VMD-L Mailing List

From: Phillips, Carolyn L. (cphillips_at_anl.gov)
Date: Tue Mar 04 2014 - 12:09:54 CST

I would assume so?

Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce GT 750M 2 SM_3.0 @ 0.93 GHz, 2.0GB RAM, KTO, OIO, ZCP

On Mar 4, 2014, at 10:16 AM, Maxim Belkin <mbelkin_at_ks.uiuc.edu<mailto:mbelkin_at_ks.uiuc.edu>> wrote:

This is a great news! Out of curiosity, is your GPU supported in the latest CUDA driver update? Basically, are there VMD Info) lines that look like that:

Info) Detected 1 available CUDA accelerator:
Info) [0] GeForce GT 330M 6 SM_1.2 @ 1.10 GHz, 255MB RAM, KTO, OIO, ZCP

I haven’t found an official list of supported GPUs for 5.5.47, but yours is not on the list for 5.5.45.

Maxim

On Mar 4, 2014, at 11:09 AM, Phillips, Carolyn L. <cphillips_at_anl.gov<mailto:cphillips_at_anl.gov>> wrote:

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

• 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> 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> 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> 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/