Typical HPC Day - Win

Case: You have developed your R code on your workstation, but the machine is not sufficient to run your entire data set   You have requested an account on the HPC and you need to test your code with some sample data before you submit your first job against your large data set.

VPN Use global protect

In the connection settings of Global Protect, add vpn-groups.kennesaw.edu
In you system tray, use the globe icon to click ‘Connect’

Use SFTP to upload  your new data. FileZilla (https://filezilla-project.org)

Open an SSH in Putty

Server: hpc.kennesaw.edu Port: 22
Username: your_netid
Password: your_netid_password

08/22: SSH now requires a Duo authentication step to access the HPC
     (1 - Duo push, 2 - Phone call)

Use interact or reserve a node

$ interact
or
$  qsub -I -q batch -l nodes=1:ppn=24,walltime=1:00:00

Load the software you want to use.

$ module load R

Run R interactively

$ R

R version 3.4.0 (2017-04-21) -- "You Stupid Darkness"
Copyright (C) 2017 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.

> new_data<-runif(10, min=0, max=100)

> new_data<-round(new_data, 2)

> new_data

 [1] 36.05 40.69  9.76  1.91  5.91  1.73 22.79 11.85 48.79  8.83

> new_data<-sort(new_data)

> new_data

 [1]  1.73  1.91  5.91  8.83  9.76 11.85 22.79 36.05 40.69 48.79

> mean(new_data)

[1] 18.831

> sum(new_data)

[1] 188.31

> sd(new_data)

[1] 17.20555

> jpeg('new_data_plot.jpg')

> plot(new_data)

> dev.off

> q()

Save workspace image? [y/n/c]: n

View my new report or graph

$ ls -l new_data_plot.jpg

-rw-rw-r-- 1 user group 10917 Apr 16 19:29 new_data_plot.jpg

Move a copy of my work to my local machine (FileZilla or SSH)

$ scp your_netid@hpc.kennesaw.edu:/data/home/your_netid/new_data_plot.jpg .