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 at 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 * * * * * * * * * * * * * 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.
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 at 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 at 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
>
>
> * * * * * * * * * * * * * 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.
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
On 18/07/2013 10:37, ONKELINX, Thierry 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?Learn how to use the R documentation. ??limit gave me some useful hits, including to how I would do this. However, as ?setTimeLimit points out, if this is running in C code, it cannot be interrupted from the R interpreter. In that case, use separate processes and your OS facilities (man ulimit, for example).> > 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 at 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 TukeyAnd 'Asking on R-help is no substitute for doing your own homework'> > > * * * * * * * * * * * * * 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. > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595