From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Thu Oct 14 2004 - 13:20:59 CDT
HI Alberto
Ramp down the optimization for namd and add the ++debug switch when
running the namd test case. I have seen this error before but it was a
long time ago. It might have even been a input script problem when I saw
it. So just check the system size parameters for any extraneous
characters.
Brian
On Thu, 14 Oct 2004, Alberto Santana wrote:
> I followed Florian's suggestion and built charm++ with:
>
> build charm++ mpi-linux icc gm2 -O2 -L/usr/rels/mpich/lib/shared
> -I/usr/rels/mpich/include -L/usr/rels/mpich/lib
> -L/opt/gm/lib -I/opt/gm/include -lmpich -lgm -DCMK_OPTIMIZE=1
>
> and added -lpmpich and -lpthread before compiling namd2, otherwise it won't
> compile.
>
> The charm++ test goes well. When running the BPTI files used to do the
> benchmark it aborts with
> ...
> Info: 2643 DEGREES OF FREEDOM
> Info: 449 HYDROGEN GROUPS
> Info: TOTAL MASS = 6446.48 amu
> Info: TOTAL CHARGE = 6 e
> Info: *****************************
> Info: Entering startup phase 0 with 43082 kB of memory in use.
> Info: Entering startup phase 1 with 43082 kB of memory in use.
> Info: Entering startup phase 2 with 43272 kB of memory in use.
> Info: Entering startup phase 3 with 43278 kB of memory in use.
> FATAL ERROR: Bug in PatchMap::initialize - negative grid dimension.
> FATAL ERROR: Bug in PatchMap::initialize - negative grid dimension.
> [0] MPI Abort by user Aborting program !
> [0] Aborting program!
>
> Note that I used -O2 as suggested by Gengbin
> (http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/0693.html)
>
> Alberto
>
> On Monday 11 October 2004 08:49 pm, you wrote:
> > Hello Alberto,
> >
> > i recently (two days ago) compiled NAMD 2.5 on my linux cluster with
> > myrinet. in order for charm to work with myrinet i compiled it with
> >
> > ./build charm++ mpi-linux gm2 -O3 -I$MPICH/include -L$MPICH/lib
> > -L$GM/lib -lmpich -lgm -DCMK_OPTIMIZE=1
> >
> > note the gm2 flag for gm version 2.xx. as i have athlon cpus i didn't
> > use icc but gcc3.3 instead. you must have mpich-gm >1.2.5..12 installed
> > in oder for everything to work (at least with the mpi-linux version).
> > mpich-gm should be compiled with the same compiler used for building charm.
> >
> > Regards
> >
> > Florian Barth
>
*****************************************************************
**Brian Bennion, Ph.D. **
**Computational and Systems Biology Division **
**Biology and Biotechnology Research Program **
**Lawrence Livermore National Laboratory **
**P.O. Box 808, L-448 bennion1_at_llnl.gov **
**7000 East Avenue phone: (925) 422-5722 **
**Livermore, CA 94550 fax: (925) 424-6605 **
*****************************************************************
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:38:55 CST