[gmx-users] Performance
Szilárd Páll
pall.szilard at gmail.com
Tue Apr 3 20:46:37 CEST 2018
Hi,
Your system is exploding, some atoms end up with coordinates of around
10^9 which then throw off the PBC code that tries to put atoms back in
the box. This will normally not happen as constraining will already
fail with such huge coordinates, I think, so technically it is a bug,
we could handle this corner-case better.
However, if you need to verify your system setup as it is unstable
(not well equilibrated or the time-step too long).
--
Szilárd
On Thu, Mar 29, 2018 at 3:50 PM, Myunggi Yi <myunggi at pukyong.ac.kr> wrote:
> 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
>> >> > > > --
>> >> > > > 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.
>> >>
>> > --
>> > 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.
More information about the gromacs.org_gmx-users
mailing list