VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Mar 05 2014 - 16:49:42 CST

Carolyn,
  Well, that's either indicative of a serious OpenGL driver oops
(which have turned up many times in the past on MacOS X in particular)
or that the debugger just isn't cooperating. If you type "frame 12"
and then "where", what does it say?

Cheers,
  John

On Wed, Mar 05, 2014 at 10:47:09PM +0000, Phillips, Carolyn L. wrote:
> I think that might be all the frames there are!
> See below
> (gdb) backtrace 10
> #0 0x0000000100777e42 in ?? ()
> #1 0x00007fff5fbfbb80 in ?? ()
> #2 0x00000001007299ed in ?? ()
> #3 0x0000000100b5c720 in ?? ()
> #4 0x7fffffffffffffff in ?? ()
> #5 0x00007fff5fbfbc20 in ?? ()
> #6 0x00007fff8af7787e in ?? ()
> #7 0x00007fff5fbfbbb0 in ?? ()
> #8 0x0000000100b5c720 in ?? ()
> #9 0x00007fff5fbfbe70 in ?? ()
> (More stack frames follow...)
> (gdb) backtrace 11
> #0 0x0000000100777e42 in ?? ()
> #1 0x00007fff5fbfbb80 in ?? ()
> #2 0x00000001007299ed in ?? ()
> #3 0x0000000100b5c720 in ?? ()
> #4 0x7fffffffffffffff in ?? ()
> #5 0x00007fff5fbfbc20 in ?? ()
> #6 0x00007fff8af7787e in ?? ()
> #7 0x00007fff5fbfbbb0 in ?? ()
> #8 0x0000000100b5c720 in ?? ()
> #9 0x00007fff5fbfbe70 in ?? ()
> #10 0x0000000000000000 in ?? ()
> On Mar 5, 2014, at 3:40 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> That's very odd that it stops at only 10 frames. The Apple
> debugger must be modified in some way. Can you use the
> built-in "help" command to see if you can get it to give a more complete
> traceback and not only the last 10 stack frames? I would normally
> expect a crash inside VMD to result in a traceback that's at least 20
> or 30 frames deep if it occurs during rendering, so what you've got
> there either indicates evil driver badness or that it's just showing
> you an incomplete traceback...
>
> Cheers,
> John
>
> On Wed, Mar 05, 2014 at 10:38:16PM +0000, Phillips, Carolyn L. wrote:
>
> HI John,
> Thanks for digging into this deeper.
> This is the output of backtrace 60
> (gdb) backtrace 60
> #0 0x0000000100777e42 in ?? ()
> #1 0x00007fff5fbfbb80 in ?? ()
> #2 0x00000001007299ed in ?? ()
> #3 0x0000000100b5c720 in ?? ()
> #4 0x7fffffffffffffff in ?? ()
> #5 0x00007fff5fbfbc20 in ?? ()
> #6 0x00007fff8af7787e in ?? ()
> #7 0x00007fff5fbfbbb0 in ?? ()
> #8 0x0000000100b5c720 in ?? ()
> #9 0x00007fff5fbfbe70 in ?? ()
> #10 0x0000000000000000 in ?? ()
> On Mar 5, 2014, at 3:15 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Carolyn,
> Okay, if you still get no symbols, that would indicate that the
> crash
> is occuring in one of the system's runtime libraries, in this case
> it's
> likely an OpenGL issue. We can dig deeper to figure this out
> however.
> What happens if you type "backtrace 60" in the debugger?
>
> Cheers,
> John
>
> On Wed, Mar 05, 2014 at 10:07:25PM +0000, Phillips, Carolyn L.
> wrote:
>
> Hi John
> That is a traceback from my build. I did exactly what you
> suggest
> (added
> -g to the compiler flags). It did not change the output.
> This
> surprised
> me as well.
> I do not actually use a CUDA build of vmd
> Here are my configure options
>
> ./configure MACOSXX86_64 FLTKOPENGL FLTK IMD TK TCL SILENT
> PTHREADS
> LIBTACHYON NETCDF PYTHON NUMPY LP64
>
> So perhaps it is my OpenGL driver. However I have worked with
> another
> code that uses OpenGL without seeing any problems.
> -Carolyn
> On Mar 5, 2014, at 8:43 AM, John Stone <johns_at_ks.uiuc.edu>
> wrote:
>
> Carolyn,
> Is that traceback from your build, or from one of the stock
> VMD
> binaries? If it's from your build, you can just edit your
> Makefiles
> to add "-g" to your compiler flags, and then you'll have
> debugging
> symbols for the code in VMD. I would guess from your
> description
> that there's some issue with the OpenGL driver on your
> machine,
> although I hadn't heard anyone else report something like
> this on
> MacOS X Mavericks yet. You appear to have a very new
> machine
> though
> (based on your GPU model), so this may be specific to your
> particular
> type of GPU. Just to verify, you have the same problem when
> you
> run
> a non-CUDA build of VMD, or not? I ask because there's an
> interaction
> between CUDA and OpenGL in that they both make use of
> NVIDIA's special TLS (thread local storage) library, and if
> there's
> any mismatched version going on there, I could envision that
> causing
> trouble. If the same problem occurs both with and without
> CUDA,
> then
> I would assume it is purely an OpenGL issue.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Wed, Mar 05, 2014 at 01:50:32AM +0000, Phillips, Carolyn
> L.
> wrote:
>
> 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>
> 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>
> 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>
> 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
>
> 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/
>
> --
> 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/ 

-- 
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/