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<font size=3>Following up on Weihai's response:<br><br>
I think the problem you are encountering is caused, as you suspect, by
conflicts in files that are being created as the multiple copies of admb
program run. Each time you call glmm.admb it is running the same
admb executable program in the same directory and thus you have multiple
calls modifying the same output files such as admb.cov. When we run
admb programs in parallel on the HPCC (Michigan State's High Performance
Compute Center) servers, we either set up multiple copies of our compiled
programs in different directories or we have our shell script make the
copies.<br><br>
Ideally we would just pass calls to our program an arg that would tell it
where to save the output files different from where the program starts
(does anyone know a way to do this?) and then we would not need to set up
multiple copies of the executable in different places.<br><br>
You have the added challenge that even if there is any easy way to change
the location for output files, you need to be able to pass that info
through your R call to glmm.admb. I recall that recently there was
expression that it would be nice to add the capability of passing
arbitrary args to glmm.admb, so I suspect that capability does not yet
exist.<br><br>
Jim Bence<br><br>
So At 02:38 PM 7/29/2011, Tara Crewe wrote:<br>
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Good afternoon,<br><br>
I'm running glmmADMB (0.5-2) with negative binomial and zinegbin
distribution on count data in R (version 2.12.2). Currently I'm
using a cluster
(<a href="http://www.sharcnet.ca/" eudora="autourl">www.sharcnet.ca</a>)
to submit multiple datasets to be analyzed by the same R program in
parallel (i.e., serial farming). <br><br>
Other R packages work fine in parallel this way (e.g., glmer), and the
code for ADMB works fine on a single dataset. However, as soon as I
submit a second dataset to be analyzed in parallel, ADMB fails with the
following error messages:<br><br>
Error in dvar_matrix write<br>
Error in glmm.admb(ObservationCount ~ c.year + poly(c.day, 2) +
poly(c.hour, : <br>
The function maximizer failed<br>
Calls: glmm.zinb.trnd.admb.yr -> glmm.admb<br>
In addition: Warning messages:<br>
1: In system(cmd2, intern = !verbose) :<br>
line 1 may be truncated in call to system(, intern = TRUE)<br>
2: In system(cmd2, intern = !verbose) :<br>
line 1 may be truncated in call to system(, intern = TRUE)<br>
3: In system(cmd2, intern = !verbose) :<br>
line 1 may be truncated in call to system(, intern = TRUE)<br>
4: In system(cmd2, intern = !verbose) :<br>
line 1 may be truncated in call to system(, intern = TRUE)<br>
5: running command './nbmm -maxfn 500 ' had status 1 <br>
Execution halted<br><br>
I searched these error messages online, and haven't found any
documentation. Question is, is it possible to run ADMB in
parallel? I suspect (with my very limited knowledge) that the error
may have to do with how temporary files are written/stored by
ADMB?? <br><br>
I haven't attached sample data, because for now I'd simply like to know
if parallel processing is possible with ADMB? If so, is there
documentation that could help me out? I am also happy to supply
data and R code if it will help.<br><br>
Thanks so much,<br><br>
Tara<br><br>
--<br>
Tara L. Crewe, PhD Candidate<br><br>
Department of Biology<br>
University of Western Ontario<br>
1151 Richmond Street<br>
London, Ontario, Canada, <br>
N6A 3K7<br><br>
Tel: 519-661-2111 x 84646<br>
email: tcrewe2@uwo.ca <br>
_______________________________________________<br>
Users mailing list<br>
Users@admb-project.org<br>
<a href="http://lists.admb-project.org/mailman/listinfo/users" eudora="autourl">http://lists.admb-project.org/mailman/listinfo/users</a></blockquote>
<x-sigsep><p></x-sigsep>
Jim Bence<br>
Dept. of Fisheries and Wildlife <br>
Michigan State University<br>
<a href="http://www.msu.edu/user/bence/" eudora="autourl">http://www.msu.edu/user/bence/</a></font></body>
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