From: Phillips, Carolyn L. (cphillips_at_anl.gov)
Date: Tue Mar 04 2014 - 19:50:32 CST

Fyi, I figured out to change the “vmd” script so it calls ggdb instead, but the output when it crashes is not very helpful (to me at least)

This appears when I grab and rotate the molecule

vmd > [New Thread 0x160b of process 52175]
[New Thread 0x1703 of process 52175]
[New Thread 0x1803 of process 52175]
[New Thread 0x1903 of process 52175]
[New Thread 0x1a03 of process 52175]
[New Thread 0x1b03 of process 52175]
[New Thread 0x1c03 of process 52175]
[New Thread 0x1d03 of process 52175]
[New Thread 0x1e03 of process 52175]
[New Thread 0x1f03 of process 52175]

Program received signal SIGSEGV, Segmentation fault.
0x0000000100777e42 in ?? ()
(gdb) where
#0 0x0000000100777e42 in ?? ()
#1 0x00007fff5fbfbac0 in ?? ()
#2 0x00000001007299ed in ?? ()
#3 0x0000000113f097d0 in ?? ()
#4 0x7fffffffffffffff in ?? ()
#5 0x00007fff5fbfbb60 in ?? ()
#6 0x00007fff8af7787e in ?? ()
#7 0x00007fff5fbfbaf0 in ?? ()
#8 0x0000000113f097d0 in ?? ()
#9 0x00007fff5fbfbdb0 in ?? ()
#10 0x0000000000000000 in ?? ()

On Mar 4, 2014, at 6:39 PM, Phillips, Carolyn L. <cphillips_at_anl.gov<mailto:cphillips_at_anl.gov>> wrote:

Ignore my last.
I forgot what caused crashing. From my local build from source, I can open a molecule file, but the moment I try to rotate it, I get the following.

rlwrap: warning: vmd killed by SIGSEGV.
rlwrap has not crashed, but for transparency,
it will now kill itself (without dumping core)with the same signal

Segmentation fault

John, you had some advice on how to apply a debugger to vmd?

ggdb vmd does not work because
"/usr/local/bin/vmd": not in executable format: File format not recognize”

On Mar 4, 2014, at 6:31 PM, Phillips, Carolyn L. <cphillips_at_anl.gov<mailto:cphillips_at_anl.gov>> wrote:

FYI, fixing this problem fixed my local build of VMD from sources as well. All is good again in the world.

Thanks for your help.
Carolyn

On Mar 4, 2014, at 2:39 PM, John Stone <johns_at_ks.uiuc.edu<mailto:johns_at_ks.uiuc.edu>> wrote:

Joshua,
I suspect that the intent of the SDK directions there is make it easy
to run the CUDA samples, but the unintended consequence is that it
will break _all_ apps like VMD that do ship with their own .dylib,
if that version is not precisely the same rev that was installed
with the toolkit.

Using the static libcudart will cure this, but that requires using
CUDA 5.5, which obsoletes older revs of MacOS, and the versions
of OptiX that I've had the most mileage on were based on CUDA 5.0
which doesn't have the static lib, so it's always tricky with
these library versioning issues.

I'm going to try a VMD MacOS build for CUDA 5.5 using the static CUDA libs
and see how far I get with that as one of the options in the early
beta revs of VMD 1.9.2.

Cheers,
John Stone
vmd_at_ks.uiuc.edu<mailto:vmd_at_ks.uiuc.edu>

On Tue, Mar 04, 2014 at 12:01:15PM -0700, Joshua Anderson wrote:
Yes, the NVIDIA docs do say that - but they also tell application developers to bundle libcudart and link to the bundled lib so that users do not need to install the CUDA toolkit.

I haven't checked recently, but you may need DYLD_LIBRARY_PATH set to run simple applications built by "nvcc -o output input.cu". It was needed back in the CUDA 1.0 days. Executables built by cmake link insert an rpath to the lib and do not need a DYLD_LIBRARY_PATH set.
------
Joshua A. Anderson, Ph.D.
Research Area Specialist, Chemical Engineering, University of Michigan
Phone: 734-647-8244
http://www-personal.umich.edu/~joaander/

On Mar 4, 2014, at 10:09 AM, 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

? 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/