basic_shell_logging.Rmd

---
title: "SSH onto a HPC"
subtitle: ""
author: "Alexis Lucattini"
date: "2017/08/17"
output:
  xaringan::moon_reader:
    lib_dir: libs
    nature:
      highlightStyle: github
      highlightLines: true
      countIncrementalSlides: false
---

# Installing commandline tools (Mac OSX)
### (0 to 10 minutes)
Mac OSX by default does not have command line tools installed.  
This is a simple fix as shown [here](http://railsapps.github.io/xcode-command-line-tools.html)

Open up 'Terminal' and type in the following.
```{bash, eval=FALSE}
xcode-select -p
```

`/Applications/Apple Dev Tools/Xcode.app/Contents/Developer` shoud appear as the output.
If not, type:
```{bash, eval=FALSE}
xcode-select --install
```

You will also need homebrew. Type the following line into terminal.
```{bash, eval=FALSE}
ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
```

---

# Installing commandline tools (Windows)
### (0 to 10 minutes)
Install [Git Bash](https://gitforwindows.org/).  
Open up the Git Bash app.

```{bash, eval=FALSE}
# Ensure ssh and ssh-copy-id commands exist
which ssh
which ssh-copy-id
# These two commands should return these two outputs respectively.
/usr/bin/ssh/
/usr/bin/ssh-copy-id 
```

---

# SSH into the cluster.
Let's first try and ssh into the cluster. SSH stands for *secure shell login*

```{bash, eval=FALSE}
# Use your login credentials to ssh onto the server
ssh <username>@<server_name>
# This should prompt you for your password
```

The following commands will be needed to navigate around:  
`pwd, ls, cd`  
The following commands will be needed to move and transfer files:  
`mv, cp, rm, touch`  
You can practise these on your own computer first before trying on the server.  
Type `exit` to leave the server and return to your computer.


---

# Passwords are annoying.
Let's use a key so that we don't have to continue entering our password when logging in.
```{bash, eval=FALSE}
# Install ssh-copy-id
brew install ssh-copy-id
# Create an ssh-key
ssh-keygen -t rsa # Then press enter twice.
# Now copy ssh key to server, you will be prompted for your password, one last time
ssh-copy-id -i ~/.ssh/id_rsa <username>@<server_name>
# Now try log in.
ssh username@<server_name>
```

---

# Troubleshooting
## I have copied across my id, but it still won't log in automatically.
Try change the permissions on your .ssh folder
```{bash, eval=FALSE}
chmod -R 700 ~/.ssh
```

If this still doesn't work, make sure that only you have permissions on your home directory.
View this [Stack-Exchange Thread](https://unix.stackexchange.com/questions/37164/ssh-and-home-directory-permissions) for more details.

---

# Troubleshooting
## I can't install brew or ssh-copy-id (Mac OSX)
That's okay, we can copy our id onto the server
```{bash, eval=FALSE}
scp ~/.ssh/id_rsa.pub <username>@<server>:
ssh <username>@<server_name>
# Now we're on the server; Create a .ssh directory for the server
mkdir -p -m 700 ~/.ssh
# Now append that id_rsa.pub key to our list of authorized keys
cat id_rsa.pub >> ~/.ssh/authorized_keys
# Our work here is done. Let's delete the .pub file and leave the server
rm id_rsa.pub
exit
```

---

# Further reading.

### Steve Parker: Shell scripting
Very comprehensive guide to using the 'Terminal'.
Starts at the very basics.
https://www.amazon.com.au/Shell-Scripting-Tutorial-Steve-Parker-ebook/dp/B00C2EGNSA

Free version is here:
https://www.shellscript.sh