Hi Peter, Bruce, and Zeke,
Thank you all for the various input. According to the tutorial Peter posted, the handful of subjects I've done look good. I ran another subject with -openmp 4 flag and it shaved the processing down to <4 hours, so that is a very nice saving! The System Monitor app in Ubuntu indeed lists 8 CPUs so the hyper threading makes Ubuntu "think" it has 8 cores. Given the 32gb of ram I have, I'll try -openmp 8 flag and see how it goes.
Does anyone have some tips on how to setup parallel processing? Is it better to set up, say, 4 participants all with the -openmp 2 flag in 4 separate tcsh sessions in order to saturate the 8 cores and 32gb ram? Or is there a more sophisticated way of doing it that I should consider?
Cheers, Linden
On 18 June 2014 07:27, Z K zkaufman@nmr.mgh.harvard.edu wrote:
Linden,
Its my understanding that that with hyperthreading enabled, you can run a subject for each processor the computer "thinks" it has. For instance, on CentOS (Im not sure the equivalent command on Ubuntu) if I 'cat /proc/cpuinfo' I see 4 processors listed. In this case I would be able to process 4 subjects using the --openmp 4 flag. Though it is sometimes recommended to process n-1 subjects in order to keep one processor available to the user.
Something to keep in mind is the available RAM. We recommend 4gigs of RAM per subject so in the case of 4 subjects, the machine should have 16gig of RAM available. And if you are going to process 8 subjects than you would want 32gigs.
-Zeke
On 06/17/2014 06:50 AM, Linden Parkes wrote:
Hi FSers,
I have an Ubuntu machine (14.04 LTS) with a quad-core i7 4770k/32gb RAM and recon-all is taking me approximately 6 hours per subject without using openmp (haven't tried this yet). According to the terminal, it finishes without errors. I've read (e.g., https://surfer.nmr.mgh.harvard.edu/fswiki/FsQuizAnswers) and heard that recon-all should take 20-24 hours per participant to complete. So, should I be celebrating my 6 hour run time or should I be very suspicious of it?
Also, how does freesurfer go with hyper threaded CPUs? (as is the case with the 4770k; 4 cores, 8 threads). I've read that you should restrict parallel processing to one subject per core. Can I take advantage of the hyper threading and run 8 subjects simultaneously or should I be more conservative and only run 4?
Cheers, Linden
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