R

R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.

R provides a wide variety of statistical (linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, …) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.

More information can be found at: http://www.r-project.org/

R on the HPCC

R is installed on all HPCC compute hosts.

R (and GCC) Versions

R version 3.6.0 and GCC version 4.8.5 are the current system default, but these are now quite old. Many R packages will no longer properly install in that combination of versions. We highly recommend using newer versions of R and GCC!

To list the available versions:

qlogin -now no
module avail R 
-------------------------------------- /etc/modulefiles ---------------------------------------
R/R-3.5.1 R/R-3.6.1 R/R-3.6.3 R/R-4.0.2 R/R-4.0.4 R/R-4.1.2 R/R-4.2.2

module avail gcc

-------------------------------------- /etc/modulefiles ---------------------------------------
gcc/gcc-10.3.0 gcc/gcc-11.3.0 gcc/gcc-7.5.0 gcc/gcc-9.2.0
gcc/gcc-11.1.0 gcc/gcc-6.3.0 gcc/gcc-8.2.0

Note: there may be more-recent versions, as well.

To use these newer version (and recommended latest GCC compiler), please modify your ~/.bashrc file as follows:

## START MPI SELECTION
if [[ $(hostname -s | grep -e "^hpcc[0-9]*$" -e "^aws-") ]]; then
    ... other modules ...
    module load R/R-4.2.2
    module load gcc/gcc-11.3.0
fi
## END MPI SELECTION

Create R Commands File

Create a .R file with your commands, for example:

D <- data.frame(x=c(1,2,3,1), y=c(7,19,2,2))
D

# Sort on x
indexes <- order(D$x)
D[indexes,]

# Print out sorted dataset, sorted in reverse by y
D[rev(order(D$y)),]

 Create R Job Script

Create a .sh file with at least the following contents:

#!/bin/bash

Rscript --no-save your-commands-file.R

More information: HPCC Job Management

Interactive R Sessions

• Graphical: via our HPCC Desktop environment (recommended)
• Textual:

  qrsh R --no-save

Installing R Packages

NOTE (2018-02-14): we no longer install all CRAN and BioConductor packages in the cluster!

Here’s how to install R packages in your home directory / shared workspace.

Manual Installation

• log on to a compute node with qlogin
• download the package with wget (if it’s not a CRAN package)
• install (different depending on whether it’s CRAN or not)

Here are two examples (Copy/Pastable except for the package URL in wget and package name in R CMD INSTALL):

If it IS a CRAN package:

qlogin -now no
R --no-save
...
> install.packages("anRpackage")

Installing package into ‘/usr/local/lib/R/library-X.X.X’
(as ‘lib’ is unspecified)
Warning in install.packages("anRpackage") :
  'lib = "/usr/local/lib/R/library-X.X.X"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
Would you like to create a personal library
‘~/R/x86_64-redhat-linux-gnu-library/X.X’
to install packages into? (yes/No/cancel) yes

qlogin -now no
wget 'http://some.server.edu/anRpackage_version.tar.gz'
R CMD INSTALL -l $R_LIBS anRpackage_version.tar.gz
exit

# Array of packages to be checked and installed if not already
myPKGs <- c('PKG1', 'PKG2', ..., 'PKGN')

# check to see if each package is installed, and if not add it to a list to install
InstalledPKGs <- names(installed.packages()[,'Package'])
InstallThesePKGs <- myPKGs[!myPKGs %in% InstalledPKGs]

# install any needed packages
if (length(InstallThesePKGs) > 0) install.packages(InstallThesePKGs)

grep -e library -e require *.R | awk -F'[()]' '{print $2}' | sed ':a;N;$!ba;s/\n/" , "/g'

rstan is one of the trickier packages to install, due to specific C++ variables, and the need for a more-recent C/C++ version. A more-recent R version is recommended, as well.

Edit your ~/.bashrc file (‘nano ~/.bashrc‘ is an easy way to do this), and add (or uncomment) the following ‘module load ..‘ lines:

if [[ $(hostname -s | grep -e "^aws-" -e "^hpcc[0-9]*$") ]]; then
    module load mpi/openmpi-x86_64
    module load R/R-4.0.4
    module load gcc/gcc-9.2.0
fi

Then you need to set up two specific R ‘Makevars’ before installation. That goes in your ~/.R/Makevars file, which should look like:

CXX14FLAGS=-O3 -march=native -mtune=native -fPIC
CXX14=g++

To do that, from the command line, do:

mkdir ~/.R
echo -e "CXX14FLAGS=-O3 -march=native -mtune=native -fPIC\nCXX14=g++" >> ~/.R/Makevars

Now you are ready to log on to an HPCC compute node, and install rstan.

qlogin -now no
R --no-save
> install.packages("rstan", repos = "https://cloud.r-project.org/")
Warning in install.packages("rstan", repos = "https://cloud.r-project.org/") :
'lib = "/usr/local/R-4.0.4/lib64/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
Would you like to create a personal library
‘~/R/x86_64-pc-linux-gnu-library/4.0’
to install packages into? (yes/No/cancel) yes

This will take a long time (~30 minutes). Once installation is complete, you can test that rstan is working correctly:

> library(rstan)
> options(mc.cores = strtoi(Sys.getenv('OMP_NUM_THREADS')))
> rstan_options(auto_write = TRUE)
> example(stan_model, package = "rstan", run.dontrun = TRUE)

Please Note: the ‘options(mc.cores = strtoi(Sys.getenv(‘OMP_NUM_THREADS’)))‘!! For best performance, ALWAYS use that option for cores on Wharton’s HPCC systems. Do not use ‘detectCores()‘, as this will be inaccurate, and degrade your performance. By default, OMP_NUM_THREADS = 1. To use more than 1 core for a job, you will need to request it at job start, either at the command line:

qsub -pe openmp 4

Or in your job script:

#$ -pe openmp 4

sf Package

sf requires some very specific libraries to be available before installing, or using, as well as a newer C/C++ version. To do that, edit your ~/.bashrc file (‘nano ~/.bashrc‘ is an easy way to do this), and add (or uncomment) the following ‘module load ..‘ lines:

if [[ $(hostname -s | grep -e "^aws-" -e "^hpcc[0-9]*$") ]]; then
    module load mpi/openmpi-x86_64
    module load R/R-4.0.4
    module load gcc/gcc-9.2.0
    module load gdal
fi

That will load all required library paths, and then you can install the sf package, per normal installation methods:

qlogin -now no
R --no-save
> install.packages("sf")

This can take a while, as sf has a number of dependencies to install prior to its own installation. After installation, to run some example code, also install sp package:

> install.packages("sp")

Then the examples at https://cran.r-project.org/web/packages/sf/sf.pdf should run correctly.