RAxML
Description
RAxML (Randomized Axelerated Maximum Likelihood) is a popular program for phylogenetic analyses of large datasets under maximum likelihood.
License
Usage
Upcoming modulesystem change alert!
Due to large number of applications and their versions it is not practical to keep them explicitly listed at our wiki pages. Therefore an upgrade of modulefiles is underway. A feature of this upgrade will be the existence of default module for every application. This default choice does not need version number and it will load some (usually latest) version.
You can test the new version now by adding a line
source /cvmfs/software.metacentrum.cz/modulefiles/5.1.0/loadmodules
to your script before loading a module. Then, you can list all versions of raxml and load default version of raxml as
module avail raxml/ # list available modules module load raxml # load (default) module
If you wish to keep up to the current system, it is still possible. Simply list all modules by
module avail raxml
and choose explicit version you want to use.
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 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