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) 48 nodes > 2) What is the compute node architecture? (e.g. dual 3GHz Xeon, dual > Opteron) dual 3.2GHz Xeon > 3) Do your compute nodes have local hard drives or are they diskless? Local hard disk > 4) What is the cluster interconnect? (e.g. GigE) GigE > 5) What application(s) primarily run on your cluster (e.g. BLAST, HMMER) sequest, tandem, statistical/mathematical ad-hoc scripts > 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) NA > 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? Seperate > 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) Quad Intel Xeon 3.0 GHz with Dual Path Fiber Connect IBM TotalStorage FAStT600 Turbo > 10) What is the ratio of NFS servers to compute nodes in your cluster? 8:48 > 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? 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) In all i have around 3TB of storage attached with this cluster consisting of 36 Fiber Channel Hard Disks > 13) What is the ratio of NAS servers to compute nodes in your cluster? 1:48 > 14) What is the throughput of your NAS server(s)/SAN? around 35-39 MB/s > 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? Yes/No > 17) What are the two biggest problems you have with your cluster > filesystem solution? Bottleneck is NFS due to excessive amount of file I/O over NFS > 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) Try different file systems > 19) What NFS server/compute node or NAS-SAN/compute node ratio will you > aim for with the next cluster you build or upgrade? Still evaluating > 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). Feel free thanks Anand --- Anand Singh Bisen http://www.abisen.com > _______________________________________________ > Bioclusters maillist - Bioclusters at bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters >