[gmx-developers] DCD / Licence
Roland Schulz
roland at utk.edu
Sat Jul 4 13:23:41 CEST 2009
On Fri, Jul 3, 2009 at 4:42 PM, Axel Kohlmeyer
<akohlmey at cmm.chem.upenn.edu>wrote:
> On Fri, 2009-07-03 at 16:06 -0400, Roland Schulz wrote:
> >
> >
> > On Fri, Jul 3, 2009 at 1:12 PM, Axel Kohlmeyer
> > <akohlmey at cmm.chem.upenn.edu> wrote:
> > On Fri, 2009-07-03 at 12:58 -0400, Roland Schulz wrote:
>
>
> i would not include the whole code, just the molfile API interface
> and then dlopen() the individual plugins. so one can use, e.g. an
> existing VMD installation (provided the API matches).
Erik, David, Berk: What do you think about that? Do you like that idea?
If so: At what stage do we want to configure the path to the molfile plugin
folder?
We could:
- add to configure a --with-vmd option
- that would set a variable (e.g. GMX_VMD) in GMXRC
- trxio would read GMX_VMD and if it finds the plugins allow also reading of
the molfile formats
- if it does not find the plugin (or GMX_VMD is not set) and one tries to
read e.g. a dcd it would give an error
In a first stage only trajectory formats would be supported. Of course later
one could also support structure format, so that charges could be read for
e.g. g_diplole.
Do we want to support only dynamic linking (dlopen) for the vmd plugins or
as an alternative also static?
> interface the mofile read API to fortran. for dynamic linkage
> and plugin management, i suggest you look at the PluginMgr.C
> source from VMD. it references also vmddlopen.c as a portable
> wrapper for dlopen.c. BTW, the VMD license allows you to use
> up to 10% of the code for other purposes... ;-)
Thanks for pointing that out. Does for less than 10% count the Illinois Open
Source License?
Or where do I find out the requirements to add license/copyright information
to the file/package under that 10% clause?
> I kept the changes very few (basically just removing the plugin api).
> > But of course your solution is much better if one wants more than just
> > DCD.
>
> i'm mainly concerned about maintainability and project fragmentation.
> you have a valid point in supporting only DCD and having a simple
> interface. if your changes could be implemented with a couple of
> well crafted #ifdefs, it would still be possible to have the source
> in the VMD plugin cvs to be _the_ authoritative source. i.e. if somebody
> in gromacs fixes a bug, it can be easily integrated back into VMD
> and vice versa.
I think I could do it with a few #ifdefs if we don't want to go the molfile
path.
> one of the big weaknesses of the MD community compared to,
> say, astrophysics, is the fragmentation of project and lack
> of interoperability in file formats and data management.
Yes I agree. That is very suboptimal.
> my hope is that popular projects like VMD, gromacs, NAMD, pymol
> (which also supports molfile, btw) and others start to converge
> to be ready for future challenges like handling multi-million
> atom simulations, efficient lossless and lossy compression,
> mult-resolution data storage, efficient parallel and out-of-core
> data access. too much is currently done with ad-hoc solutions,
> but supporting mutual APIs will allow to mutually benefit from
> improvements.
It would be great but would need very well designed APIs. E.g. molfile is
not ready for the future as it does not support parallel IO (just as one
example). So a constant update of the APIs is required and of course the
APIs should be decided by the community and not just by one group.
p.s.: sorry if i'm getting too political at the end. this is
> something that i'm very passionate about. just disregard it,
> if you think i'm going too far. ;-)
No I think this is very interesting. Is there some mailinglist / forum
where this would be more on-topic?
I would be interested in follow up on this.
Roland
>
>
>
> >
> > Roland
> >
> >
> >
> > cheers,
> > axel.
> >
> >
> >
> > > Roland
> > >
> > > On Fri, Jul 3, 2009 at 11:59 AM, Axel Kohlmeyer
> > > <akohlmey at cmm.chem.upenn.edu> wrote:
> > > roland,
> > >
> > > On Fri, Jul 3, 2009 at 6:44 AM, Roland
> > Schulz<roland at utk.edu>
> > > wrote:
> > > > Hi,
> > > >
> > > > what do you think about adding DCD read support to
> > the
> > > tools? Quite a few
> > > > people in our group use the tools but (for a
> > number of
> > > reasons) do the
> > > > simulation still with other MD packages. It is
> > inconvenient
> > > to have to
> > > > convert the trajectories.
