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

[Changwon Yang]

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:
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>   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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