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 ?
•
written
by
Khader Shameer
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
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.
Log in to answer this question.
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!