[gmx-users] GPU performance, regarding

[Mark Abraham]

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 *
> > > > --
> > > > Gromacs Users mailing list
> > > >
> > > > * Please search the archive at
> > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > > posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > send
> > > > a mail to gmx-users-request at gromacs.org.
> > > >
> > >
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at
> > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > > posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> >
> >
> > --
> > *Regards,*
> > *Rahul *
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>