[gmx-users] Gromacs 4 bug?
bernhard.knapp at meduniwien.ac.at
Fri Dec 12 09:43:29 CET 2008
I have a problem with gromacs 4 (also tried 4.0.2). If I start a
simulation it is calculating for some time but after about one day it
gets somehow stuck. This means that the simulation is still running and
the top commands says md still uses all 4 cores of the computer:
5487 bknapp 20 0 123m 41m 6864 R 100 2.0 1388:25
5488 bknapp 20 0 114m 35m 6432 R 100 1.8 1388:33
5489 bknapp 20 0 114m 35m 6432 R 100 1.8 1388:00
5490 bknapp 20 0 113m 34m 6424 R 100 1.7 1388:16 mdrun
but no output is written anymore. I redirect the output of std::err to
job.1sjh.md.err (which contains then the steps done and the prediction
how long it will take to finish):
-rw-r--r-- 1 bknapp users 258713 2008-12-12 06:25 job.1sjh.md.err
bknapp at quoVadis01:~/gromacsRuns/_validation> date
Fri Dec 12 09:30:12 CET 2008
It seems that it is still calculation (something?) but not writing
output anymore. In this case it stops after 423900 steps or 847ps. If I
simply re-run the same simulation it stops again but at a different
time. If I perform exactly the same commands on gromacs 3.3 it works
fine (I stopped the simulation by myself after 20ns).
Is this a known bug or is there a work-around?
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