VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 06 2005 - 17:28:14 CST

Daniel, Axel,
  If the LD_ASSUME_KERNEL trick that Axel suggests does cure the problem,
I'd like to have you test to see if that's necessary in order to run the
new VMD 1.8.3 test versions. If not, then there'd be no reason to add
that to the new startup script, but if so, then I agree that may be a
smart move, to prevent this problem from affecting others. Honestly though,
this is really a problem with the Linux threads runtime and not VMD itself.
I'd rather that the Linux distros fix their threads library to avoid this
kind of problem in the first place. No other OS has this type of
problem, AFAIK. I'll consider adding this to the VMD startup script
if we can gather enough evidence that this change will help avoid
this problem and not cause a new one with a subsequent rev of linux.

  John

On Thu, Jan 06, 2005 at 04:42:26PM +0100, Axel Kohlmeyer wrote:
>
> On Thu, 6 Jan 2005, Dr. Daniel James White PhD wrote:
>
> daniel,
>
> please try using
> export LD_ASSUME_KERNEL=2.4.20
>
> before you start up VMD.
> AFAIK, this is needed for all threaded applications,
> that were compiled under an older installation. i had
> this on several occasions already, also when running
> 32-bit x86 applications under x86_64.
>
> john, if this is a usable workaround, perhaps you could
> put something like the following into the linux specific
> architecture detection code of the vmd startup script:
>
> set kernelmajor=`uname -r | cut -c 1-1`
> set kernelminor=`uname -r | cut -c 3-3`
> if ( $kernelmajor == 2 && $kernelminor > 4 ) then
> setenv LD_ASSUME_KERNEL 2.4.20
> endif
>
> axel.
>
>
> DW> Hi John,
> DW>
> DW> I hadn't used VMD or a while
> DW> after I had upgraded my linux installation
> DW> so I tried to fire it up
> DW> but it quits straight away, after the main little window flashes up and
> DW> then vanishes,
> DW> leaving what looks like the process ID in my terminal window before
> DW> returning to the bash prompt.
> DW>
> DW> I removed the old installation, got a new copy, configured and
> DW> installed it,
> DW> then command
> DW> vmd
> DW> gave the same result as before.
> DW>
> DW> system:
> DW> athlon 1.? GHz
> DW> 1.5G ram
> DW> nVidia quadro 980 XGL running 6629 nVidia drivers
> DW> Fedora core linux 3
> DW> kernel 2.6.9-1.667
> DW>
> DW> how can I get more info so you can help me fix this problem
> DW>
> DW> cheers
> DW>
> DW> Dan
> DW>
> DW>
> DW>
> DW>
> DW> Dr. Daniel James White BSc. (Hons.) PhD
> DW> Cell Biology, Ambiotica C242
> DW> Department of biological and environmental science
> DW> PO Box 35
> DW> University of Jyväskylä
> DW> Jyväskylä FIN 40014
> DW> Finland
> DW> +358 14 260 4183 (work)
> DW> +358 468102840 (mobile)
> DW>
> DW> http://www.chalkie.org.uk
> DW> dan_at_chalkie.org.uk
> DW> white_at_cc.jyu.fi
> DW>
> DW>
>
> --
>
> =======================================================================
> Dr. Axel Kohlmeyer e-mail: axel.kohlmeyer_at_theochem.ruhr-uni-bochum.de
> Lehrstuhl fuer Theoretische Chemie Phone: ++49 (0)234/32-26673
> Ruhr-Universitaet Bochum - NC 03/53 Fax: ++49 (0)234/32-14045
> D-44780 Bochum http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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