any experiences with executing parallel NAMD in a NAMD simulation

From: Yinglong Miao (yimiao_at_indiana.edu)
Date: Mon Feb 09 2009 - 15:59:07 CST

Dear NAMD developers/users,

I have been trying to embed a parallel NAMD run in a bigger NAMD simulation;
that is by calling "exec mpirun -np $nprocessors -machinefile $machinelist
namd2 ${str}.conf" in a NAMD configuration script to run a different
structure and generate proper output for the big simulation. The program
runs fine except that the embedded part is executed much more slowly than
expected (~1/5 of the speed) and sometimes such error messages pop up: "Max
retransmit retries reached (829) for message". I thought it's because the
message passing is slowed down and the MPI environment is messed up upon
NAMD exit for the embedded run. Is there anybody have experiences with this?
How to run the embedded part with normal speed? Any suggestions will be
greatly appreciated.

Thanks!

-- 
Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981

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