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FastTreeMP on multicore system

Hi There,

I am trying to run FastTreeMP on multicore system (32 processors). The command is FastTreeMP -nt -gtr -boot 1 -gamma < input.fa > output.phy. The program is using only one core.

Could someone please explain why is it happening?

Thanks.

fasttree phylogeny
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updated by GenoMax GenoMax • written by bluebug • bluebug

Is this on a standalone machine or a legit SMP cluster?

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written by GenoMax GenoMax

Hi @genomax2. This is standalone server.

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written by bluebug • bluebug

I am not familiar with FastTreeMP but if the MP stands for real parallel processing then you would need a parallel execution environment installed on your machine (like OpenMP or so it appears from FastTreeMP site).

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written by GenoMax GenoMax

Thanks. I will check that.

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written by bluebug • bluebug

What is the output from:

$ ./FastTreeMP -help

It should display something like

FastTree 2.1.9 SSE3, OpenMP (24 threads):
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written by fanli.gcb fanli.gcb

Same as you have mentioned

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written by bluebug • bluebug

Huh, then it appears to be configured correctly. Are you sure it's only using one core throughout? There may be certain portions of the tree building that only use a single core

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written by fanli.gcb fanli.gcb

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