From: QMarcus_R=F6lz=22?= (m.roelz_at_gmx.de)
Date: Tue Sep 18 2007 - 08:17:15 CDT
Hello folks,
i am observing severe performance problems on our Linux-Cluster.
If i double the namd-processes from 1 to 2 performance doubles and processor load is about 90%, but if i double up from 6 to 12 processes performance even drops below the 6 processor performance and cpu usage is about 20%.
The setup is the following:
-32 machines, 2 dualcore processors each
-Linux version 2.6.16.21-0.8-smp
-Gigabit ethernet
-simulated system with about 12.000 atoms
I measured the network-performance with netperf and got about 900 Mbit/sec which should be fine. The clusternodes i use are not heavily loaded.
I am running out of ideas what to debug next. There must be a way to systematically debug these performance issues - but i didn't figure it out yet.
Any help & good ideas would greatly be appreciated.
Marcus (University of Greifswald)
My config-file: (i already experimented with stepspercycle, twoAwayX, outputtiming)
structure ./allwater_ws.psf
coordinates ./allwater_ws.pdb
set temperature 310
set outputname allwater_wsout
firsttimestep 0
paraTypeCharmm on
parameters ./par_all27_prot_na.prm
temperature $temperature
# Force-Field Parameters
exclude scaled1-4
1-4scaling 1.0
cutoff 12.
switching on
switchdist 10.
pairlistdist 14.5 ##13.5
# Integrator Parameters
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq 1
fullElectFrequency 2
stepspercycle 30
twoAwayX yes
outputTiming 20
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 5 ;# damping coefficient (gamma) of 5/ps
langevinTemp $temperature
langevinHydrogen off ;# don't couple langevin bath to hydrogens
# Output
outputName $outputname
restartfreq 5000 ;# 500steps = every 1ps
dcdfreq 250
outputEnergies 100
outputPressure 100
# Spherical boundary conditions
sphericalBC on
sphericalBCcenter 21.3367443085 29.2859230042 26.6932468414
sphericalBCr1 31.4426914717
sphericalBCk1 10
sphericalBCexp1 2
# Minimization
minimize 900 ;#100
reinitvels $temperature
run 30000000 ;# 5ps = 2500
-- Der GMX SmartSurfer hilft bis zu 70% Ihrer Onlinekosten zu sparen! Ideal für Modem und ISDN: http://www.gmx.net/de/go/smartsurfer
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:16 CST