If you are compiling with clang openmp might not work. Peace,
Matt. On 5/2/14, 2:13 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Lukas > >sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going >on? >Does OpenMP have to be enabled somehow? > >Bruce > > >On Fri, 2 May 2014, >lukas.sch...@ukb.uni-bonn.de wrote: > >> Hi Bruce! >> >> I just run: recon-all -s ernie2 -autorecon2 -openmp 4 >> >> mri_ca_register uses 100.9% CPU at most ... >> >> Any idea? Should I try to recompile FS for the current MacOS release? >>If >> so, do I have to take care on special librariwa in order to enable the >> openmp option? >> >> Best wishes, >> >> Lukas >> >> >Hi Bruce! >> > >> >Thanks for the fast response. I used the current stable version 5.3.0.1 >> >(freesurfer-Darwin-lion-stable-pub-v5.3.0.1). >> >So I will try as you have suggested ... >> > >> >Best wishes, >> > >> >Lukas >> >> >> Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 >> >> >> >> Hi Luke >> >> >> >> what version of FS are you running? We see significant speedups. Try >> >> running top in a unix terminal and seeing if the cpu usage of >> >> mri_ca_register (during autorecon2, the longest single step) is >>morethan >> >>100% >> >> >> >> cheers >> >> Bruce >> >> >> >> On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: >> >> >> >> >> >> > Hi folks! >> > > > >> >> > I try to use -openmp option on an iMAC with 4 cores. >>Unfortunately, I >> > >>do not >> >> > see any accelartion when processing a single data set with or >>without >> > >>the >> >> > flag -openmp flag set. >> >> > >> >> > recon-all -s ernie_1 -all >> >> > >> >> > leads to ~6,4h processing time. >> >> > >> >> > Unfortunately >> >> > recon-all -s ernie_2 -all -openmp 4 >> >> > >> >> > did not change anything. Do I miss anything? Do I have to prepare >>my >> > >>system >> >> > in a special way? Or run any scripts in advance? >> >> > >> >> > (System: iMac, 32GbRam,Intel i5, 4 cores, Mac Os 10.9, latest FS >> >> >version) >> >> > >> >> > Best wishes, >> >> > >> >> > Luke >> >> >> >> >>_______________________________________________ >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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
