Phylobayes MPI (PBMPI)

Overview

Phylobayes MPI is a Bayesian software for phylogenetic reconstruction using mixture models which can run in parallel using MPI.

Version 1.8 is installed on the CSF. It has been compiled with the Intel 15.0.3 compiler.

Restrictions on use

There are no restrictions on accessing this software on the CSF. It is release under the GNU GPL v2 license and all use must adhere to that license.

Set up procedure

To access the software you must first load the modulefile:

# Single node (2-24 cores) parallel jobs
module load apps/intel-15.0/pbmpi/1.8

# Multi node (48 cores or more in multiples of 24) parallel jobs
module load apps/intel-15.0/pbmpi/1.8-ib

Running the application

Please do not run pbmpi tools on the login node. Jobs should be submitted to the compute nodes via batch. There are a number of command-line tools available:

bpcomp    cvrep    pb_mpi    readpb_mpi    tracecomp

You may run each command without any args / parameters on the login node to see the help text. For example:

pb_mpi

mpirun -np  pb_mpi -d  [options] 
	creates a new chain, sampling from the posterior distribution, conditional on specified data

mpirun -np  pb_mpi 
	starts an already existing chain

	mpirun -np      : number of parallel processes (should be at least 2)

	-cat -dp            : infinite mixture (Dirichlet process) of equilibirium frequency profiles
	-ncat         : finite mixture of equilibirium frequency profiles

...

Single node Parallel batch job submission

Make sure you have the modulefile loaded then create a batch submission script, for example:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd             # Job will run from the current directory
#$ -V               # Job will inherit current environment settings
#$ -pe smp.pe 8     # Number of cores for single node jobs (2-24)

mpirun -n $NSLOTS pb_mpi inputfile
                            #
                            # Will load inputfile.param from the current dir

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Multi-node Parallel batch job submission

For larger multinode jobs ensure you have the -ib modulefile loaded, then submit a jobscript similar to:

#!/bin/bash
#$ -S /bin/bash
#$ -cwd                     # Job will run from the current directory
#$ -V                       # Job will inherit current environment settings
#$ -pe orte-24-ib.pe 48     # Must be 48 or more cores in multiples of 24

mpirun -n $NSLOTS pb_mpi inputfile
                            #
                            # Will load inputfile.param from the current dir

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Further info

• The manual is available on the CSF using evince $PBMPIHOME/pb_mpiManual1.8.pdf
• pbmpi github repo

Updates

None.