Re: [Freesurfer] launchpad help
Hi Chindhuri remove the "-l nodes=1:opteron" from your command line. Also, you probably want to send emails like this to h...@nmr.mgh.harvard.edu in the future, as they are Martinos-specific. cheers Bruce On Wed, 22 Jun 2011, Chindhuri Selvadurai wrote: > > > I thought the default was p10, so I just used that to try again, however > I'm still getting that error with no extra info in the log. what is the > name of the queue, maybe that is my problem: > > command: > > pbsubmit -q p10 -l nodes=1:opteron -m chinsel -c 'recon-all -s RMAUT021 > -all -i > /cluster/archive/292/siemens/TrioTim-35006-20110508-105030-353000/353000-04-01.dcm > -mail chin...@nmr.mgh.harvard.edu -force' > > output: > > Opening pbsjob_4 > qsub -V -S /bin/sh -m abe -M chinsel -q p10 -l nodes=1:opteron -r n > /pbs/chinsel/pbsjob_4 > qsub: Job exceeds queue resource limits MSG=cannot locate feasible nodes > FATAL: qsub call failed. Check above for error messages. > [1] + Done gedit pbsjob_3 > > > >> What exact website page are you using for help on launchpad? launchpad > has no >> opteron nodes so you should not be specifying that resource. Its queue > names >> are also different than seychelles. There is no sergeant queue. Read: >>https://www.nmr.mgh.harvard.edu/martinos/itgroup/launchpad.html >> On Tue, 21 Jun 2011, Chindhuri Selvadurai wrote: >>> Hello, >>> I am trying to do recon-all using launchpad, and I am not sure how to > fix >>> the error I am getting. I checked IT's launchpad help website, but > can't seem to figure it out. >>> Using fs v4 >>> subjects_dir: /space/ventzl/36/users/RespMon12C/subjects >>> command: pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c >>> 'recon-all >>> -s RMAUT021 -all -i >>> /cluster/archive/292/siemens/TrioTim-35006-20110508-105030-353000/353000-04-01.dcm > -mail chin...@nmr.mgh.harvard.edu -force' >>> This is the output I'm getting: >>> Opening pbsjob_3 >>> qsub -V -S /bin/sh -m abe -M chinsel -q sergeant -l nodes=1:opteron > -r n >>> /pbs/chinsel/pbsjob_3 >>> qsub: Unknown queue MSG=cannot locate queue >>> FATAL: qsub call failed. Check above for error messages. >>> I'm also not getting any e-mails. Is there a way to check an error log > like on seychelles? >>> 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 >> --- >> Paul Rainesemail: raines at nmr.mgh.harvard.edu >> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging >> 149 (2301) 13th Street Charlestown, MA 02129 USA > > > Best, > > Chindhuri Selvadurai > > Psychiatric Neuroimaging, Manoach Lab > Martinos Center for Biomedical Imaging, MGH > Phone: (617)726-0307 > > > > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] launchpad help
I thought the default was p10, so I just used that to try again, however I'm still getting that error with no extra info in the log. what is the name of the queue, maybe that is my problem: command: pbsubmit -q p10 -l nodes=1:opteron -m chinsel -c 'recon-all -s RMAUT021 -all -i /cluster/archive/292/siemens/TrioTim-35006-20110508-105030-353000/353000-04-01.dcm -mail chin...@nmr.mgh.harvard.edu -force' output: Opening pbsjob_4 qsub -V -S /bin/sh -m abe -M chinsel -q p10 -l nodes=1:opteron -r n /pbs/chinsel/pbsjob_4 qsub: Job exceeds queue resource limits MSG=cannot locate feasible nodes FATAL: qsub call failed. Check above for error messages. [1] + Done gedit pbsjob_3 > What exact website page are you using for help on launchpad? launchpad has no > opteron nodes so you should not be specifying that resource. Its queue names > are also different than seychelles. There is no sergeant queue. Read: >https://www.nmr.mgh.harvard.edu/martinos/itgroup/launchpad.html > On Tue, 21 Jun 2011, Chindhuri Selvadurai wrote: >> Hello, >> I am trying to do recon-all using launchpad, and I am not sure how to fix >> the error I am getting. I checked IT's launchpad help website, but can't seem to figure it out. >> Using fs v4 >> subjects_dir: /space/ventzl/36/users/RespMon12C/subjects >> command: pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c >> 'recon-all >> -s RMAUT021 -all -i >> /cluster/archive/292/siemens/TrioTim-35006-20110508-105030-353000/353000-04-01.dcm -mail chin...@nmr.mgh.harvard.edu -force' >> This is the output I'm getting: >> Opening pbsjob_3 >> qsub -V -S /bin/sh -m abe -M chinsel -q sergeant -l nodes=1:opteron -r n >> /pbs/chinsel/pbsjob_3 >> qsub: Unknown queue MSG=cannot locate queue >> FATAL: qsub call failed. Check above for error messages. >> I'm also not getting any e-mails. Is there a way to check an error log like on seychelles? >> 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 > --- > Paul Rainesemail: raines at nmr.mgh.harvard.edu > MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging > 149 (2301) 13th Street Charlestown, MA 02129 USA Best, Chindhuri Selvadurai Psychiatric Neuroimaging, Manoach Lab Martinos Center for Biomedical Imaging, MGH Phone: (617)726-0307 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 The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] launchpad help
What exact website page are you using for help on launchpad? launchpad has no opteron nodes so you should not be specifying that resource. Its queue names are also different than seychelles. There is no sergeant queue. Read: https://www.nmr.mgh.harvard.edu/martinos/itgroup/launchpad.html On Tue, 21 Jun 2011, Chindhuri Selvadurai wrote: > Hello, > > I am trying to do recon-all using launchpad, and I am not sure how to fix > the error I am getting. I checked IT's launchpad help website, but can't > seem to figure it out. > > Using fs v4 > subjects_dir: /space/ventzl/36/users/RespMon12C/subjects > > command: pbsubmit -q sergeant -l nodes=1:opteron -m chinsel -c 'recon-all > -s RMAUT021 -all -i > /cluster/archive/292/siemens/TrioTim-35006-20110508-105030-353000/353000-04-01.dcm > -mail chin...@nmr.mgh.harvard.edu -force' > > This is the output I'm getting: > > Opening pbsjob_3 > qsub -V -S /bin/sh -m abe -M chinsel -q sergeant -l nodes=1:opteron -r n > /pbs/chinsel/pbsjob_3 > qsub: Unknown queue MSG=cannot locate queue > FATAL: qsub call failed. Check above for error messages. > > I'm also not getting any e-mails. Is there a way to check an error log > like on seychelles? > > 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 > > > --- Paul Rainesemail: raines at nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street Charlestown, MA 02129USA ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
