[gmx-users] Segfault with the v-rescale thermostat in Gromacs 4.0.3

[Berk Hess]

Hi,

Please file a bug report on bugzilla.gromacs.org
and attach the tpr file.

Berk

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