[R] optim & .C / Crashing on run

[Patrick Burns]

When invoking R, you can add

  -d valgrind

to run it under valgrind.

On 04/11/2012 11:35, Paul Browne wrote:
> It looks like my attached files didn't go through, so I'll put them in a
> public Dropbox folder instead; optim_rhelp.tar.gz
> <http://dl.dropbox.com/u/1113102/optim_rhelp.tar.gz>
>
> Thanks, I'll run a compiled binary of the C++ code through Valgrind &
> see what it reports, then perhaps I'll try an Rscript execution of the R
> code calling the C++ in optim (not sure if Valgrind can process that
> though!).
>
> It does seem to be a memory error of some kind, since occasionally the
> OS pops up a crash report referencing a segmentation fault after optim
> crashes the R session. Though it is strange that the code has never
> crashed from a straight .C call in R, or when run from a compiled C++
> binary.
>
> - Paul
>
> On 4 November 2012 09:35, Patrick Burns <pburns at pburns.seanet.com
> <mailto:pburns at pburns.seanet.com>> wrote:
>
>     That is a symptom of the C/C++ code doing
>     something like using memory beyond the proper
>     range.  It's entirely possible to have crashes
>     in some contexts but not others.
>
>     If you can run the C code under valgrind,
>     that would be the easiest way to find the
>     problem.
>
>     Pat
>
>
>     On 03/11/2012 18:15, Paul Browne wrote:
>
>         Hello,
>
>         I am attempting to use optim under the default Nelder-Mead
>         algorithm for
>         model fitting, minimizing a Chi^2 statistic whose value is
>         determined by a
>         .C call to an external shared library compiled from C & C++ code.
>
>         My problem has been that the R session will immediately crash
>         upon starting
>         the simplex run, without it taking a single step.
>
>         This is strange, as the .C call itself works, is error-free (as
>         far as I
>         can tell!) & does not return NAN or Inf under any initial starting
>         parameters that I have tested it with in R. It only ever crashes
>         the R
>         session when the Chi^2 function to be minimized is called from
>         optim, not
>         under any other circumstances.
>
>         In the interests of reproducibility, I attach R code that reads
>         attached
>         data files & attempts a N-M optim run. The required shared library
>         containing the external code (compiled in Ubuntu 12.04 x64 with
>         g++ 4.6.3)
>         is also attached. Calculating an initial Chi^2 value for a
>         starting set of
>         model parameters works, then the R session crashes when the
>         optim call is
>         made.
>
>         Is there something I'm perhaps doing wrong in the specification
>         of the
>         optim run? Is it inadvisable to use external code with optim?
>         There doesn't
>         seem to be a problem with the external code itself, so I'm very
>         stumped as
>         to the source of the crashes.
>
>
>
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>         and provide commented, minimal, self-contained, reproducible code.
>
>
>     --
>     Patrick Burns
>     pburns at pburns.seanet.com <mailto:pburns at pburns.seanet.com>
>     twitter: @portfolioprobe
>     http://www.portfolioprobe.com/__blog
>     <http://www.portfolioprobe.com/blog>
>     http://www.burns-stat.com
>     (home of 'Some hints for the R beginner'
>     and 'The R Inferno')
>
>

-- 
Patrick Burns
pburns at pburns.seanet.com
twitter: @portfolioprobe
http://www.portfolioprobe.com/blog
http://www.burns-stat.com
(home of 'Some hints for the R beginner'
and 'The R Inferno')