VMD-L Mailing List

From: shiladitya_at_jncasr.ac.in
Date: Mon Sep 22 2008 - 18:45:30 CDT

Hi all,

> 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.
>

this is a 64 vit machine .. uname -i returns x86_64

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

i will get chance to check all these things only in the next week end.
till then i am not going to bother you all about this ...

thanks for the help ...

regards,
shiladitya sengupta
TSU
JNCASR

> 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.
>