From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Sep 17 2003 - 13:07:47 CDT
What system is this running? Does it happen with the apoa1 benchmark at
http://www.ks.uiuc.edu/Research/namd/utilities/apoa1.tar.gz ?
Both of these errors indicate a breakdown of NAMD's spatial decomposition,
either due to simulation instability or possibly some data corruption.
-Jim
On Wed, 17 Sep 2003, Jerry Ebalunode wrote:
> Hi Jim,
> I got this removed this warning by taking blocking out the CXXO...
> optimization line. However I now have this new warning " BUG ALERT: Bad
> global exclusion count!" and also this new warning when I turn on PME.
>
> OPENING EXTENDED SYSTEM TRAJECTORY FILE
> ERROR: Stray PME grid charges detected: 8 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 8 sending to 15 for planes 117 118 119
> ERROR: Stray PME grid charges detected: 12 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 12 sending to 15 for planes 117 118
> 119
> ERROR: Stray PME grid charges detected: 6 sending to 15 for planes 117 118 119
> ERROR: Stray PME grid charges detected: 16 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 15 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 13 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 14 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 11 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 11 sending to 15 for planes 117 118
> 119
> ERROR: Stray PME grid charges detected: 10 sending to 15 for planes 117 118
> 119
> ERROR: Stray PME grid charges detected: 10 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 9 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 9 sending to 15 for planes 117 118 119
> ERROR: Stray PME grid charges detected: 7 sending to 15 for planes 117 118 119
> ERROR: Stray PME grid charges detected: 7 sending to 3 for planes 0
> ERROR: Stray PME grid charges detected: 5 sending to 15 for planes 117 118 119
> ERROR: Stray PME grid charges detected: 4 sending to 15 for planes 117 118 119
>
>
> On Wednesday 17 September 2003 01:11 am, you wrote:
> > Hi Jerry,
> > I am running NAMD on linux debian and I get the same message. I was
> > using the older version 2.5b1 and someone suggest I try the new version
> > 2.5b. Now, I get a another warning Bad global exclusion count,
> > possible error. The previous version would end with segmentaion fault
> > but this new version doesn't seg fault it just stalls at the same
> > spot. I have now narrowed it to a problem with the pdb or psf
> > files...who knows if I'm correct, I've posted another meassage. Other
> > proteins I run do not give this problem which is why I think it might
> > be pdb or psf. Does your program work with other proteins or gives
> > this on all you try?
> > Cheers,
> > Cheri
> >
> >
> >
> >
> > ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> > Cheri M. Turman
> > Graduate Student
> > University of Texas-Houston Medical School
> > 6431 Fannin
> > Houston, TX 77030
> >
> > e-mail: cheri.m.turman_at_uth.tmc.edu
> > Ph.: 713-500-6126
> > Fax: 713-500-0652
> >
> > ----- Original Message -----
> > From: Jerry Ebalunode <jebalunode_at_UH.EDU>
> > Date: Tuesday, September 16, 2003 1:44 pm
> > Subject: namd-l: output warning in using namd2 "Warning: Not all atoms
> > have unique coordinates."
> >
> > > Hi all,
> > > I just compiled namd2.5b2 on an itanium2 cluster that uses
> > > SCALI's
> > > implementation of the mpi. When I run the binary, I always get
> > > this warning
> > > "Warning: Not all atoms have unique coordinates." in the output
> > > log. Does
> > > anyone know how to correct this problem? I initially thought it
> > > had to do
> > > with the tcl or fftw libraries I was using, so used the
> > > precompiled
> > > libraries from http://www.ks.uiuc.edu/Research/namd/libraries/
> > > meant for my
> > > architecture. However, after recompiling and running namd2 I
> > > still had the
> > > same problems.
> > >
> > >
> > > Compiler information
> > > intel C/C++ compiler for itanium ecc version 7.1
> > >
> > > --
> > > Cheers,
> > >
> > > Jerry Ebalunode
> > > Graduate Research Assistant
> > > RM 402F Houston Science Center
> > > Phone: 713-743-8367
> > > Dept. of Biology and Biochemistry
> > > University of Houston.
> > > 4800 Calhoun Road
> > > Houston, TX 77204
>
> --
> Cheers,
>
> Jerry Ebalunode
> Graduate Research Assistant
> RM 402F Houston Science Center
> Phone: 713-743-8367
> Dept. of Biology and Biochemistry
> University of Houston.
> 4800 Calhoun Road
> Houston, TX 77204
>
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