[gmx-users] fatal error with mpi

[Stefano Guglielmo]

Actually this is not a cluster but a single machine with two cpu's and 16
cores/cpu and in fact the non-MPI (tMPI) version works fine; I needed to
switch to the MPI version because I patched plumed which does not recognize
tMPI and need gromacs to be compiled with the same MPI used for it.

Stefano

2018-06-22 16:01 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> Just exiting without a simulation crash suggests different problems, eg
> that your cluster lost the network for MPI to use, etc. Talk to your system
> administrators about their experience and thoughts there.
>
> Mark
>
> On Fri, Jun 22, 2018, 15:57 Stefano Guglielmo <stefano.guglielmo at unito.it>
> wrote:
>
> > Thanks Mark. I must say that I tried reducing timestep (as low as 0.5
> fs-1)
> > and temperature as well (5K both in NvT and NpT) but the simulation
> crashed
> > in any case with warning about cutoff, lincs or bad water. The very
> > previous day I had run the same simulation on the same machine but with
> the
> > non-MPI version of gromacs 2016.5 and everything went smoothly; as I
> > switched to the MPI version I encountered the issue, and in the end I was
> > afraid to have missed something during compilation, so I decided to try
> and
> > recompile and now it is running.
> > Anyway I will check the trajectory as you said.
> > Thanks
> > Stefano
> >
> > 2018-06-22 15:36 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
> >
> > > Hi,
> > >
> > > Recompiling won't fix anything relevant. Molecular frustration isn't
> just
> > > about long bonds. Rearrangment of side chain groupings can do similar
> > > things despite looking happy. The sudden injection of KE means
> collisions
> > > can be more violent than normal, and the timestep is now too large. But
> > you
> > > need to look at the trajectory to understand if this might be the case.
> > >
> > > Mark
> > >
> > > On Fri, Jun 22, 2018 at 3:19 PM Stefano Guglielmo <
> > > stefano.guglielmo at unito.it> wrote:
> > >
> > > > Dear Mark,
> > > >
> > > > thanks for your answer. The version is 2016.5, but I apparently
> solved
> > > the
> > > > problem recompiling gromacs: now the simulation is running quite
> > stable.
> > > I
> > > > had minimized and gradually equilibrated the system and I could not
> see
> > > any
> > > > weird bonds or contacts. So in the end, as extrema ratio, I decided
> to
> > > > recompile.
> > > >
> > > > Thanks again
> > > > Stefano
> > > >
> > > > 2018-06-22 15:07 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
> > > >
> > > > > Hi,
> > > > >
> > > > > This could easily be that your system is actually not yet well
> > > > equilibrated
> > > > > (e.g. something was trapped in a high energy state that eventually
> > > > relaxed
> > > > > sharply). Or it could be a code bug. What version were you using?
> > > > >
> > > > > Mark
> > > > >
> > > > > On Thu, Jun 21, 2018 at 2:36 PM Stefano Guglielmo <
> > > > > stefano.guglielmo at unito.it> wrote:
> > > > >
> > > > > > Dear users,
> > > > > >
> > > > > > I have installed gromacs with MPI instead of its native tMPI and
> I
> > am
> > > > > > encountering the following error:
> > > > > > "Fatal error:
> > > > > > 4 particles communicated to PME rank 5 are more than 2/3 times
> the
> > > > > cut-off
> > > > > > out
> > > > > > of the domain decomposition cell of their charge group in
> dimension
> > > y.
> > > > > > This usually means that your system is not well equilibrated."
> > > > > >
> > > > > > I am using 8 MPI ranks with 4 omp threads per rank (it was the
> > > > > > configuration used on the same machine by tMPI), but I also
> tried 4
> > > > ranks
> > > > > > with 8 threads, but it did not solve the problem.
> > > > > >
> > > > > > I don't think this is an issue related to my system because the
> > same
> > > > > system
> > > > > > run with the native tMPI works properly (it has already been
> > > termalized
> > > > > and
> > > > > > gradually equilibrated); neverthless I tried to reduce dt and
> > > > temperature
> > > > > > but without any benefit. Does anybody have any suggestions?
> > > > > >
> > > > > > Thanks in advance
> > > > > > Stefano
> > > > > >
> > > > > > --
> > > > > > Stefano GUGLIELMO PhD
> > > > > > Assistant Professor of Medicinal Chemistry
> > > > > > Department of Drug Science and Technology
> > > > > > Via P. Giuria 9
> > > > > > 10125 Turin, ITALY
> > > > > > ph. +39 (0)11 6707178 <011-670%2071%2078> <011-670%2071%2078>
> > > > > > --
> > > > > > 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.
> > > > >
> > > >
> > > >
> > > >
> > > > --
> > > > Stefano GUGLIELMO PhD
> > > > Assistant Professor of Medicinal Chemistry
> > > > Department of Drug Science and Technology
> > > > Via P. Giuria 9
> > > > 10125 Turin, ITALY
> > > > ph. +39 (0)11 6707178 <011-670%2071%2078>
> > > > --
> > > > 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.
> > >
> >
> >
> >
> > --
> > Stefano GUGLIELMO PhD
> > Assistant Professor of Medicinal Chemistry
> > Department of Drug Science and Technology
> > Via P. Giuria 9
> > 10125 Turin, ITALY
> > ph. +39 (0)11 6707178
> > --
> > 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.
>



-- 
Stefano GUGLIELMO PhD
Assistant Professor of Medicinal Chemistry
Department of Drug Science and Technology
Via P. Giuria 9
10125 Turin, ITALY
ph. +39 (0)11 6707178