[gmx-users] fatal error with mpi

Sat Jun 23 15:43:41 CEST 2018

Hi,

Ah well, we sometimes get reports of strange behaviour with PLUMED. We have
no idea how well things work, after they've changed the source code, so you
might have better luck enquiring on their fora.

Mark

On Fri, Jun 22, 2018 at 4:14 PM Stefano Guglielmo <
stefano.guglielmo at unito.it> wrote:

> 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>
> <011-670%2071%2078>
> > > > > > > --
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> > > > > --
> > > > > 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>
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> > > --
> > > 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>
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> --
> 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>
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