VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 19 2006 - 14:43:06 CDT

Jinhua,
  What video card do you have in your machine? The debugging output
you included shows that you're using the Mesa GLX driver. Depending on
which video card you've got, you may get much better results from using
a vendor-provided OpenGL driver. The MESA GLX Indirect driver ought to work,
though it will be tremendously slow compared to a fully accelerated driver.
In your case, the MESA driver is crashing due to an internal assertion
failure in the driver, so your best option will be to switch to a different
driver. If you cannot switch to a different driver, you may get more stability
by setting the environment variable:
  setenv VMDSIMPLEGRAPHICS 1

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 19, 2006 at 11:28:18AM -0700, Jinhua Zhang wrote:
> Hi,
>
> I recently installed VMD1.8.4 on our IBM cluster (Dual
> Core AMD Opteron(tm) Processor 275 and Fedora Core 5
> Linux).
>
> VMD1.8.4 crashes immediately after I press the “Load”
> button for a selected .pdb file without any error
> message (similar to the one observed in VMD-L Mailing
> list:
> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5379.html).
>
> The output of running VMD within a debugger following
> the instructions given by John Stone
> (http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/5380.html)
> as follows:
>
>
>
> [jzhang_at_polyn proteins]$ tcsh
> [jzhang_at_polyn ~/proteins]$ source
> /home/program/bin/vmd
> [1] 26793
> [jzhang_at_polyn ~/proteins]$ gdb
> /home/program/CHEMISTRY/vmd/vmd_LINUXAMD64
> GNU gdb Red Hat Linux (6.3.0.0-1.122rh)
> Copyright 2004 Free Software Foundation, Inc.
> GDB is free software, covered by the GNU General
> Public License, and you are
> welcome to change it and/or distribute copies of it
> under certain conditions.
> Type "show copying" to see the conditions.
> There is absolutely no warranty for GDB. Type "show
> warranty" for details.
> This GDB was configured as
> "x86_64-redhat-linux-gnu"...(no debugging symbols
> found)
> Using host libthread_db library
> "/lib64/libthread_db.so.1".
>
> (gdb) run
> Starting program:
> /home/program/CHEMISTRY/vmd/vmd_LINUXAMD64
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> [Thread debugging using libthread_db enabled]
> [New Thread 47314080657984 (LWP 26813)]
> (no debugging symbols found)
> .
> .
> .
> (no debugging symbols found)
> Info) VMD for LINUXAMD64, version 1.8.4 (April 17,
> 2006)
> 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, 2 CPUs detected.
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> (no debugging symbols found)
> Info) OpenGL renderer: Mesa GLX Indirect
> Info) Features: STENCIL RN MDE MTX PP PS
> Info) GLSL rendering mode is NOT available.
> Info) Textures: 2-D (2048x2048), Multitexture (8)
> no debugging symbols found)
> .
> .
> .
> (no debugging symbols found)
> vmd > Info) Using plugin pdb for structure file
> /home/jzhang/proteins/alanin.pdb
> Info) Using plugin pdb for coordinates from file
> /home/jzhang/proteins/alanin.pdb
> Info) Determining bond structure from distance search
> ...
> Info) Analyzing structure ...
> Info) Atoms: 66
> Info) Bonds: 65
> Info) Residues: 12
> Info) Waters: 0
> Warning) Unusual bond between residues: 1 (none) and
> 2 (protein)
> Warning) Unusual bond between residues: 11 (protein)
> and 12 (none)
> Info) Segments: 1
> Info) Fragments: 1 Protein: 1 Nucleic: 0
> Info) Finished with coordinate file
> /home/jzhang/proteins/alanin.pdb.
> vmd_LINUXAMD64: indirect_vertex_array.c:659:
> emit_DrawArrays_old: Assertion `elements_per_request
> >= count' failed.
>
> Program received signal SIGABRT, Aborted.
> [Switching to Thread 47314080657984 (LWP 26813)]
> 0x000000323e32f765 in raise () from /lib64/libc.so.6
> (gdb) where
> #0 0x000000323e32f765 in raise () from
> /lib64/libc.so.6
> #1 0x000000323e331050 in abort () from
> /lib64/libc.so.6
> #2 0x000000323e328ed6 in __assert_fail () from
> /lib64/libc.so.6
> #3 0x0000003247f447cf in __glXPopArrayState () from
> /usr/lib64/libGL.so.1
> #4 0x0000003247f43fe1 in __glXPopArrayState () from
> /usr/lib64/libGL.so.1
> #5 0x000000000049aef5 in OpenGLRenderer::render ()
> #6 0x00000000004d644b in Displayable::draw ()
> #7 0x00000000004d646d in Displayable::draw ()
> #8 0x00000000004d646d in Displayable::draw ()
> #9 0x0000000000541f06 in Scene::draw ()
> #10 0x000000000054dd24 in VMDApp::VMDupdate ()
> #11 0x00000000005698c9 in main ()
>
> Jinhua
>
>
>
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-- 
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