[gmx-developers] parallelization

[K.A.Feenstra]

Justin MacCallum wrote:
 >
> I looked into some automatic documentation tools.  The most promising one
> is called doxygen (www.doxygen.org).  It extracts all functions, global
> variables, enums, and structs from the source code and makes nice
> cross-linked web pages.  It will also extract specially formatted comments
> from the source and incorperate them into the web page.  The comment
> format is relatively unobtrusive.  I would be willing to convert the
> existing comments to doxygen format, as well as host the documentation as
> long as that isn't a problem with any other developers, and as long as
> they would be willing to use the new format when updating or adding
> comments.

That sounds like a splendid idea. Could you give a short example of how
comments would have to be formatted? Just so we can get an idea of how
much work that would be. If it is too involved (I've seen some examples
of similar systems, which are in practice absolutely unworkable), it
would probably not be worth wile, since nobody will make the effort...

> I also plan to produce some how-to/tutorial pages for developers.  For the
> first one, I want to put some answers to questions I had when I was just
> starting out.  Things like how to add a new program to the makefile, how
> to compile for debugging, how to debug MPI, etc.  This could probably even
> go into the developer FAQ.  I'd also like to produce a document to help
> people getting starting writing analysis programs.  We need this for our
> group anyway.

I know someone in our group (MD group in Groningen), who has been doing
some things in this direction while implementing a QM/MM hybrid interface
into gromacs. I'll BCC this to him (though I think he is on the list), so
you could join forces...


-- 
Groetjes,

Anton
  ________ __________________________________________________________
|        | Anton Feenstra                                           |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam   |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands  |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610              |
| ' __   | Feenstra at chem.vu.nl - www.chem.vu.nl/afdelingen/FAR      |
|  /  \  |----------------------------------------------------------|
| |    | | Dept. of Biophysical Chemistry - University of Groningen |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands       |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton  |
| |    | |----------------------------------------------------------|
|  \__/  | "You Try to Run the Universe" (Tricky)                   |
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