Yeah, it works. I am able to see the load on multi cores. Regards, Krishnaprasad
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Bruce Fischl Sent: Montag, 12. Januar 2015 14:51 To: Freesurfer support list Subject: Re: [Freesurfer] Openmp option does not work in Ubuntu 12.04 yes, in 5.3 there is only openmp support in a couple of binaries. Those stages are reached maybe 15 minutes into recon-all depending on your hardware. cheers Bruce On Mon, 12 Jan 2015, Narayanan, Krishnaprasad wrote: > Hi Bruce, > > Thanks for your reply. May be I should not have said it is not working. Sorry > for that. > > The command that I used was "recon-all -i > /usr/local/freesurfer/subjects/bert/mri/T1.mgz -subjid exampledata1 -all > -openmp 8". > Yeah, I observed the core usage using htop until the end of first minute. > Until the end of first minute, I saw the CPU utilization only on one of the > core and not on all the specified cores. > > I guess I have found the mistake. The multi core option is enabled only > during the mri_em_register_stage and mri_ca_register stage. > > Can I know approximately at what point in time are these two stages reached? > > Regards, > Krishnaprasad > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Bruce > Fischl > Sent: Montag, 12. Januar 2015 14:30 > To: Freesurfer support list > Subject: Re: [Freesurfer] Openmp option does not work in Ubuntu 12.04 > > Hi Krishnaprasad > > what is your full recon-all command line? And how do you know it isn't > working? Have you tried running "top" during the mri_ca_register stage? > The upcoming (one of these months!) release will have much more in the > way of openmp optimization > > cheers > Bruce > > > On Mon, 12 Jan 2015, Narayanan, Krishnaprasad > wrote: > >> >> Hallo all, >> >> >> >> I have installed freesurfer v5.3 on Ubuntu 12.04 LTS. The GCC version >> is 4.6. I use the recon-all using –all and -openmp option. I observed >> that openmp does not seem to have any effect in the execution of >> freesurfer. I verified the installation of openmp using dpkg --status >> libgomp1 and found that the package was installed. >> >> >> >> Do I have to install or enable any additional library or flags? Can >> I kindly get help from the forum to resolve this problem? >> >> >> >> Best regards, >> >> Krishnaprasad >> >> >> > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list [email protected] 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.
