On Thu, Mar 27, 2014 at 6:00 AM, Dario Strbenac <[email protected]> wrote: > Running the example in the documentation causes R to crash. > > dario@bioinfo:~$ R > > R version 3.0.3 (2014-03-06) -- "Warm Puppy" > Copyright (C) 2014 The R Foundation for Statistical Computing > Platform: x86_64-pc-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> library(parallel) >> simplify2array(mclapply(rep(4, 5), rnorm)) > > *** caught segfault *** > address 0x7fee2a7229d0, cause 'memory not mapped' > > Traceback: > 1: mcexit(0L) > 2: FUN(1:2[[1L]], ...) > 3: lapply(seq_len(cores), inner.do) > 4: mclapply(rep(4, 5), rnorm) > 5: lapply(x, length) > 6: unlist(lapply(x, length)) > 7: unique(unlist(lapply(x, length))) > 8: simplify2array(mclapply(rep(4, 5), rnorm)) > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: > *** caught segfault *** > address 0x7fee2a7229d0, cause 'memory not mapped' > > Traceback: > 1: mcexit(0L) > 2: FUN(1:2[[2L]], ...) > 3: lapply(seq_len(cores), inner.do) > 4: mclapply(rep(4, 5), rnorm) > 5: lapply(x, length) > 6: unlist(lapply(x, length)) > 7: unique(unlist(lapply(x, length))) > 8: simplify2array(mclapply(rep(4, 5), rnorm)) > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: [,1] [,2] [,3] [,4] [,5] > [1,] -1.147559 0.05071552 -0.8661278 1.3939602 -1.8899639 > [2,] 1.092394 -0.28870308 1.5201952 0.5470172 -1.1965282 > [3,] 2.338910 -0.62201329 -0.5306457 -0.4862363 -0.1221119 > [4,] -0.181282 0.21907111 -1.0803414 -0.1504892 -0.2067919 >> > > dario@bioinfo:~$ lsb_release -a > No LSB modules are available. > Distributor ID: Ubuntu > Description: Ubuntu 13.10 > Release: 13.10 > Codename: saucy > > The same code does not crash on Debian. > > /nb$ R > > R version 3.0.3 (2014-03-06) -- "Warm Puppy" > Copyright (C) 2014 The R Foundation for Statistical Computing > Platform: x86_64-pc-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > >> library(parallel) >> simplify2array(mclapply(rep(4, 5), rnorm)) > [,1] [,2] [,3] [,4] [,5] > [1,] 1.25103304 0.71090925 -0.2416887 -1.0442886 0.826455644 > [2,] -0.08600017 -1.55204619 0.3531317 -0.2971294 -0.098026007 > [3,] 1.03296764 -0.02248264 1.0171218 -1.8507103 -1.246730487 > [4,] -0.11282003 -1.19287737 0.6241989 -0.5765659 -0.003024582 >> ^Z > [1]+ Stopped R > /nb$ lsb_release -a > No LSB modules are available. > Distributor ID: Debian > Description: Debian GNU/Linux 7.4 (wheezy) > Release: 7.4 > Codename: wheezy > > How can I fix it ? I read it could be caused by particular versions of BLAS. > The libraries on the Ubuntu system are > > dario@bioinfo:~$ ldconfig -p | grep blas > libnetblast.so.6 (libc6,x86-64) => > /usr/lib/x86_64-linux-gnu/libnetblast.so.6 > libblastcompadj.so.6 (libc6,x86-64) => > /usr/lib/x86_64-linux-gnu/libblastcompadj.so.6 > libblastapi.so.6 (libc6,x86-64) => > /usr/lib/x86_64-linux-gnu/libblastapi.so.6 > libblast.so.6 (libc6,x86-64) => > /usr/lib/x86_64-linux-gnu/libblast.so.6 > libblas.so.3 (libc6,x86-64) => /usr/lib/libblas.so.3 > libblas.so (libc6,x86-64) => /usr/lib/libblas.so > > There is no OpenBLAS present. > > -------------------------------------- > Dario Strbenac > PhD Student > University of Sydney > Camperdown NSW 2050 > _______________________________________________ > R-SIG-Debian mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-debian
The code runs here without problems also. ldd /usr/lib/R/bin/exec/R | grep -i blas $ ldd /usr/lib/R/bin/exec/R | grep -i blas libblas.so.3 => /usr/lib/libblas.so.3 (0x00007fbd4676c000) $ ldconfig -p | grep blas libgslcblas.so.0 (libc6,x86-64) => /usr/lib/libgslcblas.so.0 libf77blas.so.3 (libc6,x86-64) => /usr/lib/libf77blas.so.3 libcblas.so.3 (libc6,x86-64) => /usr/lib/libcblas.so.3 libblas.so.3 (libc6,x86-64) => /usr/lib/libblas.so.3 libblas.so (libc6,x86-64) => /usr/lib/libblas.so (Note that I still haven't upgraded to 3.0.3) > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-pc-linux-gnu (64-bit) $ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 13.10 Release: 13.10 Codename: saucy Scott -- Scott Kostyshak Economics PhD Candidate Princeton University _______________________________________________ R-SIG-Debian mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-debian
