[gmx-users] why it is so slow in Blue gene?

[Albert]

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<mailmd2011 at 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.