[gmx-developers] DCD / Licence
Axel Kohlmeyer
akohlmey at cmm.chem.upenn.edu
Wed Jul 8 18:11:28 CEST 2009
On Sat, 2009-07-04 at 07:23 -0400, Roland Schulz wrote:
all,
to resolve this thread here.
the files needed for plugin management in VMD have been
re-licensed with the UIUC open source license, so multiple
ways to include file format support through the molfile
plugins from VMD are now open.
> 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.
the question is how to manage the API design process? i've been involved
in several attempts to do this and they were all doomed from the start,
because people wanted to do too much, and basically it always seemed
more about "world domination" than interoperability. recently, it has
become even more complicated, due to the (almost religious) belief that
some people put in xml.
we hope that the approach of molfile has a chance to get around this
by first working on an API that is independent of the format and thus
one can change the "back end" if needed. also being driven by analysis
and visualization, the pressure for compatibility is higher. since
when writing an application, you don't care that much, but rather
want to "get the data out" somehow and in first order approximation,
you only have to be compatible to yourself (which is fine).
that being said, the molfile API will need a lot of rewrites over the
next years to accommodate additional requirements, particularly for
the upcoming multi-million particle simulations. we've noticed while
working on support for quantum chemical data sets (to reconstruct
molecular orbitals on the fly from population data), that a lot of
the issues only show up while implementing it, and then you get a
second round of problems, if you want to port the interface to
additional codes. quite often we got stuck in discussions about
principal stuff and how to treat (increasingly unlikely) corner cases.
we would still be discussing, if it was not for having first agreed
on just implementing what we can do now and then rewrite the API
later once we have real-life usage examples. right now we are just
3-4 people and that have overlapping but not identical needs.
that keeps the pressure to do a good (enough) job high, but also
the understanding is that we want to try and slowly incorporate
input from additional groups and their requirements so that we
slowly evolve the API into something that can serve the majority
of needs of people in the field.
> 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.
the ones that i was on, all died because of being dominated
by politics rather than pragmatism. right now, i communicate
with the other people involved through the VMD biocore chat
facilities, since VMD is the common element.
cheers,
axel.
> 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
> > > >
> > >
> > > >
> _______________________________________________
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> > >
> > >
> > >
> > > --
> > >
> > >
> >
> =======================================================================
> > > 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.
> > >
> > >
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> > >
> > > --
> > > ORNL/UT Center for Molecular Biophysics
> cmb.ornl.gov
> > > 865-241-1537, ORNL PO BOX 2008 MS6309
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> > --
> >
> =======================================================================
> > 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.
> >
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> > --
> > ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> > 865-241-1537, ORNL PO BOX 2008 MS6309
> > _______________________________________________
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> --
> =======================================================================
> 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.
>
>
> _______________________________________________
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>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
> _______________________________________________
> gmx-developers mailing list
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--
=======================================================================
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.
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