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

Ondrej Marsalek ondrej.marsalek at gmail.com
Sat Feb 21 17:47:44 CET 2009

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]
[isis:23154] [ 2]
[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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