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.)<br><br>2009/11/5 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au" target="_blank">Mark.Abraham@anu.edu.au</a>></span><div class="im">
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</div></div>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.<br></blockquote><font color="#888888">
</font><br></div>MVAPICH 1.1<br>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.<br><br>2009/11/5 Berk Hess <span dir="ltr"><<a href="mailto:gmx3@hotmail.com" target="_blank">gmx3@hotmail.com</a>></span><div class="im"><br>
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Hi,<br><br>I can vaguely remember an issue like this which I have fixed.<br>But I don't recall if this was in 4.0.5 or in git master.<br><br>Do you continue on exactly the same number of nodes?<br></div></blockquote>
</div><div><br>Yes, exactly the same.<br> </div><div class="im"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Do you use separate PME nodes?<br>
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</div><div><br>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.<br> </div><div class="im"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div>Which integrator do you use?<br></div></blockquote></div><br>MD