On 12/17/12 8:47 PM, Christopher Samuel wrote:
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On 17/12/12 21:57, ananyachatterjee wrote:
[ganga:04205] *** Process received signal *** [ganga:04205] Signal:
Segmentation fault (11) [ganga:04205] Signal code: Address not
mapped (1) [ganga:04205] Failing at address: 0x201a01c20
Segmentation faults are usually bugs in the program where it is trying
to access memory it shouldn't be. Very occasionally they can be
caused by hardware issues corrupting pointers, but usually it's just a
bug.
If, as Justin suggests, it's a problem in your simulation then I would
suggest that the program should detect it and tell you, not got off
into the weeds and trigger a condition that causes the OS kernel to
kill it with a SEGV.
Might be worth reporting a bug and seeing what the maintainers say.
The presence of the printed warning indicates it's not a bug:
"t = 239.934 ps: Water molecule starting at atom 75561 can not be settled.
Check for bad contacts and/or reduce the timestep.
Wrote pdb files with previous and current coordinates"
Whenever this happens, the integration is failing. Perhaps the seg fault isn't
elegant, but I don't know if it's unavoidable or not. When the constraints
fail, typically molecules are careening across the system with (approaching)
infinite velocity and/or coordinates. There are various environment variables
to allow more leeway when this happens and/or suppress coordinate dumping, but
they're rarely used because this is not something one should usually try to
blindly circumvent.
In 99.9999% of cases (rough guess ;), this is a failure due to instability
caused by insufficient minimization/equilibration, bad topology, or unstable run
settings and not a bug.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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