VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jun 21 2007 - 10:45:07 CDT

Indeed, quite possibly. I wish these things were simpler, but as always,
these systems have grown far more complex with time.

  John

On Thu, Jun 21, 2007 at 11:37:44AM -0400, Axel Kohlmeyer wrote:
> hi!
>
> kernel 2.6.9-5 on RHEL-4 is one of those with
> the multi-threading bug (and the machine is reporting
> two processors!). vmd will start in text mode, but crash
> when loading .pdb or .xyz files.
>
> so it might well be, that you are seeing two problems at
> the same time.
>
> cheers,
> axel.
>
> On 6/21/07, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >Hi,
> > I'm going to guess that the root of your problem is the
> >generic video driver. What graphics chip/board is in this machine?
> >If you have an ATI or NVIDIA card, then you should be running
> >the OpenGL video drivers provided by the vendors. If it is some
> >random other GPU/chipset, then you may not have very many options
> >except to upgrade to a video board that is better supported on Linux.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Thu, Jun 21, 2007 at 10:01:27AM +0530, Vijaya Brahma wrote:
> >> Sir,
> >>
> >> Regarding the previous mail dealing with the problem of inability to load
> >> graphical represenation in VMD 1.8.6 for Linux (32-bit x86) using OpenGL
> >> I am hereby mentioning the specifications of my system:-
> >>
> >> linux Distribution version
> >> Linux version 2.6.9-5.ELsmp (bhcompile_at_decompose.build.redhat.com)
> >> (gcc version 3.4.3 20041212 (Red Hat 3.4.3-9.EL4)) #1 SMP
> >>
> >> kernel:
> >> Linux 2.6.9-5.ELsmp #1 SMP
> >> i686 i686 i386 GNU/Linux
> >>
> >> CPU type:
> >> i686
> >>
> >> CPU model:
> >> model name : Intel(R) Pentium(R) 4 CPU 3.60GHz
> >>
> >> libc version:
> >> libtermcap.so.2 => /lib/libtermcap.so.2 (0x00b36000)
> >> libdl.so.2 => /lib/libdl.so.2 (0x00928000)
> >> libc.so.6 => /lib/tls/libc.so.6 (0x007d8000)
> >> /lib/ld-linux.so.2 (0x007bb000)
> >>
> >> video card:
> >> VESA driver generic
> >>
> >> Video Driver:
> >> server glx vendor string: SGI
> >> server glx version string: 1.2
> >> client glx vendor string: SGI
> >> client glx version string: 1.4
> >> OpenGL vendor string: Mesa project: www.mesa3d.org
> >> OpenGL renderer string: Mesa GLX Indirect
> >> OpenGL version string: 1.2 (1.5 Mesa 6.1)
> >>
> >>
> >> I was wondering if there is problem is in VMD finding the Mesa/OpenGL
> >> shared libraries,the command
> >> vmd -dispdev text
> >> confirmed that the problem does not lie there as it started
> >> normally,showing absolutely no error . The result was as follows :-
> >> Info) VMD for LINUX, version 1.8.6 (April 6, 2007)
> >> 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.
> >> Info) Free system memory: 612MB (60%)
> >> vmd >
> >>
> >>
> >> Kindly help
> >>
> >> Regards,
> >> --
> >> ....................................................................
> >> VIJAYA BRAHMA
> >> ...................................................................
> >> Research Scholar
> >> Protein Science & Engineering
> >> Institute of Microbial Technology(IMTECH)
> >> Chandigarh
> >> India
> >> http://www.imtech.res.in/bic/phd.html
> >>
> >> >
> >> > Hi,
> >> > Judging by the behavior you're observing, the system hang indicates
> >> > either a bad kernel, or a bad video driver. Since your email doesn't
> >> > indicate what video card or driver you're using, it's hard for me to
> >> > judge specifically. Those are the two most likely candidates leading
