Re: NAMD on Linux cluster with Myrinet

From: Alberto Santana (asantana_at_uprm.edu)
Date: Thu Oct 14 2004 - 13:59:27 CDT

Compiled with the -O0 option. Ran namd2 with the ++debug and it went very
well, no problems nor warnings of any kind. My guess is that now I can start
increasing the optimization level until it breaks.

Alberto

On Thursday 14 October 2004 02:20 pm, you wrote:
> 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 **
> *****************************************************************

-- 
							 Best wishes,
                                                         Alberto
+-------------------------------------------------------------------+
Alberto Santana, PhD
Department of Chemistry
University of Puerto Rico - Mayaguez
P.O. Box 9019
Mayaguez PR 00681-9019
Phone: (787) 832-4040 x3760
http://www.uprm.edu/~asantana
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