VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 04 2014 - 11:26:01 CST

Carolyn,
  Thanks for that link. I'll talk tot he NVIDIA devs about this
and see if we can suggest that they change this documentation to
better accomodate scenarios like ours. Going forward, another
thing that will hopefully occur is that we'll compile against a
the new static library version of libcudart, and that should eliminate
the need for these complexities with shared libraries.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 04, 2014 at 05:09:46PM +0000, Phillips, Carolyn L. 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
> 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> 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/ 

-- 
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/