How optimis and activate hyper-threading to give BLAST more virtual cores

sequenceserver
#1

I am interesting to optimize core of my blast, by default it will be less, so how to configure or where the file need to look for

#2

Hi Jaeyres,

Thanks for your interest in sequence server. I have to admit I’m not quite sure exactly what you are asking. Sequence server is able to use parallelised blast - you can specify the number of CPUs to be used in your sequenceserver.conf file. However even when this is set blast does not always use that number of CPUs, as it seems not all steps of the pipeline are parallelised.

ben

#3

my sequenceserver.conf doesn’t specify CPU, but it does have a num_threads, which I have to assume is the same thing. I set mine for 6 (my machine has 8 cores), and it definitely does use more cores for some routines than others. blastp for example tends to really use 4-6 cores, whereas blastn doesn’t seem to use more than 1. Not sure why, but like Ben said, it’s probably a BLAST pipeline thing.