[gmx-users] checkpoint file

[Mark Abraham]

On 14/08/2012 6:08 AM, 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.

You have to look at the stderr, stdout and .log file for information. 
You can't solve the problem without that.

Mark

>   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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>