Hi all, I have here R-3.3.1 built with foss-2016b. Ganglia showed me lots of red on the nodes where this R is running. I found out that by default this R will spawn number of threads equal to number of cpus on the node (does this come from openblas?), irregardless of what slurm is limiting the job to. So I prepared some prolog scripts that set OMP_NUM_THREADS based on --cpus-per-task and did some testing with http://r.research.att.com/benchmarks/R-benchmark-25.R These are the numbers: cores 1 37.77user 0.93system 0:39.49elapsed 98%CPU 2 39.70user 5.83system 0:36.90elapsed 123%CPU 4 42.12user 12.13system 0:34.71elapsed 156%CPU 8 46.62user 25.82system 0:33.80elapsed 214%CPU 16 52.83user 53.06system 0:33.29elapsed 318%CPU Trend is obvious ...
I want to know is this is expected R behaviour, since my experience with it is limited. Also my google-fu for single letter things is limited, so I would appreciate any pointers to articles I have to read or experience you can share. Thanks. -- Jurij Pečar HPC Engineer, IT Operations, IT Services EMBL Heidelberg, Meyerhofstraße 1, 69117, Heidelberg, Germany Room 13-401
