[gmx-users] Performance

Szilárd Páll pall.szilard at gmail.com
Thu Mar 29 13:58:13 CEST 2018


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
>> > > > --
>> > > > Gromacs Users mailing list
>> > > >
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