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Dear Dr. Greve,

I have 45 subjects as input. SLURM is also a parallel processing pipeline similar to PBS, Grid Engine, or Condor: https://en.wikipedia.org/wiki/Slurm_Workload_Manager I am not sure how can I speed up the mri_glmfit-sim processing.

Thanks !

On Thu, Dec 6, 2018 at 11:07 AM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

I don't know what Slurm is, so I guess the answer is no. If you have multiple processors on your machine, you can use the --bg option. In general, I have not seen it take that long to run. How many input subjects do you have?

On 12/06/2018 12:55 PM, Sahil Bajaj wrote:

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Hello experts,

I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm 1000 1.3 abs --cwp 0.05 --2spaces command, but its taking forever even if I reduce # of permutations from 1000 to 10.

I was just wondering if there’s a version of FreeSurfer for Slurm parallel processing clusters.

Thanks ! Sahil

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Thanks Dr. Greve, actually I was using --bg 2 in my command line. Removing --bg has now speeded up the process.

Thanks again for your help.

Regards, Sahil

On Thu, Dec 6, 2018 at 12:04 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:

I think something is wrong if you only have 45 subjects, it should not take that long. Can you send your mri_glmfit command line and the terminal output of mri_glmfit-sim?

On 12/06/2018 01:14 PM, Sahil Bajaj wrote:

...

    External Email - Use Caution

Dear Dr. Greve,

I have 45 subjects as input. SLURM is also a parallel processing pipeline similar to PBS, Grid Engine, or Condor: https://en.wikipedia.org/wiki/Slurm_Workload_Manager I am not sure how can I speed up the mri_glmfit-sim processing.

Thanks !

On Thu, Dec 6, 2018 at 11:07 AM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:

I don't know what Slurm is, so I guess the answer is no. If you have
multiple processors on your machine, you can use the --bg option. In
general, I have not seen it take that long to run. How many input
subjects do you have?

On 12/06/2018 12:55 PM, Sahil Bajaj wrote:
>
>         External Email - Use Caution
>
> Hello experts,
>
> I was trying to run mri_glmfit-sim --glmdir XY.glmdir --perm
1000 1.3
> abs --cwp 0.05 --2spaces command, but its taking forever even if I
> reduce # of permutations from 1000 to 10.
>
> I was just wondering if there’s a version of FreeSurfer for Slurm
> parallel processing clusters.
>
> Thanks !
> Sahil
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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