Question: Number of Threads for BWA MEM
0
gravatar for haiying.kong
14 months ago by
haiying.kong220
Germany
haiying.kong220 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 • 1.6k views
ADD COMMENTlink modified 6 months ago by Raony Guimarães820 • written 14 months ago by haiying.kong220
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 14 months ago • written 14 months ago by genomax52k

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

ADD REPLYlink written 14 months ago by st.ph.n2.3k

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

ADD REPLYlink written 14 months ago by haiying.kong220

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 14 months ago by CMosychuk20
2
gravatar for Raony Guimarães
6 months ago by
Dublin / Ireland
Raony Guimarães820 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 6 months ago by Raony Guimarães820
0
gravatar for fwuffy
6 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 6 months ago by fwuffy50
2

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

ADD REPLYlink written 6 months ago by WouterDeCoster30k
1

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

ADD REPLYlink written 6 months ago by Chris Miller20k

There will be a theoretical optimum

Did you mean Amdahl's law?

ADD REPLYlink written 6 months ago by kloetzl960
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: 464 users visited in the last hour