[Bioclusters] Taking a poll

[Rodney Dyer]

On Tue, 2005-06-21 at 15:18 -0700, Glen Otero wrote:
> Greetings biocluster intelligentsia!
> 
> I have some new BioBrew (biobrew.org) feature ideas that I'd like to  
> scrutinize against the collective intelligence and experience of this  
> community. I've written a few information gathering questions that,  
> if answered, ought to help me judge the feasibility of my ideas.  
> What's in it for those of you who take a few minutes to respond?  
> Well, the first 20 folks to email me (offline at  
> gotero at linuxprophet.com) with sufficient answers to *all* 20  
> questions will receive a $10 ThinkGeek gift certificate. The next 10  
> people with answers to all the questions will receive a $5 ThinkGeek  
> gift certificate. The questions are below with example answers in  
> parentheses (sometimes). Be as detailed as you like, because more  
> detailed answers will win in the event of a tie breaker : )
> 
> Thanks for your help!!-- Glen
> 
> 1) What is the size of your Linux cluster? (e.g. 128 nodes)

4 nodes


> 2) What is the compute node architecture? (e.g. dual 3GHz Xeon, dual  
> Opteron)

Dual PowerPC

> 3) Do your compute nodes have local hard drives or are they diskless?

They have hard drives, but boot over the network

> 4) What is the cluster interconnect? (e.g. GigE)

GigE

> 5) What application(s) primarily run on your cluster (e.g. BLAST, HMMER)

BLAST, Migrate, graph analysis, homegrown stuff


> 6) If BLAST is running on your cluster, describe the type of BLAST  
> jobs (e.g. blastn- genome vs. genome, blastn-genome annotation with  
> ESTs)

genome vs. genome

> 7) What type of cluster filesystem is in use on your cluster? (e.g.  
> NFS, GFS, proprietary)

NFS

> 8) If you use NFS, is your NFS server the same as the cluster head  
> node or is it a separate server?

Separate server

> 9) If you use NFS, what type of machine is your NFS server? (e.g.  
> dual Xeon Linux Box w/ x number of yGB hard drives)

Sun v20 Dual Opteron dual 2x73G SCSI

> 10) What is the ratio of NFS servers to compute nodes in your cluster?

1:4

> 11) How do you benchmark the throughput of your NFS server, i.e. what  
> application(s) do you use to stress the NFS server and what tool(s)  
> do you use to measure throughput?

I don't, my node count is small enough to not be a problem

> 12) If you have a NAS/SAN, what type of machine(s) are they? (e.g.  
> NetApp w/ x number of yGB hard drives)

None

> 13) What is the ratio of NAS servers to compute nodes in your cluster?

0:4

> 14) What is the throughput of your NAS server(s)/SAN?

NA

> 15) How do you benchmark the throughput of your NAS server/SAN, i.e.  
> what application(s) do you use to stress the servers and what tool(s)  
> do you use to measure throughput?

NA

> 16) Are you satisfied overall with your cluster filesystem solution?

No but it gets the work done right now

> 17) What are the two biggest problems you have with your cluster  
> filesystem solution?

Speed and reliability

> 18) With regard to cluster filesystems, what would you do differently  
> when building your next cluster? (e.g. increase NFS servers/compute  
> node ratio, different filesystem)

GFS looks nice, but I haven't spent much time on it yet.

> 19) What NFS server/compute node or NAS-SAN/compute node ratio will  
> you aim for with the next cluster you build or upgrade?

Haven't thought about it yet.

> 20) If necessary, do you mind if Glen emails you offli
> ne to seek  
> clarification on some of your answers? (Answering "Yes" is not  
> necessary to be eligible for a gift certificate).

Sure

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