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

[Justin Lemkul]

On 9/15/12 10:17 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
>

That means mdrun expects your files to be named "md_init" not "md_initial" as 
you said they were named.  It seems that file naming has gotten confused 
somewhere along the way.  You can always, of course, choose -noappend and simply 
concatenate later.

-Justin

> 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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-- 
========================================

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

========================================