[Debian-med-packaging] MP patch for PhyML

[Diego Darriba]

Hi Stephane et al,

I'm keen to modify the patch for the trunk version of PhyML. I will 
include also the necessary changes in every .h and .ac file and I will 
send you the diff files. This patch allows shared memory parallel 
execution of PhyML using OpenMP, so it takes advantage of multi-core 
processors.

Kind regards,

Diego.


El 15/02/11 08:04, Andreas Tille escribió:
> Hi Stephane,
>
> thanks for your quick response.  I wonder if David as the author of this
> MP patch would be willing to provide it for the latest development
> release (because I personally do not use phyml and do not even have an
> idea how to test it).  I'm volunteering to provide help (perhaps via the
> competence of the Debian mailing list in build system questions.
>
> For the moment I can provide a phyml.1 manpage (attached).  Feel free to
> (change and) include it into your official PhyML code.
>
> Kind regards
>
>         Andreas.
>
> On Tue, Feb 15, 2011 at 02:51:35PM +1300, Stephane Guindon wrote:
>> 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.
>>>
>> -- 
>> Stephane Guindon
>> Department of Statistics
>> University of Auckland
>> http://www.stat.auckland.ac.nz
>>

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