Hi, Freesufer experts

Sorry for the late reply, I have tried again with openmp 8 flag and added the cpus-per-task=16 for a subject. I have cut the recon-all processing time from 06:17:14 to 03:32:21! So excited.

By the way, Could you help me to understand this command?

export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

From what I understand, if I apply this code for recon-all, this command assigns the total threads of recon-all task = number of the cpu used in the recon-all task? I know a cpu can handle multiples threads, is this mean that only one thread to one cpu for the recon-all task?

Best,
Wei

On Fri, Jan 29, 2021 at 10:53 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

No, all the results are fine. By "broken" I mean that it might crash in
places that it would not have crashed in v6 or that it just would not
have been running in parallel when you think it was.

On 1/28/2021 3:48 PM, Michael Krause wrote:
> External Email - Use Caution
>
> On 1/28/21 6:00 PM, Douglas N. Greve wrote:
>> No, use of -threads or -openmp will always trigger the openmp code. The
>> -parallel may introduce other parallel. I did not write this part of the
>> code so I'm not sure, and I think I might have broken the -parallel
>> implementation when I did the last recon-all rewrite
> Ah, that's good to know. I will remove the redundancy in our scripts then.
>
> What do you mean by "may have broken"? Broken as in we have to worry about
> results? We are currently running a couple of thousand subjects with 7.1.1
> and they appear to be running fine so far *with* -parallel and -openmp 4
> with an average core utilization of around 2.4 out of the possible 4.
>
> cheers
> Michael Krause
>
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