[Beowulf] Performance degrading

Jörg Saßmannshausen sassy1 at gmx.de
Tue Dec 15 17:22:11 EST 2009


Hi Gus,

thanks for your comments. The problem is not that there are 5 NWChem running. 
I am only starting 4 processes and the additional one is the master which 
does nothing more but coordinating the slaves. 

Other parts of the program behaving more as you expect it (again parallel 
between nodes, taken from one node):
14902 sassy     25   0 2161m 325m 124m R  100  2.8  14258:15 nwchem
14903 sassy     25   0 2169m 335m 128m R  100  2.9  14231:15 nwchem
14901 sassy     25   0 2177m 338m 133m R  100  2.9  14277:23 nwchem
14904 sassy     25   0 2161m 333m 132m R   97  2.9  14213:44 nwchem
14906 sassy     15   0  978m  71m  69m S    3  0.6 582:57.22 nwchem

As you can see, there are 5 NWChem running but the fifth one does very little. 
So for me it looks like that the internode communication is a problem here and 
I would like to pin that down.

For example, on the new dual quadcore I can get:
13555 sassy     20   0 2073m 212m 113m R  100  0.9 367:57.27 nwchem
13556 sassy     20   0 2074m 209m 109m R  100  0.9 369:11.21 nwchem
13557 sassy     20   0 2074m 206m 107m R  100  0.9 369:13.76 nwchem
13558 sassy     20   0 2072m 203m 103m R  100  0.8 368:18.53 nwchem
13559 sassy     20   0 2072m 178m  78m R  100  0.7 369:11.49 nwchem
13560 sassy     20   0 2072m 172m  73m R  100  0.7 369:14.35 nwchem
13561 sassy     20   0 2074m 171m  72m R  100  0.7 369:12.34 nwchem
13562 sassy     20   0 2072m 170m  72m R  100  0.7 368:56.30 nwchem
So here there is no internode communication and hence I get the performance I 
would expect.

The main problem is I am no longer the administrator of that cluster so 
anything which requires root access is not possible for me :-(

But thanks for your 2 cent! :-)

All the best

Jörg

Am Dienstag 15 Dezember 2009 schrieb beowulf-request at beowulf.org:
> Hi Jorg
>
> If you have single quad core nodes as you said,
> then top shows that you are oversubscribing the cores.
> There are five nwchem processes are running.
>
> In my experience, oversubscription only works in relatively
> light MPI programs (say the example programs that come with OpenMPI or
> MPICH).
> Real world applications tend to be very inefficient,
> and can even hang on oversubscribed CPUs.
>
> What happens when you launch four or less processes
> on a node instead of five?
>
> My $0.02.
> Gus Correa
> ---------------------------------------------------------------------
> Gustavo Correa
> Lamont-Doherty Earth Observatory - Columbia University
> Palisades, NY, 10964-8000 - USA
> ---------------------------------------------------------------------


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