Hi,
Am 15.12.2009 um 23:22 schrieb Jörg Saßmannshausen:
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.
isn't NWChem using Global Arrays internally, and Open MPI is only
used for communication? Which version of GA is included with your
current NWChem?
-- Reuti
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-requ...@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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