[gmx-users] checkpoint file

Justin Lemkul jalemkul at vt.edu
Mon Aug 13 22:10:26 CEST 2012

On 8/13/12 4:08 PM, Juliette N. wrote:
> Yes this is to continue a crashed run, but I dont know why my runs
> crash at the very beginnig of the simulation. I am using 4.5.4 so
> -append should work by default. I tried a simulation from time zero
> and it works as before (   mpirun -np 8 mdrun_mpi -deffnm md -s -o -c
> -g -e -x ) but as soon as I include the -cpi flag the it doesn work
> and  I get:
> 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.
> While as I said if I try to start from the very beginning it doesnt crash...
> Any ideas..

Before OpenMPI exits, there should be a reason why mdrun is exiting that is 
printed to the same stream.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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