[Beowulf] advice for newbie

Duke Nguyen duke.lists at gmx.com
Sun Aug 19 21:55:22 PDT 2012


Hi folks,

First let me start that I am total novice with cluster and/or beowulf. I 
am familiar with unix/linux and have a few years working in a cluster 
(HPC) environment, but I never have a chance to design and admin a cluster.

Now my new institute decides to build a (small) cluster for our next 
research focus area: genome research. The requirements are simple: 
expandable and capable of doing genome research. The budget is low, 
about $15,000, and we have decided:

  * cluster is a box cluster, not rack (well, mainly because our funding 
is low)
  * cluster OS is scientific linux with OpenMPI
  * cluster is about 16-node with a master node, expandable is a must

Now next step for us is to decide hardwares and other aspects:

  * any recommendation for a reliable 24-port gigabit switch for the 
cluster? I heard of HP ProCurve 2824 but it is a little bit hard to find 
it in my country
  * should our boxes be diskless or should they have a hard disk inside? 
I am still not very clear the advantages if the clients has about 80GB 
hard disk internally except that their OS are independent and does not 
depend on the master node, and maybe faster data processing (temporay), 
but 80GB each for genome research is too small
  * hard drives/data storage: we want to have storage of about 10TB but 
I am not sure how to design this. Should all the hard disk be in the 
master node, or they can be on each of the node, or should it be a NAS?
  * any recommendation for a mainboard (gigabit network, at least 4 RAM 
slots) about $200-$300 good for cluster?

I would love to hear any advice/suggestion from you, especially if you 
had built a similar cluster with similar purpose.

Thank you in advance,

Duke.



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