[ADMB Users] ADMB NBMM for R: running ADMB in parallel?

[Weihai Liu]

We can run the same admb program for different dataset by using the job
array, also called pleasantly parallel on our hpcc, it works fine if you
don't need each job within the array to communicate with other job during
the run. More details see link
https://wiki.hpcc.msu.edu/display/~colbrydi@msu.edu/2011/07/08/Pleasantly+Parallel+Presentation,
click the pdf for more slides.

I am not using glmmadmb, but you can try to separate each dataset in its own
directory, then call the program or submit the job for each directory, since
admb has not implement parallel yet and create the temporary files during
its run.


weihai

On Fri, Jul 29, 2011 at 2:38 PM, Tara Crewe <tcrewe2 at uwo.ca> wrote:

> Good afternoon,
>
> 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 (www.sharcnet.ca) to submit multiple datasets to be analyzed by
> the same R program in parallel (i.e., serial farming).
>
> 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:
>
>  Error in dvar_matrix write
> Error in glmm.admb(ObservationCount ~ c.year + poly(c.day, 2) +
> poly(c.hour,  :
>   The function maximizer failed
> Calls: glmm.zinb.trnd.admb.yr -> glmm.admb
> In addition: Warning messages:
> 1: In system(cmd2, intern = !verbose) :
>   line 1 may be truncated in call to system(, intern = TRUE)
> 2: In system(cmd2, intern = !verbose) :
>   line 1 may be truncated in call to system(, intern = TRUE)
> 3: In system(cmd2, intern = !verbose) :
>   line 1 may be truncated in call to system(, intern = TRUE)
> 4: In system(cmd2, intern = !verbose) :
>   line 1 may be truncated in call to system(, intern = TRUE)
> 5: running command './nbmm -maxfn 500 ' had status 1
> Execution halted
>
> 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??
>
> 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.
>
> Thanks so much,
>
> Tara
>
> --
> Tara L. Crewe, PhD Candidate
>
> Department of Biology
> University of Western Ontario
> 1151 Richmond Street
> London, Ontario, Canada,
> N6A 3K7
>
> Tel: 519-661-2111 x 84646
> email: tcrewe2 at uwo.ca
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>
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