From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Wed Sep 17 2003 - 07:54:46 CDT
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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