> > >
> > >
> > > instead of adopting code to only read .dcd files,
> > > why don't you write an interface to the VMD molfile
> > API?
> > > should be even less work and then you would
> > interface
> > > gromacs to a large number of file formats. also it
> > would
> > > avoid replicating and code (and problems with
> > diverging
> > > developments and missing bugfixes) and also you can
> > add
> > > new file formats or updated readers/writers
> > > on the fly through the dynamic loading of plugins.
> > >
> > > cheers,
> > > axel.
> > >
> > > p.s.: we're also in the process of gradually
> > revising the
> > > molfile API to make it more flexible and powerful
> > and
> > > particularly add support for "out-of-core"
> > processing of
> > > a collection of files (primarily for VMD but not
> > limited to
> > > it).
> > > that might be interesting for gromacs tools just as
> > well.
> > >
> > >
> > > >
> > > > Is it OK to add code which is under the University
> > of
> > > Illinois Open Source
> > > > License? It is GPL compatible so does not cause
> > license
> > > conflicts
> > > >
> > >
> > (
> http://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License
> ).
> > > >
> > > > Roland
> > > >
> > > > --
> > > > ORNL/UT Center for Molecular Biophysics
> > cmb.ornl.gov
> > > > 865-241-1537, ORNL PO BOX 2008 MS6309
> > > >
> > >
> > > > _______________________________________________
> > > > gmx-developers mailing list
> > > > gmx-developers at gromacs.org
> > > >
> > http://lists.gromacs.org/mailman/listinfo/gmx-developers
> > > > Please don't post (un)subscribe requests to the
> > list. Use
> > > the
> > > > www interface or send it to
> > > gmx-developers-request at gromacs.org.
> > > >
> > >
> > >
> > >
> > > --
> > >
> > >
> >
> =======================================================================
> > > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu
> > > http://www.cmm.upenn.edu
> > > Center for Molecular Modeling -- University of
> > > Pennsylvania
> > > Department of Chemistry, 231 S.34th Street,
> > Philadelphia, PA
> > > 19104-6323
> > > tel: 1-215-898-1582, fax: 1-215-573-6233,
> > office-tel:
> > > 1-215-898-5425
> > >
> >
> =======================================================================
> > > If you make something idiot-proof, the universe
> > creates a
> > > better idiot.
> > >
> > > _______________________________________________
> > > gmx-developers mailing list
> > > gmx-developers at gromacs.org
> > >
> > http://lists.gromacs.org/mailman/listinfo/gmx-developers
> > > Please don't post (un)subscribe requests to the
> > list. Use the
> > > www interface or send it to
> > > gmx-developers-request at gromacs.org.
> > >
> > >
> > >
> > >
> > > --
> > > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> > > 865-241-1537, ORNL PO BOX 2008 MS6309
> > > _______________________________________________
> > > gmx-developers mailing list
> > > gmx-developers at gromacs.org
> > > http://lists.gromacs.org/mailman/listinfo/gmx-developers
> > > Please don't post (un)subscribe requests to the list. Use
> > the
> > > www interface or send it to
> > gmx-developers-request at gromacs.org.
> >
> > --
> >
> =======================================================================
> > Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu
> > http://www.cmm.upenn.edu
> > Center for Molecular Modeling -- University of
> > Pennsylvania
> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA
> > 19104-6323
> > tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:
> > 1-215-898-5425
> >
> =======================================================================
> > If you make something idiot-proof, the universe creates a
> > better idiot.
> >
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to
> > gmx-developers-request at gromacs.org.
> >
> >
> >
> >
> > --
> > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> > 865-241-1537, ORNL PO BOX 2008 MS6309
> > _______________________________________________
> > gmx-developers mailing list
> > gmx-developers at gromacs.org
> > http://lists.gromacs.org/mailman/listinfo/gmx-developers
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-developers-request at gromacs.org.
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey at cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>
> _______________________________________________
> gmx-developers mailing list
> gmx-developers at gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-developers
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-developers-request at gromacs.org.
>
--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20090704/ce75eaae/attachment.html>
More information about the gromacs.org_gmx-developers
mailing list