[gmx-users] Performance

[Szilárd Páll]

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 <myunggi at 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
> --
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