Bernhard Knapp wrote:
Mark wrote:
What's happening in the log files? What's the latest information in
the checkpoint files? Could there be some issue with file system
availability?
Hi Mark
Unfortunaltey I already deleted the simulation files which got stuck
after 847ps. But here is the output of another simulation done on the
same system but with an other pdb file. This one gets stuck after 179ps
with the following output:
The latest thing the checkpoint file says is:
"imb F 3% step 89700, will finish Wed Jul 1 09:11:00 2009
imb F 3% step 89800, will finish Wed Jul 1 09:02:51 2009"
OK so there's no indication from GROMACS that it's experiencing trauma
within the simulation. So now you need to try to restart close to the
point you saw problems to see if the problem is reproducible. If it's
not reproducible, then my guess, as last time, is that an NFS share is
becoming unavailable, or some such. There are lots of other
possibilities - a bug in GROMACS seems unlikely at this stage.
Mark
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