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Hi,<br><br>Please file a bug report on bugzilla.gromacs.org<br>and attach the tpr file.<br><br>Berk<br><br>> Date: Sat, 21 Feb 2009 17:47:44 +0100<br>> From: ondrej.marsalek@gmail.com<br>> To: gmx-users@gromacs.org<br>> Subject: [gmx-users] Segfault with the v-rescale thermostat in Gromacs 4.0.3<br>> <br>> Dear Gromacs users and developers,<br>> <br>> I have encountered a segmentation fault with Gromacs 4.0.3. It only<br>> happens in a parallel run (particle decomposition, open boundary<br>> conditions), the same setup runs fine in serial. I can provide a small<br>> test case that should reproduce it, if anyone is interested. The stack<br>> trace is:<br>> <br>> starting mdrun 'Neat water'<br>> 500000 steps, 500.0 ps.<br>> [isis:23154] *** Process received signal ***<br>> [isis:23154] Signal: Segmentation fault (11)<br>> [isis:23154] Signal code: Address not mapped (1)<br>> [isis:23154] Failing at address: (nil)<br>> [isis:23154] [ 0] /lib/libpthread.so.0 [0x7f41e64050f0]<br>> [isis:23154] [ 1]<br>> /opt/gromacs-4.0.3/double/lib/libmd_mpi_d.so.5(vrescale_tcoupl+0x184)<br>> [0x7f41e8b3048c]<br>> [isis:23154] [ 2]<br>> /opt/gromacs-4.0.3/double/lib/libmd_mpi_d.so.5(update+0x1fa)<br>> [0x7f41e8bad03c]<br>> [isis:23154] [ 3] mdrun_d(do_md+0x25f9) [0x416ed1]<br>> [isis:23154] [ 4] mdrun_d(mdrunner+0xf35) [0x419bd3]<br>> [isis:23154] [ 5] mdrun_d(main+0x55f) [0x41a35f]<br>> [isis:23154] [ 6] /lib/libc.so.6(__libc_start_main+0xe6) [0x7f41e60a2466]<br>> [isis:23154] [ 7] mdrun_d [0x4062d9]<br>> [isis:23154] *** End of error message ***<br>> --------------------------------------------------------------------------<br>> mpirun noticed that process rank 1 with PID 23154 on node isis exited<br>> on signal 11 (Segmentation fault).<br>> --------------------------------------------------------------------------<br>> <br>> Seeing where the problem occurs, I have tried to switch to the the<br>> Berendsen thermostat. Then the calculation runs fine even in parallel.<br>> This looks like a bug to me, has anyone else seen this?<br>> <br>> Best regards,<br>> Ondrej Marsalek<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.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 />Express yourself instantly with MSN Messenger! <a href='http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/' target='_new'>MSN Messenger</a></body>
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