Re: [Freesurfer] Setting -openmp flag to more than 8

2017-05-02 Thread Douglas Greve
You should also know that the memory management during openmp mri_em_register execution is not optimal (as found by the HCP group. If you are oversubscribing your processors (ie, have 20 cpus, but run 3 jobs each with 8 cpus), then mri_em_register will slow way down. This appears to be due to s

Re: [Freesurfer] Setting -openmp flag to more than 8

2017-05-02 Thread Chris Gorgolewski
Thank you - this is very useful! On Tue, May 2, 2017 at 12:05 PM, Bruce Fischl wrote: > Hi Chris > > we have found an almost linear speed improvement up to 4, then it starts > to fall off, with not much at all after 8. > > cheers > Bruce > > On Tue, 2 May 2017, Chris Gorgolewski wrote: > > Hi, >

Re: [Freesurfer] Setting -openmp flag to more than 8

2017-05-02 Thread Bruce Fischl
Hi Chris we have found an almost linear speed improvement up to 4, then it starts to fall off, with not much at all after 8. cheers Bruce On Tue, 2 May 2017, Chris Gorgolewski wrote: Hi, We are running freesurfer as part of a bigger pipelines with other steps that can be performed in paral