From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 04 2014 - 09:51:08 CST

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> 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>
> 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.
>
> --
> 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/