[gmx-users] GPU performance, regarding
RAHUL SURESH
drrahulsuresh at gmail.com
Thu Dec 12 16:23:11 CET 2019
Hi Mark
Multiple energy groups is not implemented for GPUs, falling back to the
CPU. For better performance, run on the GPU without energy groups and then
do gmx mdrun -rerun option on the trajectory with an energy group .tpr file.
I got this line on the log file.
gmx_mpi mdrun -v -deffnm md work without gpu but on adding -nb gpu the
error prevails.
the output from gmx_mpi dump says
integrator = md
tinit = 0
dt = 0.002
nsteps = 50000000
init-step = 0
simulation-part = 1
comm-mode = Linear
nstcomm = 100
bd-fric = 0
ld-seed = 396053596
emtol = 10
emstep = 0.01
niter = 20
fcstep = 0
nstcgsteep = 1000
nbfgscorr = 10
rtpi = 0.05
nstxout = 5000
nstvout = 5000
nstfout = 0
nstlog = 5000
nstcalcenergy = 100
nstenergy = 5000
nstxout-compressed = 0
compressed-x-precision = 1000
cutoff-scheme = Verlet
nstlist = 20
ns-type = Grid
pbc = xyz
periodic-molecules = false
verlet-buffer-tolerance = 0.005
rlist = 1.417
coulombtype = PME
coulomb-modifier = Potential-shift
rcoulomb-switch = 0
rcoulomb = 1.4
epsilon-r = 1
epsilon-rf = inf
vdw-type = Cut-off
vdw-modifier = Potential-shift
rvdw-switch = 0
rvdw = 1.4
DispCorr = EnerPres
table-extension = 1
fourierspacing = 0.16
fourier-nx = 28
fourier-ny = 28
fourier-nz = 28
pme-order = 4
ewald-rtol = 1e-05
ewald-rtol-lj = 0.001
lj-pme-comb-rule = Geometric
ewald-geometry = 0
epsilon-surface = 0
implicit-solvent = No
gb-algorithm = Still
nstgbradii = 1
rgbradii = 1
gb-epsilon-solvent = 80
gb-saltconc = 0
gb-obc-alpha = 1
gb-obc-beta = 0.8
gb-obc-gamma = 4.85
gb-dielectric-offset = 0.009
sa-algorithm = Ace-approximation
sa-surface-tension = 2.05016
tcoupl = V-rescale
nsttcouple = 20
nh-chain-length = 0
print-nose-hoover-chain-variables = false
pcoupl = Parrinello-Rahman
pcoupltype = Isotropic
nstpcouple = 20
tau-p = 2
compressibility = 4.5e-05 4.5e-05 4.5e-05 0 0 0
ref-p = 1 1 1 0 0 0
refcoord-scaling = No
posres-com = 0 0 0
posres-comB = 0 0 0
QMMM = false
QMconstraints = 0
QMMMscheme = 0
MMChargeScaleFactor = 1
qm-opts:
ngQM = 0
constraint-algorithm = Lincs
continuation = true
Shake-SOR = false
shake-tol = 0.0001
lincs-order = 4
lincs-iter = 1
lincs-warnangle = 30
nwall = 0
wall-type = 9-3
wall-r-linpot = -1
wall-atomtype[0] = -1
wall-atomtype[1] = -1
wall-density[0] = 0
wall-density[1] = 0
wall-ewald-zfac = 3
pull = false
awh = false
rotation = false
interactiveMD = false
disre = No
disre-weighting = Conservative
disre-mixed = false
dr-fc = 1000
dr-tau = 0
nstdisreout = 100
orire-fc = 0
orire-tau = 0
nstorireout = 100
free-energy = no
cos-acceleration = 0
deform = 0 0 0 0 0 0
simulated-tempering = false
swapcoords = no
userint1 = 0
userint2 = 0
userint3 = 0
userint4 = 0
userreal1 = 0
userreal2 = 0
userreal3 = 0
userreal4 = 0
nrdf = 1252.78 16119.2
ref-t = 300 300
tau-t = 0.1 0.1
annealing = No No
annealing-npoints = 0 0
acc: 0 0 0
nfreeze: N N N
energygrp-flags[ 0]: 0 0
energygrp-flags[ 1]: 0 0
thank you
On Thu, 12 Dec, 2019, 7:32 PM Mark Abraham, <mark.j.abraham at gmail.com>
wrote:
> Hi,
>
> On Thu, 12 Dec 2019 at 14:35, Mateusz Bieniek <bieniekmat at gmail.com>
> wrote:
>
> > Hi Gromacs,
> >
> > A small digression: Ideally Gromacs would make it more clear in the error
> > message explaining which part is not implemented for the GPUs.
