[gmx-users] checkpoint file
joojoojooon at gmail.com
Mon Aug 13 22:16:54 CEST 2012
Sorry Justin, but I dont see whats happening...
Do I have to remove mpi or -np from the line while using -cpi *.cpt ?
mdrun -deffnm md -s -o -c -g -e -x -cpi >& output
On 13 August 2012 16:10, Justin Lemkul <jalemkul at vt.edu> wrote:
> 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
>> 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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