Hardware Benchmarking Tasks For A High-Performance Bioinformatics Cluster

Question

[Khader Shameer]

Is there any bioinformatics specific task to asses performance of a high-performance cluster ? How do you benchmark your brand-new locally accessible hardware designated for biocomputing ?

[Zev.Kronenberg]

IO slam your fancy new cluster. Here is a list of software that can help with benchmarking IO http://www.mcs.anl.gov/~thakur/pio-benchmarks.html. We often bottleneck our IO. You could also do a whole bunch of alignments on FASTQ. congrats on a new setup!

Answer 1

[Mndoci]

IO, IO, IO. The list by Zev is good, but at the very least run Fio [1] and and network tests (ping pong, single flow, etc)

Also, make sure you run STREAM [2]. You want to test memory bandwidth.

You could run HPCC [3], which has a number of different types of benchmark

1. http://www.cs.virginia.edu/stream/
2. http://freecode.com/projects/fio
3. http://icl.cs.utk.edu/hpcc/

[Khader Shameer]

Thanks Deepak. I am new to this whole benchmarking scene. It will be great if you could add a couple of links about the tests you mentioned in answer.

[Mndoci]

Added links to various benchmarks