Re: [Rd] repeatable segfault - on Mac

From: Rob Goedman <robjgoedman_at_me.com>
Date: Thu, 08 Sep 2011 08:31:41 -0700

It is intermittent on both my systems.

Rob

On Sep 8, 2011, at 8:00 AM, luke-tierney_at_uiowa.edu wrote:

> On Thu, 8 Sep 2011, Martin Maechler wrote:
>

>>>>>>> Simon Urbanek <simon.urbanek_at_r-project.org>
>>>>>>>    on Thu, 8 Sep 2011 09:33:23 -0400 writes:
>> 
>>   > On Sep 8, 2011, at 4:01 AM, Martin Maechler wrote:
>> 
>>   >>>>>>> David Winsemius <dwinsemius_at_comcast.net>
>>   >>>>>>> on Tue, 6 Sep 2011 00:38:13 -0400 writes:
>>   >>
>>   >>> I can reproduce:
>>   >>> eigen(crossprod(matrix(1:2000, 50)) + (0+0i), T, T)
>>   >>
>>   >>> *** caught segfault ***
>>   >>> address 0x102d0e028, cause 'memory not mapped'
>>   >>
>>   >>> Traceback:
>>   >>> 1: .Call("La_rs_cmplx", x, only.values, PACKAGE = "base")
>>   >>> 2: eigen(crossprod(matrix(1:2000, 50)) + (0 + (0+0i)), T, T)
>>   >>> ##---- after restart
>>   >>>> sessionInfo()
>>   >>> R version 2.13.1 (2011-07-08)
>>   >>> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>>   >>
>>   >>> locale:
>>   >>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>   >>
>>   >>> attached base packages:
>>   >>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>   >>
>>   >>> With OSX 10.5.8
>>   >>
>>   >>> Also happens with 32 bit R
>>   >>> [R.app GUI 1.41 (5874) i386-apple-darwin9.8.0]
>>   >>
>>   >> It does not happen on Linux (different versions)
>>   >> nor Windows (2.13.1 patched, early August).
>>   >>
>>   >> As this is calling LAPACK code,
>>   >> I guess that this is yet another case where the Mac version
>>   >> of optimized BLAS / LAPACK is playing wrongly.
>>   >>
>> 
>>   > Nope, this is R's BLAS / LAPACK!
>> 
>> yes, it seems, as Peter is confirming as well.
>> 
>> *BUT* as far as we currently know, the problem was never seen
>> outside of MacOS X , right?
>> 

>
> My experience is that the Mac OS malloc is less forgiving of writing
> outside allocated memory than the one usually used on Linux, so some
> things show up only on macs or are easier to trigger on macs even
> though the problems exist else where as well. Valgrind probably makes
> up for that most of the time but maybe not always.
>
> Best,
>
> luke
>
>
>> Martin Maechler
>> 
>>   >>> David Winsemius
>>   >>
>>   >>> On Sep 6, 2011, at 12:12 AM, robin hankin wrote:
>>   >>
>>   >>>> Hi.  macosx 10.6.8
>>   >>>>
>>   >>>> With R-2.13.1 and also revision 56948 I get the following repeatable
>>   >>>> segfault:
>>   >>>>
>>   >>>>
>>   >>>>
>>   >>>> wt118:~% R --vanilla --quiet
>>   >>>>> R.Version()
>>   >>>> $platform
>>   >>>> [1] "x86_64-apple-darwin9.8.0"
>>   >>>>
>>   >>>> $arch
>>   >>>> [1] "x86_64"
>>   >>>>
>>   >>>> $os
>>   >>>> [1] "darwin9.8.0"
>>   >>>>
>>   >>>> $system
>>   >>>> [1] "x86_64, darwin9.8.0"
>>   >>>>
>>   >>>> $status
>>   >>>> [1] ""
>>   >>>>
>>   >>>> $major
>>   >>>> [1] "2"
>>   >>>>
>>   >>>> $minor
>>   >>>> [1] "13.1"
>>   >>>>
>>   >>>> $year
>>   >>>> [1] "2011"
>>   >>>>
>>   >>>> $month
>>   >>>> [1] "07"
>>   >>>>
>>   >>>> $day
>>   >>>> [1] "08"
>>   >>>>
>>   >>>> $`svn rev`
>>   >>>> [1] "56322"
>>   >>>>
>>   >>>> $language
>>   >>>> [1] "R"
>>   >>>>
>>   >>>> $version.string
>>   >>>> [1] "R version 2.13.1 (2011-07-08)"
>>   >>>>
>>   >>>>> eigen(crossprod(matrix(1:2000, 50)) + (0+0i), T, T)
>>   >>>>
>>   >>>> *** caught segfault ***
>>   >>>> address 0x1038000a8, cause 'memory not mapped'
>>   >>>>
>>   >>>> Traceback:
>>   >>>> 1: .Call("La_rs_cmplx", x, only.values, PACKAGE = "base")
>>   >>>> 2: eigen(crossprod(matrix(1:2000, 50)) + (0 + (0+0i)), T, T)
>>   >>>>
>>   >>>> 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: 2
>>   >>>> wt118:~%
>>   >>>>
>>   >>>>
>>   >>>>
>>   >>>>
>>   >>>>
>>   >>>> --
>>   >>>> Robin Hankin
>>   >>>> Uncertainty Analyst
>>   >>>> hankin.robin_at_gmail.com
>>   >>>>
>>   >>>> ______________________________________________
>>   >>>> R-devel_at_r-project.org mailing list
>>   >>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>   >>
>>   >>> David Winsemius, MD
>>   >>> Heritage Laboratories
>>   >>> West Hartford, CT
>>   >>
>>   >>> ______________________________________________
>>   >>> R-devel_at_r-project.org mailing list
>>   >>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>   >>
>>   >> ______________________________________________
>>   >> R-devel_at_r-project.org mailing list
>>   >> https://stat.ethz.ch/mailman/listinfo/r-devel
>>   >>
>>   >>
>> 
>> ______________________________________________
>> R-devel_at_r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 

>
> --
> Luke Tierney
> Chair, Statistics and Actuarial Science
> Ralph E. Wareham Professor of Mathematical Sciences
> University of Iowa Phone: 319-335-3386
> Department of Statistics and Fax: 319-335-3017
> Actuarial Science
> 241 Schaeffer Hall email: luke_at_stat.uiowa.edu
> Iowa City, IA 52242 WWW: http://www.stat.uiowa.edu
>
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