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Bug #456

git gromacs and -dlb yes

Added by Carsten Kutzner over 9 years ago. Updated over 9 years ago.

Status:
Closed
Priority:
Normal
Assignee:
Erik Lindahl
Category:
mdrun
Target version:
Affected version - extra info:
Affected version:
Difficulty:
uncategorized
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Description

Created an attachment (id=483)
DPPC with PME tpr file

When explicitly switching on dynamic load balancing

mpirun -np 4 mdrun -s ../tpr/Dppc.tpr -dlb yes

Git gromacs crashes instantly with the following error (the number
of particles varies depending on the number of PME nodes):
-------------------------------------------------------
Program mdrun, VERSION 4.0.99-dev-20100629-e965458
Source code file: pme.c, line: 535

Fatal error:
228 particles communicated to PME node 3 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y.
...
-------------------------------------------------------

When leaving the -dlb flag away, or setting it to no, the system runs fine.
I experienced this error on at least two different MD systems and on different
computers.

Dppc.tpr (3.27 MB) Dppc.tpr DPPC with PME tpr file Carsten Kutzner, 06/29/2010 04:14 PM

History

#1 Updated by Berk Hess over 9 years ago

Ah, apparently I never tried a box with y larger than x!
I thought this worked, but I don't know if I intended to have
PME decomposition along x or y in that case. Anyhow the code messed
up the dimension and dimension index in this case.
I fixed it now such that 1xNx1 should run as fast as Nx1x1.

This might explain some other bug reports (not in bugzilla) as well.

Berk

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