[gmx-users] Performance

[Myunggi Yi]

I am attaching the file.

Thank you.

Myunggi Yi

On Wed, Mar 28, 2018 at 11:40 AM, Szilárd Páll <pall.szilard at gmail.com>
wrote:

> 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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