VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 13 2018 - 16:48:50 CDT

Axel,
  Thanks for the warning on that.
What about making the plugin use a set of runtime-set function pointers
for it's I/O calls? In practice, when opening a file with the .gz suffix,
it would use function pointers that point to gzgets(), gzprintf(), etc,
but when opening a file without the suffix, the function pointers would
point to the stdio calls, fgets(), printf(), etc. The code required
for that would only be very slightly more involved than what it is doing
now with the compile-time macros, and it should run as fast as it can
without creating compilation complications. This would seem to resolve
both issues at low cost as far as code complexity goes.

Best,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 13, 2018 at 05:32:37PM -0400, Axel Kohlmeyer wrote:
> On Tue, Mar 13, 2018 at 3:29 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> > Hi,
> > While I didn't do it yet, this is on my short list of things
> > going into VMD 1.9.4, because zlib is a dependency for libpng,
> > and I would like to enable (and thus have to redistribute) libpng
> > with VMD, at least on linux perhaps on all platforms, by default.
> >
>
> ???hi john,
>
> we probably should figure out a way to have two different plugin binaries
> for this: one with compression enabled and without.
> adding zlib support, significantly slows down uncompressed reading, which
> is why it is an add-on define that is disabled by default.
>
> axel.???
>
>
>
> > I'm currently swamped so I wasn't planning to work on this for a
> > couple of weeks, but if you can wait a bit longer, I hope to have
> > this resolved in the near future, and I will definitely have
> > a look at the LAMMPS plugin when I'm adding libz to the build/redistrib
> > directories.
> >
> > Best,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Mar 13, 2018 at 12:19:48PM -0700, Christian Leitold wrote:
> > > Hello,
> > > I recently wanted to read gzippped LAMMPS trajectories with VMD, and
> > it
> > > turns out this is possible when the right option is defined. In
> > > particular, lammpsplugin.c looks for the preprocessor variable
> > _USE_ZLIB.
> > > This was also mentioned for a similar case in post a few weeks ago:
> > > [1]http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28540.html
> > > My question is rather basic: HOW exactly do I activate the
> > preprocessor
> > > macro in practice? When I just add "#define _USE_ZLIB" it
> > > in lammpsplugin.c, the compilation fails because apparently it cannot
> > > find the zlib functions:
> > > lammpsplugin.c:(.text+0x2e3d): undefined reference to `gzgets'
> > > My guess is that I will need to add a "-lz" linker option at some
> > point,
> > > but I failed to find out where exactly.
> > > Thanks,
> > > Christian
> > >
> > > References
> > >
> > > Visible links
> > > 1. http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/28540.html
> >
> > --
> > 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/
> >
> >
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science & Technology, Temple University, Philadelphia PA, USA
> International Centre for Theoretical Physics, Trieste. Italy. 

-- 
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/