[gmx-users] checkpoint file

[Juliette N.]

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..

Thanks


On 13 August 2012 15:51, Matthias Ernst <matthias.ernst2 at student.kit.edu> wrote:
>
>
> Am 13.08.2012 21:42, schrieb Juliette N.:
>
>> Thank you. I am using
>>
>>   mpirun -np 8 mdrun_mpi -deffnm md -s -o -c -g -e -x  -cpi md_prev.cpt
>
> I see a "md_prev.cpt". If I presume correctly that this is for the
> continuation of the crashed run: Why and did you read what I wrote?
>
>
>>
>> but I dont get any output and the issued command terminates in the
>> terminal.
>>
>> Do I have to remove the -o -c -g -e -x flags from the command line?
>>
>> Appreciate your help,
>>
>>
>> On 13 August 2012 15:28, Matthias Ernst <matthias.ernst2 at student.kit.edu>
>> wrote:
>>>
>>> Long story short: backup everything (since it's a backup, and hopefully
>>> you
>>> won't need it), then use the [whatever].cpt file. You don't want to do
>>> work
>>> twice, do you? If you use the [whatever]_prev.cpi file, you will
>>> calculate
>>> some frames *again* that are already there.
>>> If you use an up-to-date version of Gromacs (4.5.5 is the most recent
>>> one),
>>> then the files will be continued and not overwritten. This is stated on
>>> the
>>> page you already found (hint: "remaining output will be appended to the
>>> existing files (energy, trajectory, log, etc).")
>>>
>>> Good luck,
>>> Matthias
>>>
>>> Am 13.08.2012 21:07, schrieb Juliette N.:
>>>
>>>> Hello all,
>>>>
>>>> I am going to restart my crashed simulations, but I am not sure which
>>>> of  *_prev.cpt or *.cpt to use as they contain different written
>>>> frames.
>>>>
>>>>    *_prev.cpt >>>> Last frame         -1 time 7462.900
>>>>
>>>>    *.cpt           >>>> Last frame         -1 time 7468.965
>>>>
>>>> Also on the gmx site it is stated that :
>>>>
>>>> Before doing anything, back up your files! Then use
>>>>
>>>> mdrun -s topol.tpr -cpi state.cpt
>>>>
>>>>
>>>> What files do I need to back up? the edr. trr .. files that were
>>>> written before crash? Is the new run going to overwrite the old files?
>>>>
>>>>
>>>> Thanks,
>>>
>>>
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>>
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-- 
Thanks,
J. N.