From: Jerry Ebalunode (jebalunode_at_UH.EDU)
Date: Wed Sep 17 2003 - 06:21:53 CDT
Hi Jim,
Thanks. Commenting the CXXNOALIASOPTS line helped in preventing this error
warning. Thanks again.
On Wednesday 17 September 2003 02:19 am, Jim Phillips wrote:
> This error happens on every test simulation, and they used to work? Hmmm.
> Your compiler and processor are both newer that what I've gotten to test
> at NCSA, and the "unique coordinates" warning really means that extra
> exclusions were calculated, which is very unusual. You might want to back
> off on the optimization of ComputeNonbonded..., maybe start by commenting
> out CXXNOALIASOPTS from arch/Linux-ia64-ecc.arch. If that eliminates the
> warning then we're at least on the right track (but Itanium is pretty
> pointless without those optimization flags).
>
> -Jim
>
> On Tue, 16 Sep 2003, Jerry Ebalunode wrote:
> > 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
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:37:02 CST