VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun Sep 21 2008 - 03:13:41 CDT

On Sun, 21 Sep 2008, shiladitya_at_jncasr.ac.in wrote:

SS> Hi Axel and others,
SS>
SS> first we used the env VMDSIMPLEGRAPHICS=1 vmd to launch vmd . it could
SS> load a mollecule(small xyz file) . but then the machine got hung.
SS>
SS> then we installed the latest nvidea graphics driver from their site. now
SS> we can load a molecule with or without env VMDSIMPLEGRAPHICS=1 option.
SS>
SS> but , only that, then the machine becomes slow and finally got hung. top
SS> shows that vmd_linux uses 99.9 % of cpu.

hmmm... this is very unusual. can you run other OpenGL programs without
problems, e.g., glxgears (a demo application that is usually installed)?

SS>
SS> we also ran with -debug (env VMDSIMPLEGRAPHICS=1 vmd -debug) option. however
SS> gdb does not show any error message.
SS>
SS>
SS> if i want to reinstall vmd, how to uninstall vmd?

you can just delete the directory where vmd installs itself.

SS> we are using linux opengl version (vmd-1.8.6.bin.LINUX.opengl.tar.gz)
SS> is it correct version for intel xeon processor based 64 bit machine?

well, that depends on whether you have installed a 64-bit OS version.
this kind of cpu runs just as fine with 32-bit...

try running: uname -i

if it returns i386 then you have the correct version,
if it returns x86_64, then you can try the LINUXAMD64 version.
nevertheless, the LINUX version of VMD should work under
x86_64 just as well. it may only happen, that you have to
install the 32-bit version of the latest nividia drivers
_and_ the 64-bit version, to get the proper runtime libraries
for both installed.

the symptoms you describe could also be related to the
graphics card overheating. i suggest to inspect the machine,
get rid of dust that may have been collected inside and
check that the heatsink fan is operating properly.

cheers,
   axel.

SS>
SS> regards,
SS> shiladitya sengupta
SS> TSU
SS> JNCASR
SS>
SS>
SS>
SS> > On Fri, 19 Sep 2008, shiladitya_at_jncasr.ac.in wrote:
SS> >
SS> > SS> Hello friends,
SS> > SS>
SS> > SS> we recently installed vmd 1.8.6 in a workstation.
SS> > SS>
SS> > SS> typing vmd on the terminal , successfully launches the vmd windows. SS>
SS> > SS> but then the machine gets hung up. neither mouse nor keyboard works
SS> .
SS> > the
SS> > SS> only way to get back to normal condition seems to reboot.
SS> >
SS> > that sounds a lot like a buggy or misconfigured graphics driver.
SS> >
SS> > please see the linux release notes on the VMD homepage for a list of
SS> known problems and workarounds. for starters, i would suggest to try
SS> launching VMD with: env VMDSIMPLEGRAPHICS=1 vmd
SS> > that will turn off most of the advanced features in the OpenGL support.
SS> >
SS> > SS> i tried to ssh login from a remote machine and killed the process
SS> vmd.
SS> > SS> even after the process got killed , the vmd windows remain (hung up
SS> state)
SS> > SS>
SS> > SS> it is a 64 bit machine.
SS> > SS> the os is redhat enterprise linux (2.6.9-22.ELsmp).
SS> >
SS> > also please make sure that you have the latest updates for your
SS> > OS and the graphics driver. sometime, updates of the OS overwrite parts
SS> of the graphics driver and a re-install of the driver is
SS> > required.
SS> >
SS> > cheers,
SS> > axel.
SS> >
SS> > SS>
SS> > SS> the following is the startup message in the vmd-console :
SS> > SS>
SS> > SS> Info) Please include this reference in published work using VMD: SS>
SS> Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual SS>
SS> Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
SS> Info)
SS> > SS> ------------------------------------------------------------- Info)
SS> SS> Multithreading available, 8 CPUs detected.
SS> > SS> Info) Free system memory: 7750MB (97%)
SS> > SS> Info) OpenGL renderer: Quadro FX 1700/PCI/SSE2
SS> > SS> Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVF)
SS> Info)
SS> > SS> Full GLSL rendering mode is available.
SS> > SS> Info) Textures: 2-D (8192x8192), 3-D (2048x2048x2048),
SS> Multitexture
SS> > (4)
SS> > SS> vmd >
SS> > SS>
SS> > SS>
SS> > SS> please help.
SS> > SS>
SS> > SS> regards,
SS> > SS>
SS> > SS> shiladitya sengupta
SS> > SS> TSU
SS> > SS> JNCASR
SS> > SS>
SS> > SS>
SS> > SS>
SS> > SS>
SS> > SS>
SS> >
SS> > --
SS> > =======================================================================
SS> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
SS> > Center for Molecular Modeling -- University of Pennsylvania
SS> > Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
SS> tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
SS> =======================================================================
SS> If you make something idiot-proof, the universe creates a better idiot.
SS> >
SS>
SS>
SS> 

-- 
=======================================================================
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.