Question: Bwa: Number Of Threads
3
gravatar for Pierre Lindenbaum
9.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k 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 14 months ago by RamRS24k • written 9.4 years ago by Pierre Lindenbaum124k
5
gravatar for Aaron Statham
9.4 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 9.4 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 14 months ago by RamRS24k • written 9.4 years ago by Stefano Berri4.1k
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