Question: Number of Threads for BWA MEM
1
gravatar for haiying.kong
23 months ago by
haiying.kong250
Germany
haiying.kong250 wrote:

Is it recommended to use number of threads for BWA MEM, 2**N (4, 8, 16, 32...)? Or any number is as good as well as long as the memory can support?

bwa • 3.3k views
ADD COMMENTlink modified 15 months ago by Raony Guimarães980 • written 23 months ago by haiying.kong250
1

You can't use more than what is available on your computer for a start. Experiment with a small set of reads (100K) to see what core # works best with your system in terms of time to complete. You will saturate something (PCI-E/memory bus) and will see a plateau in performance beyond a certain number of cores/threads.

ADD REPLYlink modified 23 months ago • written 23 months ago by genomax65k

If your machine/cluster can support it, using many threads with -t should be fine.

ADD REPLYlink written 23 months ago by st.ph.n2.4k

It does not have advantage if the number of thread is 2**N, is this correct?

ADD REPLYlink written 23 months ago by haiying.kong250

I'd stick to the greatest number of threads your processor can support, unless you're on a workstation and you actually need to do other stuff while bwa runs.

ADD REPLYlink written 23 months ago by CMosychuk20
2
gravatar for Raony Guimarães
15 months ago by
Dublin / Ireland
Raony Guimarães980 wrote:

Are you looking for something like this ?

alt text

Source: http://en.community.dell.com/techcenter/high-performance-computing/b/genomics

ADD COMMENTlink written 15 months ago by Raony Guimarães980
0
gravatar for fwuffy
15 months ago by
fwuffy50
Michigan, USA
fwuffy50 wrote:

Bump. You can not run bwa with 1000 threads on one host and expect it to be 1000x faster than single thread. There will be a theoretical optimum which is a function of memory available per thread and reference genome size. Has anyone actually done tests?

ADD COMMENTlink written 15 months ago by fwuffy50
2

This will very likely depend on your computer architecture, for example I/O speed.

ADD REPLYlink written 15 months ago by WouterDeCoster38k
1

+1 - for most setups, alignment will be I/O bound before any other bottleneck gets hit.

ADD REPLYlink written 15 months ago by Chris Miller20k

There will be a theoretical optimum

Did you mean Amdahl's law?

ADD REPLYlink written 15 months ago by kloetzl1.0k
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