[gmx-users] Free-energy on GMX-2019.1 ( lower performance on GPU)
Mark Abraham
mark.j.abraham at gmail.com
Fri Mar 15 07:59:36 CET 2019
Hi,
How large is your perturbed region and your normal region? The FEP
short-ranged kernels run on the CPU, and are not written very well for
performance. So the larger the perturbed region, the worse things get.
Because there's a lot of extra CPU work when running FEP, you may see
improvements from also adding -pme gpu -bonded gpu to your mdrun
invocation, by moving such work off the CPU.
BTW lincs-order=12 is uselessly large, but is not the problem here.
Mark
On Fri, 15 Mar 2019 at 06:16 praveen kumar <praveenche at gmail.com> wrote:
> Dear All
>
> I am trying to run the free-energy simulation using TI method in gromacs
> 2019.1 in a GPU machine (containing two Nvidia Geforce 1080 TI cards ).
> But unfortunately, am unable to run the free-energy simulation run on GPU.
>
> The normal MD simulation (without free-energy )is able to run perfectly by
> making use of GPU, which gives us excellent speed up in the simulation.
> for example, 100 K atoms system is able to give us ~ 80 ns per day on a gpu
> card. (It uses > 80 % GPU usage)
> When I am trying to run the free-energy simulations for the same system,
> the performance drastically falls down to ~0.02 ns per day. (It uses 0 %
> GPU usage).
>
> I am pasting the MDP files for Normal MD simulation and Free-energy
> simulation below.
> npt. mdp (MD simulation)
>
>
> #####################################################################
> title = MD simulation
> ; Run parameters
> integrator = md ; leap-frog integrator
> nsteps = 100000000 ; 2 * 60000000 = 200 ns
> dt = 0.002 ; 2 fs
> ; Output control
> nstxout = 100000 ; save coordinates every 10.0 ps
> nstvout = 100000 ; save velocities every 10.0 ps
> nstfout = 100000 ; save forces every 10.0 ps
> nstenergy = 500 ; save energies every 10.0 ps
> nstlog = 5000 ; update log file every 10.0 ps
> nstxout-compressed = 5000 ; save compressed coordinates every
> 10.0 ps, nstxout-compressed replaces nstxtcout
> compressed-x-grps = System ; replaces xtc-grps
> ; Bond parameters
> continuation = yes ; Restarting after NVT
> constraint_algorithm = lincs ; holonomic constraints
> constraints = h-bonds ; 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 cells
> nstlist = 10 ; 20 fs, largely irrelevant with Verlet
> rcoulomb = 1.2 ; short-range electrostatic cutoff (in nm)
> rvdw = 1.2 ; short-range van der Waals cutoff (in nm)
> rvdw-switch = 1.0
> vdwtype = cutoff
> vdw-modifier = force-switch
> rlist = 1.2
> ; 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 = system ; Water ; two coupling
> groups - more accurate
> tau_t = 0.1 ; 0.1 ; time constant, in ps
> ref_t = 360 ; 340 ; reference
> temperature, one for each group, in K
> ; Pressure coupling is on
> ;pcoupl =no
> 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 ;1.0 ; reference pressure, in
> bar
> compressibility = 4.5e-5 ; 4.5e-5 ; isothermal
> compressibility of water, bar^-1
> ; Periodic boundary conditions
> pbc = xyz ; 3-D PBC
> ; Dispersion correction
> DispCorr = no ; account for cut-off vdW scheme
> ; Velocity generation
> gen_vel = no ; Velocity generation is off
> ######################################################################
> npt. mdp ( for free-energy simulation)
> ##########################################################################
>
> ; Run control
> integrator = sd ; Langevin dynamics
> tinit = 0
> dt = 0.002
> nsteps = 50000 ; 100 ps
> nstcomm = 100
> ; Output control
> nstxout = 500
> nstvout = 500
> nstfout = 0
> nstlog = 500
> nstenergy = 500
> nstxout-compressed = 0
> ; Neighborsearching and short-range nonbonded interactions
> cutoff-scheme = verlet
> nstlist = 20
> ns_type = grid
> pbc = xyz
> rlist = 1.2
> ; Electrostatics
> coulombtype = PME
> rcoulomb = 1.2
> ; van der Waals
> vdwtype = cutoff
> vdw-modifier = potential-switch
> rvdw-switch = 1.0
> rvdw = 1.2
> ; Apply long range dispersion corrections for Energy and Pressure
> DispCorr = EnerPres
> ; Spacing for the PME/PPPM FFT grid
> fourierspacing = 0.12
> ; EWALD/PME/PPPM parameters
> pme_order = 6
> ewald_rtol = 1e-06
> epsilon_surface = 0
> ; Temperature coupling
> ; tcoupl is implicitly handled by the sd integrator
> tc_grps = system
> tau_t = 1.0
> ref_t = 298
> ; Pressure coupling is on for NPT
> Pcoupl = berendsen
> tau_p = 1.0
> compressibility = 4.5e-05
> ref_p = 1.0
> ; Free energy control stuff
> free_energy = yes
> init_lambda_state = 0
> delta_lambda = 0
> calc_lambda_neighbors = 1 ; only immediate neighboring windows
> couple-moltype = IO ; name of moleculetype to decouple
> couple-lambda0 = vdw ; only van der Waals interactions
> couple-lambda1 = vdw-q ; turn off everything, in this case
> only vdW
> couple-intramol = no
> ; Vectors of lambda specified here
> ; Each combination is an index that is retrieved from init_lambda_state for
> each simulation
> ; init_lambda_state 0 1 2 3 4 5 6 7 8
> 9 10 11 12 13 14 15 16 17 18 19 20
> vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40
> 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00
> coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> ; We are not transforming any bonded or restrained interactions
> bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> ; Masses are not changing (particle identities are the same at lambda = 0
> and lambda = 1)
> mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> ; Not doing simulated temperting here
> temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00
> ; Options for the decoupling
> sc-alpha = 0.5
> sc-coul = no ; linear interpolation of Coulomb (none
> in this case)
> sc-power = 1
> sc-sigma = 0.3
> nstdhdl = 10
> ; Do not generate velocities
> gen_vel = no
> ; options for bonds
> constraints = h-bonds ; we only have C-H bonds here
> ; Type of constraint algorithm
> constraint-algorithm = lincs
> ; Constrain the starting configuration
> ; since we are continuing from NVT
> continuation = yes
> ; Highest order in the expansion of the constraint coupling matrix
> lincs-order = 12
>
> ################################################################################
>
> for running simulation I am using the command below.:
>
> "gmx mdrun -v -s MD.tpr -deffnm MD -nb gpu -ntomp 10 -gpu_id 0 "
>
> Any help in solving this issue is much appreciated
>
> Thanking you in Advance
>
> Praveen
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