[Beowulf] Performance degrading

Jörg Saßmannshausen jorg.sassmannshausen at strath.ac.uk
Mon Dec 14 10:17:15 EST 2009


Dear all,

I am scratching my head but apart from getting splinters into my fingers I 
cannot find a good answer for the following problem:
I am running a DFT program (NWChem) in parallel on our cluster (AMD Opterons, 
single quad cores in the node, 12 GB of RAM, Gigabit network) and at certain 
stages of the run top is presenting me with that:

top - 15:10:48 up 13 days, 22:20,  1 user,  load average: 0.26, 0.24, 0.19
Tasks: 106 total,   1 running, 105 sleeping,   0 stopped,   0 zombie
Cpu0  :  8.0% us,  2.7% sy,  0.0% ni, 82.7% id,  0.0% wa,  1.3% hi,  5.3% si
Cpu1  :  4.1% us,  1.4% sy,  0.0% ni, 94.6% id,  0.0% wa,  0.0% hi,  0.0% si
Cpu2  :  2.7% us,  0.0% sy,  0.0% ni, 97.3% id,  0.0% wa,  0.0% hi,  0.0% si
Cpu3  :  0.0% us,  0.0% sy,  0.0% ni, 100.0% id,  0.0% wa,  0.0% hi,  0.0% si
Mem:  12250540k total,  5581756k used,  6668784k free,   273396k buffers
Swap: 16779884k total,        0k used, 16779884k free,  3841688k cached

  PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
16885 sassy     15   0 3928m 1.7g 1.4g S    4 14.4 312:19.92 nwchem
16886 sassy     15   0 3928m 1.7g 1.4g S    4 14.5 313:08.77 nwchem
16887 sassy     15   0 3920m 1.7g 1.4g S    3 14.4 316:18.24 nwchem
16888 sassy     15   0 3923m 1.6g 1.3g S    3 13.3 316:13.55 nwchem
16890 sassy     15   0 2943m 1.7g 1.7g S    3 14.8 104:32.33 nwchem

It is not a few seconds it does it, it appears to be for a prolonged period of 
time. I checked it randomly for say 1 min and the performance is well below 
50 % (most of the time around 20 %). I have not noticed that when I am 
running the job within one node.

I have the suspicion that the Gigabit network is the problem, but I really 
would like to pinpoint that so I can get my boss to upgrade to a better 
network for parallel computing (hence my previous question about Open-MX). 
Now how, as I am not an admin of that cluster, would I be able to do that?

Thanks for your comments.

Best wishes from Glasgow!

Jörg

-- 
*************************************************************
Jörg Saßmannshausen
Research Fellow
University of Strathclyde
Department of Pure and Applied Chemistry
295 Cathedral St.
Glasgow
G1 1XL

email: jorg.sassmannshausen at strath.ac.uk
web: http://sassy.formativ.net

Please avoid sending me Word or PowerPoint attachments.
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