From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Oct 11 2010 - 08:55:41 CDT
dear jianing,
> It seems that GPU version NAMD-CUDA could only show limited accelerate capacity,
> even worse, in all the simulation processes, the utilization of GPU is only 50%-60%.
on what kind of analysis do you base this assertion?
you get about 6x acceleration out of the first case
and about 7x out of the second case. you only seem
to have one GPU, so when oversubscribing it, you can
only get additional acceleration out of it, since the GPU
is already mostly occupied by the first host thread.
> So, is this the normal performance of the GPU-version of NAMD?
> Or is there something wrong with my job? If so, how can I improve the performance of my job?
rather than your input, it would have been important to
list what kind of hardware you are using.
cheers,
axel.
> P. S.
> Here is my input file:
> #############################################################
> ## ADJUSTABLE PARAMETERS ##
> #############################################################
>
> structure ../../kcsa_popcwi.psf
> coordinates ../../kcsa_popcwi.pdb
> outputName kcsa_! popcwieq-05_8cpu
>
> set temperature 310
>
> # Continuing a job from the restart files
> if {1} {
> set inputname kcsa_popcwieq-04
> binCoordinates ../../step4/$inputname.restart.coor
> binVelocities ../../step4/$inputname.restart.vel ;# remove the "temperature" entry if you use this!
> extendedSystem ../../step4/$inputname.restart.xsc
> }
>
> firsttimestep 752000
>
>
> #############################################################
> ## SIMULATION PARAMETERS ##
> #############################################################
>
> # Input
> paraTypeCharmm on
> pa! rameters ! ../../p ar_all27_prot_lipidNBFIX.prm
> if {0} {
> cellBasisVector1 98. 0. 0.
> cellBasisVector2 0. 98. 0.
> cellBasisVector3 0. 0. 96.
> cellOrigin -0.0390621498227 -0.0503903478384 0.05063835904
> }
> wrapWater on
> wrapAll on
> # Force-Field Parameters
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 10! .
> pairlistdist 13.5
>
>
> # Integrator Parameters
> timestep 2.0 ;# 2fs/step
> rigidBonds all ;# needed for 2fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
>
> #PME (for full-system periodic electrostatics)
> if {1} {
> PME yes
> PMEGridSizeX 100
> PMEGridSizeY 100
> PMEGridSizeZ 90
> }
>
>
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping &! nbsp; 1 ;# damping coefficient (! gamma) o f 5/ps
> langevinTemp $temperature
>
> # Constant Pressure Control (variable volume)
> if {1} {
> useGroupPressure yes ;# needed for 2fs steps
> #useFlexibleCell yes ;# no for water box, yes for membrane
> #useConstantArea yes ;# no for water box, yes for membrane
>
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 50.
> langevinPistonTemp $temperature
>
> }
>
>
> restartfreq 1000 ;# 1000steps = every 2ps
> dcdfreq 1000
> xstFreq 1000
> outpu! tEnergies 100
> outputPressure 50
>
>
> # Fixed Atoms Constraint (set PDB beta-column to 1)
> if {0} {
> fixedAtoms on
> fixedAtomsFile nottails.fix.pdb
> fixedAtomsCol B
> fixedAtomsForces on
> }
>
>
> #############################################################
> ## EXECUTION SCRIPT ##
> #############################################################
>
> # Minimization
> if {0} {
> minimize 1000
> reinitvels $tem! perature
> }
>
> run 5000 ;# 10 ps
>
>
> !
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://sites.google.com/site/akohlmey/ Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
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