[gmx-users] replica restart from checkpoints

[Berk Hess]

Hi,

If that is really the end of the log file, you are indeed having the problem that 
certain replicas are waiting for communication during exchange, while other
have stopped due to reaching -maxh.
This problem will also be addressed in 4.1, but for the moment you will have
to limit nsteps (as I mailed before) instead of using -maxh.

PS: if you are interested in the conformations are higher temperatures
you should use NPT.

Berk

From: massimiliano.bonomi at gmail.com
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] replica restart from checkpoints
Date: Fri, 20 Feb 2009 10:47:21 +0100


On Feb 20, 2009, at 10:07 AM, Berk Hess wrote:Hi,

I guess that actually the -maxh procedure might be the problem in your case.
If all replicas stop correctly after -maxh, they will all be between the same exchange events,
so it should work.
The only issue I can see is that one (or more) replica reaches an exchange attempt step
early and waits for communication, while the others are late and get stopped by -maxh.
Have you checked that the simulation terminated properly?
This is the last output line of one md.log
Step 4834163: Run time exceeded 23.760 hours, will terminate the run           Step           Time         Lambda        4834164     9668.32800        0.00000
No checkpoints are created after this point.The same for all the other replicas.Is this a correct stop or the code should have print out a "final" checkpoint before stopping?
PS: simulations are in the NVT ensemble...
Massimiliano


If this is the case, currently the only solution is not to use -maxh,
but to make tpr files with nsteps short enough to finish in time and then use tpbconv
to extend the tpr files (without trajectory and energy) and then run mdrun -cpi.

Berk

From: massimiliano.bonomi at gmail.com
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] replica restart from checkpoints
Date: Thu, 19 Feb 2009 22:47:23 +0100

Thanks for your reply...
Which version are you using?
In 4.0.3 I made things slightly better by allowing checkpoints
to have different step numbers, as long as they fall within
the same exchange attempt steps.

I'm using 4.0.3. Same problem with the former versions 4.0.x.
This could still cause problems when the steps in the checkpoints
differ very much. But if you use -maxh all simulations should finish
closely within each other.
Actually I'm using -maxh!

(you can always go back to using tpbconv)


Unfortunately I have no trr files, but just xtc with only solute...
Synchronizing the checkpoint writing is a bit complicated
and will probably only be done in 4.1.

Is it not possible to define the writing stride in terms of MD steps?
Thanks again,Massimiliano
Berk

> From: massimiliano.bonomi at gmail.com
> To: gmx-users at gromacs.org
> Date: Thu, 19 Feb 2009 20:14:15 +0100
> Subject: [gmx-users] replica restart from checkpoints
> 
> Dear Gromacs Users,
> 
> I'm experiencing some problems when restarting a replica exchange run 
> from previous checkpoint files.
> It often happens to me that the number of MD steps done in the 
> previous run is not the
> same for all the replica. If this is the case, the program stops.
> This may happen since checkpoints are written with a stride expressed
> in REAL time (every 15 minutes) and replica on different processors 
> may have run
> for different number of steps in the same amount of time.
> 
> Is it possible to specify the checkpoint writing stride in number of 
> steps instead of real time?
> 
> Regards,
> Massimiliano Bonomi
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