VMD-L Mailing List

From: Vijaya Brahma (vbrahma_at_imtech.res.in)
Date: Thu Jun 21 2007 - 22:40:47 CDT

Dear Sirs
Thanks for your reply, So since we are seeing two problems at the same
time what do yu suggest is the final solution to the problem???

....................................................................
>> >> VIJAYA BRAHMA
>> >> ...................................................................
>> >> Research Scholar
>> >> Protein Science & Engineering
>> >> Institute of Microbial Technology(IMTECH)
>> >> Chandigarh
>> >> India

>
> 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
> 

-- 
....................................................................
VIJAYA BRAHMA
...................................................................
Research Scholar
Protein Science & Engineering
Institute of Microbial Technology(IMTECH)
Chandigarh
India
http://www.imtech.res.in/bic/phd.html