Hi, thanks for the hints. I am quite sure that at some points R stalls as I am used to monitor the progress of simulations (with a custom function similar to pbmclapply) and save partial results: whenever all R instances collapse into one, then no more updates show up. I was able to set OPENBLAS_NUM_THREADS=1 (1=the value calculated by using the formula you provided) as suggested here https://stat.ethz.ch/pipermail/r-sig-debian/2016-August/002588.html, but it seemed to have no effect on the machine I am using. However, I managed to force R to use standard BLAS/LAPACK libraries, hope this is going to solve the problem
sessionInfo() R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.6 LTS Matrix products: default BLAS: /usr/lib/libblas/libblas.so.3.6.0 LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 Il giorno gio 6 giu 2019 alle ore 13:20 Ivan Krylov <krylov.r...@gmail.com> ha scritto: > On Mon, 3 Jun 2019 06:37:46 +0200 > Nicola Lunardon <nicola.lunardon...@gmail.com> wrote: > > > R seems to be running, but simulations do not progress further. > > Have you tried message() (or REprintf() in C code) to narrow down the > specific part of the code where simulations stop in their progress? > It's less convenient than a good debugger, but with parallel code it is > sometimes the only way to reproduce the problem and get some > information about it. > > > If I run simulations on 16 cores I end up having an R instance with > > CPU usage about 1600%, never experienced such a behaviour. > > > BLAS: /usr/lib/openblas-base/libblas.so.3 > > LAPACK: /usr/lib/libopenblasp-r0.2.18.so > > OpenBLAS can, indeed, use multiple threads on its own, inside a single > process. Combined with mclapply, this might create a situation when > there are far more threads competing for CPU time than CPU cores > available. Does it help if you set an environment variable such as > OPENBLAS_NUM_THREADS [*] to a number less than or equal to (number of > CPU cores / mc.cores mclapply argument)? > > -- > Best regards, > Ivan > > [*] > > https://github.com/xianyi/OpenBLAS#setting-the-number-of-threads-using-environment-variables > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.