FastTreeMP on multicore system

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7.4 years ago

bluebug ▴ 10

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 • 3.5k views

ADD COMMENT • link updated 7.4 years ago by GenoMax 141k • written 7.4 years ago by bluebug ▴ 10

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

ADD REPLY • link 7.4 years ago by GenoMax 141k

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Hi @genomax2. This is standalone server.

ADD REPLY • link 7.4 years ago by bluebug ▴ 10

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What is the output from:

$ ./FastTreeMP -help

It should display something like

FastTree 2.1.9 SSE3, OpenMP (24 threads):

ADD REPLY • link 7.4 years ago by fanli.gcb ▴ 730

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Same as you have mentioned

ADD REPLY • link 7.4 years ago by bluebug ▴ 10

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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

ADD REPLY • link 7.4 years ago by fanli.gcb ▴ 730

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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).