Again, please share the exact log files / description of inputs. What does "bad performance" mean? -- Szilárd
On Wed, Mar 28, 2018 at 5:31 PM, Myunggi Yi <myun...@pukyong.ac.kr> wrote: > Dear users, > > I have two questions. > > > 1. I used to run typical simulations with the following command. > > gmx mdrun -deffnm md > > I had no problem. > > > Now I am running a simulation with "Dry_Martini" FF with the following > input. > > > integrator = sd > tinit = 0.0 > dt = 0.040 > nsteps = 1000000 > > nstlog = 5000 > nstenergy = 5000 > nstxout-compressed = 5000 > compressed-x-precision = 100 > > cutoff-scheme = Verlet > nstlist = 10 > ns_type = grid > pbc = xyz > verlet-buffer-tolerance = 0.005 > > epsilon_r = 15 > coulombtype = reaction-field > rcoulomb = 1.1 > vdw_type = cutoff > vdw-modifier = Potential-shift-verlet > rvdw = 1.1 > > tc-grps = system > tau_t = 4.0 > ref_t = 310 > > ; Pressure coupling: > Pcoupl = no > > ; GENERATE VELOCITIES FOR STARTUP RUN: > gen_vel = yes > gen_temp = 310 > gen_seed = 1521731368 > > > > If I use the same command to submit the job. > I got the following error. I don't know why. > > ------------------------------------------------------- > Program: gmx mdrun, version 2018.1 > Source file: src/gromacs/taskassignment/resourcedivision.cpp (line 224) > > Fatal error: > When using GPUs, setting the number of OpenMP threads without specifying the > number of ranks can lead to conflicting demands. Please specify the number > of > thread-MPI ranks as well (option -ntmpi). > > For more information and tips for troubleshooting, please check the GROMACS > website at http://www.gromacs.org/Documentation/Errors > ------------------------------------------------------- > > > So I did run simulation with the following command. > > > gmx mdrun -deffnm md -ntmpi 1 > > > Now the performance is extremely bad. > Since yesterday, the log file still reporting the first step's energy. > > 2. This is the second question. Why? > > Can anyone help? > > > Myunggi Yi > -- > 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.
