Re: [AMBER] Random segfaults (invalid memory reference) in sander

From: <scanya.interia.eu> Date: Fri, 03 May 2019 16:23:10 +0200

----
Regards,
Scanya
Od: "Daniel Roe" <daniel.r.roe.gmail.com>
Do: "AMBER Mailing List" <amber.ambermd.org>; 
Wysłane: 14:30 Piątek 2019-05-03
Temat: Re: [AMBER] Random segfaults (invalid memory reference) in sander
> Hmm - I think both of you are using OpenMPI. Do you have another MPI
> library (mpich, mvapich, intel mpi) that you can test with?
> 
> -Dan
> 
> On Fri, May 3, 2019 at 5:12 AM Margarita I. Bernal-Uruchurtu
>  wrote:
> >
> > Hi All!
> >
> > Charo del Genio's message struck me this morning as something I've also
> > been experiencing.
> > It has been quite difficult to follow due to its randomness.
> > I'm using sander with SEBOMD and the error seems to come quite unexpectedly
> > and is not related to convergence in SEBOMD. It has happened with systems
> > of different sizes and in different thermodynamical conditions.
> > The strange thing is that I can build a restart file from the last stored
> > configuration and continue the trajectory without problems.
> > And also as posted by Charo, it happens in different nodes in the local
> > cluster.
> >
> > -----------
> > /sw/target/CentOS-7.5-avx2/prl/openmpi/openmpi-2.1.5_gcc-7.3.0_C++-bindings/bin/mpirun
> >
> >
> > Program received signal SIGSEGV: Segmentation fault - invalid memory
> > reference.
> >
> >
> > Backtrace for this error:
> >
> > #0  0x7f7e9fc6c2ef in ???
> >
> > #1  0x7f7e9f2d5e9d in ???
> >
> > #2  0x7f7e9f28559b in ???
> >
> > #3  0x7f7ea0db0d54 in ???
> >
> > #4  0x7f7ea0e0a309 in ???
> >
> > #5  0x7f7ea0dc51b9 in ???
> >
> > #6  0x7f7ea11cd5e2 in ???
> >
> > #7  0x5b5360 in ???
> >
> > #8  0x574684 in ???
> >
> > #9  0x577394 in ???
> >
> > #10  0x7e4097 in ???
> >
> > #11  0x53b8e4 in ???
> >
> > #12  0x4ea46f in ???
> >
> > #13  0x4de8f2 in ???
> >
> > #14  0x4de9e4 in ???
> >
> > #15  0x7f7e9fc58444 in ???
> >
> > #16  0x4592e6 in ???
> >
> > #17  0xffffffffffffffff in ???
> >
> > --------------------------------------------------------------------------
> >
> > mpirun noticed that process rank 0 with PID 60283 on node nnode037 exited
> > on signal 11 (Segmentation fault).
> >
> > --------------------------------------------------------------------------
> >
> >
> > Science is built with facts as a house is with stones, but a collection of
> > facts is no more a science than a heap of stones is a house. - Henri
> > Poincaré
> > °°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°°
> > Margarita I. Bernal-Uruchurtu
> > Centro de Investigaciones Química, UAEM
> > +52.777.329.7000 ext 6003
> > mabel.uaem.mx
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> 
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