From: Phillips, Carolyn L. (cphillips_at_anl.gov)
Date: Tue Mar 04 2014 - 11:09:46 CST

I removed it from my .bashrc, and indeed now VMD starts up without a problem!

This is the opposite of what NVIDA advises you to do, btw… curious

http://docs.nvidia.com/cuda/cuda-getting-started-guide-for-mac-os-x/index.html

  1. Define the environment variables.
     * The PATH variable needs to include /Developer/NVIDIA/CUDA-5.5/bin
     * DYLD_LIBRARY_PATH needs to contain /Developer/NVIDIA/CUDA-5.5/lib

To change the environment variables for 32-bit operating systems:

export PATH=/Developer/NVIDIA/CUDA-5.5/bin:$PATH
export DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-5.5/lib:$DYLD_LIBRARY_PATH

To change the environment variables for 64-bit operating systems:

export PATH=/Developer/NVIDIA/CUDA-5.5/bin:$PATH
export DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-5.5/lib:$DYLD_LIBRARY_PATH

On Mar 4, 2014, at 9:55 AM, Maxim Belkin <mbelkin_at_ks.uiuc.edu<mailto:mbelkin_at_ks.uiuc.edu>> wrote:

Hi Carolyn,

As John suggested, I was able to reproduce your problem by setting DYLD_LIBRARY_PATH. Run “unset DYLD_LIBRARY_PATH” and try launching VMD then.

Maxim

On Mar 4, 2014, at 9:51 AM, John Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:

Carolyn,
Have you checked your environment variables to see if they are
interfering with VMD's usage of the .dylib that's shipped with it?
Anything in DYLD_FRAMEWORK_PATH or LD_LIBRARY_PATH that adds CUDA?

Cheers,
John

On Tue, Mar 04, 2014 at 03:45:23PM +0000, Phillips, Carolyn L. wrote:
 So I have now updated my cuda driver to 5.5.47 and then grabbed the VMD
 1.9.1 binary again
 Same problem
 /Applications/VMD\ 1.9.1\ 2.app/Contents/MacOS/startup.command ; exit;
 dyld: Library not loaded: @executable_path/libcudart.dylib
   Referenced from: /Applications/VMD 1.9.1
 2.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
 /Applications/VMD 1.9.1 2.app/Contents/MacOS/startup.command: line 7:
 47884 Trace/BPT trap: 5 "$p/../Resources/VMD.app/Contents/MacOS/VMD"
 $*
 logout
 From the error message above I wonder if your install_name_tool and otool
 is finding the libcudart.dylib at all. (version 0.0.0 ??)
 Also, I noticed that the the /usr/local/cuda directory all points to the
 Developer folder as well
 lrwxr-xr-x 1 root wheel 35 Nov 21 09:06 EULA.txt ->
 /Developer/NVIDIA/CUDA-5.5/EULA.txt
 lrwxr-xr-x 1 root wheel 30 Nov 21 09:06 bin ->
 /Developer/NVIDIA/CUDA-5.5/bin
 lrwxr-xr-x 1 root wheel 30 Nov 21 09:06 doc ->
 /Developer/NVIDIA/CUDA-5.5/doc
 lrwxr-xr-x 1 root wheel 33 Nov 21 09:06 extras ->
 /Developer/NVIDIA/CUDA-5.5/extras
 lrwxr-xr-x 1 root wheel 34 Nov 21 09:06 include ->
 /Developer/NVIDIA/CUDA-5.5/include
 drwxr-xr-x 28 root wheel 952 Mar 4 08:34 lib
 lrwxr-xr-x 1 root wheel 36 Nov 21 09:06 libnsight ->
 /Developer/NVIDIA/CUDA-5.5/libnsight
 lrwxr-xr-x 1 root wheel 34 Nov 21 09:06 libnvvp ->
 /Developer/NVIDIA/CUDA-5.5/libnvvp
 lrwxr-xr-x 1 root wheel 31 Nov 21 09:06 nvvm ->
 /Developer/NVIDIA/CUDA-5.5/nvvm
 lrwxr-xr-x 1 root wheel 33 Nov 21 09:06 open64 ->
 /Developer/NVIDIA/CUDA-5.5/open64
 lrwxr-xr-x 1 root wheel 34 Nov 21 09:06 samples ->
 /Developer/NVIDIA/CUDA-5.5/samples
 lrwxr-xr-x 1 root wheel 30 Nov 21 09:06 src ->
 /Developer/NVIDIA/CUDA-5.5/src
 lrwxr-xr-x 1 root wheel 32 Nov 21 09:06 tools ->
 /Developer/NVIDIA/CUDA-5.5/tools
 and in lib
 lrwxr-xr-x 1 root wheel 46 Nov 21 09:06 libcudart.dylib ->
 /Developer/NVIDIA/CUDA-5.5/lib/libcudart.dylib
 On Mar 3, 2014, at 9:08 AM, John Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:

   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<mailto: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<mailto:akohlmey_at_gmail.com>>
       wrote:

         On Sun, Mar 2, 2014 at 3:42 PM, Phillips, Carolyn L.
         <cphillips_at_anl.gov<mailto: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<mailto: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/

--
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/