Dear AMBER users and developers,
I would like to ask partitioning issue of sander. I noticed that similar
questions invoked in this ML forum, but could not find the solution.
So, please let me allow to invoke this issue again.
If you know the page providing the solution, please let me know just
the page in this ML.
I used sander to perform MD of protein using 8-core parallel computer
system, and detected the following error message;
----------------------------------------
partition error in shake on processor 0
this processor has atoms 1 through 9100
atom 9098 is within this range
atom 9101 is not within this range !
------------------------------------------
In the case of using 4 cores, sander works well, but for more than 8
cores, it does not, as mentioned (i.e., the above-mentioned error
message appears).
This system includes 16,799 water molecules. (Case 1)
Next, I added +3,989 water molecules to this model system by using
SolvateBox in LEaP, and noticed that sander worked well on a 16-core
parallel computer system, and that it did not on a 32-core parallel
system. (Case 2)
Then, I added +28,313 water molecules to this model system by
LEaP, and noticed that sander worked well even on a 32-core
parallel system. But it takes much more time than the Case 2.
(Case 3)
For this model system (Case 3), I removed 108 waters to build a
smaller calculation system, and tried the calculation again; as a result
of this modification, sander did not work on 32-core parallel
computer system (i.e., the above-mentioned error message appears).
Thus, the number of available cores looks very sensitive to sander
for this protein.
I would like to use 32-core parallel system even when using calculation
models 1 and/or 2 (Cases 1 and/or 2).
If you could let me know some instructions of this issue, I would much
appreciate it.
best regards,
Tetsuhiko
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Received on Sun Apr 15 2012 - 19:30:03 PDT
