Question: Number of Threads for BWA MEM
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gravatar for haiying.kong
8 months ago by
haiying.kong180
Germany
haiying.kong180 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 • 699 views
ADD COMMENTlink modified 12 days ago by Raony Guimarães760 • written 8 months ago by haiying.kong180

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 8 months ago • written 8 months ago by genomax40k

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

ADD REPLYlink written 8 months ago by st.ph.n2.0k

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

ADD REPLYlink written 8 months ago by haiying.kong180

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 8 months ago by CMosychuk20
1
gravatar for Raony Guimarães
12 days ago by
Dublin / Ireland
Raony Guimarães760 wrote:

Are you looking for something like this ?

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

ADD COMMENTlink written 12 days ago by Raony Guimarães760
0
gravatar for fwuffy
12 days 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 12 days ago by fwuffy50
1

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

ADD REPLYlink written 12 days ago by WouterDeCoster24k
1

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

ADD REPLYlink written 12 days ago by Chris Miller19k

There will be a theoretical optimum

Did you mean Amdahl's law?

ADD REPLYlink written 12 days ago by kloetzl750
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