Please file a Bugzilla, being sure to attach your .tpr files and be explicit about the GROMACS version.
Mark ----- Original Message ----- From: Changwon Yang <[email protected]> Date: Friday, August 13, 2010 14:15 Subject: [gmx-users] Re: gmx-users Digest, Vol 76, Issue 53 To: [email protected] > I tried openmpi v 1.3.3 > but, I got a same error. > mdrun_mpi -multi works fine. REMD has a problem. > > ## error message ## > > step 500, will finish Fri Aug 13 16:43:25 2010[localhost:20171] > *** Process received signal *** > [localhost:20172] *** Process received signal *** > [localhost:20172] Signal: Segmentation fault (11) > [localhost:20172] Signal code: Address not mapped (1) > [localhost:20172] Failing at address: (nil) > [localhost:20171] Signal: Segmentation fault (11) > [localhost:20171] Signal code: Address not mapped (1) > [localhost:20171] Failing at address: (nil) > [localhost:20172] [ 0] /lib64/libpthread.so.0 [0x36e9e0eb10] > [localhost:20172] [ 1] mdrun_mpi_d(replica_exchange+0x1136) [0x42a446] > [localhost:20172] [ 2] mdrun_mpi_d(do_md+0x48a8) [0x433ca8] > [localhost:20172] [ 3] mdrun_mpi_d(mdrunner+0x11f1) [0x42f181] > [localhost:20172] [ 4] mdrun_mpi_d(main+0x9f1) [0x438101] > [localhost:20172] [ 5] /lib64/libc.so.6(__libc_start_main+0xf4) > [0x36e921d994][localhost:20172] [ 6] mdrun_mpi_d [0x420359] > [localhost:20172] *** End of error message *** > [localhost:20171] [ 0] /lib64/libpthread.so.0 [0x36e9e0eb10] > [localhost:20171] [ 1] mdrun_mpi_d(replica_exchange+0x1136) [0x42a446] > [localhost:20171] [ 2] mdrun_mpi_d(do_md+0x48a8) [0x433ca8] > [localhost:20171] [ 3] mdrun_mpi_d(mdrunner+0x11f1) [0x42f181] > [localhost:20171] [ 4] mdrun_mpi_d(main+0x9f1) [0x438101] > [localhost:20171] [ 5] /lib64/libc.so.6(__libc_start_main+0xf4) > [0x36e921d994][localhost:20171] [ 6] mdrun_mpi_d [0x420359] > [localhost:20171] *** End of error message *** > ----------------------------------------------------------------- > --------- > mpiexec noticed that process rank 2 with PID 20172 on node > localhost.localdomain exited on signal 11 (Segmentation fault). > ----------------------------------------------------------------- > --------- > > > > -------------------------------------------------- > From: <[email protected]> > Sent: Wednesday, August 11, 2010 7:00 PM > To: <[email protected]> > Subject: gmx-users Digest, Vol 76, Issue 53 > > > Send gmx-users mailing list submissions to > > [email protected] > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > or, via email, send a message with subject or body 'help' to > > [email protected] > > > > You can reach the person managing the list at > > [email protected] > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of gmx-users digest..." > > > > > > Today's Topics: > > > > 1. RE: Replica Exchange problem in gmx-4.5 beta3 > (Berk Hess) > > > > > > --------------------------------------------------------------- > ------- > > > > Message: 1 > > Date: Wed, 11 Aug 2010 11:23:54 +0200 > > From: Berk Hess <[email protected]> > > Subject: RE: [gmx-users] Replica Exchange problem in gmx-4.5 beta3 > > To: Discussion list for GROMACS users <[email protected]> > > Message-ID: <[email protected]> > > Content-Type: text/plain; charset="iso-8859-1" > > > > > > Hi, > > > > This could be due to problems with MPICH. > > Could you please try openmpi and report back? > > > > Thanks, > > > > Berk > > > > From: [email protected] > > To: [email protected] > > Date: Wed, 11 Aug 2010 18:09:00 +0900 > > Subject: [gmx-users] Replica Exchange problem in gmx-4.5 beta3 > > > > > > > > > > > > > > > > > > Hello! > > I'm doing a simple REMD test with 4 > > replicas. > > Time step : 2 fs > > Exchange : every 500fs > > > > md_0.tpr md_1.tpr md_2.tpr md_3.tpr > > > > mpiexec(or mpirun) -np 4 mdrun_mpi_d -deffnm md_ > > -multi 4 -replex 200 > > I got a error message. > > > > ##error## > > 1000000 steps, 2000.0 ps. > > step 600 rank > > 3 in job 10 localhost.localdomain_50305 > caused collective > > abort of all ranks > > exit status of rank 3: killed by signal 11 > > rank > > 2 in job 10 localhost.localdomain_50305 > caused collective > > abort of all ranks > > exit status of rank 2: killed by signal 11 > > > > > > Using gmx4.0.7 , It works fine. > > Is this bug in gmx-4.5 beta ? > > In log files, no error message were > > found. > > gmx-4.5 beta3 was compiled with icc 11.0 > > and mpich2-1.2.1p1. > > > > > > > > -- > > gmx-users mailing list [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search > before posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [email protected]. > > Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > > -------------- next part -------------- > > An HTML attachment was scrubbed... > > URL: http://lists.gromacs.org/pipermail/gmx- > users/attachments/20100811/b4d58a9c/attachment-0001.html > > > > ------------------------------ > > > > -- > > gmx-users mailing list > > [email protected] > > http://lists.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search > before posting! > > > > End of gmx-users Digest, Vol 76, Issue 53 > > ***************************************** > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search > before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [email protected]. > Can't post? 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