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

[James R. Bence]

All sorry,

Just looked at the help file for glmm.admb.  Should have done this before I 
posted.  I see that the ability to pass args is there.  But even more 
interesting to me is the "save.dir" argument that Ben mentions below.  That 
is really nice and seems designed just for this.  I am very curious what 
that is actually doing beneath the surface since my interest is for other 
admb applications not just the glmmADMB package in R.  When I look through 
available admb argsI don't see one that does this.  Is this changing env 
variables or...?

Jim



At 04:55 PM 7/29/2011, Ben Bolker wrote:
>-----BEGIN PGP SIGNED MESSAGE-----
>Hash: SHA1
>
>   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>
> >     _______________________________________________
> >     Users mailing list
> >     Users at admb-project.org <mailto:Users at admb-project.org>
> >     http://lists.admb-project.org/mailman/listinfo/users
> >
> >
> >
> >
> > _______________________________________________
> > Users mailing list
> > Users at admb-project.org
> > http://lists.admb-project.org/mailman/listinfo/users
>
>-----BEGIN PGP SIGNATURE-----
>Version: GnuPG v1.4.10 (GNU/Linux)
>Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org/
>
>iEYEARECAAYFAk4zHkIACgkQc5UpGjwzenMx9QCggIQZ5tlzSe2yZ/5P7Yw95TUA
>Ec8AoIWiNx66p34/72m01oBstbg6JQzL
>=eDyF
>-----END PGP SIGNATURE-----
>_______________________________________________
>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/ 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.admb-project.org/pipermail/users/attachments/20110729/e05245e6/attachment.html>