<br><br><div class="gmail_quote">On Fri, Jul 3, 2009 at 4:42 PM, Axel Kohlmeyer <span dir="ltr"><<a href="mailto:akohlmey@cmm.chem.upenn.edu">akohlmey@cmm.chem.upenn.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">On Fri, 2009-07-03 at 16:06 -0400, Roland Schulz wrote:<br>
><br>
><br>
> On Fri, Jul 3, 2009 at 1:12 PM, Axel Kohlmeyer<br>
> <<a href="mailto:akohlmey@cmm.chem.upenn.edu">akohlmey@cmm.chem.upenn.edu</a>> wrote:<br>
> On Fri, 2009-07-03 at 12:58 -0400, Roland Schulz wrote:<br>
<br>
<br>
</div>i would not include the whole code, just the molfile API interface<br>
and then dlopen() the individual plugins. so one can use, e.g. an<br>
existing VMD installation (provided the API matches).</blockquote><div><br>Erik, David, Berk: What do you think about that? Do you like that idea? <br><br>If so: At what stage do we want to configure the path to the molfile plugin folder? <br>
We could:<br>- add to configure a --with-vmd option<br>- that would set a variable (e.g. GMX_VMD) in GMXRC<br>- trxio would read GMX_VMD and if it finds the plugins allow also reading of the molfile formats<br>- 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<br>
<br>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.<br><br>Do we want to support only dynamic linking (dlopen) for the vmd plugins or as an alternative also static?<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
interface the mofile read API to fortran. for dynamic linkage<br>
and plugin management, i suggest you look at the PluginMgr.C<br>
source from VMD. it references also vmddlopen.c as a portable<br>
wrapper for dlopen.c. BTW, the VMD license allows you to use<br>
up to 10% of the code for other purposes... ;-)</blockquote><div> <br>Thanks for pointing that out. Does for less than 10% count the Illinois Open Source License? <br>Or where do I find out the requirements to add license/copyright information to the file/package under that 10% clause?<br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">> I kept the changes very few (basically just removing the plugin api).<br><div class="im">
> But of course your solution is much better if one wants more than just<br>
> DCD.<br>
<br>
</div>i'm mainly concerned about maintainability and project fragmentation.<br>
you have a valid point in supporting only DCD and having a simple<br>
interface. if your changes could be implemented with a couple of<br>
well crafted #ifdefs, it would still be possible to have the source<br>
in the VMD plugin cvs to be _the_ authoritative source. i.e. if somebody<br>
in gromacs fixes a bug, it can be easily integrated back into VMD<br>
and vice versa.</blockquote><div><br>I think I could do it with a few #ifdefs if we don't want to go the molfile path. <br></div><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
one of the big weaknesses of the MD community compared to,<br>
say, astrophysics, is the fragmentation of project and lack<br>
of interoperability in file formats and data management.</blockquote><div><br>Yes I agree. That is very suboptimal. <br></div><div> </div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
my hope is that popular projects like VMD, gromacs, NAMD, pymol<br>
(which also supports molfile, btw) and others start to converge<br>
to be ready for future challenges like handling multi-million<br>
atom simulations, efficient lossless and lossy compression,<br>
mult-resolution data storage, efficient parallel and out-of-core<br>
data access. too much is currently done with ad-hoc solutions,<br>
but supporting mutual APIs will allow to mutually benefit from<br>
improvements.</blockquote><div><br>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. <br>
<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
p.s.: sorry if i'm getting too political at the end. this is<br>
something that i'm very passionate about. just disregard it,<br>
if you think i'm going too far. ;-)</blockquote><div><br>No I think this is very interesting. Is there some mailinglist / forum where this would be more on-topic?<br>I would be interested in follow up on this.<br><br>
Roland<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>
<div><div></div><div class="h5"><br>
<br>
><br>
> Roland<br>
><br>
><br>
><br>
> cheers,<br>
> axel.<br>
><br>
><br>
><br>
> > Roland<br>
> ><br>
> > On Fri, Jul 3, 2009 at 11:59 AM, Axel Kohlmeyer<br>
> > <<a href="mailto:akohlmey@cmm.chem.upenn.edu">akohlmey@cmm.chem.upenn.edu</a>> wrote:<br>
> > roland,<br>
> ><br>
> > On Fri, Jul 3, 2009 at 6:44 AM, Roland<br>
> Schulz<<a href="mailto:roland@utk.edu">roland@utk.edu</a>><br>
> > wrote:<br>
> > > Hi,<br>
> > ><br>
> > > what do you think about adding DCD read support to<br>
> the<br>
> > tools? Quite a few<br>
> > > people in our group use the tools but (for a<br>
> number of<br>
> > reasons) do the<br>
> > > simulation still with other MD packages. It is<br>
> inconvenient<br>
> > to have to<br>
> > > convert the trajectories.<br>
> ><br>
> ><br>
> > instead of adopting code to only read .dcd files,<br>
> > why don't you write an interface to the VMD molfile<br>
> API?<br>
> > should be even less work and then you would<br>
> interface<br>
> > gromacs to a large number of file formats. also it<br>
> would<br>
> > avoid replicating and code (and problems with<br>
> diverging<br>
> > developments and missing bugfixes) and also you can<br>
> add<br>
> > new file formats or updated readers/writers<br>
> > on the fly through the dynamic loading of plugins.<br>
> ><br>
> > cheers,<br>
> > axel.<br>
> ><br>
> > p.s.: we're also in the process of gradually<br>
> revising the<br>
