|mpiRAxML: RAxML for parallel bootstrap analysis|
RAxML is a highly optimized derivative of fastDNAml that allows for the maximum likelihood-based inference of phylogenetic trees with enormous datasets. The parallel version allows for the efficient bootstrapped evaluation of thousands of taxa.
Using mpiRAxML on HPC
The parallel version of RAxML has been compiled with GNU OpenMPI, so your MOAB script needs to source that environment. The command to launch mpiRAxML is "mpiraxml" or, as listed in the documentation, "raxmlHPC-MPI." You should specify one more process than the number of CPUs that you designate, since one process is just a 'bookkeeper.' The "-b" option designates the bootstrap seed number, though parallel bootstrap runs are not reproducable. A minimal sample MOAB script to perform 100 bootstraps using ten HPC nodes on a sample DNA dataset is given here:
#!/bin/bash #MOAB -l nodes=10 #MOAB -j oe #MOAB -m abe #MOAB -N RAXML-OPENMPI source /usr/local/profile.d/openmpi-gnu.sh mpirun -np 11 /opt/Bio/raxml/mpiraxml -s $HOME/test/subset.phy \ -m GTRMIX -b 12345 -# 100 -n bootstrappedraxml