[gmx-users] 4.0_beta1: 1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition cell of their charge group

[andrea spitaleri]

Hi there,
my system is about 200,000 atoms. we have installed the latest version (4.0_beta1) on our cluster 
but i get the follow error after few calculation ps :

1 particles communicated to PME node 9 are more than a cell length out of the domain decomposition 
cell of their charge group

similar to what reported few months ago 
(http://www.gromacs.org/pipermail/gmx-revision/2008-July/000213.html).

Using the version 3.3.99_development_200800503 on Louhi (csc.fi) the run goes fine.

In our cluster with 4.0_beta1 i am using 36 cpus (with no -dd option) whereas on louhi 64 cpus 
(using -dd 4 4 4 option).

I hope this help in gmx debugging

Regards,

andrea




-- 
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Andrea Spitaleri PhD
Dulbecco Telethon Institute
c/o DIBIT Scientific Institute
Biomolecular NMR, 1B4
Via Olgettina 58
20132 Milano (Italy)
http://biomolecularnmr.ihsr.dom/
Tel: 0039-0226434348/5622/3497/4922
Fax: 0039-0226434153
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