[gmx-users] Checkpointing

[Jack Shultz]

So you mean something like -cpi state.cpt -cpo state.cpt ? If so, I'll
try this approach again. I had a little trouble doing it this way
previously. I think I had trouble with the extension scripts doing it
this way.

On Tue, Feb 2, 2010 at 11:56 PM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> On 03/02/10 15:44, Jack Shultz wrote:
>>
>> I will try it without the checkpointing flags.
>
> That's not quite what I said. I suggested not using *different* filenames
> for -cpo and -cpi. What you want is the output file from a former run to
> transparently become the input file for the subsequent one, and I expect
> GROMACS will handle this for you if you let it. Try some things and see.
>
> Mark
>
>> If that fails, maybe
>> I'll introduce some python into this integration. Check if the
>> checkpoint already exists.
>>
>> On Tue, Feb 2, 2010 at 6:18 PM, Mark Abraham<mark.abraham at anu.edu.au>
>>  wrote:
>>>
>>>
>>> ----- Original Message -----
>>> From: Jack Shultz<js at drugdiscoveryathome.com>
>>> Date: Wednesday, February 3, 2010 2:36
>>> Subject: [gmx-users] Checkpointing
>>> To: Discussion list for GROMACS users<gmx-users at gromacs.org>, Andrey
>>> Voronkov<av at drugdiscoveryathome.com>
>>>
>>>> We have mdrun integrated into our distributed computing project. When
>>>> your users suspend or close the manger it checkpoints, so when they
>>>> open again it continues mdrun where it left off. However, when users
>>>> reboot, it starts from the beginning. We are using this command line
>>>> to execute the work.
>>>>
>>>> mdrun.exe (-v -x -c -o md.pdb -e -cpo md.next -cpi md.cpt -
>>>> deffnm md)
>>>
>>> If you're using this input line always, then you're getting what you're
>>> asking for - an mdrun that begins from the state in md.cpt. Since you're
>>> never updating that, it doesn't change.
>>>
>>> Try not stipulating different -cpo and -cpi and see what the native
>>> coping mechanism is. Otherwise, you'll have to write a bunch of scripting
>>> logic to decide which .cpt to use each restart.
>>>
>>> Mark
>>>
>>>> I have a seperate checkpoint for output so after this simulation we
>>>> can extend the workunit. Should we try using this append option?
>>>>
>>>> Checkpoints containing the complete state of the system are
>>>> written at
>>>> regular intervals (option -cpt) to the file -cpo, unless option -cpt
>>>> is set to -1. A simulation can be continued by reading the full state
>>>> from file with option -cpi. This option is intelligent in the
>>>> way that
>>>> if no checkpoint file is found, Gromacs just assumes a normal
>>>> run and
>>>> starts from the first step of the tpr file.
>>>>
>>>> With checkpointing you can also use the option -append to just
>>>> continue writing to the previous output files. This is not
>>>> enabled by
>>>> default since it is potentially dangerous if you move files, but if
>>>> you just leave all your files in place and restart mdrun with exactly
>>>> the same command (with options -cpi and -append) the result will be
>>>> the same as from a single run. The contents will be binary identical
>>>> (unless you use dynamic load balancing), but for technical reasons
>>>> there might be some extra energy frames when using checkpointing
>>>> (necessary for restarts without appending).
>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Jack
>>>>
>>>> http://drugdiscoveryathome.com
>>>> http://hydrogenathome.org
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>>
>>
>>
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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org