Suman Chakrabarty wrote:
Hi,
I am trying brownian dynamics simulation of a single polymer chain
consisting of 100 atoms in vacuum. All bonds are constrained by LINCS.
I am trying to use the particle decomposition scheme for parallel run
since for a molecule in vacuum domain decomposition seems to be a
waste. I am using the 4.0.4 version.
But for whatever number of nodes I choose (> 1), I am getting the
following error (in this case the number of nodes was 4):
=================================================================================
The number of constraints is 99
Center of mass motion removal mode is Linear
We have the following groups for center of mass motion removal:
0: rest
There are: 100 Atoms
splitting topology...
There are 100 charge group borders and 1 shake borders
There are 100 total borders
Division over nodes in atoms:
25 25 25 25
Walking down the molecule graph to make constraint-blocks
-------------------------------------------------------
Program mdrun_mpi_d, VERSION 4.0.4
Source code file: splitter.c, line: 130
Fatal error:
Shake block crossing node boundaries
constraint between atoms (75,76)
-------------------------------------------------------
==================================================================
Parallel lincs does not work with particle decomposition unfortunately.
Try DD.
So is there any way to avoid such an error and still have a particle
decomposed parallel run or I am forced to use single processor always?
Thanks.
Regards,
Suman.
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Professor of Biology
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[email protected] [email protected] http://folding.bmc.uu.se
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