From: Phillips, Carolyn L. (cphillips_at_anl.gov)
Date: Tue Mar 04 2014 - 10:35:49 CST

DYLD_LIBRARY_PATH=/Developer/NVIDIA/CUDA-5.5/lib:/Developer/NVIDIA/CUDA-5.5/lib:

LD_LIBRARY_PATH is not set.

On Mar 4, 2014, at 8:51 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/