[gmx-users] Re: Re: nodes error

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 6 13:14:37 CET 2012

Albert wrote:
> is there any solution to fix this?

The only solution is to use fewer nodes.  You cannot simply split any system 
into an arbitrarily-chosen number of nodes.  The DD algorithm, for the reasons 
described below, imparts a limit on how many nodes can be used based on how many 
DD cells are constructed.


> On 01/06/2012 09:52 AM, gmx-users-request at gromacs.org wrote:
>> "The minimum cell size is controlled by the size of the largest charge
>> group or bonded interaction and the largest of rvdw, rlist and rcoulomb,
>> some other effects of bond constraints, and a safety margin. *Thus it is
>> not possible to run a small simulation with large numbers of 
>> processors.*"
>> Based on the information you provided, the only thing I can say is, MAYBE
>> your system is "too small" to run with 256 processors.
>> Cheers
>> Terry


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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