Running an R application - GeoSSE (Geographic State Speciation and

Extinction) analyses run using R and parallel functions

Victor Soria-Carrascov.soria-carrasco@shef.ac.uk

Download this filehttp://goo.gl/rQL8Hd

GeoSSE• Belongs to a family of likelihood-based methods for

studying diversification and character evolution using phylogenetic trees (BiSSE - Binary State Speciation and Extinction)

• GeoSSE models the reciprocal effects between geographic range evolution and diversification (speciation and extinction)

• It estimates region-dependent rates of speciation, extinction and dispersal.

• R package diversitree

A shell script is used to call the R script

#!/bin/bash#$ -l h_rt=08:00:00#$ -l mem=2G#$ -m bea#$ -M user@sheffield.ac.uk

R CMD BATCH --vanilla myscript.R

# Load diversitree packagelibrary (diversitree)

# Load phylogenetic treestrees<-read.tree(“mytrees.new”)

# Load statesstates<-read.table(“mytable.txt”, header=T)...

R_job.sh myscript.R

$ qsub R_job.sh -j y -o rjob.log

Example 1

Running R usingmultiple cores of 1 node

(shared memory)

# Launch an interactive session

$ qrsh

# Copy the input files (trees and table with geographic states) to your home folder

$ cp /usr/local/extras/Genomics/HPC_course/R_GeoSSE/example_trees_10.new $HOME/

$ cp /usr/local/extras/Genomics/HPC_course/R_GeoSSE/example_states.txt $HOME/

# Copy the R script to your home folder

$ cp /usr/local/extras/Genomics/submit_scripts/geosse_openmp.R $HOME/

# Copy the shell script to call the R script to your home folder

$ cp /usr/local/extras/Genomics/submit_scripts/R_job_openmp.sh $HOME/

Example 1. Run GeoSSE using multiple cores of 1 node (shared memory)

# If you experience problems, you can download all the files from the web:

$ wget http://goo.gl/9GVykX$ tar -xvf R_GeoSSE.tar.gz$ rm R_GeoSSE.tar.gz

Example 1. Run GeoSSE using multiple cores of 1 node (shared memory)

# Check you have the following 4 files in your home directory:

example_states.txtexample_trees_10.newgeosse_openmp.RR_job_openmp.sh

# Edit the shell script to change number of processors, e-mail address, and path to R script

$ nano $HOME/R_job_openmp.sh

Example 1. Run GeoSSE using multiple cores of 1 node (shared memory)

#!/bin/bash#$ -l h_rt=08:00:00#$ -l mem=2G#$ -pe openmp 2#$ -m bea#$ -M user@sheffield.ac.uk

# Number of cores to be usedexport OMP_NUM_THREADS=2

# Add path to software repository librariesexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/extras/Genomics/lib/lib

R='/usr/local/extras/Genomics/apps/R/current/bin/R'

# Change R script pathRSCRIPT="$HOME/geosse_openmp.R"

# Some options## --slave# Don't print input commands## --vanilla (highly recommended)# Don't load anything from previous sessions, # and don't save data at the end of the current session

$R CMD BATCH --vanilla $RSCRIPT

R_job_openmp.sh

# Edit the R script to change input and output files

$ nano $HOME/geosse_openmp.R

Example 1. Run GeoSSE using multiple cores of 1 node (shared memory)

# Load parallel packagelibrary(parallel)

# Number of coresncores<-2

# Load diversitree packagelibrary(diversitree)

# Load phylogenetic treestrees<-read.tree(“/home/user/example_trees_10.new”)

# Load statesstates<-read.table(”/home/user/example_states.txt”, header=T)tip.states<-states$statenames(tip.states)<-states$taxon

# Fit birth-death model to get an extinction/speciation ratio (eps)# and use it as starting value for GeoSSEbd.rates<-mclapply(trees, birthdeath)

geosse_openmp.R (1)

# Fit GeoSSE model by maximum likelihood to the treesML.est<-mclapply(1:length(trees), function(x){ model<-make.geosse( tree=trees[[x]], states=tip.states) start.values<-starting.point.geosse(trees[[x]], eps=bd.rates[[x]]$par[1]) res<-find.mle(model, x.init=start.values, method="subplex") cat("Job # ", x, " finished\n", sep="") return(res) }, mc.cores=ncores) # Format results into a table ML.est.pars.table<-as.data.frame(do.call("rbind", lapply(ML.est, function(x) c(x$par, npar=length(x$par), lnl=x$lnLik)))) # Write the table to a file output<-paste(Sys.getenv("HOME"), "/example_openmp_output.txt", sep='') write.table(ML.est.pars.table, file=output, row.names=F, quote=F, sep="\t") # Save image of this session image<-paste(Sys.getenv("HOME"), "/example_openmp_image.RData", sep='') save.image(file=image, compress="bzip2")

geosse_openmp.R (2)

