On 25/04/2012 3:24 PM, Albert wrote:
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.
Yes, but your system is too small to make use of 128 processors. Also,
get rid of -launch and -nt from your command line, since they do nothing.
It is even slower than my own workstation with 16 core.........
here is the log file I get:
No, that's the stdout file. Look at the end of the .log file.
-------------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 guaranteed to lead to woeful performance with your .mdp
settings, but you will have to look towards the beginning of the .log
file to find out why mdrun selected this. Odds are good that your system
size is so small that the minimum particle-particle cell size
(constrained by rcoulomb) doesn't give mdrun any good options that use
all the processors. You'd likely get better raw performance with twice
the number of atoms or half the number of processors.
Mark
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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