[gmx-developers] unbundling the lmfit library bundled with Gromacs

David van der Spoel spoel at xray.bmc.uu.se
Tue Dec 1 19:42:17 CET 2015

On 01/12/15 01:21, Dominik 'Rathann' Mierzejewski wrote:
> Hi,
> On Tuesday, 24 November 2015 at 08:20, David van der Spoel wrote:
>> On 24/11/15 03:00, Roland Schulz wrote:
>>> Hi,
>>> Dominik, any contribution should be posted to gerrit.gromacs.org
>>> <http://gerrit.gromacs.org>. The current situation would only cause a
>>> problem if an application tried to link both to libgromacs and liblmfit
>>> correct? Because we don't have the lmfit API as public (but we currently
>>> still export all symbols so this currently only affects that the headers
>>> aren't installed).
>>> David, why did you change the source style for those files (e.g.
>>> brackets, doxygen, ...)? I think for any external code, we want to keep
>>> files as close to the original as possible to be able to look at the
>>> difference and also be able to update to a newer version if needed. I
>>> think if there is no special reason why this is needed we should undo
>>> those style changes.
>> I changed the interface to the routine as well. Since this is a fitting
>> function I introduced a weighting array (errors in y). This is therefore a
>> derived work now. Best way around clashes would be to rename the functions
>> inside gromacs I guess.
> Since the latest release of lmfit provides new API call that allows
> specifying a weighting array, wouldn't it make more sense to support
> building against that version (6.0) instead of carrying a copy in
> gromacs?
Thanks for the information.

It would make some sense to have a newer version, however it is extra 
work, and it is not ubiquitous enough to be able to count on it being 
installed everywhere. That means we will need an internal version anyway 
since not everyone runs the latest Linux.

> Regards,
> Dominik

David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se

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