VMD-L Mailing List

From: Rene Salmon (rsalmon_at_tulane.edu)
Date: Tue Mar 06 2007 - 10:18:18 CST

Hi,

Thanks for the reply. I installed the 32bit version and now everything
seems to be working fine.

Thanks again

Rene

> 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 3/5/07 4:16 PM, "Rene Salmon" <rsalmon_at_tulane.edu> 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