# useful server basics
PUBS 2018 | Jean Costello

## log in/out
To log in:

- $ ssh username@servername.domainname.edu

Enter your password when prompted.

To log out (use any):

- $ logout
- $ exit
- $ ctrl+D


## create an alias
To avoid having to type out the full server name and domain every time, create an alias.

1. open the file ~/.ssh/config
2. add the following three lines to the file:
  - Host *nickname*
  - HostName *domain*
  - User *username*
3. save and exit
4. login by typing: ssh *nickname*

An example in vim:

1. $ vim ~/.ssh/config
2. type "i" to inter insert mode
3. enter the text (example):
  - Host pubs
  - HostName derisilab105.ucsf.edu
  - User my_pubs_group
4. type esc to exit insert mode
5. type ":wq" to save and quit (if the program says you may not edit the file, use ! to override: :wq!)
6. $ ssh pubs

## transfer files
To move files between your local machine and the server, use the scp (securely copy files) command.

**local to remote**

- $ scp username@server:file.txt /local/directory/

Or, if you've set up an alias:

- $ scp nickname:file.txt /local/directory/

**remote to local**

- $ scp file.txt username@server:/remote/directory/
- $ scp file.txt nickname:/remote/directory/

**directories**

To transfer directories, use the option r:

- $ scp -r /local/directory/ nickname:/remote/directory/
- $ scp -r nickname:/remote/directory/ /local/directory/

## files
List files and file sizes:

- $ ls -lh

List the number of lines in a file:

- $ wc -l file.txt

Display the first n lines in a file:

- $ head -n file.text

Display the last n lines in a file:

- $ tail -n file.txt

Zip a file:

- $ gzip file.txt

Unzip a file:

- $ gunzip file.txt.gz

## continue processes after logout
prefix your command with nohup:

- $ nohup command arguments

Example:

- $ nohup python myscript.py

This allows you to logout or disconnect from the server or exit the shell without aborting the command.

To save the output to a file:

- $ nohup python myscript.py > file.txt

## return to shell prompt immediately
suffix your command with &

- $ nohup command arguments &

The command will run in the background.

## viewing and killing processes
To view processes (use either):

- $ top
- $ htop

To exit out of the process view:
- q

To kill, use top or htop to find the job PID.

- $ kill *PID*

If that doesn't work, use signal 9:

- $ kill -9 *PID*