RAxML installations at NSC


This is an untested installation! NSC recommends that you proceed with caution and report any problems to support@nsc.liu.se.

Level of support

Tier 3 NSC will not be able to help you much with this program, either because we lack the in-house experience, or because it is a test installation. In general, these types of installations are untested, and will not be updated unless you send a request to NSC.

Please see the page describing our software support categories for more information.
You can also contact support@nsc.liu.se for further information.

Randomized Axelerated Maximum Likelihood

Developer’s homepage: sco.h-its.org/exelixis/web/software/raxml

Naming scheme for binaries

Name Description
raxmlHPC-AVX serial version
raxmlHPC-PTHREADS-AVX Pthreads parallel version
raxmlHPC-MPI-AVX MPI parallel version
raxmlHPC-HYBRID-AVX MPI-Pthreads parallel version

How to run

To run the serial or Pthreads version, just load the raxml module and execute the binary with the desired options. To run the MPI-parallel version, use mpprun and the full path to the MPI binary. Please see the example batch scripts below.

Example batch scripts

Using the Pthreads version:

#!/bin/bash

#SBATCH --nodes=1
#SBATCH --time=4:00:00
#SBATCH --exclusive
#SBATCH --account=snicxxx-yyy

module load raxml/7.9.1
raxmlHPC-PTHREADS-AVX -T 16 other-options

Using the MPI version:

#SBATCH --nodes=1
#SBATCH --time=4:00:00
#SBATCH --exclusive
#SBATCH --account=snicxxx-yyy

mpprun /software/apps/raxml/7.9.1/build01/raxmlHPC-MPI-AVX other-options

mpprun will automatically start the number of MPI ranks that matches the requested allocation.

NOTE: You will, of course, need to change other-options to whatever options RAxML needs to run the desired job. The -h option will print the list of available options and some help text.

Remember to change the account string, snicxxx-yyy, to the string for the project that you want to charge the job to. You can find the account string in NSC Express or using the projinfo command. If you are only included in one project, then you don’t need this line at all.