have started moving our data to a different location, however, since this is all new data, I don't see how this could be the problem.
I am using freesurfer 4, so I set this var before sourcing the script:
setenv USE_STABLE_4_5_0 source /usr/local/freesurfer/stable4
My subjects_dir is /space/ventzl/36/users/RespMon12C/subjects And my command is what it has always been:
/usr/bin/pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all
-s RMOCD025 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110504-155020-764000/764000-000004-000001.dcm -mail chinsel@nmr.mgh.harvard.edu -force'
I would appreciate your help!
Thank you, Chindhuri S
---------------------------- Original Message ---------------------------- Subject: PBS JOB 1380351.seychelles.nmr.mgh.harvard.edu From: "adm" adm@nmr.mgh.harvard.edu Date: Thu, June 2, 2011 2:03 pm To: chinsel@nmr.mgh.harvard.edu --------------------------------------------------------------------------
PBS Job Id: 1380351.seychelles.nmr.mgh.harvard.edu Job Name: pbsjob_14 Execution terminated Exit_status=1 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:01
Best,
Chindhuri Selvadurai
Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307
Hi Chindhuri,
we'll need to know what the error was that resulted in the non-zero exit status.
cheers Bruce On Thu, 2 Jun 2011, Chindhuri Selvadurai wrote:
Hello,
I am not able to do a regular recon-all of my data on seychelles-- I am doing the same thing I used to do. We have started moving our data to a different location, however, since this is all new data, I don't see how this could be the problem.
I am using freesurfer 4, so I set this var before sourcing the script:
setenv USE_STABLE_4_5_0 source /usr/local/freesurfer/stable4
My subjects_dir is /space/ventzl/36/users/RespMon12C/subjects And my command is what it has always been:
/usr/bin/pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all
-s RMOCD025 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110504-155020-764000/764000-000004-000001.dcm -mail chinsel@nmr.mgh.harvard.edu -force'
I would appreciate your help!
Thank you, Chindhuri S
---------------------------- Original Message ---------------------------- Subject: PBS JOB 1380351.seychelles.nmr.mgh.harvard.edu From: "adm" adm@nmr.mgh.harvard.edu Date: Thu, June 2, 2011 2:03 pm To: chinsel@nmr.mgh.harvard.edu
PBS Job Id: 1380351.seychelles.nmr.mgh.harvard.edu Job Name: pbsjob_14 Execution terminated Exit_status=1 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:01
Best,
Chindhuri Selvadurai
Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I'm not sure how to get that information. It does not give me an error message in the terminal. Is there a log I could look at? Is there anything that I need to do prior to the recon-all?
Hi Chindhuri,
we'll need to know what the error was that resulted in the non-zero exit status.
cheers Bruce On Thu, 2 Jun 2011, Chindhuri Selvadurai wrote:
Hello,
I am not able to do a regular recon-all of my data on seychelles-- I am doing the same thing I used to do. We have started moving our data to a different location, however, since this is all new data, I don't see how this could be the problem.
I am using freesurfer 4, so I set this var before sourcing the script:
setenv USE_STABLE_4_5_0 source /usr/local/freesurfer/stable4
My subjects_dir is /space/ventzl/36/users/RespMon12C/subjects And my command is what it has always been:
/usr/bin/pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all
-s RMOCD025 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110504-155020-764000/764000-000004-000001.dcm -mail chinsel@nmr.mgh.harvard.edu -force'
I would appreciate your help!
Thank you, Chindhuri S
---------------------------- Original Message
Subject: PBS JOB 1380351.seychelles.nmr.mgh.harvard.edu From: "adm" adm@nmr.mgh.harvard.edu Date: Thu, June 2, 2011 2:03 pm To: chinsel@nmr.mgh.harvard.edu
PBS Job Id: 1380351.seychelles.nmr.mgh.harvard.edu Job Name: pbsjob_14 Execution terminated Exit_status=1 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:01
Best,
Chindhuri Selvadurai
Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Best,
Chindhuri Selvadurai
Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307
http://www.nmr.mgh.harvard.edu/martinos/itgroup/seychelles.html
describes the cluster use. It will tell you how to check errors (there are pbsjob files in your folder that contain output and error messages.
Best, Martin
On Thu, 2011-06-02 at 14:54 -0400, Chindhuri Selvadurai wrote:
I'm not sure how to get that information. It does not give me an error message in the terminal. Is there a log I could look at? Is there anything that I need to do prior to the recon-all?
Hi Chindhuri,
we'll need to know what the error was that resulted in the non-zero exit status.
cheers Bruce On Thu, 2 Jun 2011, Chindhuri Selvadurai wrote:
Hello,
I am not able to do a regular recon-all of my data on seychelles-- I am doing the same thing I used to do. We have started moving our data to a different location, however, since this is all new data, I don't see how this could be the problem.
I am using freesurfer 4, so I set this var before sourcing the script:
setenv USE_STABLE_4_5_0 source /usr/local/freesurfer/stable4
My subjects_dir is /space/ventzl/36/users/RespMon12C/subjects And my command is what it has always been:
/usr/bin/pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all
-s RMOCD025 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110504-155020-764000/764000-000004-000001.dcm -mail chinsel@nmr.mgh.harvard.edu -force'
I would appreciate your help!
Thank you, Chindhuri S
---------------------------- Original Message
Subject: PBS JOB 1380351.seychelles.nmr.mgh.harvard.edu From: "adm" adm@nmr.mgh.harvard.edu Date: Thu, June 2, 2011 2:03 pm To: chinsel@nmr.mgh.harvard.edu
PBS Job Id: 1380351.seychelles.nmr.mgh.harvard.edu Job Name: pbsjob_14 Execution terminated Exit_status=1 resources_used.cput=00:00:00 resources_used.mem=0kb resources_used.vmem=0kb resources_used.walltime=00:00:01
Best,
Chindhuri Selvadurai
Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Best,
Chindhuri Selvadurai
Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Chindhuri Selvadurai -
Martin Reuter