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====== Using R ======

**R** has been installed in ''/apps/chpc/bio/R/?'' and is compiled using openmpi and the GNU compilers. R modules have been created so simply adding:
<code>
module add chpc/R/3.2.3-gcc5.1.0
</code>

to your scripts will set up the appropriate paths to R, the compilers (if you want to add your own R packages) and the mpi libraries. Note that there may be several versions of R installed and can be seen by running the: <code>module avail 2>&1 | grep "R"</code> command.


===== Parallel R =====

The ''Rmpi'', ''doMPI'' and other packages are already installed to allow R to use MPI to distribute its work across multiple nodes of the cluster. **Please submit a request to helpdesk should you need any other packages installed.**

Once you've created your R script file, called ''myScRipt.r'', you will need to create a job script file to submit to the PBSPro scheduler.

Example job script file:

<file bash my_R_job.qsub>
#!/bin/bash
#PBS -l select=2:ncpus=24:mpiprocs=24
#PBS -P SHORTNAME
#PBS -q normal
#PBS -l walltime=4:00:00
#PBS -o /mnt/lustre/users/USERNAME/my_R_data/stdout.txt
#PBS -e /mnt/lustre/users/USERNAME/my_R_data/stderr.txt
#PBS -N RJob
#PBS -M myemailaddress@someplace.com
#PBS -m abe

# Add R module (includes appropriate openMPI and gcc modules)
module add chpc/R/3.2.3-gcc5.1.0

# explicitly calculate number of processes.
nproc=`cat $PBS_NODEFILE | wc -l`

# make sure we're in the correct working directory.
cd /mnt/lustre/users/USERNAME/my_R_data

mpirun -np $nproc -machinefile $PBS_NODEFILE  R --slave -f myScRipt.r
</file>

**Notes:**
  * Replace ''USERNAME'' with **your** user name.
  * Replace ''SHORTNAME'' with **your research programme's** short name.
  * Replace ''myemailaddress@someplace.com'' with **your** email address.
  * And replace ''my_R_data'' with your program's //working directory// (which **must** be under ''/mnt/lustre/users/USERNAME/'').
  * And change ''myScRipt.r'' to be your //script file name//.

===Running the script===

Submit to the scheduler
<code>
qsub my_R_job.qsub
</code>

Check the list of current jobs in the queue
<code>
qstat -w
</code>

==== R/bioconductor ====

Here is a more complete example

=== pbdR example ===
== Job scripts ==
<file bash pbdtest.qsub>
#PBS -l select=2:ncpus=24:mpiprocs=24:place=excl
#PBS -l walltime=00:01:00
#PBS -q normal
#PBS -P SHORTNAME
#PBS -M YOUREMAILADDRESS
#PBS -m be
#PBS -e /mnt/luster/users/USERNAME/pbdR_test/std_err.txt
#PBS -o /mnt/lustre/users/USERNAME/pbdR_test/std_out.txt
#PBS -N PBDR_TEST
#PBS -mb

module add chpc/R/3.2.3-gcc5.1.0

NP=`cat ${PBS_NODEFILE} | wc -l`

cd /mnt/lustre/users/USERNAME/pbdR_test/
mpirun -np ${NP} -machinefile ${PBS_NODEFILE} Rscript test_script.R

</file>
Note: __USERNAME__ should contain your actual user name!

<file R test_script.R>
library(pbdMPI, quiet=TRUE)
init()
my.rank <- comm.rank()
comm.print(my.rank, all.rank=TRUE)

finalize()
</file>

== Submit your job ==
Finally submit your job using:<code bash>user@login01:~ $ qsub pbdtest.qsub</code>
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