Be careful with your benchmarks as they can be meaningless or misleading. You will find that the speed of blast distributed within a cluster or compute farm is directly related to 2 things: (a) the amount of physical memory in the compute nodes and (b) the speed of your storage or disk I/O system. You can have the fastest server on earth but if you searching with blast against an NFS mounted database and your network or fileserver is slow then your blast searching speeds will be horrible. Give me a small number of speedy linux boxes and I can bring a $300,000 NFS/NAS system to its knees. Storage does matter. Blast performance also depends on you tune your DRM (gridengine or LSF etc. etc.) and how you adjust your workflow with respect to splitting large databases, locally caching data on compute nodes etc. etc. What are you trying to benchmark for? Picking the right CPU? Some people on this list may have already done this. My personal preference is Intel Pentium III's right now because: o P IV's are way too expensive o P III's are dirt cheap o There are a ton of dual-CPU motherboard options for the PIII allowing me flexible choices of system packaging and vendor o Athalon / AMDs are super fast but your motherboard choices are limited and you need to be really careful about cooling and ventilation --Chris http://bioteam.net On Monday, September 16, 2002, at 07:24 PM, Romualdo Zayas Lagunas wrote: > Hello everyone, > > I am part of a computational genomics team at CIFN-UNAM in Mexico. > Currently, we are trying to purchase a cluster (Linux and 32 or 48 > dual nodes), but since we lack experience in the field we > would like to perform some tests on some clusters first. Can you give > me > any pointers to URLs or any resources where I can download parallel > blast or scripts that run blast in parallel (and its different command > line options)? > > I will really appreciate any help you can give me. > > > Thanks a lot in advance > ~~~~~~~~~~~~~~~~~~~~~~~~~~~ > M.C. Romualdo Zayas Lagunas > CIFN-UNAM > rzayas@cifn.unam.mx > ~~~~~~~~~~~~~~~~~~~~~~~~~~~ > > _______________________________________________ > Bioclusters maillist - Bioclusters@bioinformatics.org > https://bioinformatics.org/mailman/listinfo/bioclusters