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How to run R on clusters



Notes:

1. We have two different R version installed in the system. R 2.6 and R 2.8, please load correct modules before using them

2. R 2.6 has bioconductor installed by default. R 2.8 has RMPI module installed.

Step 1: Please read "how to setup your working environment" and do the following:

a. Include the sentence of "module load r/2.6/default" in the module-loading blocks in your .bashrc file

. Basically, you shall contain the following block in the .bashrc file.

# modules definitions
if [ -n "$MODULESHOME" ]; then
  module use /shr/modules
  module load r/2.6/default
fi

[testy@n137 ~]$ . .bashrc
[testy@n137 ~]$ module list
Currently Loaded Modulefiles:
   1) r/2.6/default
[testy@n137 ~]$ which R
/source/R_2.6/bin/R

#!/bin/bash

# enable your environment, which will use .bashrc configuration in your home directory
#BSUB -L /bin/bash

# the name of your job showing on the queue system
#BSUB -J rtest

# the queue that you will use, the example here use the queue called "normal", it will end in 3 hours.
# use long queue if you job will run more than 3 hours
# please use bqueus command to check the available queues, or consult system administrator to use other queues
#BSUB -q normal


# the system output and error message output, %J will show as your jobID
#BSUB -o %J.out
#BSUB -e %J.err

#the CPU number that you will collect for each job
#BSUB -n 1

# The following configuration will allow you exclusively allocate one node so that
# you can use all the entire memory of the allocated computing node. Here we comment it out by using two "#"
# if you want to enable it, delete one "#"
##BSUB -x

#when job finish that you will get email notification, change it to your own email address
#BSUB -u yourID@partners.org
#BSUB -N


#enter your working directory, change to your own dir
cd /shr/home/$USER/r_example


#Finally, Start the blast program
R --no-save < example.R > r_example.out

 [testy@n137 ~] bsub < rjob.lsf