[gmx-users] Resuming of calculation from last *.cpt

[Mark Abraham]

On 16/09/2012 12:17 AM, James Starlight wrote:
> In that case I've obtain error
>
> Fatal error:
> Failed to lock: md_init.log. Already running simulation?
>
> What does it means ? the md_init.log is present in the wor dir

Appending to an old run requires that all the filenames are identical 
between the two runs. It looks to me like your .log file was called 
md_init.log originally. You can use gmxdump -cp on your checkpoint file 
to see what the output filenames used to be, and thus what they must now 
be called if you want to use appending.

Mark

>
> 2012/9/15 Justin Lemkul <jalemkul at vt.edu>:
>>
>> On 9/15/12 10:11 AM, James Starlight wrote:
>>> Jusin,
>>>
>>> yes, the initial files were named as the md_initial
>>>
>>> the simulation was resumed correctly but all output data was saved
>>> into new set of files with the default names. In my case I want that
>>> the resummed simulation data will write to the existing (md_initial)
>>> files without creation of new trajectory and other files.
>>>
>> mdrun -cpi -append -deffnm md_initial
>>
>> Should do the trick.
>>
>> -Justin
>>
>>
>>> James
>>>
>>> 2012/9/15 Justin Lemkul <jalemkul at vt.edu>:
>>>>
>>>>
>>>> On 9/15/12 10:03 AM, James Starlight wrote:
>>>>>
>>>>> Justin,
>>>>>
>>>>> In accordance to the manual I've re-launched my simulation by the
>>>>> command
>>>>> mpiexec -np 48 mdrun_mpi.openmpi -v -s md_initial  -cpi md_initial
>>>>> -append
>>>>>
>>>>>
>>>>> where md_initial is the name of the files from the run which I want to
>>>>> continue.
>>>>>
>>>>> As the result this produce new files with the default names traj.trr
>>>>> ener.edr etc. In those files the trajectory have been calculated from
>>>>> the last frame of the md_initial.cpt file. So as the result I've
>>>>> obtain again 2 set of output files ( from old and new runs). IS it
>>>>> possible to continue the calculations and save output within the
>>>>> existing files (md_initial) without creation of new ones ?
>>>>>
>>>> The names of the files produced depend on what is stored in the .cpt
>>>> file.
>>>> mdrun will only append to files with those names.  I don't have a clear
>>>> picture of what you've done so it's impossible to say whether or not this
>>>> is
>>>> the expected outcome, but the checkpointing feature is very robust so I
>>>> suspect it is.  Were all of  your file names originally called
>>>> md_initial?
>>>> If you've re-named them, the appending will fail for that very reason.
>>>>
>>>>
>>>> -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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>>
>> --
>> ========================================
>>
>> 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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