Question: FastTreeMP on multicore system
0
gravatar for bluebug
3.9 years ago by
bluebug10
bluebug10 wrote:

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 • 1.6k views
ADD COMMENTlink modified 3.9 years ago by genomax89k • written 3.9 years ago by bluebug10

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

ADD REPLYlink written 3.9 years ago by genomax89k

Hi @genomax2. This is standalone server.

ADD REPLYlink written 3.9 years ago by bluebug10
1

What is the output from:

$ ./FastTreeMP -help

It should display something like

FastTree 2.1.9 SSE3, OpenMP (24 threads):
ADD REPLYlink written 3.9 years ago by fanli.gcb690

Same as you have mentioned

ADD REPLYlink written 3.9 years ago by bluebug10

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 REPLYlink written 3.8 years ago by fanli.gcb690

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).

ADD REPLYlink written 3.9 years ago by genomax89k

Thanks. I will check that.

ADD REPLYlink written 3.9 years ago by bluebug10
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