Hello,
I want some inputs on observed performance of protein-in-water
simulations run on a single server with 2 Intel Xeon E5-2660
processors. Each processor has 8C/16T, so total 16C/32T. My system is
composed of 1643 beta-microglobulin atoms and 24699 water atoms.
I ran several 500ps simulations with either 1, 2, or 4 simultaneous
simulations on one server. Performance using the verlet and group
schemes are reported below:
For Verlet:
mdrun -ntomp N -deffnm file where N is the no. of threads
for Single simulation, 32 ns/day (N= 32 threads)
Two simultaneous simulations, 4 + 0.25 = 4.25ns/day ( with N= 16
threads each)
Four simultaneous simulations, 3.36+0.11+0.11+0.10=3.68ns/day.
(N=8 threads each)
mdrun -nt N -deffnm file where N is the no. of threads
this gave me different results!
for Single simulation, 28 ns/day (N= 32 threads)
Two simulations, 13.8+13.5=27.3 ns/day ( with N= 16 threads each)
-----------------------------------------------------------------------------------------------------------------------------------------------------------------------
For Group:
-ntomp option is not available with Group cutoff-scheme.
mdrun -nt N -deffnm file where N is the no. of threads
for Single simulation, 38.5ns/day (N= 32 threads)
Two simulations, 22.1+22.1=44.2 ns/day ( with N= 16 threads each)
Four simulations, 12+11.9+12.2+11.8=48 ns/day ( N=8 threads each).
Also, using -nt gives a warning to use -pin on , pinoffset option but
if I use this option I get reduction in the performance again! the
commands that I followed are:
For Group cutoff-scheme and two simultaneous simulations --
mdrun -nt 16 -pin on -pinoffset 0 -deffnm file
mdrun -nt 16 -pin on -pinoffset 8 -deffnm file
the performance was 13.063+12.250=25.313 ns/day
It is not clear to me why the performance decreases drastically on
running simultaneous simulations with the verlet scheme. What is the
correct way to use'-pin' option when running simultaneous simulations
on a single server with multiple processors?
The .mdp file that i used is (for Group, 'cutoff-scheme' option was omitted):
; Run parameters
integrator = md ; leap-frog integrator
nsteps = 250000 ; 2 * 250000 = 500 ps, 0.5 ns
dt = 0.002 ; 2 fs
; Output control
nstxout = 100 ; save coordinates every 2 ps
nstvout = 100 ; save velocities every 2 ps
nstxtcout = 100 ; xtc compressed trajectory output every 2 ps
nstenergy = 100 ; save energies every 2 ps
nstlog = 100 ; update log file every 2 ps
; Bond parameters
continuation = yes ; Restarting after NPT
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H bonds)
constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cells
nstlist = 5 ; 10 fs
rlist = 1.0 ; short-range neighborlist cutoff (in nm)
rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm)
rvdw = 1.0 ; short-range van der Waals cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for long-range
electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
; Temperature coupling is on
tcoupl = V-rescale ; modified Berendsen thermostat
tc-grps = Protein Non-Protein ; two coupling groups - more accurate
tau_t = 0.1 0.1 ; time constant, in ps
ref_t = 300 300 ; reference temperature, one for each
group, in K
; Pressure coupling is on
pcoupl = Parrinello-Rahman ; Pressure coupling on in NPT
pcoupltype = isotropic ; uniform scaling of box vectors
tau_p = 2.0 ; time constant, in ps
ref_p = 1.0 ; reference pressure, in bar
compressibility = 4.5e-5 ; isothermal compressibility of water, bar^-1
; Periodic boundary conditions
pbc = xyz ; 3-D PBC
; Dispersion correction
DispCorr = EnerPres ; account for cut-off vdW scheme
; Velocity generation
gen_vel = no ; Velocity generation is off
; CUTOFF SCHEME
cutoff-scheme = Verlet
Thanks for your time.
--
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