Suggestions for small Beowulf?

David Mathog mathog at
Wed Jul 31 10:12:19 PDT 2002

I'm shopping for a cluster to replace our current 9 node DS10 beowulf
and would like to get a bit of feedback before buying anything.

It's going to be 20 nodes in small ATX cases with 1Gb memorynode
and a smallish disk (40 GB or so, probably ATA.)  100BaseT networking.
We already have a SCSI U160 server which will NFS
serve to them and be the master for YP, SGE, etc.   I looked at racks
can't justify the cost now, and we have power/cooling/space for the
separate boxes.  The primary task for this server is to scan through
protein/DNA sequence databases which will normally live in file
cache, and will reload from the local disk if they happen to swap out.
(BLAST, for instance - I don't know if that's memory bandwidth limited
or CPU limited on the latest systems.)  It will also be used for POVray
rendering to make movies of molecules.

In each case please explain why rather than just stating a part number.

1.  Which 24 port switch?
2.  Which CPU/motherboard?  (In particular, is a nonECC solution
 viable with this many nodes???)
3.  Which additional compilers (besides gcc)?
4.  SGE, PVM, and Mpich will be installed.  What other cluster software
is worth having?
5.  What changes to RH 7.3?  (Upgrade kernel...?)
6.  Add a cheap video card or plunk one in if/when a node has problems?

Thank you,

David Mathog
mathog at
Manager, Sequence Analysis Facility, Biology Division, Caltech

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