> >
>
> Indeed, and this case it is supposed to have already written on the log
> file that multiple energy groups are not supported with NB on GPUs. So I
> suggest Rahul look for that. If we see it, then I suspect Rahul's reported
> mdp file was not what generated his tpr file. What does gmx dump -s say
> about the energy groups in the tpr file?
>
> Mark
>
> Thanks, Mat
> >
> > On Thu, 12 Dec 2019 at 13:01, RAHUL SURESH <drrahulsuresh at gmail.com>
> > wrote:
> >
> > > Hi John
> > >
> > > Thank you and adding here the mdp settings
> > >
> > > title = Protein-gas molecule interaction MD simulation
> > > ; Run parameters
> > > integrator = md
> > > nsteps = 200000000
> > > dt = 0.002 ; 2 fs
> > > ; Output control
> > > nstxout = 5000 ;
> > > nstvout = 5000 ;
> > > nstenergy = 5000 ;
> > > nstlog = 5000 ;
> > > energygrps = Protein
> > > ; Bond parameters
> > > continuation = yes ;
> > > constraint_algorithm = lincs
> > > constraints = all-bonds ;
> > > lincs_iter = 1 ;
> > > lincs_order = 4
> > > ; Neighborsearching
> > > cutoff-scheme = Verlet
> > > ns_type = grid ;
> > > nstlist = 20 ; 10 fs
> > > rlist = 1.4 ;
> > > rcoulomb = 1.4 ;
> > > rvdw = 1.4 ;
> > > ; Electrostatics
> > > coulombtype = PME ;
> > > pme_order = 4 ;
> > > fourierspacing = 0.16 ;
> > > ; Temperature coupling
> > > tcoupl = V-rescale ;
> > > tc-grps = Protein_NO2 Water_and_ions ;
> > > tau_t = 0.1 0.1 ;
> > > ref_t = 300 300 ;
> > > ; Pressure coupling
> > > pcoupl = Parrinello-Rahman ;
> > > pcoupltype = isotropic ;
> > > tau_p = 2.0 ;
> > > ref_p = 1.0 ;
> > > compressibility = 4.5e-5
> > > ; Periodic boundary conditions
> > > pbc = xyz ; 3-D PBC
> > > ; Dispersion correction
> > > DispCorr = EnerPres ;
> > > ; Velocity generation
> > > gen_vel = no
> > >
> > > On Thu, Dec 12, 2019 at 6:01 PM John Whittaker <
> > > johnwhittake at zedat.fu-berlin.de> wrote:
> > >
> > > > Hi,
> > > >
> > > > > Hi Users.
> > > > >
> > > > > I am simulating a peptide of 40 residues with small molecules using
> > > > oplsaa
> > > > > ff in Gromacs 2018.20 installed in CUDA environment.. The
> workstation
> > > has
> > > > > 16 Cores and 2 1080Ti card On execution of command gmx_mpi mdrun -v
> > > > > -deffnm
> > > > > md for 100ns it shows no usage of gpu card. For the command
> gmx_mpi
> > > > mdrun
> > > > > -v -deffnm md -gputasks 01 -nb gpu, the job is terminated with note
> > > > > " NB interaction on the gpu were required but not supported for
> > these
> > > > > simulation settings. change your settings or do not require using
> > > gpus."
> > > >
> > > > You should provide the content of your .mdp file. According to the
> > error
> > > > message, some of your settings are not compatible with GPU
> > acceleration.
> > > > Without some information about your settings, no one can really help.
> > > >
> > > > - John
> > > >
> > > > >
> > > > > Could anyone explain a solution on this issue?
> > > > >
> > > > > Thank you
> > > > >
> > > > > --
> > > > > *Regards,*
> > > > > *Rahul *
> > > > > --
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> > > *Regards,*
> > > *Rahul *
> > > --
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