# Submit the job to the cluster

$ qsub -j y -o geosse_openmp.log R_job_openmp.sh

# Check if the job is running

$ Qstat

# When the job finishes, look at the logs and the output

$ less -S geosse_openmp.log$ less -S geosse_openmp.Rout$ less -S example_openmp_output.txt

Example 1. Run GeoSSE using multiple cores of 1 node (shared memory)

Example 2

Running R usingmultiple nodes

(distributed memory)

# Copy the R script to your home folder

$ cp /usr/local/extras/Genomics/submit_scripts/geosse_mpi.R $HOME/

# Copy the shell script to call the R script to your home folder

$ cp /usr/local/extras/Genomics/submit_scripts/R_job_mpi.sh $HOME/

# Check you have the following 4 files in your home directory:example_states.txtexample_trees_10.newgeosse_mpi.RR_job_mpi.sh

# Edit the shell script to change number of nodes, e-mail address, and path to R script

$ nano $HOME/R_job_mpi.sh

Example 2. Run GeoSSE using multiple nodes (distributed memory)

#!/bin/bash#$ -l h_rt=08:00:00#$ -l mem=2G#$ -pe ompigige 4#$ -m bea#$ -M user@sheffield.ac.uk

# Required for running Rmpimodule add mpi/gcc/openmpi/1.4.4export MPI_ROOT='/usr/local/mpi/gcc/openmpi/1.4.4/'export OMPI_MCA_mtl=^psm

# Add path to software repository librariesexport LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/extras/Genomics/lib/lib

R='/usr/local/extras/Genomics/apps/R/current/bin/R'

# Change R script pathRSCRIPT=”$HOME/geosse_mpi.R"

# Some options## --slave# Don't print input commands## --vanilla (highly recommended)# Don't load anything from previous sessions, # and don't save data at the end of the current session

$R CMD BATCH --vanilla $RSCRIPT

R_job_mpi.sh

# Edit the R script to change input and output files

$ nano $HOME/geosse_mpi.R

Example 2. Run GeoSSE using multiple nodes (distributed memory)

# This R script uses multiple nodes to fit a GeoSSE model# to multiple phylogenetic trees

# Ignore Infiniband interfaceSys.setenv(OMPI_MCA_mtl='^psm')

# Echo commandsoptions(echo=T)

# Load Rmpi packagelibrary (Rmpi)# Load diversitree packagelibrary (diversitree)

# Load phylogenetic treestrees<-read.tree(“/home/user/example_trees_10.new”)

# Load statesstates<-read.table(”/home/user/example_states.txt”, header=T)tip.states<-states$statenames(tip.states)<-states$taxon

geosse_mpi.R (1)

# Number of nodesnnodes<-4

# spawn mpi slavesmpi.spawn.Rslaves(nslaves=nnodes, needlog=T)

# load diversitree on slavesmpi.bcast.cmd(library(diversitree))

# Broadcast trees to slavesmpi.bcast.Robj2slave(trees)

# Broadcast tip.states to slavesmpi.bcast.Robj2slave(tip.states)

# Fit birth-death model to get an extinction/speciation ratio (eps)# and use it as starting value for GeoSSEbd.rates<-mpi.parLapply(trees, birthdeath)

# Broadcast bd.rates to slavesmpi.bcast.Robj2slave(bd.rates)

geosse_mpi.R (2)

# Fit GeoSSE model by maximum likelihoodML.est<-mpi.parLapply(1:length(trees), function(x){ model<-make.geosse( tree=trees[[x]], states=tip.states) start.values<-starting.point.geosse(trees[[x]], eps=bd.rates[[x]]$par[1]) res<-find.mle(model, x.init=start.values, method="subplex") cat("Job # ", x, " finished\n", sep="") return(res) }, job.num=nnodes)

# Format results into a tableML.est.pars.table<-as.data.frame(do.call("rbind", lapply(ML.est, function(x) c(x$par, npar=length(x$par), lnl=x$lnLik))))

# Write the table to a fileoutput<-paste(Sys.getenv("HOME"), "/example_mpi_output.txt", sep='')write.table(ML.est.pars.table, file=output, row.names=F, quote=F, sep="\t")

# Save an image of this sessionimage<-paste(Sys.getenv("HOME"), "/example_mpi_image.RData", sep='')save.image(file=image, compress="bzip2")

geosse_mpi.R (3)

# Submit the job to the cluster

$ qsub -j y -o geosse_mpi.log R_job_mpi.sh

# Check if the job is running

$ Qstat

# When the job finishes, look at the logs$ less -S geosse_mpi.log$ less -S geosse_mpi.Rout

# look at the log for each node$ find . -name "*node*.log" -exec sh -c "echo {}; cat {} | sed 's/^/\t/g'" \;

# Output (results)$ less -S example_mpi_output.txt

Example 2. Run GeoSSE using multiple nodes (distributed memory)

https://myapps.shef.ac.uk

bo4cm14 / gen0mics