From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Fri May 04 2012 - 16:30:26 CDT
Hi Aron, if you're in doubt, have a look at the .txt files that are
generated, it should clarify which state files are the most recent.
Each replica/walker should be restarted *from its own most recent state file
*, with no exceptions. Just keep running each one as a regular NAMD
simulation, they will communicate with one other on their own.
In any case, if you have e.g. replicaID = "R001" in the configuration file
of one replica/walker, and you feed to it the state file from the walker
"R002" it should give you an error. So you should see for yourself which
one is the right way :-)
If one walker has been offline for a long time (e.g. because it crashed and
you're now restarting it), there will be of course a sudden jump in its
PMF, because at that moment it reads all the hills that the other walkers
have been accumulating in the meantime. So it makes no sense to compare
the PMFs before and after a restart, if one replica/walker has been
off-sync for a while.
What makes sense instead is to compare the PMFs written by different
replicas/walkers within minutes from each other. Those should be
essentially the same: if they turned out wildly different, please send me
the details so that I can try to figure it out.
On Fri, May 4, 2012 at 4:54 PM, Aron Broom <broomsday_at_gmail.com> wrote:
> sorry, just as a second follow-up question. If what I've said in the
> previous message is true, is it also possible to restart a walker that has
> crashed while the other walkers are still running, and they will again
> start picking up the new hills?
> On Fri, May 4, 2012 at 4:52 PM, Aron Broom <broomsday_at_gmail.com> wrote:
>> I've been running a few preliminary experiments with the multiple walkers
>> MetaDynamics, and I'm wondering about restarts. I've had some issues with
>> a few nodes crashing, and have had to restart some of the walkers. What
>> I've noticed is that the pmfs for different walkers at the same timestep
>> don't match once there has been some kind of crash, which I guess makes
>> sense, as there is no inefficiency of synchronizing them, so they are all
>> semi-independent (or maybe I'm confused on that).
>> Anyway, my question then is, if all my walkers have stopped (having
>> finished whatever short chunk of time they get run for, or all having
>> crashed, or some combination of the two), and I want to continue with the
>> next chunk of simulation, should I take the *.colvars.state file from the
>> most progressed walker (the one with the most hills) and replace all the
>> other walkers with that, so that they now start at the most advanced stage?
>> Aron Broom M.Sc
>> PhD Student
>> Department of Chemistry
>> University of Waterloo
> Aron Broom M.Sc
> PhD Student
> Department of Chemistry
> University of Waterloo
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