Some additional notes: OpenMP isn't something that needs to be "enabled" on a system, it is compiled into the executables.
Given that you mention 32 cores, a warning about multi-socket systems: OpenMP doesn't detect multi-socket systems, and may naively run on all cores - this is a problem because memory access across sockets is notably slower than access to memory attached to the same socket the thread is running on, and becomes a bottleneck, and can make the operation take longer than on a single-socket system. You can use the environment variable OMP_NUM_THREADS to set a maximum number of threads for OpenMP executables to use, but in order for the threads to end up on a single socket and not hit this issue, you may need to do some additional configuration at the OS level (or the OS might already be smart enough to put associated threads on one socket when possible, try it and see). Tim On Mon, May 23, 2016 at 2:15 PM, Glasser, Matthew <[email protected]> wrote: > You could try running a wb_command like smoothing on a random dense > timeseries dataset. It should use multiple cores if everything is working > correctly with that. > > Peace, > > Matt. > > From: <[email protected]> on behalf of Gengyan Zhao < > [email protected]> > Date: Monday, May 23, 2016 at 10:57 AM > To: "[email protected]" <[email protected]> > Subject: [HCP-Users] Questions about Run Diffusion Preprocessing > Parallelly > > Hello HCP Masters, > > > I have a question about the "DiffusionPreprocessingBatch.sh". I want to > run it in a multi-thread manner and involve as many cores as possible. > There is a line in the script saying: > > > #Assume that submission nodes have OPENMP enabled (needed for eddy - at > least 8 cores suggested for HCP data) > > > What shall I do to enable OPENMP? or OPENMP is ready to go? My current > state is that the pipeline has just been run with SGE on a Ubuntu 14.04 > machine having 32 cores. Thank you very much. > > > Best, > > Gengyan > > > Research Assistant > > Medical Physics, UW-Madison > > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. If you have received this email > in error, please immediately notify the sender via telephone or return mail. > > _______________________________________________ > HCP-Users mailing list > [email protected] > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
