VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jun 21 2007 - 10:37:44 CDT

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
=======================================================================
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