First, let’s get on the cluster
- Open the terminal or PuTTY
- Type
ssh yourusername@enigma2.jhsph.edu
- Now you’re on enigma!
- Type
qrsh to get on a node
- Now you’re on a node! Do everything from a node except submitting batch jobs, which can only be done from enigma
- When you’re done, type
exit to go back to enigma
- Type
exit again to exit enigma
Basic Unix commands (1 of 2)
- Change directory:
cd
- Subdirectory:
cd [subdir]
- Home directory:
cd ~/
- New directory:
cd /new/path/
- Go up a directory:
cd ..
- Print current working directory:
pwd
- List files:
ls
- Create new directory:
mkdir [dirname]
- Copy file:
cp [filename]
- Delete file:
rm [filename]
- Move or rename file:
- Move:
mv [filename] [newlocation]
- Rename:
mv [oldname] [newname]
Basic Unix commands (2 of 2)
- View or edit text files:
- This includes .txt, .sh, .R, etc.
cat [filename] to view entire filehead [filename] or tail [filename] to preview fileless [filename] or more [filename] to scroll through file (hit q to exit)emacs -nw [filename] to view and edit file- Options with “
-”. Examples include:
ls -l lists files and includes file informationrm -f [filename] forces removal of file without promptingmatlab -nodisplay opens MATLAB on the command line (without the interactive display window)- Tab completion (for file or directory names)
- Google is your friend!
Exercise
- Get onto enigma and qrsh to get onto a node
- List the files in your home directory (that’s where you are)
- Create a new directory called “BST753” within your home directory
- Copy a file from your home directory into BST753
- Go into BST753 and look at the files
- Go back to your home directory
Working Interactively in R
- First, make sure you are on a node!
- Type
R
- Do stuff!
- Reading and saving data
- Read files from locations on the cluster
- Save R data files (.Rdata, .rda) within your home directory
- Plotting
- If X11 is set up, plots will display
- Otherwise, save plots using
pdf() or png() functions
- When finished, exit R by typing
q()
Submitting batch jobs
- Get on enigma
- Go to the directory where your code is using
cd path/to/code
- Create a “shell script” that will run your R code using
emacs -nw shellscriptname.sh
- Write shell script (next slide)
- Exit emacs and save file by typing
Ctrl-X Ctrl-C then y
- Submit job by typing
qsub shellscriptname.sh
Shell script
#!/bin/sh
#$ -cwd
#$ -l mf=40G,h_vmem=40G,h_fsize=10G
#$ -m e -M youremail@jhsph.edu
R CMD BATCH --no-save --no-restore Rfilename.R