[gmx-users] parallel run breaks !!

[Mark Abraham]

On 4/18/2011 4:39 PM, delara aghaie wrote:
>
>
> Dear Gromacs users
> I run DPPC monolayer on Tip4p2005 water layer system with gromacs 3.3
> I had no problem before but when I run the system with command
> grompp_mpi -c .gro -f .mdp -n .ndx -p .top -o .tpr -np 8
> and then qsub .ll
> the run starts but it has break down several times, each ime after for 
> ex 987654 steps or more steps or less.
>

If you've changed nothing, and it used to work, and now doesn't, then 
something about your computer has changed. We can't really help there - 
and there must be better people to ask.

Mark

> I get in .o.ii file this message:
> ----
> PBS has allocated the following nodes:
> cx1-25-8-4
> cx1-25-8-4
> cx1-25-8-4
> cx1-25-8-4
> cx1-25-8-4
> cx1-25-8-4
> cx1-25-8-4
> cx1-25-8-4
> ---
> mpiexec.intel -genv I_MPI_DEVICE ssm -genv I_MPI_DEBUG 0 -genv 
> I_MPI_PIN yes -genv I_MPI_PIN_MODE lib -genv I_MPI_FALLBACK_DEVICE 
> disable -genv DAPL_MAX_CM_RETRIES 500 -genv DAPL_MAX_CM_RESPONSE_TIME 
> 300 -genv I_MPI_DAPL_CONNECTION_TIMEOUT 300 -machinefile 
> /tmp/pbs.5455562.cx1/tmp.VRhkM11825 -n 8 -wdir /tmp/pbs.5455562.cx1 
> mdrun_mpi -v -s topol.tpr -np 8
> Job output begins below
> -----------------------
> mpdallexit: cannot connect to local mpd 
> (/tmp/pbs.5455562.cx1/mpd2.console_dmohamma_110411.074928); possible 
> causes:
>   1. no mpd is running on this host
>   2. an mpd is running but was started without a "console" (-n option)
> ---
> what can be the solvation of the possible problem?
> Thanks
> D. Aghaie
>




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