Forum:How To Correctly Speed Up Blast Using Num_Threads

Question

[commonsnook]

Hello, I did a short blast comparison using multiple cores to see how they behave. I published it in my blog and thought it would be a good idea to share it here.

http://voorloopnul.com/blog/how-to-correctly-speed-up-blast-using-num_threads/

[PoGibas]

You should modify y-axis (start from 0), for me it wasn't clear.

Edit:

Some time ago I asked similar question on http://unix.stackexchange.com/ -- got really informative answers.

Why using more threads makes it slower than using less threads

Answer 1

[Istvan Albert]

Benchmarking on VPS servers is tricky since everything is virtualized: CPU, harddrive etc.

Also the size of the database and size of a typical query may also be a factor. Each of these could turn a blast lookup from being CPU bound to IO bound and could substantially alter the results of the test.

[commonsnook]

Hello Istvan,

Most of your concerns are stated in the "Disclaimer" section, since the article is not intended to be a "One size fits all".

But Indeed, benchmarking on a VPS is really tricky, I had to switch one of the VMs because it was giving me absurd results, I believe the physical server hosting this particular VM was with high load.