VMD-L Mailing List

From: Phillips, Carolyn L. (cphillips_at_anl.gov)
Date: Tue Mar 04 2014 - 09:45:23 CST

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<mailto: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<mailto: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<mailto:akohlmey_at_gmail.com>> wrote:

On Sun, Mar 2, 2014 at 3:42 PM, Phillips, Carolyn L. <cphillips_at_anl.gov<mailto: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<mailto: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/