[gmx-users] GPU performance question

[Mark Abraham]

Hi,

It certainly can be normal :-) Having four people cook your dinner instead
of one isn't going to make it take a quarter of the time unless it was
already going to be a banquet! Do check out the end of the log file for
analysis from mdrun.

Mark

On Fri, Oct 7, 2016 at 8:23 PM Irem Altan <irem.altan at duke.edu> wrote:

> Hi,
>
> I had been running simulations using our local cluster, but now I’m doing
> some tests on SDSC’s Comet. Even though I use considerably higher
> resources, the speed-up is only two-fold. I was wondering if I was doing an
> error while setting the simulations up, that result in lower performance.
>
> My previous setup (1 node):
>
> 1 MPI thread, 6 OpenMP threads, 1 GPU
> (nVidia Tesla K80, 6 cores, 6 logical cores (intel xeon e5-2690))
>
> ==> 52.705 ns/day
>
> the command was:
>
> gmx mdrun -v -deffnm npt
>
> ————————————————
>
> The current setup (1 node):
>
> 4 MPI processes, 6 OpenMP threads per MPI process, 4 GPUs
> (nVidia Tesla K80, 24 cores, 24 logical cores (intel xeon e5-2680))
>
> ==> 100.577 ns/day
>
> the command:
>
> ibrun gmx_mpi mdrun -v -deffnm npt
> (found it in an example in Comet)
> ___________
>
> The .mdp file was identical (see end of e-mail for the contents). The
> speed-up is only two-fold, despite the fact that I quadruple the resources.
> Is this normal? If not, how can I optimize my setup? (Note: the simulation
> in the second setup has ~20,000 less
>
> Best,
> Irem
>
> .mdp file:
>
> itle       = NPT Equilibration
> define      = -DPOSRES          ; position restrain the protein
> ; Run parameters
> integrator  = md                ; leap-frog integrator
> nsteps      = 500000             ; 2 * 50000 = 100 ps
> dt          = 0.002             ; 2 fs
> ; Output control
> nstxout     = 5000              ; save coordinates every 2 ps
> nstvout     = 5000              ; save velocities every 2 ps
> nstenergy   = 5000              ; save energies every 2 ps
> nstlog      = 5000              ; update log file every 2 ps
> ; Bond parameters
> continuation         = no        ; Initial simulation
> 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
> cutoff-scheme = Verlet
> ns_type     = grid              ; search neighboring grid cels
> nstlist     = 20                 ; 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             ; Weak coupling for initial
> equilibration
> tc-grps     = Protein   Non-Protein ; two coupling groups - more accurate
> tau_t       = 0.1 0.1         ; time constant, in ps
> ref_t       = 277 277         ; reference temperature, one for each group,
> in K
> ; Pressure coupling is on
> pcoupl              = Berendsen     ; Pressure coupling on in NPT, also
> weak coupling
> pcoupltype          = isotropic     ; uniform scaling of x-y-z box vectors
> tau_p               = 2.0           ; time constant, in ps
> ref_p               = 1.0           ; reference pressure (in bar)
> compressibility     = 4.5e-5        ; isothermal compressibility, bar^-1
> refcoord_scaling    = com
> ; Periodic boundary conditions
> pbc     = xyz                   ; 3-D PBC
> ; Dispersion correction
> DispCorr    = EnerPres          ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel     = yes               ; Velocity generation is on
> gen_temp    = 277               ; temperature for velocity generation
> gen_seed    = -1                ; random seed
> ; COM motion removal
> ; These options remove COM motion of the system
> nstcomm         = 10
> comm-mode = Linear
> comm-grps = System
> --
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