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

[Nanzhen]

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]

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]

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

> --
> You received this message because you are subscribed to the Google Groups "raxml" group.
> To unsubscribe from this group and stop receiving emails from it, send an email to
> raxml+un...@googlegroups.com <mailto:raxml+un...@googlegroups.com>.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/raxml/47de404d-6b92-4c8a-a1b7-ad7b980d9170n%40googlegroups.com
> <https://groups.google.com/d/msgid/raxml/47de404d-6b92-4c8a-a1b7-ad7b980d9170n%40googlegroups.com?utm_medium=email&utm_source=footer>.

[Nanzhen]

Hi Grimm and Alexey,

Many thanks for the help!

Best,

Nanzhen