AMBER Archive (2004)

Subject: AMBER: sander8 performance

From: Oliver Hucke (
Date: Tue Jun 01 2004 - 12:53:46 CDT

Dear Amber users/developers,

I am using sander of amber8 compiled with ifort on dual processor nodes
of a linux cluster (Fedora 1.0). I am using the shmem device of mpich,
which gave me a speedup of a factor of ~1.5 compared to the ch_p4
device. I am working with Dual Xeon nodes running at 2.4 GHz, with 1 GB RAM.

With a sytem of ~50000 atoms, PME, cut=8.0, I get 75000 steps per day,
using two processors. This seems rather poor compared to the 117000
steps that were obtained in the hemoglobin benchmark with two Xeon
processors (2.0 GHz), with ifc7 compiled amber8, as I read on the amber
benchmarks page.

Do you have ideas on how to increase the performance?
What about using lam instead of mpich?
Should the hyperthreading capability rather be switched on or off?

I would like to use sander instead of pmemd because I want to compare
results from MM-PBSA with those from TI calculations - TI is not
possible with pmemd, right?

Thanks very much,


Oliver Hucke, Dr. Health Sciences Building - K418C University of Washington 1959 NE Pacific St. Dept. of Biochemistry phone: (206) 685 7046 Box 357742 fax : (206) 685 7002 Seattle, WA 98195-7742 email: _______________________________________________________________

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