VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 14 2015 - 14:45:46 CDT

Hi,
  I think that the issue with loading the h5md plugin might be
caused by either an unresovled dependency (from the perspective of
the h5mdplugin.so shared object at the point when VMD calls dlopen()),
or by the MacOS X runtime not searching the directory where the
libraries it depends on are located. To get VMD to be completely
self-contained, we have to override the normal MacOS X search path
by using "otool" to set the search path for things like Tcl so that
they are relative to the VMD install folder. If you have compiled
h5mdplugin.so against other libraries, MacOS X may or may not do
the right thing with resolving dependencies if the libraries it needs
aren't already in your framework or dyld search paths.

Yet another potential problem might be caused by mixing code compiled
via clang vs. code compiled with GNU gcc/g++. All of the existing
shipping versions of VMD were compiled using gcc/g++ rather than clang
since this produces binaries that will run on any later version of
MacOS X. It is possible that clang and gcc are incompatible in various
ways and this might explain why h5mdplugin.so doesn't load if you used
clang to compile it.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 06, 2015 at 10:26:13PM +0000, Hart, David Blaine wrote:
> Hi John,
>
> On 7/6/15, 3:42 PM, "John Stone" <johns_at_ks.uiuc.edu> wrote:
>
> >Hi,
> > I'm fairly certain that the issue here is that there are unresolved
> >dependencies in the H5MD when VMD calls dlopen()/dlsym() on the
> >H5MD plugin shared library file, resulting in dlopen()/dlsym() returning
> >an error, which VMD then reports as a plugin load failure.
> >
> >What output do you get if you run this command?:
> > otool -L h5mdplugin.so
>
> h5mdplugin.so:
> h5mdplugin.so (compatibility version 0.0.0, current version 0.0.0)
> libh5md.so (compatibility version 0.0.0, current version 0.0.0)
> /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version
> 1213.0.0)
>
>
> >
> >Perhaps we should include the H5MD plugin authors on this email
> >exchange...
>
> I believe Jonas is the author, and I believe he is on this list;
>
>
> If I understand correctly, you are suggesting that the h5mdplugin/libh5md
> (both created by the plugin) arenšt properly linked to the HDF5-1.5
> libraries?
>
> Thanks,
>
> David
> 

-- 
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/