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

[James Starlight]

There is no errors in the filenames

In the above example init and initial names were used for simplicity :)
Actually the name of the simulation was md_a2a_pope_SD

so I've used
mpiexec -np 48 mdrun_mpi.openmpi -v -cpi md_a2a_pope_SD -deffnm
md_a2a_pope_SD -append

and eror was

Fatal error:
Failed to lock: md_a2a_pope_SD.log. Already running simulation?


from cpt file after dump

output filename = md_a2a_pope_SD.log

James



2012/9/15 Mark Abraham <Mark.Abraham at anu.edu.au>:
> 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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