[gmx-users] Performance

[Myunggi Yi]

I see.

I am trying again.
​
 ves
<https://drive.google.com/drive/folders/1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl>
​

Myunggi Yi  (이명기, Ph. D.), Professor

Department of Biomedical Engineering (의공학과 bme.pknu.ac.kr), College of
Engineering
Interdisciplinary Program of Biomedical Mechanical & Electrical Engineering
Center for Marine-Integrated Biomedical Technology (BK21+)
College of Engineering
Pukyong National University (부경대학교 www.pknu.ac.kr)
45 Yongso-ro, Nam-gu (남구 용소로 45)
Busan, 48513, South Korea
Phone: +82 51 629 5773
Fax: +82 51 629 5779

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
> > > >
> > > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > > >
> > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > > >
> > > > * For (un)subscribe requests visit
> > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or
> > > send a mail to gmx-users-request at gromacs.org.
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at
> > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> > posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>