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Hi,<br><br>I fixed the bug for 4.0.8 (if it will ever be released).<br><br>You can work around it by put your protein in a big box and using long cut-off's<br>with domain decomposition (or simple run in serial).<br><br>The next version of Gromacs will support domain decomposition also<br>for vacuum simulations, even without cut-off's.<br><br>Berk<br><br>> Date: Wed, 20 Jan 2010 09:34:45 +0100<br>> From: sdonnin@gwdg.de<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] problem with vsite and particle decomposition<br>> <br>> Hi,<br>> <br>> yes, I've just filed a bugzilla and attached the tpr.<br>> Thanks,<br>> <br>> Serena<br>> <br>> > Hi,<br>> ><br>> > This is clearly a bug.<br>> > Could you file a bugzilla and attach the tpr file?<br>> > <br>> > Thanks,<br>> > <br>> > Berk<br>> <br>> >/ Date: Wed, 20 Jan 2010 08:52:27 +0100<br>> />/ From: sdonnin at gwdg.de <http://lists.gromacs.org/mailman/listinfo/gmx-users><br>> />/ To: gmx-users at gromacs.org <http://lists.gromacs.org/mailman/listinfo/gmx-users><br>> />/ Subject: [gmx-users] problem with vsite and particle decomposition<br>> />/ <br>> />/ Hallo,<br>> />/ <br>> />/ I had a problem when running with virtual sites (-vsite hydrogens) and<br>> />/ particle decomposition (mdrun -pd) on more than one processor with<br>> />/ gromacs 4.0.7. I could run without problems the same files without<br>> />/ virtual site description. The error message looks like this:<br>> />/ <br>> />/ [node036:28870] *** An error occurred in MPI_Wait<br>> />/ [node036:28870] *** on communicator MPI_COMM_WORLD<br>> />/ [node036:28870] *** MPI_ERR_TRUNCATE: message truncated<br>> />/ [node036:28870] *** MPI_ERRORS_ARE_FATAL (goodbye)<br>> />/ <br>> />/ It seems that the error message comes from move_cgcm() in<br>> />/ sim_util.c, line 157, but the cause could as well<br>> />/ be MPI communication that happens before move_cgcm.<br>> />/ <br>> />/ Did anybody experienced similar problems or can help with this issue?<br>> />/ Thanks,<br>> />/ <br>> />/ Serena<br>> />/ <br>> />/ <br>> />/ -- <br>> /<br>> <br>> <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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