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

[Tara Crewe]

Thanks for all the helpful responses - save.dir worked as you expected, Ben... so perfectly simple!

Tara
________________________________________
From: users-bounces at admb-project.org [users-bounces at admb-project.org] On Behalf Of Ben Bolker [bbolker at gmail.com]
Sent: July 29, 2011 4:55 PM
To: users at admb-project.org
Subject: Re: [ADMB Users] ADMB NBMM for R: running ADMB in parallel?

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  Yes, separating the examples into separate subdirectories should do
the trick.  I *think* you should also be able to specify the "save.dir"
argument to take care of this, but I admit I haven't tested it ...

  Ben Bolker


On 11-07-29 04:03 PM, Weihai Liu wrote:
> 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
> <mailto: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 <http://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 <tel:519-661-2111%20x%2084646>
>     email: tcrewe2 at uwo.ca <mailto:tcrewe2 at uwo.ca>
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>
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