VMD-L Mailing List

From: Rene Salmon (rsalmon_at_tulane.edu)
Date: Mon Mar 05 2007 - 16:16:01 CST

Hi list,

I am getting a core dump while trying to run vmd-1.8.5 on IRIX 6.5.28.
I started vmd in debug mode and ran the following two commands and got a
core dump.

rsalmon_at_ccs1 107> vmd -debug
***
*** Running VMD in debugger, type 'run' at debugger prompt
***
dbx version 7.3.7 (96015_Nov16 MR) Nov 16 2004 07:34:16
*STRIPPED* Executable /usr/local/opt/vmd-1.8.5/lib/vmd/vmd_IRIX6_64
(dbx) run
Process 46079 (vmd_IRIX6_64) started
Info) VMD for IRIX6_64, version 1.8.5 (August 25, 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, 8 CPUs detected.
Info) OpenGL renderer: ATI Radeon 9000 OpenGL Engine
Info) Features: STENCIL
Info) Textures: 2-D (2048x2048)
vmd > display projection Orthographic
vmd > solvate bpti.psf bpti.pdb -o bpti.solv -rotate -t 9.0
Loading the structure for rotation...
Info) Using plugin pdb for structure file bpti.pdb
Info) Using plugin pdb for coordinates from file bpti.pdb
Info) Determining bond structure from distance search ...
Info) Analyzing structure ...
Info) Atoms: 882
Info) Bonds: 901
Info) Residues: 57
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
done
Initial volume is 126792.0358
Rotating the system...
done

New volume is 100729.129175
The system was rotated by 230.0 degrees around Z axis and 310.0 degrees
around X axis.
Info) Opened coordinate file bpti.pdb-rotated-tmp.pdb for writing.
Info) Using plugin psf for structure file bpti.psf
Info) Analyzing structure ...
Info) Atoms: 882
Info) Bonds: 896
Info) Residues: 57
Info) Waters: 0
Info) Segments: 1
Info) Fragments: 1 Protein: 1 Nucleic: 0
Info) Using plugin pdb for coordinates from file bpti.pdb-rotated-tmp.pdb
Info) Finished with coordinate file bpti.pdb-rotated-tmp.pdb.
Process 46079 Thread 0x10000 (vmd_IRIX6_64) stopped on signal SIGSEGV:
Segmentation violation (default) at [realfree:527 +0x4,0xd9fc948]
         Source (of
/xlv44/6.5.28m/work/irix/lib/libc/libc_64_M4/gen/malloc.c) not available for
Process 46079
(dbx)

These same exact two commands seem to work fine on our Linux box. Any
ideas? Thanks

Rene 

-- 
        Rene Salmon
        Tulane University
        Center for Computational Science
        http://www.ccs.tulane.edu
        rsalmon_at_tulane.edu
        Tel 504-862-8393
        Fax 504-862-8392