RAxML

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Description

RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood.

Availability

Version 7.2.8-alpha, 7.3.0, 8.1.17 (approx from 23.2.2015) and 8.2.4

Licence

GNU GPL v3

Use

Add module

module add raxml-8.2.4

now you can use single processor, thread or MPI version by issue command

raxmlHPC
raxmlHPC-PTHREADS
mpirun raxmlHPC-MPI

Addition of module recognizes processor architecture (if it supports AVX or not).

Notice: This application supports parallel computing (MPI, OpenMP) which can have weird consequences. For more details about parallel computing visit the page How to compute/Parallelization.

Selection of particular CPU type

RAxML provides various binaries for different CPU types (CPUs with different extensions). If user wishes to use particular CPU type, it is necessary to do this manually.

First list available extensions:

pbsnodes -a | grep resources_available.cpu_flag | awk '{print $3}' | tr "," "\n" | sort -u

Currently, the fastest option is avx2. It is then possible to request particular CPU type:

qsub -l select=cpu_flag=avx2 ...

Documentation

https://github.com/stamatak/standard-RAxML/tree/master/manual

Program manager

meta@cesnet.cz

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