[gmx-users] Performance
Myunggi Yi
myunggi at pukyong.ac.kr
Thu Mar 29 15:42:26 CEST 2018
Thanks.
I used the exactly same program (same installation and same environment
variable).
How come this error depends on the *.mdp file?
I don't get it with typical simulations such as md with PME etc,
but I get it with this Dry_Martini mdp file (using sd, reaction field etc.).
Myunggi Yi
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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