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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>Do you use separate PME nodes?<br>Which integrator do you use?<br><br>Berk<br><br>> Date: Thu, 5 Nov 2009 18:37:07 +1100<br>> From: Mark.Abraham@anu.edu.au<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] MPI_BCAST : Message truncated [when restarting from checkpoint]<br>> <br>> Vasilii Artyukhov wrote:<br>> > Dear colleagues,<br>> > <br>> > I encountered the following error messages when trying out the <br>> > checkpoint continuation functionality with MPI:<br>> > <br>> > Reading file topol.tpr, VERSION 4.0.5 (single precision)<br>> > <br>> > Reading checkpoint file state.cpt generated: Tue Oct 27 22:37:23 2009<br>> > <br>> > 8 - MPI_BCAST : Message truncated<br>> > [8] [] Aborting Program!<br>> > Abort signaled by rank 8: Aborting program !<br>> > Exit code -3 signaled from [node address]<br>> > Killing remote processes...<br>> > <br>> > <br>> > From a short google search I've come under the impression that this has <br>> > to do with sending messages between the nodes that are larger than the <br>> > receive buffer (note my total lack of practical experience with MPI <br>> > programming). However, I have no idea where, if this is true, it might <br>> > be happening.<br>> > <br>> > My system has 44091 atoms, and the .cpt file size is 1.1M, which doesn't <br>> > seems too large. Restarting works seemingly fine with serial mdrun.<br>> <br>> Hmm, that's an issue I've not seen before. Perhaps your MPI is <br>> configured with quite a small buffer for such things. What MPI style and <br>> version is it? Checking about this with your system admins is a good idea.<br>> <br>> Mark<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://lists.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br> <br /><hr />New Windows 7: Find the right PC for you. <a href='http://windows.microsoft.com/shop' target='_new'>Learn more.</a></body>
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