<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi,<div><br></div><div>Having optional support for a dlopen API sounds great. You probably don't want to make it default, since that could screw up compilation on many platforms.</div><div><br></div><div>Our only hard requirements are:</div><div><br></div><div>1) We need to be able to distribute the code as GPL/LGPL (instead of a combination of licenses). The 10% clause probably doesn't fly with this, since the one could imagine 10 different people copy 10% each, distribute as GPL, then somebody else (who gets it under strict GPL, where there cannot be side clauses) merges it and has the original code under GPL. </div><div><br></div><div>2) The basic code must be possible to compile without any extra libraries. Optional stuff can use them, though!</div><div><br></div><div>Cheers,</div><div><br></div><div>Erik</div><div><br><div><div>On Jul 4, 2009, at 1:23 PM, Roland Schulz wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><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> _______________________________________________<br>gmx-developers mailing list<br><a href="mailto:gmx-developers@gromacs.org">gmx-developers@gromacs.org</a><br>http://lists.gromacs.org/mailman/listinfo/gmx-developers<br>Please don't post (un)subscribe requests to the list. Use the <br>www interface or send it to gmx-developers-request@gromacs.org.</blockquote></div><br></div></body></html>