Error - Option -T does not have any effect with the sequential or parallel MPI version.

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Nanzhen

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Aug 24, 2021, 10:57:35 PMAug 24
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Hey there,

I used raxmlHPC -f a -x 12345 -p 12345 -#500 -m PROTGAMMAILGF -s Lac_core_alignment_2.fasta -n ex -T 70, but it showed that "Option -T does not have any effect with the sequential or parallel MPI version.".

Do you have any suggestions on how to speed up the process?

Thanks.
Best

Grimm

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Aug 25, 2021, 8:08:51 AMAug 25
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Hi Nanzhe,

first, as always, you should swap to and install RAxML-ng, which is even faster than classic RAxML.
second, if you want to stick with the classic (stand-alone) version, you have to call not raxmlHPC executable but the ...-PTHREADS version, which is the parallising variant where you can set the number of cores to be used using -T

Cheers, G.

Alexey Kozlov

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Aug 25, 2021, 8:21:33 AMAug 25
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thanks Grimm!

Just a small correction: with old RAxML, you most probably want to use "raxmlHPC­-PTHREADS­-AVX"
executable, which is parallelized *and* vectorized.

Please see section V. in the manual for details:

https://cme.h-its.org/exelixis/resource/download/NewManual.pdf


Best,
Alexey
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Nanzhen

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Aug 29, 2021, 12:39:33 AMAug 29
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Hi Grimm and Alexey,

Many thanks for the help!

Best,
Nanzhen

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