Prerequisites

Topics

Extras

9. Running Interactive Jobs

Managing R Software Libraries and Versions

The R software is installed system-wide, allowing each user to maintain their own set of R packages within their home directory by default. Furthermore, each R version has its dedicated library, distinct from other versions.
Every R version will also have its own library separate from other versions. For example, R 4.0 will have its user-installed packages side by side with R 4.2 library containing the user-installed packages specific to that version.

When upgrading your R version (e.g., to run code with a newly released R version), you must first install packages that are needed for your script to run for that specific R version. However, once the package is installed, you can load it in your scripts without the need for repeated installations upon each login.

Moreover, if you require access to a newer software version that is not currently available on the system, please don’t hesitate to contact DARC to request its installation.

Installing R packages without a Graphical Interface

Load the R module with the version that you want (R 4.2 is the current default).

For example, let’s use the newest R version available on the yens:

$ ml R

Start interactive R console by typing R.

You should see:

R version 4.2.1 (2022-06-23) -- "Funny-Looking Kid"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

>

Let’s install two multiprocessing packages on the yens that we will use for the R example.

> install.packages('foreach')

If this is your first time installing R package for this R version on the Yens, you will be asked to create a personal library (because users do not have write permissions to the system R library). Answer yes to both questions:

Warning in install.packages("foreach") :
  'lib = "/software/free/R/R-4.2.1/lib/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/4.2’
to install packages into? (yes/No/cancel) yes

This creates a new personal R 4.2 library in your home directory. The library path is ~/R/x86_64-pc-linux-gnu-library/4.2 where all of the user packages will be installed. Once the library is created, next package will be installed there automatically.

Pick any mirror in the US.

Installing package into ‘/home/users/nrapstin/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Secure CRAN mirrors

 1: 0-Cloud [https]
 2: Australia (Canberra) [https]
...
74: USA (IA) [https]
75: USA (MI) [https]
76: USA (OH) [https]
77: USA (OR) [https]
78: USA (TN) [https]
79: USA (TX 1) [https]
80: Uruguay [https]
81: (other mirrors)

Selection: 77

If the package is successfully installed, you should see:

* DONE (foreach)

The downloaded source packages are in
	‘/tmp/RtmpsYpzoP/downloaded_packages’

Then install doParallel package:

> install.packages("doParallel")

When the package is done installing, you will see:

* DONE (doParallel)

The downloaded source packages are in
	‘/tmp/Rtmpwy8WeV/downloaded_packages’

Running R Script Interactively

Now that we have loaded R module and installed R packages that we are going to use, we are ready to run our code. You can run R code line by line interactively by copying-and-pasting into the R console. For example,

> print('Hello!')
[1] "Hello!"

The advantage of interactive console is that the results are printed to the screen immediately and if you are developing code or debugging, it can be very powerful. But the disadvantage is that if you close the terminal window or lose connection, the session is not saved and you will need to reload the R module and paste all of the commands again. So, use this method for when you need interactive development / debugging environment. Another disadvantage is that if you did not login with the graphical interface (X forwarding) you will not be able to plot anything in the interactive console. So, if you need plots and graphs, either use -Y flag when connecting to the Yens or use RStudio on JupyterHub.

We can then quit out of R without saving workspace image:

> q()
Save workspace image? [y/n/c]: n

Running R Script on the Command Line

If you want to simply run the script, you can do so from the command line.

We are going to run the same code that we ran on our local machine, investment-npv-parallel.R.

Warning: Because this R code uses multiprocessing and the yens are a shared computing environment, we need to be careful about how R sees and utilizes the shared cores on the yens.

Let’s update the script for the yens. Edit the script on JupyterHub in the Text Editor. Instead of using detectCores() function, we will hard code the number of cores for the script to use in this line in the R script:

ncore <- 1 

Thus, the investment-npv-parallel.R script on the yens should look like:

# In the context of economics and finance, Net Present Value (NPV) is used to assess 
# the profitability of investment projects or business decisions.
# This code performs a Monte Carlo simulation of Net Present Value (NPV) with 500,000 trials in parallel,
# utilizing multiple CPU cores. It randomizes input parameters for each trial, calculates the NPV,
# and stores the results for analysis.

# load necessary libraries
library(foreach)
library(doParallel)

options(warn=-1)

# set the number of cores here
ncore <- 1

# register parallel backend to limit threads to the value specified in ncore variable
registerDoParallel(ncore)

# define function for NPV calculation
npv_calculation <- function(cashflows, discount_rate) {
  # inputs: cashflows (a vector of cash flows over time) and discount_rate (the discount rate).
  npv <- sum(cashflows / (1 + discount_rate)^(0:length(cashflows)))
  return(npv)
}

# number of trials
num_trials <- 500000

# measure the execution time of the Monte Carlo simulation
system.time({
  # use the foreach package to loop through the specified number of trials (num_trials) in parallel
  # within each parallel task, random values for input parameters (cash flows and discount rate) are generated for each trial
  # these random input values represent different possible scenarios
  results <- foreach(i = 1:num_trials, .combine = rbind) %dopar% {
    # randomly generate input values for each trial
    cashflows <- runif(10000, min = -100, max = 100)  # random cash flow vector over 10,000 time periods. 
    # these cash flows can represent costs (e.g., initial investment) and benefits (e.g., revenue or savings) associated with the project
    discount_rate <- runif(1, min = 0.05, max = 0.15)  # random discount rate at which future cash flows are discounted
    
    # calculate NPV for the trial
    npv <- npv_calculation(cashflows, discount_rate)
    
  }
})


cat("Parallel NPV Calculation (using", ncore, "cores):\n")
# print summary statistics for NPV and plot a histogram of the results
# positive NPV indicates that the project is expected to generate a profit (the benefits outweigh the costs), 
# making it an economically sound decision. If the NPV is negative, it suggests that the project may not be financially viable.
summary(results)
hist(results, main = 'NPV distribution')

After loading the R module, we can run this script with Rscript command on the command line:

$ Rscript investment-npv-parallel.R

Loading required package: iterators
Loading required package: parallel
   user  system elapsed
274.631   0.433 275.130
Parallel NPV Calculation (using 1 cores):
       V1
 Min.   :-727.7947
 1st Qu.: -96.5315
 Median :  -0.0326
 Mean   :  -0.0505
 3rd Qu.:  96.3001
 Max.   : 700.4002

Again, running this script is active as long as the session is active (terminal stays open and you do not lose connection).