VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Sep 14 2009 - 14:45:02 CDT

On Mon, Sep 14, 2009 at 3:08 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> This is almost certainly a failure of your Intel OpenGL driver,
> and many others have encountered similar issues with those chipsets/drivers.
> You have a few options:
> 1) report the bug to Intel in hopes of getting a fixed driver

the intel OpenGL driver in fedora 11 is beyond hope of repair.
i have a test machine set up with it and it is a catastrophe, due
to massive rewrites in the kernel interface. the one in fedora 10
works a bit better with VMD, but still _requires_ the environment
variables VMDSIMPLEGRAPHICS to 1 _and_ vblank_mode to 0
in order to minimize crashes.

> 2) try installing a newer/different Intel graphics driver

i found that the intel driver version in the fedora 12 alpha
it working a bit better than fedora 11, but there are frequent
changes and there are still vblank issues and other features
not fully working, so at the moment there is no good solution
for running VMD with intel chipset graphics other than turning
it off and plugging in a decent card.

cheers,
   axel.

> 3) try running with the environment variable VMDSIMPLEGRAPHICS set to 1
> 4) buy/install a different brand of GPU that has better Linux driver support
>
> You'll see from searching VMD-L that the issues with the Intel chipsets
> (especially these older ones) and their Linux drivers have existed for quite
> a long time now. I always advise people to follow option 1) first, as
> the bugs won't get fixed unless people tell Intel about them. It's also

> good that Intel realizes that they are losing sales to other vendors when,
> after following the remaining steps, users end up ultimately going with
> option 4) and subsequently avoid Intel's graphics products from then on.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Sun, Sep 13, 2009 at 05:16:28PM -0700, Rob wrote:
>>
>> Hi,
>>
>> I have installed the recent VMD binaries for linux:
>> "VMD for LINUX, version 1.8.7 (August 1, 2009)"
>>
>> When I type the vmd command (located at /usr/local/bin/vmd),
>> I get following output in my terminal:
>>
>> ============================
>> $ vmd
>> Info) VMD for LINUX, version 1.8.7 (August 1, 2009)
>> Info) http://www.ks.uiuc.edu/Research/vmd/
>> Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
>> Info) Please include this reference in published work using VMD:
>> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
>> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
>> Info) -------------------------------------------------------------
>> Info) Multithreading available, 4 CPUs detected.
>> Info) Free system memory: 1549MB (77%)
>> Info) No CUDA accelerator devices available.
>> Warning) Detected X11 'Composite' extension: if incorrect display occurs
>> Warning) try disabling this optional X server feature.
>> Info) OpenGL renderer: Mesa DRI Intel(R) 965G GEM 20090114 x86/MMX/SSE2
>> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
>> Info) Full GLSL rendering mode is available.
>> Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
>> Segmentation fault
>> $
>> ==================================
>>
>> Meanwhile, the OpenGL window has come up for just a second, before
>> the segmentation fault occurs, and then that window collapses.
>>
>> In /var/log/messages, I get this line:
>>
>> kernel: vmd_LINUX[1316]: segfault at 4 ip 00157eef sp bfd7d4b0 error 4 in libX11.so.6.2.0[110000+12b000]
>>
>> When I do a strace of vmd, the following text appears when the
>> segmentation fault occurs:
>>
>> =====================================
>> ...
>> Info) OpenGL renderer: Mesa DRI Intel(R) 965G GEM 20090114 x86/MMX/SSE2
>> Info) Features: STENCIL MDE CVA MTX NPOT PP PS GLSL(OVF)
>> Info) Full GLSL rendering mode is available.
>> Info) Textures: 2-D (4096x4096), 3-D (256x256x256), Multitexture (8)
>> ) = ? ERESTARTNOHAND (To be restarted)
>> --- SIGCHLD (Child exited) @ 0 (0) ---
>> sigreturn() = ? (mask now [INT CHLD])
>> wait4(-1, [{WIFSIGNALED(s) && WTERMSIG(s) == SIGSEGV}], WNOHANG, {ru_utime={0, 977851}, ru_stime={0, 111982}, ru_maxrss=0, ru_ixrss=0, ru_idrss=0, ru_isrss=0, ru_minflt=21923, ru_majflt=0, ru_nswap=0, ru_inblock=0, ru_oublock=0, ru_msgsnd=0, ru_msgrcv=0, ru_nsignals=0, ru_nvcsw=380, ru_nivcsw=137}) = 1728
>> wait4(-1, 0xbfd357cc, WNOHANG, 0xbfd35784) = -1 ECHILD (No child processes)
>> rt_sigprocmask(SIG_SETMASK, [], NULL, 8) = 0
>> write(17, "Segmentation fault\n"..., 19Segmentation fault
>> ) = 19
>> ...
>> ====================================
>>
>> Any idea what is the problem here?
>>
>> Is this a problem with vmd, or have I updated to a buggy X library from X.org?
>>
>> Thanks,
>> Rob.
>>
>>
>>
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> 

-- 
Dr. Axel Kohlmeyer    akohlmey_at_gmail.com
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.