[gmx-users] Testing the performance of

[Richa Singh]

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.