[gmx-users] MPI_BCAST : Message truncated [when restarting from checkpoint]

Vasilii Artyukhov darth.vasya at gmail.com
Thu Nov 5 17:51:39 CET 2009

Thanks for your quick responses! (Sorry if this appears in your inboxes
twice, first time I tried to send it there were some problems with my
connection, and I don't see my message on the list archive.)

2009/11/5 Mark Abraham <Mark.Abraham at anu.edu.au>

> Hmm, that's an issue I've not seen before. Perhaps your MPI is configured
> with quite a small buffer for such things. What MPI style and version is it?
> Checking about this with your system admins is a good idea.

Never had any problem with it on 4.0.5 or 3.3.3 (well, aside from random
halting sometimes) - right until the present issue with checkpoint restarts.

2009/11/5 Berk Hess <gmx3 at hotmail.com>

> I can vaguely remember an issue like this which I have fixed.
> But I don't recall if this was in 4.0.5 or in git master.
> Do you continue on exactly the same number of nodes?

Yes, exactly the same.

> Do you use separate PME nodes?

I think so; this depends on which is the default :) I didn't get any deep
into these things and just let mdrun decide for itself, but the log file
does mention PME and particle nodes.

> Which integrator do you use?

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