> On 3 Sep 2015, at 10:10, mohamad reza khodaei <[log in to unmask]> wrote:
>
> I used the qstat command to check bedpost state:
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
>
> [m.khodaei@cluster bio]$ qstat -u m.khodaei
>
>
> job-ID prior name user state submit/start at queue slots ja-task-ID
> -----------------------------------------------------------------------------------------------------------------
> 89 0.55500 bpx_prepro m.khodaei qw 09/02/2015 03:43:45 1
> 90 0.00000 bedpostx m.khodaei hqw 09/02/2015 03:43:47 1 1-145:1
> 91 0.00000 bpx_postpr m.khodaei hqw 09/02/2015 03:43:47 1
>
> -------------------------------------------------------------------------------------------------------------------------------------------------
> qw (job is waiting in the queue)
Try "qstat -j 89" to see if it can tell you the specific issue with this job.
>
> Any idea?
>
> Best regards
>
> On Wed, Sep 2, 2015 at 12:16 AM, mohamad reza khodaei <[log in to unmask]> wrote:
> Thank you so much, i really appreciate it, the error is fixed, it seems like i am getting somewhere...
>
> There is one major problem. After running bedpostx on my data, every thing looks fine and there is no error:
>
> _______________________________________
>
> [m.khodaei@cluster bio]$ bedpostx dti -c
>
> subjectdir is /home/m.khodaei/bio/dti
> Making bedpostx directory structure
> Queuing preprocessing stages
> Queuing parallel processing stage
> Queuing post processing stage
>
> Type /home/m.khodaei/bio/dti.bedpostX/monitor to show progress.
> Type /home/m.khodaei/bio/dti.bedpostX/cancel to terminate all the queued tasks.
>
> You will get an email at the end of the post-processing stage.
> _________________________________________
>
> but there isn't any progress in bedpost operation,and the dti.bedpostX folders remain empty
>
> any idea?
>
>
> Best regards
>
>
>
>
> On Tue, Sep 1, 2015 at 1:10 PM, paul mccarthy <[log in to unmask]> wrote:
> Hi Khodaei,
>
> Try running bedpostx with the '-c' option.
>
> Cheers,
>
> Paul
>
> On 30 August 2015 at 11:09, mohamad reza khodaei <[log in to unmask]> wrote:
> Thanks for your response,i really appreciate it.
>
> I edited the fsl_sub file and the short.q and long.q errors are fixed.
> but ''No cluster queue or queue instance matches the phrase "cuda.q" '' error still exists.
>
> Any idea?
>
> Best regards
>
> On Mon, Aug 24, 2015 at 12:47 PM, paul mccarthy <[log in to unmask]> wrote:
> Hi Khodaei,
>
> You need to edit 'fsl_sub' to customise it for your local system. This file is well commented, so it should be fairly straightforward.
>
> Cheers,
>
> Paul
>
> On 22 August 2015 at 11:21, mohamad reza khodaei <[log in to unmask]> wrote:
> Dear fsl experts
>
>
> I have installed fsl on my computing cluster, but when i run bepostx, i face the following errors:
>
> [m.khodaei@cluster bio]$ bedpostx dti
>
>
> No cluster queue or queue instance matches the phrase "cuda.q"
> subjectdir is /home/m.khodaei/bio/dti
> Making bedpostx directory structure
> Queuing preprocessing stages
> Unable to run job: Job was rejected because job requests unknown queue "short.q".
> Exiting.
> Queuing parallel processing stage
> Unable to run job: Job was rejected because job requests unknown queue "long.q".
> Exiting.
> Queuing post processing stage
>
> Type /home/m.khodaei/bio/dti.bedpostX/monitor to show progress.
> Type /home/m.khodaei/bio/dti.bedpostX/cancel to terminate all the queued tasks.
>
> You will get an email at the end of the post-processing stage.
> -------------------------------------------------------------------
>
> I really appreciate any help you can provide.
>
>
> Best regards,
> Khodaei
>
>
> --
> Mohammad Reza Khodaei
> M.Sc. student of Biomedical Engineering,
> School of medicine,
> Shahid Beheshti university,
> Tehran, Iran
>
>
>
>
>
> --
> Mohammad Reza Khodaei
> M.Sc. student of Biomedical Engineering,
> School of medicine,
> Shahid Beheshti university,
> Tehran, Iran
>
>
>
>
>
> --
> Mohammad Reza Khodaei
> M.Sc. student of Biomedical Engineering,
> School of medicine,
> Shahid Beheshti university,
> Tehran, Iran
>
>
>
>
> --
> Mohammad Reza Khodaei
> M.Sc. student of Biomedical Engineering,
> School of medicine,
> Shahid Beheshti university,
> Tehran, Iran
>
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