> > molfile API to make it more flexible and powerful<br>
> and<br>
> > particularly add support for "out-of-core"<br>
> processing of<br>
> > a collection of files (primarily for VMD but not<br>
> limited to<br>
> > it).<br>
> > that might be interesting for gromacs tools just as<br>
> well.<br>
> ><br>
> ><br>
> > ><br>
> > > Is it OK to add code which is under the University<br>
> of<br>
> > Illinois Open Source<br>
> > > License? It is GPL compatible so does not cause<br>
> license<br>
> > conflicts<br>
> > ><br>
> ><br>
> (<a href="http://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License" target="_blank">http://en.wikipedia.org/wiki/University_of_Illinois/NCSA_Open_Source_License</a>).<br>
> > ><br>
> > > Roland<br>
> > ><br>
> > > --<br>
> > > ORNL/UT Center for Molecular Biophysics<br>
> <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
> > > 865-241-1537, ORNL PO BOX 2008 MS6309<br>
> > ><br>
> ><br>
> > > _______________________________________________<br>
> > > gmx-developers mailing list<br>
> > > <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> > ><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
> > > Please don't post (un)subscribe requests to the<br>
> list. Use<br>
> > the<br>
> > > www interface or send it to<br>
> > <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
> > ><br>
> ><br>
> ><br>
> ><br>
> > --<br>
> ><br>
> ><br>
> =======================================================================<br>
> > Axel Kohlmeyer <a href="mailto:akohlmey@cmm.chem.upenn.edu">akohlmey@cmm.chem.upenn.edu</a><br>
> > <a href="http://www.cmm.upenn.edu" target="_blank">http://www.cmm.upenn.edu</a><br>
> > Center for Molecular Modeling -- University of<br>
> > Pennsylvania<br>
> > Department of Chemistry, 231 S.34th Street,<br>
> Philadelphia, PA<br>
> > 19104-6323<br>
> > tel: 1-215-898-1582, fax: 1-215-573-6233,<br>
> office-tel:<br>
> > 1-215-898-5425<br>
> ><br>
> =======================================================================<br>
> > If you make something idiot-proof, the universe<br>
> creates a<br>
> > better idiot.<br>
> ><br>
> > _______________________________________________<br>
> > gmx-developers mailing list<br>
> > <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> ><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
> > Please don't post (un)subscribe requests to the<br>
> list. Use the<br>
> > www interface or send it to<br>
> > <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
> ><br>
> ><br>
> ><br>
> ><br>
> > --<br>
> > ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
> > 865-241-1537, ORNL PO BOX 2008 MS6309<br>
> > _______________________________________________<br>
> > gmx-developers mailing list<br>
> > <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> > <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
> > Please don't post (un)subscribe requests to the list. Use<br>
> the<br>
> > www interface or send it to<br>
> <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
><br>
> --<br>
> =======================================================================<br>
> Axel Kohlmeyer <a href="mailto:akohlmey@cmm.chem.upenn.edu">akohlmey@cmm.chem.upenn.edu</a><br>
> <a href="http://www.cmm.upenn.edu" target="_blank">http://www.cmm.upenn.edu</a><br>
> Center for Molecular Modeling -- University of<br>
> Pennsylvania<br>
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA<br>
> 19104-6323<br>
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel:<br>
> 1-215-898-5425<br>
> =======================================================================<br>
> If you make something idiot-proof, the universe creates a<br>
> better idiot.<br>
><br>
> _______________________________________________<br>
> gmx-developers mailing list<br>
> <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to<br>
> <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
><br>
><br>
><br>
><br>
> --<br>
> ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov" target="_blank">cmb.ornl.gov</a><br>
> 865-241-1537, ORNL PO BOX 2008 MS6309<br>
> _______________________________________________<br>
> gmx-developers mailing list<br>
> <a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
> <a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
> Please don't post (un)subscribe requests to the list. Use the<br>
> www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br>
<br>
--<br>
=======================================================================<br>
Axel Kohlmeyer <a href="mailto:akohlmey@cmm.chem.upenn.edu">akohlmey@cmm.chem.upenn.edu</a> <a href="http://www.cmm.upenn.edu" target="_blank">http://www.cmm.upenn.edu</a><br>
Center for Molecular Modeling -- University of Pennsylvania<br>
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323<br>
tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425<br>
=======================================================================<br>
If you make something idiot-proof, the universe creates a better idiot.<br>
</div></div><br>_______________________________________________<br>
gmx-developers mailing list<br>
<a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-developers" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-developers</a><br>
Please don't post (un)subscribe requests to the list. Use the<br>
www interface or send it to <a href="mailto:gmx-developers-request@gromacs.org">gmx-developers-request@gromacs.org</a>.<br></blockquote></div><br><br clear="all"><br>-- <br>ORNL/UT Center for Molecular Biophysics <a href="http://cmb.ornl.gov">cmb.ornl.gov</a><br>
865-241-1537, ORNL PO BOX 2008 MS6309<br>