On Thu, 2 Feb 2017 13:33:04 +0100 Pablo Escobar Lopez <[email protected]> wrote:
> Hi Jure, > > I have experienced similar issues in the past. I think this depends on the > R library you use for parallelization but I don't remember the details. > > I suggest that you also define OPENBLAS_NUM_THREADS with the same value as > OMP_NUM_THREADS. Defining both env vars with the same value shouldn't hurt > and In theory openblas won't respect the value of OMP_NUM_THREADS unless it > has been compiled with USE_OPENMP=1 which I think it's not the case in > foss/2016b > > Also see here https://github.com/xianyi/OpenBLAS#usages Hm, OPENBLAS_NUM_THREADS doesn't make any difference. OMP_NUM_THREADS was did what I was asking of it (limiting number of R threads from "all cores in that machine" to for example 4), but still it looks like just one thread is doing something useful while the remaining are wasting time dealing with themselves. I remember there was a talk on this topic at one of the past ISCs. Have to dig up the slides ... -- Jurij Pečar HPC Engineer, IT Operations, IT Services EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany Room 13-401
