Question: Bwa: Number Of Threads
3
gravatar for Pierre Lindenbaum
9.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

OK, I'm really not a hardware-guy: I want to run bwa and here is a snapshot of my /proc/cpuinfo

#grep "physical id" /proc/cpuinfo | sort | uniq | wc -l
4
#grep ^processor /proc/cpuinfo | wc -l
16
#grep 'cpu cores' /proc/cpuinfo | sort | uniq
cpu cores    : 4

what would you suggest as a good value for the number of threads to be used by bwa (option -t ) ?

Thank you ! :-)

ADD COMMENTlink modified 17 months ago by RamRS25k • written 9.7 years ago by Pierre Lindenbaum126k
5
gravatar for Aaron Statham
9.7 years ago by
Aaron Statham1.1k
Australia
Aaron Statham1.1k wrote:

Looks to me like you have 4xquad core CPUs - I would use 15 threads, that way you still have one core free to do other things in the meantime

ADD COMMENTlink written 9.7 years ago by Aaron Statham1.1k
2

Agreed. You could also use nice and use all processors:

nice -19 bwa -t 16 ...
ADD REPLYlink modified 17 months ago by RamRS25k • written 9.7 years ago by Stefano Berri4.1k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 789 users visited in the last hour