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

[Berk Hess]

Hi,

That is not only a quick fix, but also the real fix.
I field an issue:
http://redmine.gromacs.org/issues/1273
and the fix:
https://gerrit.gromacs.org/#/c/2432/

Cheers,

Berk

On 06/03/2013 09:24 PM, francesco oteri wrote:
> 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 
> <mailto: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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