[Developers] Running ADMB with separate exe and data dirs

[Arni Magnusson]

Hi all,

Ben raises an interesting question, regarding the behavior of ADMB when 
running a model with the executable and data in separate directories.

I think the reason the glmmADMB binaries are copied to the temporary 
directory before running them is because ADMB executable models create 
some "garbage", and R packages shouldn't create any garbage inside the R 
library tree. The same cleanliness might be required in other cases when 
the same executable is used on many input files - simulations or when 
embedding ADMB inside another application.

I use the word "garbage" here for all output files except simple.cor, 
simple.par, and simple.std. Clearly, those garbage files do indeed have 
value for the modeller, e.g. when debugging a model or accessing precise 
numbers related to the estimation.

So here are four experiments describing the behavior of ADMB 9.1, when 
running a model with the executable and data in separate directories. The 
'exe' directory contains the simple executable and the 'data' directory 
contains simple.dat. One experiment involves a 'third' empty directory.

   Experiment #1, from within exe:
   simple -ind ~/data/simple.dat
   => all results created in 'exe', and no files are added to 'data'

   Experiment #2, from within data:
   ~/exe/simple -ind simple.dat
   => useful output in 'exe' and garbage in 'data'

   Experiment #3, from within data:
   ~/exe/simple -ind ~/data/simple.dat
   => useful output in 'exe' and garbage in 'data'

   Experiment #4, from within third:
   ~/exe/simple -ind ~/data/simple.dat
   => useful output in 'exe' and garbage in 'third'

I guess what the user would expect is that in all four cases, all output 
files should appear in the same directory as the input data file.

Johnoel, I vaguely remember some earlier discussion on this topic. Will 
the new ADMB release have different behavior from the above experiments?

All the best,

Arni



On Thu, 4 Nov 2010, Ben Bolker wrote:

> I rearranged stuff a bit in glmmADMB and added the MacOS binaries Dave 
> sent; committed to R-forge.  The package passes R CMD check for me (on 
> Linux), and installs and runs the example(glmm.admb) OK on MacOS.  I 
> rearranged the structure in which the binaries are kept slightly (there 
> are now separate linux/windows/macos subdirectories). If any of you has 
> a Mac for testing, please give it a whirl -- or we can get back to the 
> MacOS users who have posted on admb-users and ask them to try it out -- 
> or we can post to the list in general.
>
> Don't know what the difference is between the old binaries on the otter 
> research site (which give an 'illegal instruction' error when I run them 
> on MacOS X.6) and the new ones provided by Dave ...
>
> PS Hans, Arni -- can you tell me offhand why the binaries are copied 
> from their installed location to the temporary directory before running 
> them under Unix?  Do ADMB binaries have a separate concept of "directory 
> where I live" and "directory from which I was called"?
>
>   cheers
>    Ben
>