[gmx-users] checkpoint file

[Juliette N.]

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

Thanks!


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
>> crash...
>>
>> Any ideas..
>>
>
> Before OpenMPI exits, there should be a reason why mdrun is exiting that is
> printed to the same stream.
>
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Thanks,
J. N.