[R-sig-Debian] mclapply Segmentation Fault for Ubuntu

[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