[gmx-users] distance restrained D simulations

[XAvier Periole]

What is happening is that you've got bonds too long and the
dd can not manage to cut things in 4 subsystems ...

try particle decomposition but you might end up with the same
problem :((

On Sep 29, 2010, at 5:35 PM, jayant james wrote:

>
> Hi!
> I am trying to perform distance restrained MD simulations of a  
> protein with Gromacs4.0.5.
> I have a bunch of FRET distances ranging from 10Angs to 40 angs that  
> I am incorporating simular to NOE distance restraints in NMR.
> When I use one processor for the simulations its all fine, but, when  
> I use multiple processors I get a bunch of errors
> lets me start with the "NOTE" found below. Well do not want to  
> increase the cut-off distance but want the program to use multiple  
> processors. How can I overcome this problem?
> I would appreciate your input
> Thanks
> JJ
>
> NOTE: atoms involved in distance restraints should be within the  
> longest cut-off distance, if this is not the case mdrun generates a  
> fatal error, in that case use particle decomposition (mdrun option - 
> pd)
>
>
> WARNING: Can not write distance restraint data to energy file with  
> domain decomposition
> Loaded with Money
>
>
> -------------------------------------------------------
> Program mdrun_mpi, VERSION 4.0.5
> Source code file: ../../../src/mdlib/domdec.c, line: 5873
>
> Fatal error:
> There is no domain decomposition for 4 nodes that is compatible with  
> the given box and a minimum cell size of 8.89355 nm
> Change the number of nodes or mdrun option -rdd or -dds
> Look in the log file for details on the domain decomposition
> -------------------------------------------------------
>
> "What Kind Of Guru are You, Anyway ?" (F. Zappa)
>
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun_mpi on CPU 0 out of 4
>
> gcq#21: "What Kind Of Guru are You, Anyway ?" (F. Zappa)
>
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 2 with PID 28700 on
> node compute-3-73.local exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> -------------------------------------------------------------------------
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode -1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
>
>
>
>
>
>
>
>
> -- 
> Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp)
>
> -- 
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