[Dockdev] FW: opteron error

[John Irwin]

[Forwarded from Demetri]

> -----Original Message-----
> From: Demetri Moustakas [mailto:moustakas at gmail.com]
> Sent: Thursday, January 20, 2005 2:39 PM
> To: jji at cgl.ucsf.edu
> Subject: re: opteron error
> 
> Hi John,
> 
> That's strange- it may be the python problem Terry mentioned, but it
> might be something else.  Actually, this system RNG is deprecated-
> perhaps could you ask this person to email you their input file?  Make
> sure they have python installed, as it might be that the sphere file
> is not reduced, leaving 4000 spheres which will crash the program.
> Usually though, this reports an "Out of Memory" type error.
> 
> Its possible that on the two architechtures, there might be different
> enough RNG that the minimizer operates differently.  This would imply,
> however, that the user is vastly undersampling orientations.  We've
> found that as the # of orientations is increased, the results converge
> regardless of platform.
> 
> I'll sign up for those lists!  I'm glad you have those established-
> they will help build the user community (or at least tie UCSF into it
> better:).
> 
> I hope things are going well- talk w/you soon.
> 
> Demer
> 
> -----Original Message-----
> From: John Irwin [mailto:jji at cgl.ucsf.edu]
> Sent: Thu 1/20/2005 1:41 PM
> To: demer at socrates.Berkeley.EDU
> Cc: 'Terry Lang'
> Subject: FW: [Dockdev] opteron error
> 
> 
> Hi Demer
> 
> Any ideas about this one? If you haven't joined 'dock-fans' and 'dockdev'
> you might want to consider joining at mailman.docking.org
> 
> Hope all is well.
> Cheers
> 
> John
> > -----Original Message-----
> > From: dockdev-bounces at docking.org [mailto:dockdev-bounces at docking.org]
> On
> > Behalf Of Tan Guangming
> > Sent: Thursday, January 20, 2005 5:52 AM
> > To: dock_bugs
> > Cc: dockdev
> > Subject: [Dockdev] opteron error
> >
> > Hello!
> > I compiled dock 5.1.1 on Opteron processor Linux platform, it shows the
> > SEGMENTATION FAULT error message when I run the demo. I traced the
> program
> > and found that one instruction j=iy/NDIV in the function
> > Random_Number_Generator::independent_rand() gived the error,i.e. iy =
> > 19371779413, NDIV=67108862, however, j = 8156!
> > Besides, the final results on AMD Opteron is different from that on
> Intel
> > Xeon!
> > Xeon:
> >  .  ...
> >       Orientations Passed : 231
> >  .....
> >       Energy score: -40.376114
> >                       vdw:  -19.698305
> >                       es:       -20.677811
> > Opteron:
> > .  ...
> >       Orientations Passed : 233
> >  .....
> >       Energy score: -50.252425
> >                       vdw:  -23.808451
> >                       es:       -21.243562
> > Why?
> >
> >
> >
> >
> >
> >         Tan Guangming
> >                          National Research Center for Intelligent
> Computing
> > Systems,
> >                          Institute of Computing Technology,
> >                          Chinese Academy of Sciences
> >
> >                          6#, South Road, Kexueyuan, Zhongguancun,
> >                      Beijing, P.R.China
> >                      P.O.Box 2704   Zip Code 100080
> >
> >                Phone: 86-10-62565533 ext. 5730
> >         tgm at ncic.ac.cn
> >           2005-01-20