VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Apr 01 2020 - 00:53:17 CDT

Hi guys,
  I'm still short on time, we had some significant computing disruptions
here and being under lockdown slowed down our responses significantly,
and I haven't had a chance to get caught up yet.

The big difference between the C++11 issue for a plugin vs. VMD itself is
that a plugin that has unresolved dependencies will not crash the entire
VMD session, whereas code included in VMD itself will. There are still
some gotchas for me to compile the C++11 code that I'll have to work through,
but there have always been a few plugins that required special non-standard
compilation, so my VMD build system can handle this case without much
difficulty I think.

In the short term I do expect to continue to make builds that support older
distros like CentOS 6.x. This isn't motivated by official end of support
dates for RHEL6/CentOS 6.x, but rather because those distros are some of
the last ones that provide completely trouble-free support for
stereoscopic displays (LCD shutter glasses, clone-mode passive stereo
projection systems, 3-D TVs, etc). We managed to get a CentOS 7.x
system to "limp" with stereoscopic display support, but it's been a
comparative nightmare. I haven't tried CentOS 8.x yet, and I've heard
it's near hopeless on Ubuntu from what others have said. The stereoscopic
display users are a minority among the full VMD user community, but
that's one of the "hold out" groups from upgrades to newer distros.

In any case, I plan to have a look at Francois-Xavier's plugin this
week and I'll let you know more as I put effort into building it and Gemmi
on a few different platforms. I'll report back when I've had a chance
to do this, and what my results on various platforms look like.

Best,
  John Stone

On Sun, Mar 29, 2020 at 11:04:55AM -0400, Giacomo Fiorin wrote:
> Hi John, thanks for clarifying that the issues are different. It was
> unclear to me (and probably will be clearer when you write back on Monday)
> how this would work. For most of us, there isn't a clear distinction
> between how VMD and the plugins are built, since their builds are bundled
> together anyway.
> It is possible that what you have in mind could be the solution to
> problems with other C++11 code, which would otherwise need to wait until a
> version later than 1.9.4 to become available in an official VMD build.
> Giacomo
> On Sat, Mar 28, 2020 at 11:11 PM John Stone <[1]johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> Â I'm pressed for time, but I never said that the plugin can't
> make it into the official builds. I said that on systems that
> lack the necessary C++11 runtime, it would fail to load.Â
> That's a different issue altogether. I will explain all of
> this in more detail when I have the time on Monday since it seems
> there are some misunderstandings here.Â
>
> Best,
> Â John
>
> On Sun, Mar 29, 2020 at 01:35:14AM +0100, FX wrote:
> > Thanks Giacomo,
> >
> > > In summary, it's a good idea to work with John on getting the plugin
> to be a part of VMD. But in my opinion you shouldn't feel obliged to
> rewrite a big chunk of code just to work around the lack of a now
> established standard.
> >
> > I???m not gonna rewrite the code because it???s not my code, it???s
> the CIF-handling headers that I need that are C++11.
> > I still wish there was a way to get the plugin in official VMD builds,
> since most people use the official builds.
> >
> > FX
>
> --
> NIH Center for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> [2]http://www.ks.uiuc.edu/~johns/Â Â Â Â Â Â Phone: 217-244-3349
> [3]http://www.ks.uiuc.edu/Research/vmd/Â Â Â
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Research collaborator, National Institutes of Health, Bethesda, MD
> [4]http://goo.gl/Q3TBQU
> [5]https://github.com/giacomofiorin
>
> References
>
> Visible links
> 1. mailto:johns_at_ks.uiuc.edu
> 2. http://www.ks.uiuc.edu/~johns/
> 3. http://www.ks.uiuc.edu/Research/vmd/
> 4. http://goo.gl/Q3TBQU
> 5. https://github.com/giacomofiorin 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/