VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jul 06 2015 - 16:42:34 CDT

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

Perhaps we should include the H5MD plugin authors on this email exchange...

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 06, 2015 at 04:56:30PM +0000, Hart, David Blaine wrote:
> I am trying to build the H5MD plugin to work with my Mac version of VMD
> (no CUDA). I'm having issues because the library versions seem to
> mismatch, and try as I might, I can't seem to get the compilation flags to
> match up. Is there a way to find out what flags/compilers were used for
> binary distribution? I don't really want to try to build the entire VMD
> program from source.
> The following is the log from VMD startup:
>
> Info) VMD for MACOSXX86, version 1.9.2 (December 29, 2014)
>
> ... Clipity clip ...
>
> Info) Multithreading available, 4 CPUs detected.
>
> Info) OpenGL renderer: Intel(R) Iris(TM) Graphics 6100
>
> Info) Features: STENCIL MDE MTX NPOT PP PS GLSL(OVF)
>
> Info) Full GLSL rendering mode is available.
>
> Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture
> (8)
>
> Warning) Unable to open dynamic library
> '/Applications/VMD.app/Contents/vmd/plugins/MACOSXX86/molfile/h5mdplugin.so'.
>
> Warning)
> dlopen(/Applications/VMD.app/Contents/vmd/plugins/MACOSXX86/molfile/h5mdplugin.so,
> 2): Library not loaded: libh5md.so
>
> Warning) Referenced from:
> /Applications/VMD.app/Contents/vmd/plugins/MACOSXX86/molfile/h5mdplugin.so
>
> Warning) Unable to dlopen
> '/Applications/VMD.app/Contents/vmd/plugins/MACOSXX86/molfile/h5mdplugin.so':
>
> Unable to dlopen plugin file
> /Applications/VMD.app/Contents/vmd/plugins/MACOSXX86/molfile/h5mdplugin.so
>
> Warning) Didn't find the register function
> in/Applications/VMD.app/Contents/vmd/plugins/MACOSXX86/molfile/libh5md.so;
> plugin(s) not loaded.
>
> Current build options are -m32 -arch=i386
> And hdf5-1.8-15-patch1 was built from scratch with the same flags to match
> (since macports only supplies a 64-bit version of the hdf5 libraries).
> MacOS X 10.10.4
>
> $ clang --version -m32
>
> Apple LLVM version 6.1.0 (clang-602.0.53) (based on LLVM 3.6.0svn)
>
> Target: i386-apple-darwin14.4.0
>
> Thread model: posix
>
> Thanks,
> David Hart 

-- 
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/