From: Gabriel Jara (gabriel.fcq.unc.ar_at_gmail.com)
Date: Thu May 13 2010 - 11:34:49 CDT
Hi all,
I am trying to run NAMD on a SGE cluster with InfiniBand and paralleled with
OpenMPI. I am looking for support because I am very
beginner.
I have many questions.
- First at all, How charmrun parallels serial processes? To do this, does it
use mpirun? Is correct to run the serial version of Namd (Linux-x86_64) in a
cluster like this because of the InfiniBand? (This version runs well, but I
don't know If I am getting the best
performance of the cluster).
- I tried to run the Linux-x86_64-ibverbs (InfiniBand via OpenFabrics OFED,
no MPI needed) but I get a Segmentation fault (or violation) message using
AMBER topologies (not with the CHARMM ones of the namd test apo1.namd)
- I tried to compile NAMD_2.7b2 and NAMD_CVS, but i had an unusual error:
FATAL ERROR: Parallel IO can not be used with langevin On.
FATAL ERROR: See http://www.ks.uiuc.edu/Research/namd/bugreport.html
- I also tried to compile NAMD2.6 using config files of 2.7b2
(mpi-linux-x86_64) but this gave me another error:
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: run
ERROR: set
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
To compile I did thi
CHARMRUN
env MPICXX=mpicxx ./build charm++ mpi-linux-x86_64 pthreads --libdir
/opt/openmpi/lib --incdir /opt/openmpi/include --no-shared -O
-DCMK_OPTIMIZE=1
NAMD
./config Linux-x86_64-g++ --charm-arch mpi-linux-x86_64-pthreads
I even tested without pthreads.
In conclusion, I want to use the full potential of my cluster using NAMD on
OpenMPI and InfiniBand, but I couldn't do it.
Any help should be really appreciated, thanks in advance
Gabriel
-- Lic. Gabriel E. Jara INFIQC - CONICET Departamento de Química Orgánica Facultad de Ciencias Químicas Universidad Nacional de Córdoba Tel: ++54-351-4334170/4173 int. 132 Fax: ++54-351-4333030 X5000HUA - Córdoba -Argentina
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