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. Confidentiality Note: This message is intended for > use only by the individual or entity to which it is addressed and may > contain information that is privileged, confidential, and exempt from > disclosure under applicable law. If the reader of this message is not > the intended recipient or the employee or agent responsible for > delivering the message to the intended recipient, you are hereby > notified that any dissemination, distribution or copying of this > communication is strictly prohibited. If you have received this > communication in error, please contact the sender immediately and > destroy the material in its entirety, whether electronic or hard copy. > Thank you. > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
