Looks like it is not an issue in the mpi version, but the normally-threaded
gromacs-4.6 beta2 version dies at 1.07 us as well.
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This is fixed in 4.6-beta1, though I am using the mpi version instead of the
single-node threaded version.
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On 11/13/12 2:56 PM, benjfitz wrote:
Are there any other tests I should run to diagnose the problem?
I doubt there's anything that can be done that will be particularly useful. You
could compile in debugging mode and try to do a backtrace when the problem
occurs, but if you have a means t
Are there any other tests I should run to diagnose the problem?
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gmx-
Justin,
The main result is that extending the run in 500 ns chunks, per your
suggestion, appears to bypass this error. I used the first method listed on
the gromacs page for extending runs.
tpbconv -s cs2-npt-1us-b.tpr -extend 50 -o cs2-npt-1pt5us-c.tpr
mdrun -s cs2-npt-1pt5us-c.tpr -cpi cs2-
On 11/6/12 9:01 AM, benjfitz wrote:
Thanks for the suggestion, I should have mentioned Tcoupl and Pcoupl in my
previous post. I changed them from Nose-Hoover/Parrinello-Rahman to
V-rescale/Berendsen and one permutation mixing the two, but it crashed all
the same.
The nodes have at least 8 GB o
Thanks for the suggestion, I should have mentioned Tcoupl and Pcoupl in my
previous post. I changed them from Nose-Hoover/Parrinello-Rahman to
V-rescale/Berendsen and one permutation mixing the two, but it crashed all
the same.
The nodes have at least 8 GB of ram and free -m shows that I'm not run
On 11/5/12 11:25 PM, benjfitz wrote:
Justin, thank you for reminding me that I need to adhere to sane parameters.
I do have a few clarifying points, as it were. I tried these simulations
again, but with a larger box and 0.9 nm cutoffs, and received a segfault at
the same simulation time.
The m
Justin, thank you for reminding me that I need to adhere to sane parameters.
I do have a few clarifying points, as it were. I tried these simulations
again, but with a larger box and 0.9 nm cutoffs, and received a segfault at
the same simulation time.
The model I am using, from the user contribute
On 10/15/12 11:45 AM, benjfitz wrote:
As a further check I ran a neat solvent box and the simulation ends abruptly
at 1.07 us.
These results suggest that your physical model is unstable. A linear model of a
triatomic species is not stable. A more appropriate approach is to use virtual
s
As a further check I ran a neat solvent box and the simulation ends abruptly
at 1.07 us.
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