[gmx-developers] No WHITE nodes found error

[Berk Hess]

Hi,

You have 3 Calcium ions in one molecule type.
That is not very elegant, but a nice test case.

I fixed the bug.

Berk

Berk Hess wrote:
> Hi,
>
> Could you send me a tpr file?
>
> Berk
>
> Carsten Kutzner wrote:
>> Hi,
>>
>> I am having some trouble with one MD system here. I am using
>> today's CVS gromacs for a (big) system which runs fine with
>> older CVS versions. I think the problem is related to the new
>> molecular topology code. The error message I get is
>>
>> -------------------------------------------------------
>> Program mdrun, VERSION 4.0_beta1
>> Source code file: mshift.c, line: 575
>>
>> Fatal error:
>> No WHITE nodes found while nW=3369
>>
>> -------------------------------------------------------
>>
>> The problem seems to me that in do_pbc_first_mtop (l. 305 of md.c)
>> at one iteration of the loop a graph with g->nnodes = 0 is created
>> by mk_graph_ilist (while at the same time g->nbound=nW=3369 in 
>> mk_mshift).
>> A bit later in  the routine first_colour the loop
>>
>> for(i=fC; (i<g->nnodes); i++)
>>
>> is not executed, since both fC and nnodes are 0, therefore the
>> first_color routine returns -1, triggering the gmx_fatal.
>>
>> Thanks for any hints.
>>
>> Carsten
>>
>>
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