[gmx-users] gromacs 4.0.2 error in continuation to triclinic skew error

Berk Hess gmx3 at hotmail.com
Wed Nov 19 15:46:54 CET 2008


That is strange.
This looks like a different box size than you mailed yesterday.
Could you mail me the tpr file that caused this error?


Date: Wed, 19 Nov 2008 14:22:29 +0000
From: lastexile7gr at yahoo.de
Subject: RE: [gmx-users] gromacs 4.0.2 error in continuation to triclinic skew	error
To: gmx-users at gromacs.org


the run didn't even start and I got this:

Initializing Domain Decomposition on 8 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Minimum cell size due to bonded interactions: 1.000 nm
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 8 cells with a minimum initial size of 1.250 nm
The maximum allowed number of cells is: X 2 Y 1 Z 4

Program mdrun, VERSION 4.0.2
Source code file: domdec.c, line: 5842

Fatal error:
There is no domain decomposition for 8 nodes that is compatible with the given box and a minimum cell size of 1.25 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain

Should I run on two nodes as before? Change something else?


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