VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Tue Mar 04 2014 - 11:16:12 CST

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> 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/
>>
>