[gmx-users] Performance

Myunggi Yi myunggi at pukyong.ac.kr
Thu Mar 29 15:51:11 CEST 2018


Dear Szilard,

Can you run this simulation?

Simulation doesn't crush and doesn't generate error message.
It take forever without updating report in log file or other output files.

Is this a bug?



On Thu, Mar 29, 2018 at 7:58 AM, Szilárd Páll <pall.szilard at gmail.com>
wrote:

> Thanks. Looks like the messages and error handling is somewhat
> confusing; you must have the OMP_NUM_THREADS environment variable set
> which (just as setting -ntomp), without setting -ntmpi too is not
> supported.
>
> Either let mdrun decide about the thread count or set -ntmpi manually.
>
> --
> Szilárd
>
>
> On Wed, Mar 28, 2018 at 7:10 PM, Myunggi Yi <myunggi at pukyong.ac.kr> wrote:
> > Does it work?
> >
> > https://drive.google.com/open?id=1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl
> >
> > How about this?
> >
> >
> > Myunggi Yi
> >
> > On Wed, Mar 28, 2018 at 12:20 PM, Mark Abraham <mark.j.abraham at gmail.com
> >
> > wrote:
> >
> >> Hi,
> >>
> >> Attachments can't be accepted on the list - please upload to a file
> sharing
> >> service and share links to those.
> >>
> >> Mark
> >>
> >> On Wed, Mar 28, 2018 at 6:16 PM Myunggi Yi <myunggi at pukyong.ac.kr>
> wrote:
> >>
> >> > 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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> >> > > >
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