VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Tue Mar 04 2014 - 10:55:22 CST

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/