VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 05 2007 - 16:30:10 CST

Hi,
  There's a dynamic linking issue with the 64-bit IRIX versions of
VMD affecting plugins that use Tcl, the main example of which is psfgen,
and by extension the other structure building tools that call psfgen,
(e.g. solvate). The problem occurs with certain versions of the IRIX
MIPSPro compilers, and since we haven't had software support for our sole
remaining SGI for many years now, we're stuck using the compiler versions
we've got. The workaround for this problem is to use the 32-bit builds
of VMD when you run the structure building tools on your IRIX machine.
Alternately, you could compile VMD from source, if you have the newest
SGI compilers and really feel the need for doing the structure building
on big systems that won't fit in 4GB of memory.

Let us know if you need more help with this.

  John

On Mon, Mar 05, 2007 at 04:16:01PM -0600, Rene Salmon wrote:
> 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
>
> 

-- 
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