[gmx-users] Re: CPMD continue running although the job is finished

[Elena Formoso]

Hey

One of the developers write to me. Everyone who is using that code is having
the same problem. This is his answer:

"You are right 'CPMD sleeps' expecting further communication from Gromacs.
This part was not taken care of in the current version. We are working on a
newer version with Gromacs-4.5; we will fix that in the newer version. "




On Thu, Apr 7, 2011 at 3:37 PM, Elena Formoso <
elena.formoso at phys.chem.ethz.ch> wrote:

> Dear users,
>
> I am trying to use gromacs/CPMD.
>
> Gromacs-3.3.1_qmmm-1.3.2
> CPMD-3.13.2
>
> To test it, I am doing a 0 step md. The problem is that CPMD runs until the
> schedule time is finished. It is waiting to ./QMCONTINUE, which is never
> going to be, because gmx has finished
>
> Does anyone know what can be the problem?
>
> These are the last lines of output.mdrun and md.log. There you can see how
> CPMD exits at 20:14:15, while gmx has finished at 18:45
>
>
>
>   INTERFACE| FORCES WRITTEN TO FILE
> ====== GROMACS reads <./qmoutput.out> and starts new step ======.
> Writing final coordinates.
> ^Mstep 0, remaining runtime:     0 s
>
>
>         M E G A - F L O P S   A C C O U N T I N G
>
>    RF=Reaction-Field  FE=Free Energy  SCFE=Soft-Core/Free Energy
>    T=Tabulated        W3=SPC/TIP3p    W4=TIP4p (single or pairs)
>    NF=No Forces
>
>  Computing:                        M-Number         M-Flops  % of Flops
> -----------------------------------------------------------------------
>  LJ                                0.298490        9.850170     0.2
>  Coulomb                           1.466383       39.592341     1.0
>  Coulomb + LJ                     65.918468     2504.901784    62.7
>  Outer nonbonded loop              0.034642        0.346420     0.0
>  1,4 nonbonded interactions        0.030585        2.752650     0.1
>  NS-Pairs                         67.762261     1423.007481    35.6
>  CG-CoM                            0.011641        0.337589     0.0
>  Bonds                             0.011748        0.505164     0.0
>  Angles                            0.021194        3.454622     0.1
>  Propers                           0.002375        0.543875     0.0
>  RB-Dihedrals                      0.024229        5.984563     0.1
>  Virial                            0.011670        0.210060     0.0
>  Update                            0.011643        0.360933     0.0
>  Calc-Ekin                         0.023286        0.628722     0.0
> -----------------------------------------------------------------------
>  Total                                          3992.476374   100.0
> -----------------------------------------------------------------------
>
>                NODE (s)   Real (s)      (%)
>        Time:      3.400   1136.000      0.3
>
> gcq#120: "You Could Be a Shadow" (The Breeders)
>
>
>  RESTART INFORMATION WRITTEN ON FILE                  ./RESTART.1
>
>  ===============================================================
>   INTERFACE| WAIT FOR CONTINUE-FILE ./QMCONTINUE
>
> mpirun: Forwarding signal 12 to job
>  ****************************************************************
>  *                                                              *
>  *             CPMD RECEIVED THE SOFT EXIT REQUEST              *
>  *      THE COMMAND WAS ISSUED AT Wed Apr  6 20:14:15 2011      *
>  *                                                              *
>
>
> [md.log]
> Finished mdrun on node 0 Wed Apr  6 18:45:09 2011
>
>
>
>
>
> Regards
>
> ***********************************
> Elena Formoso
> ETH Zürich and
> Università della Svizzera Italiana, USI
>
>
>
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