[gmx-users] problem with vsite and particle decomposition
gmx3 at hotmail.com
Wed Jan 20 11:02:23 CET 2010
I fixed the bug for 4.0.8 (if it will ever be released).
You can work around it by put your protein in a big box and using long cut-off's
with domain decomposition (or simple run in serial).
The next version of Gromacs will support domain decomposition also
for vacuum simulations, even without cut-off's.
> Date: Wed, 20 Jan 2010 09:34:45 +0100
> From: sdonnin at gwdg.de
> To: gmx-users at gromacs.org
> Subject: [gmx-users] problem with vsite and particle decomposition
> yes, I've just filed a bugzilla and attached the tpr.
> > Hi,
> > This is clearly a bug.
> > Could you file a bugzilla and attach the tpr file?
> > Thanks,
> > Berk
> >/ Date: Wed, 20 Jan 2010 08:52:27 +0100
> />/ From: sdonnin at gwdg.de <http://lists.gromacs.org/mailman/listinfo/gmx-users>
> />/ To: gmx-users at gromacs.org <http://lists.gromacs.org/mailman/listinfo/gmx-users>
> />/ Subject: [gmx-users] problem with vsite and particle decomposition
> />/ Hallo,
> />/ I had a problem when running with virtual sites (-vsite hydrogens) and
> />/ particle decomposition (mdrun -pd) on more than one processor with
> />/ gromacs 4.0.7. I could run without problems the same files without
> />/ virtual site description. The error message looks like this:
> />/ [node036:28870] *** An error occurred in MPI_Wait
> />/ [node036:28870] *** on communicator MPI_COMM_WORLD
> />/ [node036:28870] *** MPI_ERR_TRUNCATE: message truncated
> />/ [node036:28870] *** MPI_ERRORS_ARE_FATAL (goodbye)
> />/ It seems that the error message comes from move_cgcm() in
> />/ sim_util.c, line 157, but the cause could as well
> />/ be MPI communication that happens before move_cgcm.
> />/ Did anybody experienced similar problems or can help with this issue?
> />/ Thanks,
> />/ Serena
> />/ --
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