[gmx-developers] Dependence on libxml2

[David van der Spoel]

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>
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> 
> 
> 
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> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov <http://cmb.ornl.gov>
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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