VMD-L Mailing List
From: Jinhua Zhang (jhz666_at_yahoo.com)
Date: Mon Jun 19 2006 - 13:28:18 CDT
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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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