Re: [gmx-users] Low GPU utilization

[Mark Abraham]

Hi,

That sounds like it could just be normal for what you'd expect on a
small-ish system if your GPU is better than your CPU. Sharing a .log file
via a file-sharing service gives you a better chance of useful feedback.

Mark

On Mon, Feb 1, 2016 at 7:43 AM Hovakim Grabski 
wrote:

> Dear Gromacs users,
>
> I'm running a simulation between LASR receptor and Quercetin on Q6600, GTX
> 960, CPU utilization is about 90%, but GPU is only 25-30%(Nvidia X server
> tools).The system is only 28643 atoms and dt = 2 fs.
> This is the mdp settings:
> ; Run parametersdefine  = -DPOSRES_B ; Lets seeintegrator  = md
>  ; leap-frog integratornsteps  = 500  ; 2 * 50 = 1000 ps (1
> ns)dt  = 0.002 ; 2 fs; Output controlnstxout = 0 ;
> suppress .trr output nstvout = 0 ; suppress .trr
> outputnstenergy   = 1000  ; save energies every 2 psnstlog  = 1000
>  ; update log file every 2 psnstxout-compressed  = 1000  ; write
> .xtc trajectory every 2 pscompressed-x-grps   = Systemenergygrps  = Protein
> HSL; Bond parameterscontinuation= yes   ; first dynamics
> runconstraint_algorithm = lincs; holonomic constraints constraints
> = all-bonds ; all bonds (even heavy atom-H bonds) constrainedlincs_iter
>  = 1 ; accuracy of LINCSlincs_order = 4 ;
> also related to accuracy; Neighborsearchingcutoff-scheme   = Verletns_type
> = grid  ; search neighboring grid cellsnstlist = 10 ;
> 20 fsrcoulomb= 1.4rvdw= 1.4   ; short-range van der Waals
> cutoff (in nm); Electrostaticscoulombtype = PME   ; Particle Mesh
> Ewald for long-range electrostaticspme_order   = 4 ; cubic
> interpolationfourierspacing  = 0.16  ; grid spacing for FFT;
> Temperature coupling is ontcoupl  = V-rescale ;
> modified Berendsen thermostattc-grps = Protein_HSL Water_and_ions;
> two coupling groups - more accuratetau_t   = 0.1   0.1
> ; time constant, in psref_t   = 300   300 ;
> reference temperature, one for each group, in K; Pressure coupling is
> offpcoupl  = Parrinello-Rahman ; pressure coupling is on
> for NPTpcoupltype  = isotropic ; uniform scaling of box
> vectorstau_p   = 2.0   ; time constant, in
> psref_p   = 1.0   ; reference pressure, in
> barcompressibility = 4.5e-5; isothermal compressibility
> of water, bar^-1; Periodic boundary conditionspbc = xyz   ; 3-D
> PBC; Dispersion correctionDispCorr= EnerPres  ; account for cut-off vdW
> scheme; Velocity generationgen_vel = no   ; assign velocities from
> Maxwell distributiongen_temp= 300   ; temperature for Maxwell
> distributiongen_seed= -1; generate a random
> seedrefcoord_scaling = com
>
> Best regards,Hovakim Grabski
> --
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[gmx-users] Low GPU utilization

[Hovakim Grabski]

Dear Gromacs users,

I'm running a simulation between LASR receptor and Quercetin on Q6600, GTX 960, 
CPU utilization is about 90%, but GPU is only 25-30%(Nvidia X server tools).The 
system is only 28643 atoms and dt = 2 fs.
This is the mdp settings:
; Run parametersdefine      = -DPOSRES_B ; Lets seeintegrator  = md        ; 
leap-frog integratornsteps      = 500  ; 2 * 50 = 1000 ps (1 ns)dt      
    = 0.002     ; 2 fs; Output controlnstxout     = 0         ; suppress .trr 
output nstvout     = 0         ; suppress .trr outputnstenergy   = 1000      ; 
save energies every 2 psnstlog      = 1000      ; update log file every 2 
psnstxout-compressed  = 1000      ; write .xtc trajectory every 2 
pscompressed-x-grps   = Systemenergygrps  = Protein HSL; Bond 
parameterscontinuation    = yes           ; first dynamics 
runconstraint_algorithm = lincs    ; holonomic constraints constraints     = 
all-bonds     ; all bonds (even heavy atom-H bonds) constrainedlincs_iter      
= 1             ; accuracy of LINCSlincs_order     = 4             ; also 
related to accuracy; Neighborsearchingcutoff-scheme   = Verletns_type     = 
grid      ; search neighboring grid cellsnstlist     = 10         ; 20 
fsrcoulomb    = 1.4rvdw        = 1.4       ; short-range van der Waals cutoff 
(in nm); Electrostaticscoulombtype     = PME       ; Particle Mesh Ewald for 
long-range electrostaticspme_order       = 4         ; cubic 
interpolationfourierspacing  = 0.16      ; grid spacing for FFT; Temperature 
coupling is ontcoupl      = V-rescale                     ; modified Berendsen 
thermostattc-grps     = Protein_HSL Water_and_ions    ; two coupling groups - 
more accuratetau_t       = 0.1   0.1                     ; time constant, in 
psref_t       = 300   300                     ; reference temperature, one for 
each group, in K; Pressure coupling is offpcoupl      = Parrinello-Rahman       
      ; pressure coupling is on for NPTpcoupltype  = isotropic                  
   ; uniform scaling of box vectorstau_p       = 2.0                           
; time constant, in psref_p       = 1.0                           ; reference 
pressure, in barcompressibility = 4.5e-5                    ; isothermal 
compressibility of water, bar^-1; Periodic boundary conditionspbc         = xyz 
      ; 3-D PBC; Dispersion correctionDispCorr    = EnerPres  ; account for 
cut-off vdW scheme; Velocity generationgen_vel     = no       ; assign 
velocities from Maxwell distributiongen_temp    = 300       ; temperature for 
Maxwell distributiongen_seed    = -1        ; generate a random 
seedrefcoord_scaling = com

Best regards,Hovakim Grabski
-- 
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