AW: GPU/CPU workstation optimal simulation parameters for NAMD2.9 performance

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Wed Feb 19 2014 - 01:38:53 CST

Well I will list what I'm using, everything else is more or less default.

In config:

twoawayx yes #depends on system size, should be tested
twoawayy yes #worth to try if twoawayx is turned on already and brought
improvement
fullelectfrequency 4

to the namd2 binary:

+ignoresharing

In general: You shouldn't use both the GPUs together only the K20c as they
are too different. You should disable Hyper-Threading at all (BIOS).

Good luck

Norman Geist.

> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Pino, James Christopher
> Gesendet: Dienstag, 18. Februar 2014 19:01
> An: namd-l_at_ks.uiuc.edu
> Betreff: namd-l: GPU/CPU workstation optimal simulation parameters for
> NAMD2.9 performance
>
>
> Hello,
> I have a question about NAMD performance on GPU/CPU workstation. I am
> using Ubunto 12.04.
> The station has two Keplar K20c and a Quadro K5000 and two Intel Xeon
> E5 v2/cores, 8 core double threaded, 32 cpu.I have a binary multi-core
> NAMD 2.9 CUDA.CUDA-5.5
> As for my system at study, it is a lipid bilayer containing ~50k lipid
> atoms, with tip3waters and ions for a total of 189225 atoms. I am
> running NPT using Nose-Hoover langevin barostat
> I have read through the mailing list multiple times, explored various
> resources, and spent many days varying a multitude of parameters.
> I have improved the performance from 0.241213 days/ns to 0.154686
> days/ns over the past 4 weeks.
> A few things I have observed
> +p odd # is always faster, I assume this is due to freeing one
> ldbUnloadZero yes ?
> +devices 0,2 works best with a combination of 3 to 5 *(0,2)
> using charmrun doesn't increase speed, in fact decreases slightly
>
> I have rans 100s of benchmarks, using multiple combinations of
>
> twoAwayX (Y,Z)
> PMEProcessors
> +p ( all the way from 1-32)
> +p with +ppn
> with 0 , 1 or 2 gpus, with all combinations CPUs
>
> The best combination (so far) (file 10ns.namd)
> ###########################################################
> set steps 5000000
> set tstep 2.0
> set stepscycle 21
> set temp 310
> set pres 1.01325
> set dcdfrq 1000
> set rstfrq 5000
> set xstfrq 1000
> set enefrq 960
> set prsfrq 1000
> set timfrq 1000
>
> set dcdout "Prod/Prod/Prod-70-80ns/mito_equil_prod_70_80ns.dcd"
> set rstout "Prod/Prod/Prod-70-80ns/equil_prod_70_80ns"
> set prfxout "Prod/Prod/Prod-70-80ns/equil_prod_70_80ns"
> set inputname "Prod/Prod/Prod-60-70ns/equil_prod_60_70ns"
>
> ldbUnloadZero yes
> twoAwayX no
> twoAwayY no
> twoAwayZ no
>
> temperature $temp
> paraTypeCharmm on
> parameters par_all36_lipid.prm
> structure mem_solv_ions.psf
> coordinates mem_solv_ions.pdb
>
> binCoordinates $inputname.coor ;
> extendedSystem $inputname.xsc ;
>
> # NAMD OUTPUT
> outputName $prfxout ;# defined above
> restartname $rstout ;# restart prefix
> restartfreq $rstfrq ;# how often to save restart files
> DCDfile $dcdout ;# dcd file name
> DCDfreq $dcdfrq ;# how often to save trajectories
> outputEnergies $enefrq ;# how often to report energies to
> stdout
> outputPressure $prsfrq ;# how often to report pressure to
> stdout
> outputTiming $timfrq ;# how often to report CPU timings
> and wall clock timings
>
> #Other settings
> rigidBonds all ;# hold the water bonds fixed (SHAKE)
>
> #Non-Bond Parameters
> exclude scaled1-4
> cutoff 12.
> 1-4scaling 1.0
> switching on
> switchdist 10.
> pairlistdist 14.
> margin .5
>
> #PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSpacing 1
>
> # Multiple Time Step (rRESPA) Parameters
> fullElectFrequency 3
> nonbondedFreq 1
>
> # Temperature Control
> langevin on
> langevinTemp $temp
> langevinDamping 1
> XSTfile $prfxout.xst
> XSTfreq $xstfrq
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# use pseudo-molecular virial
> (group H's). required by SHAKE
> useFlexibleCell yes ;# constant ratio (x-y plane) and
> constant area (x-y) also available
> useConstantRatio yes ;# constant x-y plane ratio
> langevinPiston on
> langevinPistonTarget $pres
> langevinPistonPeriod 100.
> langevinPistonDecay 50.
> langevinPistonTemp $temp
>
> numsteps $steps ;# see above
> timestep $tstep ;# see above
> stepspercycle $stepscycle ;# the number of steps per cycle
> #######################################################################
> #####
>
> Am I varying the correct parameters when optimizing the timing of my
> simulations?
> What are the optimal conditions when running a multicore workstation
> CPU/GPU simulation ?
> Are the obvious flaws in my command line or parameters that are hurting
> the capabilities of NAMD?
> Does the NAMD performance wiki mainly apply to CPU based simulations?
>
> Thank you
> James P
>
>

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