[Bioclusters] Taking a poll

[Glen Otero]

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)
2) What is the compute node architecture? (e.g. dual 3GHz Xeon, dual  
Opteron)
3) Do your compute nodes have local hard drives or are they diskless?
4) What is the cluster interconnect? (e.g. GigE)
5) What application(s) primarily run on your cluster (e.g. BLAST, HMMER)
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)
7) What type of cluster filesystem is in use on your cluster? (e.g.  
NFS, GFS, proprietary)
8) If you use NFS, is your NFS server the same as the cluster head  
node or is it a 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)
10) What is the ratio of NFS servers to compute nodes in your cluster?
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?
12) If you have a NAS/SAN, what type of machine(s) are they? (e.g.  
NetApp w/ x number of yGB hard drives)
13) What is the ratio of NAS servers to compute nodes in your cluster?
14) What is the throughput of your NAS server(s)/SAN?
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?
16) Are you satisfied overall with your cluster filesystem solution?
17) What are the two biggest problems you have with your cluster  
filesystem solution?
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)
19) What NFS server/compute node or NAS-SAN/compute node ratio will  
you aim for with the next cluster you build or upgrade?
20) If necessary, do you mind if Glen emails you offline to seek  
clarification on some of your answers? (Answering "Yes" is not  
necessary to be eligible for a gift certificate).