[gmx-users] Re: gmx-users Digest, Vol 76, Issue 53

[Mark Abraham]

Please file a Bugzilla, being sure to attach your .tpr files and be explicit about the GROMACS version.

Mark

----- Original Message -----
From: Changwon Yang <sht_ycw79 at hotmail.com>
Date: Friday, August 13, 2010 14:15
Subject: [gmx-users] Re: gmx-users Digest, Vol 76, Issue 53
To: gmx-users at gromacs.org

> 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: <gmx-users-request at gromacs.org>
> Sent: Wednesday, August 11, 2010 7:00 PM
> To: <gmx-users at gromacs.org>
> Subject: gmx-users Digest, Vol 76, Issue 53
> 
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> > 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 <gmx3 at hotmail.com>
> > Subject: RE: [gmx-users] Replica Exchange problem in gmx-4.5 beta3
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <COL113-W4823E4BD1309887C9126078E960 at phx.gbl>
> > 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: sht_ycw79 at hotmail.com
> > To: gmx-users at gromacs.org
> > 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.
> > 
> > 
> > 
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