VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 03 2014 - 10:08:18 CST

Carolyn,
  Let us know if Maxim's suggestion makes any difference.
Maxim, Thanks for the tip.

Another thing to check is to see which CUDA runtime .dylib your locally
compiled VMD is actually picking up when it runs.
Since you have several on your system, one question I would ask is whether
anything would have changed your DYLD_FRAMEWORK_PATH or LD_LIBRARY_PATH
or similar environment variables in such a way that VMD is now picking
up the wrong .dylib where it had not previously.

In the binaries we produce, we use the MacOS X 'install_name_tool' and
'otool' commands to set some of our library dependency paths in such a
way that they are unlikely to be overridden by environment variable
changes like the ones above, but if you compile VMD from source and
don't do this on your own, then anything could potentially happen if
system-wide paths are changed such that the wrong .dylib shows up earlier
in the search path.

It should be easy to attach a debugger to your VMD during startup to
help track down what's going on there. When the debugger attaches, it will
usually print out what shared libraries the app is linked against and what
they were resolved to, and this would help track down if there's something
bad going on with mismatched .dylib files...

Cheers,
  John Stone

On Sun, Mar 02, 2014 at 05:54:44PM -0600, Maxim Belkin wrote:
> Hi Carolyn,
>
> The issue you are facing is caused by CUDA drivers. Try installing the latest CUDA 5.5.43 drivers. Until this version, CUDA didn?t work on a great deal of GPUs under Mavericks.
>
> Maxim
>
>
>
> On Mar 2, 2014, at 4:54 PM, Phillips, Carolyn L. <cphillips_at_anl.gov> wrote:
>
> > A little search turned up these versions.
> >
> > ./NVIDIA/CUDA-5.5/lib/libcudart.dylib
> > ./VMD 1.9.1.app/Contents/vmd/libcudart.dylib
> > ./MATLAB_R2013b.app/bin/maci64/libcudart.dylib
> > /local/cuda/lib/libcudart.dylib
> >
> > I think the first it the one it should be finding.
> > I don?t know why such a library is included in vmd, but I am going to assume its legitimate
> > Same for the Matlab one
> > I assume it may be the /local version that is creating the problem.
> >
> > FYI,
> >
> > which nvcc
> > /Developer/NVIDIA/CUDA-5.5/bin/nvcc
> >
> > -Carolyn
> > On Mar 2, 2014, at 3:20 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> >
> >> On Sun, Mar 2, 2014 at 3:42 PM, Phillips, Carolyn L. <cphillips_at_anl.gov> wrote:
> >>> Hello,
> >>>
> >>> I am trying to pin down why my version of VMD 1.91.1 built from source has
> >>> started seg faulting. (Note, i cannot run vmd -debug because gdb is no
> >>> longer included with Xcode on Mavericks as a command line tool, you can get
> >>> it from macports but it is now called ggdb )
> >>>
> >>> I started with verifying if I download and run the VMD1.9.1 binary that it
> >>> still works. What I found is that this version does work, MacOS X OpenGL
> >>> (32-bit Intel x86) (Apple MacOS-X 10.5.x or later).
> >>>
> >>> This version crashes, MacOS X OpenGL, CUDA (32-bit Intel x86) (Apple
> >>> MacOS-X 10.5.x or later with CUDA)
> >>>
> >>> It cannot seem to interface with the cuda library correctly
> >>>
> >>> /Volumes/VMD-1.9.1/VMD\ 1.9.1.app/Contents/MacOS/startup.command ; exit;
> >>> dyld: Library not loaded: @executable_path/libcudart.dylib
> >>> Referenced from: /Volumes/VMD-1.9.1/VMD
> >>> 1.9.1.app/Contents/MacOS/../Resources/VMD.app/Contents/MacOS/VMD
> >>> Reason: Incompatible library version: VMD requires version 1.1.0 or later,
> >>> but libcudart.dylib provides version 0.0.0
> >>
> >> hi carolyn,
> >>
> >> this looks like VMD picks up some old and incompatible version of the
> >> cuda runtime library from somewhere.
> >>
> >> axel.
> >>
> >>
> >>> /Volumes/VMD-1.9.1/VMD 1.9.1.app/Contents/MacOS/startup.command: line 7:
> >>> 2533 Trace/BPT trap: 5 "$p/../Resources/VMD.app/Contents/MacOS/VMD" $*
> >>> logout
> >>>
> >>> [Process completed]
> >>>
> >>>
> >>> My system is
> >>>
> >>> Mac OSX 10.9.1
> >>> Graphics NVIDIA GeForce GT 750M 2048 MB
> >>> Processor 2.3 GHz Intel Core i7
> >>>
> >>>
> >>> -Carolyn
> >>
> >>
> >>
> >> --
> >> 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.
> >
> 

-- 
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