[gmx-developers] Re: Problem with Run time exceeded

[francesco oteri]

A quick fix might be changing the lines:

        if ( (gs.set[eglsSTOPCOND] < 0 ) || ( (gs.set[eglsSTOPCOND] > 0 )
&& ( bNS || ir->nstlist == 0)) )
        {
            bLastStep = TRUE;
        }

in
        if ( (gs.set[eglsSTOPCOND] < 0 ) || ( (gs.set[eglsSTOPCOND] > 0 )
&& ( bNStList || ir->nstlist == 0)) )
        {
            bLastStep = TRUE;
        }

What do you think about?

Francesco




2013/6/3 francesco oteri <francesco.oteri at gmail.com>

> Dear gromacs developers,
>
> analyzing a hunging replica exchange simulation, I might have figured out
> a problem (likely a bug).
>
> Let's suppose I am running replica exchange with -maxh, -replex 50
> and neighbour searching frequence = 5 steps .
>
> If I well understood, once the code run for maxh*0.99 it stops at the next
> neighbour searching step.
>
> If the program reaches maxh*0.99 let's say at the step 50, the
> next neighbour searching step is the 55. But if 2 replicas exchange at step
> 50, it implies rebuilding the neighbour searching
> ( because in the code bExchanged=TRUE implies bNS to be TRUE).
>
> These two replicas so stop at step 51 but the other replicas continue
> until the 55th step.
> Here the problem appears. In this case mdrun performs global communication
> calling compute_global next to the line commented as:
>  /* ############## IF NOT VV, Calculate globals HERE, also iterate
> constraints  ############ */
>
> Since the 2 replicas that exchanged already ended, mdrun hungs.
>
> Maybe my analysis is incorrect and in this case I apologize.
> In any case, if nobody did, I am looking for a fix.
>
> Francesco
>
>
>


-- 
Cordiali saluti, Dr.Oteri Francesco
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