Dario Strbenac
2014-Mar-27 10:00 UTC
[R-sig-Debian] mclapply Segmentation Fault for Ubuntu
Running the example in the documentation causes R to crash. dario at 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 at 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 at 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
Johannes Ranke
2014-Mar-27 10:30 UTC
[R-sig-Debian] mclapply Segmentation Fault for Ubuntu
Hi, I checked on Ubuntu 13.10:> library(parallel) > simplify2array(mclapply(rep(4,5), rnorm))[,1] [,2] [,3] [,4] [,5] [1,] 0.5615870 -0.27748675 -0.08832828 0.4887008 -0.6710558 [2,] -0.1100447 0.04958648 -1.24414404 -0.5549061 0.4509780 [3,] 1.4462468 -0.12099765 -0.87754954 -0.3806779 -0.1440630 [4,] 0.4429913 -1.06452941 0.42370677 -1.2382726 0.2476223> quit()Save workspace image? [y/n/c]: n ich at pc:~$ lsb_release -a No LSB modules are available. Distributor ID: Ubuntu Description: Ubuntu 13.10 Release: 13.10 Codename: saucy ich at pc:~$ So no problem over here. Maybe you installed a multithreaded blas? Not sure about the current state but I remember that this combination would lead to crashes at some point. Johannes Am Donnerstag, 27. M?rz 2014, 10:00:28 schrieb Dario Strbenac:> Running the example in the documentation causes R to crash. > > dario at 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 at 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 at 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 > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debian-- PD Dr. Johannes Ranke Kronacher Str. 8 79639 Grenzach-Wyhlen
Scott Kostyshak
2014-Mar-27 11:19 UTC
[R-sig-Debian] mclapply Segmentation Fault for Ubuntu
On Thu, Mar 27, 2014 at 6:00 AM, Dario Strbenac <dstr7320 at uni.sydney.edu.au> wrote:> Running the example in the documentation causes R to crash. > > dario at 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 at 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 at 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 > R-SIG-Debian at r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-debianThe 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