R help - Apr 2008 - Stopping a function execution automatically after a given time

Dear all,

I often need to execute functions repeatedly (thousands or more times).
While doing so, I encounter two types of problems:

1.) In some models, the estimation process fails due to convergence problems
2.) Some models will run forever.

My solution to #1 is to use tryCatch around the function call so that my
script does not stop if one of the models will raise an error. This works
fine.

Nowever, with regard to #2, I am lost. I would like to set a maximum time
limit (say, 1 minute) and if my procedure is still running then, I would
like to move on to the next model.
I guess a brute-force solution would be to start a new R process for each
model from my R script and to kill the process using system commands after a
given time. However, restarting the R interpreter each time sounds very
inelegant. Are there any versions that work within a single script? Or
alternative suggestions?

Note that mostly these functions are not written by me and not R code (like
nlme for example), so it is not feasible to adapt the function itself.
Rather, it needs to be a wrapper around the function, similar to tryCatch.

Any help appreciated!
Kind regards,
  Lukas

	[[alternative HTML version deleted]]

?help.search("time")
?proc.time
?system.time

You can stick these in your code appropriately to keep track of elapsed
time. You could also count iterations, of course.

-- Bert Gunter
Genentech

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
On
Behalf Of Lukas Rode
Sent: Wednesday, April 02, 2008 8:07 AM
To: r-help at stat.math.ethz.ch
Subject: [R] Stopping a function execution automatically after a given time

Dear all,

I often need to execute functions repeatedly (thousands or more times).
While doing so, I encounter two types of problems:

1.) In some models, the estimation process fails due to convergence problems
2.) Some models will run forever.

My solution to #1 is to use tryCatch around the function call so that my
script does not stop if one of the models will raise an error. This works
fine.

Nowever, with regard to #2, I am lost. I would like to set a maximum time
limit (say, 1 minute) and if my procedure is still running then, I would
like to move on to the next model.
I guess a brute-force solution would be to start a new R process for each
model from my R script and to kill the process using system commands after a
given time. However, restarting the R interpreter each time sounds very
inelegant. Are there any versions that work within a single script? Or
alternative suggestions?

Note that mostly these functions are not written by me and not R code (like
nlme for example), so it is not feasible to adapt the function itself.
Rather, it needs to be a wrapper around the function, similar to tryCatch.

Any help appreciated!
Kind regards,
  Lukas

	[[alternative HTML version deleted]]

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Lukas Rode a ?crit :
> Nowever, with regard to #2, I am lost. I would like to set a maximum time
> limit (say, 1 minute) and if my procedure is still running then, I would
> like to move on to the next model.

begin_time = as.difftime(format(Sys.time(), '%H:%M:%S'),
units='secs');
for(...)
  {
  ...
  current_time = as.difftime(format(Sys.time(), '%H:%M:%S'),
units='secs');
  delay = current_time - begin_time;
  if (delay>60) return();
  }

a counter may also be enough