> >> > to your problem. Since the system hang occurs when you change the
> >> > graphical representation, I wonder if it might be a problem with the
> >> > video card or video driver. If you tell me more about your system,
> >> > I may have further suggestions.
> >> >
> >> > John Stone
> >> > vmd_at_ks.uiuc.edu
> >> >
> >> > On Mon, Jun 18, 2007 at 10:29:06AM +0530, Vijaya Brahma wrote:
> >> >> Sir
> >> >> With due respect i want to state the problem that I am facing while
> >> >> running VMD 1.8.6 for Linux (32-bit x86) using OpenGL, downloaded via
> >> >> http://www.ks.uiuc.edu/Research/vmd/
> >> >> The problem is that I am unable to load a PDB file, as soon I load a
> >PDB
> >> >> file the VMD crashes. I have tried to debug and run, using following
> >> >> command
> >> >> vmd -debug
> >> >> (gdb) run
> >> >> as a consequence I am able to load the PDB file but when I try to
> >change
> >> >> the graphical representation of the molecule, the system hangs:-
> >> >> these are the steps that occured in the terminal,
> >> >>
> >> >> vmd > mol new
> >> >> /home/vbrahma/Desktop/STRUCTURAL-COMPARISON/epo/PDB/1CN4.pdb
> >> >> Info) Using plugin pdb for structure file
> >> >> /home/vbrahma/Desktop/STRUCTURAL-COMPARISON/epo/PDB/1CN4.pdb
> >> >> Info) Using plugin pdb for coordinates from file
> >> >> /home/vbrahma/Desktop/STRUCTURAL-COMPARISON/epo/PDB/1CN4.pdb
> >> >> Info) Determining bond structure from distance search ...
> >> >> Info) Eliminating bonds duplicated from existing structure...
> >> >> [New Thread 45882288 (LWP 29963)]
> >> >> [Thread 45882288 (LWP 29963) exited]
> >> >> [New Thread 62696368 (LWP 29964)]
> >> >> [Thread 62696368 (LWP 29964) exited]
> >> >> Info) Analyzing structure ...
> >> >> Info) Atoms: 4604
> >> >> Info) Bonds: 4709
> >> >> Info) Residues: 604
> >> >> Info) Waters: 15
> >> >> Info) Segments: 1
> >> >> Info) Fragments: 19 Protein: 4 Nucleic: 0
> >> >> 0
> >> >> Info) Finished with coordinate file
> >> >> /home/vbrahma/Desktop/STRUCTURAL-COMPARISON/epo/PDB/1CN4.pdb.
> >> >> vmd > Info) In any publication of scientific results based in part or
> >> >> Info) completely on the use of the program STRIDE, please reference:
> >> >> Info) Frishman,D & Argos,P. (1995) Knowledge-based secondary
> >structure
> >> >> Info) assignment. Proteins: structure, function and genetics, 23,
> >> >> 566-579.
> >> >> Detaching after fork from child process 29965.
> >> >> ptrace: No such process.
> >> >> [Switching to Thread 62696368 (LWP 29964)]
> >> >> Cannot remove breakpoints because program is no longer writable.
> >> >> It might be running in another process.
> >> >> Further execution is probably impossible.
> >> >> 0x080f8fbc in BaseMolecule::~BaseMolecule$delete ()
> >> >> (gdb)
> >> >>
> >> >> Kindly help,
> >> >>
> >> >> THanking You,
> >> >>
> >> >> Regards
> >> >> --
> >> >> ...................................................................
> >> >> VIJAYA BRAHMA
> >> >> ..................................................................
> >> >> Research Scholar
> >> >> Protein Science & Engineering
> >> >> Institute of Microbial Technology(IMTECH)
> >> >> Chandigarh
> >> >> India
> >> >> http://www.imtech.res.in/bic/phd.html
> >> >
> >> > --
> >> > 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
> >> >
> >> >
> >
> >--
> >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
> >
> >
>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> Center for Molecular Modeling -- University of Pennsylvania
> Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
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