[gmx-developers] Dependence on libxml2

[David van der Spoel]

Berk Hess wrote:
> Hi,
> 
> But in Gromacs 4 xml is no longer used, is it?
> But I think xml still has to be removed from the configure script.
xml is off by default.

It is however used in the contrib section so it should stay in configure.

How to deal with file formats in the future is a separate discussion 
(which has been going on for 6-7 year already :().

> 
> Berk
> 
> David van der Spoel wrote:
>> Roland Schulz wrote:
>>> Hi,
>>>
>>> also on cross compile clusters (Cray, Bluegene), libxml(2) is not 
>>> installed on the Compute-Node but only on the frontend. Since having 
>>> to cross compile another library is a pain, it would be great if 
>>> mdrun could be compiled without libxml(2).
>>
>> Interesting challenge indeed. I guess what we have to do is to 
>> minimize the interdependencies between the code. That is, mdrun should 
>> not depend on the entire gmxlib.
>>
>>
>>>
>>> Roland
>>>
>>> On Mon, Sep 8, 2008 at 4:18 AM, Marc F. Lensink 
>>> <lensink at bigre.ulb.ac.be <mailto:lensink at bigre.ulb.ac.be>> wrote:
>>>
>>>     On Sat, Sep 06, 2008 at 02:07:42PM +0200, David van der Spoel wrote:
>>>      > Hi,
>>>      >
>>>      > the inclusion of the xml library is currently limited to stuff 
>>> in the
>>>      > contrib directory. However we have discussed on many occasions
>>>     which xml
>>>      > library to use if we were going to make the move. The de-facto
>>>     standard
>>>      > in the linux world is libxml2 (foundation of the gnome project).
>>>     Are you
>>>      > aware of any platform where this wouldn't work?
>>>      >
>>>      > Do you see any other obvious drawbacks?
>>>
>>>     libxml2 is the way to go.  however, some clusters may have been
>>>     installed with older linux distributions, eg of the SL 3 series.
>>>     ancient, but stable.  in those cases libxml2 can still be installed,
>>>     but only manually and its functionality is limited.  one of the 
>>> issues
>>>     I recall is problems with namespace support.
>>>
>>>     cheers,
>>>     marc
>>>
>>>
>>>     --
>>>     Marc F. Lensink
>>>     Centre for Structural Biology and Bioinformatics          CSBB
>>>     Université Libre de Bruxelles           marc.lensink at ulb.ac.be
>>>     <mailto:marc.lensink at ulb.ac.be>
>>>     Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
>>>     tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425
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>>>
>>>
>>> -- 
>>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 
>>> <http://cmb.ornl.gov>
>>>
>>>
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>>
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se