Glen Otero wrote: > Greetings biocluster intelligentsia! Hello, Glen. Hmm... not sure I qualify for that accolade ;-) > 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) 76 nodes > 2) What is the compute node architecture? (e.g. dual 3GHz Xeon, dual > Opteron) 34 Athlon XP 2400+ DDR266 32 Athlon XP 2600+ DDR333 8 Athlon64 DDR400 2 Opteron 146 DDR400 > 3) Do your compute nodes have local hard drives or are they diskless? NFSROOT with local hard drives for swap + /tmp > 4) What is the cluster interconnect? (e.g. GigE) Dual NIC's in each node 100base-T and Gigabit Ethernet, three NIC's in servers connected to LAN. > 5) What application(s) primarily run on your cluster (e.g. BLAST, HMMER) Statistical simulations of stocastic processes Quantum chemistry density filed theory simulations EMBOSS, clustal, phylip, BLAST, HMMER, phredPhrap, Consed, MrBayes. > 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) Local stand-alone BLAST of NCBI mirror, and contigs from DNA shotgun sequence assembly projects > 7) What type of cluster filesystem is in use on your cluster? (e.g. > NFS, GFS, proprietary) ClusterNFS + Linux kernel NFS > 8) If you use NFS, is your NFS server the same as the cluster head node > or is it a separate server? ROOTNFS server separate from 'head' node (ssh and XDMP login 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) Uniprocessor Athlon XP2400+ 3 @ 8GB SCSI drives + 1.6TB RAID shared with login server > 10) What is the ratio of NFS servers to compute nodes in your cluster? 4:72 > 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? lmdd + bonnie > 12) If you have a NAS/SAN, what type of machine(s) are they? (e.g. > NetApp w/ x number of yGB hard drives) LAN access to 2 @ NetApp filers > 13) What is the ratio of NAS servers to compute nodes in your cluster? 2:72 > 14) What is the throughput of your NAS server(s)/SAN? 4MB/s (constrained by 100Base-T LAN) > 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? lmdd > 16) Are you satisfied overall with your cluster filesystem solution? No > 17) What are the two biggest problems you have with your cluster > filesystem solution? ClusterNFS 2GB filesize limit, poor file locking, cache inconsistent > 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) 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? same > 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). Yes - don't care about gift certificate. Best wishes, Tony. -- Dr. A.J.Travis, | mailto:ajt at rri.sari.ac.uk Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751 Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687