Micheal, Im sorry but I sent you conflicting information.
The Centos4 build does NOT have openmp built into it. Our Centos4 builds use gcc version 3.4.6. It wasnt till gcc 4.2 that the gcc compiler implement openmp (v2.5) Our CentOS6 build uses gcc 4.4.7 and does have openmp built into it. Sorry for the confusion. -Zeke On 03/05/2014 10:15 AM, Weiner, Michael wrote: > Thank you for the information, I wasn't sure if the centos4 build had mp > built into it. I will try this and forward the information on to the > researcher to see how their runs can be improved. > > Regards > Michael weiner > > -----Original Message----- > From: Z K [mailto:zkauf...@nmr.mgh.harvard.edu] > Sent: Tuesday, March 04, 2014 1:17 PM > To: Weiner, Michael; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Freesurfer 5.3 and CentOS 5.10 > > Hello Michael, > > Use the Freesurfer Centos4 build for your Centos5 platform. People who > want to take advantage of of multiple cores typically use the "-openmp > <num cores>" flag when running recon-all. Theoretically the more cores > you use the faster the runtime, but we have found that that there is > little gain after 8 and when using that many we typically only see a 25% > decrease in the time it takes to run the entire recon-all stream. > > You could try and get fancy by writing up a script and breaking up the > reson-all stream into parts and parrallelizing some of the processing of > the left and right hemispere... something along the lines of: > > recon-all -s subj -autorecon1 -openmp 8 > recon-all -s subj -autorecon2-volonly -openmp 8 recon-all -s subj > -autorecon2-perhemi -hemi rh -log recon-all-hemi rh.log -notify > rh-done.log -openmp 8 & recon-all -s subj -autorecon2-perhemi -hemi lh > -log recon-all-hemi-lh.log -notify lh-done.log -openmp 8 & while > (rh-done.log AND lh-done.log do not both exist) do > sleep 1 > end loop > recon-all -s subj -autorecon3 -openmp 8 > > > -Zeke > > > > On 03/03/2014 10:21 AM, Weiner, Michael wrote: >> I have recently upgraded our server from v5.0.0 to v5.3.0 running on >> CentOS 5.10 and was a little surprised that there wasnt a version of >> Freesurfer built for this platform but rather 4 and 6. I guess my main > >> question is, was the version for centos4 built with openmpi at all? >> THe server we are running Freesurfer on has 48 cores and we are trying > >> to figure out how to make sure that while running Freesurfer we take >> advantage of all these cores. Is there any documentation that i can >> look at to help me in this endeavor or does anyone have any tips they > can share? >> >> Thank you in advance >> Michael Weiner >> Lead Analyst/UNIX Systems Administrator Lerner Research Institute >> Computing Services Lerner Research Institute Cleveland Clinic >> >> =================================== >> >> Please consider the environment before printing this e-mail >> >> Cleveland Clinic is ranked as one of the top hospitals in America by >> U.S.News & World Report (2013). Visit us online at >> http://www.clevelandclinic.org for a complete listing of our services, > >> staff and locations. 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