[gmx-users] replica restart from checkpoints

[Massimiliano Bonomi]

On Feb 20, 2009, at 10:59 AM, Berk Hess wrote:

> 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.
>
Ok! Thank you very much for the suggestions...

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

I'm just trying to reproduce some old results done with another code  
and in the NVT ensemble,
so I cannot use NPT!!

> Berk

Thanks again,

Massimiliano

>
>
> 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
> > _______________________________________________
> > gmx-users mailing list gmx-users at gromacs.org
> > http://www.gromacs.org/mailman/listinfo/gmx-users
> > Please search the archive at http://www.gromacs.org/search before  
> posting!
> > Please don't post (un)subscribe requests to the list. Use the
> > www interface or send it to gmx-users-request at gromacs.org.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> Express yourself instantly with MSN Messenger! MSN Messenger  
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> What can you do with the new Windows Live? Find out  
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
> Express yourself instantly with MSN Messenger! MSN Messenger  
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before  
> posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090220/86824ef9/attachment.html>