Some operations in wb_command automatically use OpenMP without being enabled by an argument, using however many cores it can find. You can change the number it uses by setting the environment variable OMP_NUM_THREADS. I'm not as sure about multithreading in other software used in the scripts.
As I understand it, in our cluster, we use the job control system to restrict the number of cores the process can see, in order to reduce things like cross-socket memory access. This won't help with a fixed number of threads set in a script, but it does let us keep a single process restricted to the amount of hardware we want it to use. Tim On Fri, Jun 19, 2015 at 1:04 PM, m s <mgstauff...@gmail.com> wrote: > Version 3.4.0 > > Hi, > > We're wondering if there's a clear global way to manage how many compute > threads the HCP pipeline uses. We're running on a Rocks/SGE(OGE) cluster. > > My colleague recently ran the perfusion pre-processing pipeline with 9 > slots/cores allocated via SGE/OGE and we observed the job's cpu usage on > the compute node to which the job was assigned fluctuate in steps between > 200%, 800% and 900%. > > We found one spot in an HCP script where the -openmp argument is > explicitly called and was hardcoded to 8. We've changed that to be set to > the SGE/OGE NSLOTS env var. But it seems there may be other spots where > this is hardcoded to 8, or other spots where other threading options are > set? > > Thanks, > Michael > > _______________________________________________ > HCP-Users mailing list > HCP-Users@humanconnectome.org > http://lists.humanconnectome.org/mailman/listinfo/hcp-users > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
