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

Roland Schulz roland at utk.edu
Tue Nov 24 03:00:26 CET 2015


Dominik, any contribution should be posted to 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.


On Mon, Nov 23, 2015 at 7:43 PM, Dominik 'Rathann' Mierzejewski <
dominik at greysector.net> wrote:

> Dear Developers,
> I am the maintainer of the GROMACS package in Fedora. Recently, I found
> that GROMACS bundles the lmfit library
> (http://apps.jcns.fz-juelich.de/doku/sc/lmfit), which is already packaged
> in Fedora (https://apps.fedoraproject.org/packages/lmfit). However, it
> seems that the GROMACS-included version is modified from latest 5.1
> version (cleaned-up patch showing the main differences attached) and in
> a bad way: it breaks API and ABI (lmcurve_evaluate() and lmcurve()).
> Now, this can be done properly by introducing new API that GROMACS can
> use while keeping the existing API intact. To that end, I'm attaching
> a patch that tries to do just that. I'm not claiming my solution is the
> best or even entirely correct, but it should be a start.
> I'm also attaching an initial patch for GROMACS to use a system-wide
> shared library with this new API. It's most probably not suitable
> to be applied as-is, but at least the internal test suite (make check)
> passes.
> I'm Cc'ing other interested parties, including the Fedora lmfit package
> maintainer (Miro), the lmfit author (Joachim Wuttke) and Tobias Klauser,
> who seems to have created a fork of lmfit on github
> (https://github.com/tklauser/lmfit) which contains at least one fix
> present in GROMACS fork of lmfit, too (the memleak fix:
> https://github.com/tklauser/lmfit/commit/1dfe71ae26986b52e6037fb1933904d541ab100f
> ).
> Regards,
> Dominik
> --
> Fedora http://fedoraproject.org/wiki/User:Rathann
> RPMFusion http://rpmfusion.org
> "Faith manages."
>         -- Delenn to Lennier in Babylon 5:"Confessions and Lamentations"

ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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