AMBER Archive (2006)

Subject: AMBER: PMEMD scaling

From: Tiziano Tuccinardi (tuccinardi_at_farm.unipi.it)
Date: Thu Dec 07 2006 - 02:46:49 CST

Hi all,
I 'm building a beowulf cluster: 2 (up to now) 2-cpu nodes Intel E6600
2,4 GHz Fsb 1066 4 MB cache (Core 2 Duo), 1 GB memory per node, gigabit
ethernet (switch interconnected, 3com Switch 2816) / MPICH2 1.0.4p1 /
Intel Fortran compiler 9.1.040 without Intel MKL.

I installed both amber8 and amber9 and these are my benchmark results:

AMBER8

JAC - NVE ensemble, PME, 23,558 atoms

#procs nsec/day scaling, %

    2 0.383 100
    4 0.631 82

AMBER9

JAC - NVE ensemble, PME, 23,558 atoms

#procs nsec/day scaling, %

    2 0.600 100
    4 0.857 71

FACTOR IX - NVE ensemble, PME, 90,906 atoms
#procs nsec/day scaling, %

    2 0.283 100
    4 0.395 70

Is it possible to have a decrease of scaling using "pmemd9" compared
with amber8, or I made a mistake during the installation? The
"configure" command that I used is:
./configure linux_em64t ifort mpich2

Many Thanks
Tiziano 

-- 

+++++++++++++++++++++++++++++++++++++
Tiziano Tuccinardi, PhD
Dip. Scienze Farmaceutiche
Via Bonanno 6, 56126 PISA
Tel ++39 050 2219572
Fax ++39 050 2219605
E-mail tuccinardi_at_farm.unipi.it <mailto:tuccinardi_at_farm.unipi.it>
http://www.mmvsl.farm.unipi.it/staff/tiziano-tuccinardi/
+++++++++++++++++++++++++++++++++++++

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