[R] stopping functions with long execution times

[ONKELINX, Thierry]

Hi Henrik,

That is exactly what I was looking for.

Thanks a lot.

Best regards,

Thierry

ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
Kliniekstraat 25
1070 Anderlecht
Belgium
+ 32 2 525 02 51
+ 32 54 43 61 85
Thierry.Onkelinx op inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey


-----Oorspronkelijk bericht-----
Van: henrik.bengtsson op gmail.com [mailto:henrik.bengtsson op gmail.com] Namens Henrik Bengtsson
Verzonden: donderdag 18 juli 2013 12:43
Aan: ONKELINX, Thierry
CC: r-help op r-project.org
Onderwerp: Re: [R] stopping functions with long execution times

See evalWithTimeout() of R.utils, e.g.

tryCatch({
  evalWithTimeout({
    slowFunction();
  }, timeout=7*24*3600);
}, TimeoutException=function(ex) {
  cat("Timeout. Skipping.\n");
})

help("evalWithTimeout") have more information and cross links.

/Henrik

On Thu, Jul 18, 2013 at 11:37 AM, ONKELINX, Thierry <Thierry.ONKELINX op inbo.be> wrote:
> Dear all,
>
> I am running the same model on several datasets, each dataset is a different species. The problem is that for some datasets the model is not converging. Currently I have an INLA model running for 35 days and still no results. The process still uses near 100% of the CPU and less than 1 GB RAM on virtual Ubuntu box with 8 GB RAM on a blade server.
>
> I can kill the process manual and make the script skip this model. However it would be more elegant if it was possible to automate this. E.g. let the model run but kill it automatically once it runs for more than 7 days. Once killed the model should throw an error so we can catch that in the error-handling.
>
> Any suggestions on how to do this?
>
> Best regards,
>
> Thierry
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature
> and Forest team Biometrie & Kwaliteitszorg / team Biometrics & Quality
> Assurance Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx op inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
>
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>
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* * * * * * * * * * * * * D I S C L A I M E R * * * * * * * * * * * * *
Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is door een geldig ondertekend document.
The views expressed in this message and any annex are purely those of the writer and may not be regarded as stating an official position of INBO, as long as the message is not confirmed by a duly signed document.