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

Ben Bolker bbolker at gmail.com
Fri Jul 29 14:14:45 PDT 2011

Hash: SHA1

On 11-07-29 04:53 PM, James R. Bence wrote:
> Following up on Weihai's response:
> 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.
> 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.
> 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.
> Jim Bence

   It should be there -- I added it on June 15.  If someone tries it and
it doesn't work, let me know.  I will point out that there's a
bug/feature request tracker for glmmADMB at
<https://r-forge.r-project.org/tracker/?group_id=847> -- you may need to
set up an r-forge account in order to add new bugs/requests.

> So At 02:38 PM 7/29/2011, Tara Crewe wrote:
>> Content-type: multipart/alternative;
>>  boundary="Boundary_(ID_oBtCKwtWoaJicJtof93Qog)"
>> Content-language: en
>> 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
>> email: tcrewe2 at uwo.ca
>> _______________________________________________
>> Users mailing list
>> Users at admb-project.org
>> http://lists.admb-project.org/mailman/listinfo/users
> Jim Bence
> Dept. of Fisheries and Wildlife
> Michigan State University
> http://www.msu.edu/user/bence/
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