need advice on small cluster

[Tibor Pali]

Hi,

I am reading, these two lists (beowulf and gromacs) for while now and - 
seeing so many experts here - I hope I can get some help in setting up a 
small cluster. It will initially have 4-5 nodes (and will not grow above 
8-12 nodes any soon). Primary usage will be gromacs and possibly gaussian 
and charm. It should also allow using the nodes as independent 
workstations, i.e. cluster of workstations (COW), Therefore I need  HD and 
graphic card in the nodes and a CPU switch (because the rack will be 
placed in a remote part of the building). Since I will have jobs mainly 
running on a single node (or processor) and only occasionally multinode 
jobs, I dropped GBit ethernet (I can add later if need dictates). Here is 
the setup so far (after negotiation with a local supplier):

** Board/House: MSI K7D Master MS-6501 (dual)
- http://www.msi.com.tw/program/products/mainboard/mbd/pro_mbd_detail.php?
UID=344&MODEL=MS-6501

** Chassis:
*** seems to be better (higher power, better cooling and diagnostic leds): 
Supermicro SC8221-400RC (see 
http://www.supermicro.com/PRODUCT/Chassis/SC822.htm)
*** alternative (weaker): Mapower MP-P26EX32-1 (the IDE disk version, 19", 
2U) ( see http://www.mapower.de/produkte.asp): 1.44 MB FDD, S3 3D/2X AGP 
vid.

** Processor: 2 x Athlon MP 2000+ with CoolerMaster DP-56j31C

** RAM: 512 MB DDR266 SDRAM (non-registered)

** HD: 60GB/5400

** network interface card (fast): 3Com 3C905 10/100 (M-via supports it: 
http://www.nersc.gov/research/FTG/via)

** ethernet fast switch:
*** 3Com 3C16981 12-port 10/100 switch; this is commonly called 3Com 
SupersStack 3 switch 3300 (nI don't see anymore on 3com's web page, but 
http:
//support.3com.com/infodeli/tools/switches/s_stack2/3c16980/manual.a05/index.
htm and 
http://support.3com.com/infodeli/tools/switches/s_stack2/3c16950/manual.b03/
index.htm)
*** alternative?: 3Com 3C16464C-ME
- about one third the price of the 3C16981, but: no management, VLAN and 
SNMP; and fixed store-and-forward mode.
*** alternative?: DLink DES 1016+ 16-port 10/100 switch (less than one 6th 
the price of the 3C16981!!
- http://www.dlink-me.com/products/switches/des1016.htm
- forwarding mode not clear to me

** power supply: APC 1400 VA RackMount UPS

** rack: CONTEG 42U, 8 shelves

** Keyboard-Video-Mouse switch extender: Master View ProOSD 8PC+console 
extender (upto 150m) (185 eHUF)


My, somewhat redundant, specific questions:

What are the important parameters for a switch for the above purpose?

Is the 3Com 3C905/3C16981 NIC/switch combo a good choice?

The 3Com Switch 3300 seems to have only store-and-forward forwarding mode 
(i.e. no on-the-fly or direct forward): is this critical? I read that 
on-the-fly (or direct) forwarding results in lower latency (on the cost of 
leaving error checking to other MAC devices in the chain).

Does "management" slow down node-node communication speeds or increases 
latency?


Any comment (weak points in the setup, suggestions for alternatives, etc.) 
would be greatly appreciated.

Many thannks in advance,

-- 				
Tibor