Group cutoff scheme can never run on a gpu, so none of that should matter. Use ps and find out what the command lines were.
Mark On Fri, Apr 27, 2018, 21:37 Alex <nedoma...@gmail.com> wrote: > Update: we're basically removing commands one by one from the script that > submits the jobs causing the issue. The culprit is both EM and the MD run: > and GPUs are being affected _before_ MD starts loading the CPU, i.e. this > is the initial setting up of the EM run -- CPU load is near zero, > nvidia-smi reports the mess. I wonder if this is in any way related to that > timing test we were failing a while back. > mdrun call and mdp below, though I suspect they have nothing to do with > what is happening. Any help will be very highly appreciated. > > Alex > > *** > > gmx mdrun -nt 2 -nb cpu -pme cpu -deffnm > > mdp: > > ; Run control > integrator = md-vv ; Velocity Verlet > tinit = 0 > dt = 0.002 > nsteps = 500000 ; 1 ns > nstcomm = 100 > ; Output control > nstxout = 50000 > nstvout = 50000 > nstfout = 0 > nstlog = 50000 > nstenergy = 50000 > nstxout-compressed = 0 > ; Neighborsearching and short-range nonbonded interactions > cutoff-scheme = group > nstlist = 10 > ns_type = grid > pbc = xyz > rlist = 1.4 > ; Electrostatics > coulombtype = cutoff > rcoulomb = 1.4 > ; van der Waals > vdwtype = user > vdw-modifier = none > rvdw = 1.4 > ; 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 = nose-hoover > tc_grps = system > tau_t = 1.0 > ref_t = some_temperature > ; Pressure coupling is off for NVT > Pcoupl = No > tau_p = 0.5 > compressibility = 4.5e-05 > ref_p = 1.0 > ; options for bonds > constraints = all-bonds > constraint_algorithm = lincs > > > > > > > On Fri, Apr 27, 2018 at 1:14 PM, Alex <nedoma...@gmail.com> wrote: > > > As I said, only two users, and nvidia-smi shows the process name. We're > > investigating and it does appear that it is EM that uses cutoff > > electrostatics and as a result the user did not bother with -pme cpu in > the > > mdrun call. What would be the correct way to enforce cpu-only mdrun when > > coulombtype = cutoff? > > > > Thanks, > > > > Alex > > > > On Fri, Apr 27, 2018 at 12:45 PM, Mark Abraham <mark.j.abra...@gmail.com > > > > wrote: > > > >> No. > >> > >> Look at the processes that are running, e.g. with top or ps. Either old > >> simulations or another user is running. > >> > >> Mark > >> > >> On Fri, Apr 27, 2018, 20:33 Alex <nedoma...@gmail.com> wrote: > >> > >> > Strange. There are only two people using this machine, myself being > one > >> of > >> > them, and the other person specifically forces -nb cpu -pme cpu in his > >> > calls to mdrun. Are any other GMX utilities (e.g. insert-molecules, > >> grompp, > >> > or energy) trying to use GPUs? > >> > > >> > Thanks, > >> > > >> > Alex > >> > > >> > On Fri, Apr 27, 2018 at 5:33 AM, Szilárd Páll <pall.szil...@gmail.com > > > >> > wrote: > >> > > >> > > The second column is PIDs so there is a whole lot more going on > there > >> > than > >> > > just a single simulation, single rank using two GPUs. That would be > >> one > >> > PID > >> > > and two entries for the two GPUs. Are you sure you're not running > >> other > >> > > processes? > >> > > > >> > > -- > >> > > Szilárd > >> > > > >> > > On Thu, Apr 26, 2018 at 5:52 AM, Alex <nedoma...@gmail.com> wrote: > >> > > > >> > > > Hi all, > >> > > > > >> > > > I am running GMX 2018 with gmx mdrun -pinoffset 0 -pin on -nt 24 > >> > -ntmpi 4 > >> > > > -npme 1 -pme gpu -nb gpu -gputasks 1122 > >> > > > > >> > > > Once in a while the simulation slows down and nvidia-smi reports > >> > > something > >> > > > like this: > >> > > > > >> > > > | 1 12981 C gmx > >> > > > 175MiB | > >> > > > | 2 12981 C gmx > >> > > > 217MiB | > >> > > > | 2 13083 C gmx > >> > > > 161MiB | > >> > > > | 2 13086 C gmx > >> > > > 159MiB | > >> > > > | 2 13089 C gmx > >> > > > 139MiB | > >> > > > | 2 13093 C gmx > >> > > > 163MiB | > >> > > > | 2 13096 C gmx > >> > > > 11MiB | > >> > > > | 2 13099 C gmx > >> > > > 8MiB | > >> > > > | 2 13102 C gmx > >> > > > 8MiB | > >> > > > | 2 13106 C gmx > >> > > > 8MiB | > >> > > > | 2 13109 C gmx > >> > > > 8MiB | > >> > > > | 2 13112 C gmx > >> > > > 8MiB | > >> > > > | 2 13115 C gmx > >> > > > 8MiB | > >> > > > | 2 13119 C gmx > >> > > > 8MiB | > >> > > > | 2 13122 C gmx > >> > > > 8MiB | > >> > > > | 2 13125 C gmx > >> > > > 8MiB | > >> > > > | 2 13128 C gmx > >> > > > 8MiB | > >> > > > | 2 13131 C gmx > >> > > > 8MiB | > >> > > > | 2 13134 C gmx > >> > > > 8MiB | > >> > > > | 2 13138 C gmx > >> > > > 8MiB | > >> > > > | 2 13141 C gmx > >> > > > 8MiB | > >> > > > +----------------------------------------------------------- > >> > > > ------------------+ > >> > > > > >> > > > Then goes back to the expected load. Is this normal? > >> > > > > >> > > > Thanks, > >> > > > > >> > > > Alex > >> > > > > >> > > > -- > >> > > > 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-requ...@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-requ...@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-requ...@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? 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