[Debian-med-packaging] MP patch for PhyML

[Diego Darriba]

Dear Stephan et al,

I send you the patch for the current phyml trunk. I checked the results 
with several input data, and I think I solved correctly some 
dependencies in the parallelized loops from my computer science point of 
view. In the configure.ac it is just necessary to include the *-fopenmp* 
flag for compiling (if using gcc compiler). I would modify it, but I 
prefer you to do so. That way you can create a conditional Makefile, or 
include the flag as a commentary, or whatever.

If the compilation flag is not set, the application will compile with no 
error, but it will run as before (i.e, sequentially).

Please, let me know if you have any doubt or any problem.

Kind Regards,

Diego.

El 15/02/11 02:51, Stephane Guindon escribió:
> Dear Andreas,
>
> Thank you very much for contributing to PhyML.
> Yes, it makes perfect sense to try and include this functionality
> into the latest release of the program. Please feel free to take
> a look at the most recent version of the sources on our svn server
> (http://code.google.com/p/phyml/source/browse/#svn%2Ftrunk%2Fsrc)
> and let me know how to amend the configure.ac, *.c  and *.h file
> in an appropriate manner.
>
> Regards,
>
> -Stephane-
>
> On 15/02/11 03:26, Andreas Tille wrote:
>> Hi PhyML authors,
>>
>> when discssing with Diego about a program which uses PhyML he told me
>> about his MP patch which would enable making use of hybrid memory when
>> running PhyML on clusters.  I was considering to port this patch to the
>> Debian packaged version where I intended to support two versions of
>> the package: one conventional phylip and one phylip-mp.
>>
>> When inspecting the patch I noticed that it was done against an older
>> version of PhyML (20100123).  I would consider it a reasonable idea if
>> this patch would be included into the upstream version by just wrapping
>> it into "#ifdef"s properly to enable switching between both versions by
>> simply providing different options to make.  If the patch would be taken
>> over into the official PhyML code this would simplify our work as
>> distributor (as well as Diego's work) and it might be of extra value for
>> other users.
>>
>> What do you think about this idea?
>>
>> Kind regards
>>
>>        Andreas.
>>

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