VMD-L Mailing List
From: Phillips, Carolyn L. (cphillips_at_anl.gov)
Date: Tue Mar 04 2014 - 19:31:53 CST
- Next message: Phillips, Carolyn L.: "Re: Issues using VMD 1.91. with CUDA on Mac OSX 10.9.1"
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- Next in thread: Phillips, Carolyn L.: "Re: Issues using VMD 1.91. with CUDA on Mac OSX 10.9.1"
- Reply: Phillips, Carolyn L.: "Re: Issues using VMD 1.91. with CUDA on Mac OSX 10.9.1"
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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/
- Next message: Phillips, Carolyn L.: "Re: Issues using VMD 1.91. with CUDA on Mac OSX 10.9.1"
- Previous message: Josh Vermaas: "Re: Mutate Residue Extension"
- In reply to: John Stone: "Re: Issues using VMD 1.91. with CUDA on Mac OSX 10.9.1"
- Next in thread: Phillips, Carolyn L.: "Re: Issues using VMD 1.91. with CUDA on Mac OSX 10.9.1"
- Reply: Phillips, Carolyn L.: "Re: Issues using VMD 1.91. with CUDA on Mac OSX 10.9.1"
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