[R] stopping functions with long execution times
Prof Brian Ripley
ripley at stats.ox.ac.uk
Thu Jul 18 14:30:25 CEST 2013
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,
> 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
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx at inbo.be
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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)
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