hello:
it is blue gene P. And the gromacs is single precision in the
cluster. Getting Loaded...And the administrator told me that I have to
use the multiples of 32 in the bg_size parameter. The number specified
in "-np" should be 4 times bg_size.
It is even slower than my own workstation with 16 core.........
here is the log file I get:
-------------log----------------
Reading file npt_01.tpr, VERSION 4.5.5 (single precision)
Loaded with Money
Will use 112 particle-particle and 16 PME only nodes
This is a guess, check the performance at the end of the log file
Making 3D domain decomposition 4 x 4 x 7
starting mdrun 'GRowing Old MAkes el Chrono Sweat'
500000 steps, 500.0 ps.
step 0
vol 0.64! imb F 16% pme/F 0.22 step 100, will finish Wed Apr 25 18:28:06
2012
vol 0.65! imb F 17% pme/F 0.21 step 200, will finish Wed Apr 25 18:09:54
2012
vol 0.67! imb F 18% pme/F 0.21 step 300, will finish Wed Apr 25 18:03:12
2012
vol 0.69! imb F 18% pme/F 0.21 step 400, will finish Wed Apr 25 17:58:25
2012
vol 0.67! imb F 19% pme/F 0.21 step 500, will finish Wed Apr 25 17:55:26
2012
vol 0.68! imb F 19% pme/F 0.22 step 600, will finish Wed Apr 25 17:53:31
2012
vol 0.68! imb F 19% pme/F 0.22 step 700, will finish Wed Apr 25 17:51:57
2012
vol 0.68! imb F 19% pme/F 0.22 step 800, will finish Wed Apr 25 17:50:32
2012
vol 0.68! imb F 20% pme/F 0.22 step 900, will finish Wed Apr 25 17:49:14
2012
vol 0.67! imb F 21% pme/F 0.22 step 1000, will finish Wed Apr 25
17:48:13 2012
vol 0.68! imb F 20% pme/F 0.22 step 1100, will finish Wed Apr 25
17:47:28 2012
vol 0.67! imb F 21% pme/F 0.22 step 1200, will finish Wed Apr 25
17:46:50 2012
vol 0.67! imb F 21% pme/F 0.22 step 1300, will finish Wed Apr 25
17:46:15 2012
On 04/24/2012 06:01 PM, Hannes Loeffler wrote:
On Tue, 24 Apr 2012 15:42:15 +0200
Albert<mailmd2...@gmail.com> wrote:
hello:
I am running a 60,000 atom system with 128 core in a blue gene
cluster. and it is only 1ns/day.... here is the script I used for
You don't give any information what exact system that is (L/P/Q?), if
you run single or double precision and what force field you are using.
But for a similar sized system using a united atom force field in
single precision we find about 4 ns/day on a BlueGene/P (see our
benchmarking reports on
http://www.stfc.ac.uk/CSE/randd/cbg/Benchmark/25241.aspx). I would
expect a run with the CHARMM 27 force field in double precision to be
roughly 3 times slower. We found scaling to 128 cores to be
reasonably good. Also, check our report for problems when compiling
with higher optimisation.
Hannes.
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