[maker-devel] Hyperthreading

[Carson Holt]

MAKER is more of a pipeline. It will launch external tools on as many CPUs as you give it with the mpiexec command. I’ve found that many of the tools used get a boost with hyperthreading even though optimizations are not explicitly built into their code. The short answer is you would have to try it both ways. I doubt there will be much more than a 10-15% difference in runtime.

You can pull back to 128 would if you find that you are running low on RAM or have a high IO burden (both of which will double if you go from 128 to 256 even though CPU isn’t really doubling). Also MAKER per job performance plateaus at around 200 processes due to communication overhead. Above that threshold it is often useful to divide datasets into multiple separate jobs that can run simultaneously.

—Carson



> On May 23, 2017, at 1:52 PM, System Admin <admin at genome.arizona.edu> wrote:
> 
> We are using maker in a cluster with mpich.  Currently hyperthreading is on and we use 'mpiexec -n <cores>' to start maker.  Our machinelist file for mpich specifies the total emulated cores for each node.
> With hyperthreading on, we have up to 256 total emulated cores available.
> 
> Which is the optimal scenario?
> 1. Use '-n 256'
> 2. Use '-n 128' with hyperthreading still on
> 3. Use '-n 128' with hyperthreading turned off
> 
> Thanks
> 
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