UNIX.md

MiCE 5035 UNIX Command-line Guide

These are some of the more commonly used UNIX commands.

scroll through your command history

<up/down arrow>

kill the current process (or delete what you have written on the command line)

<control>-c

search your command history

<control>-r (then type the search string)

clear your screen

clear

change into your “home” directory

cd

switch groups if you have a research lab group also

This makes sure you're not using your lab's computing allotment This is only if you already have an MSI account through a research lab.

newgrp mice5035

list the contents of this directory

ls

list the contents of the parent directory

ls ..

list the contents of some other directory

ls /path/to/other/directory

print out the full “path” to this directory. Also called the "absolute path".

pwd

make a new directory (aka folder) for your programs (binaries)

mkdir bin

make sure it got created

ls

change into the “bin” directory

cd bin

change back to the "parent" directory (the one just above this in the file system)

cd ..

unzip a file

unzip zippedfile.zip

remove a file

rm unwantedfile.txt

list the number of lines, words, and characters in a file:

wc filename.txt

remove a directory

rm -r unwanteddirectory

view the first 10 lines of a file

head myfile.txt

view the first 3 columns (fields) of a file, assuming tab delimiters

cut -f 1-3 myfile.txt

view the first 3 columns (fields) of a file, assuming comma delimiters

cut -f 1-3 -d "," myfile.txt

view the first 10 lines of the first 3 columns

cut -f 1-3 -d myfile.txt | head 

scroll through the first 3 columns of the whole file (enter q to exit)

cut -f 1-10 -d "," myfile.txt | less

scroll through the whole file

less myfile.txt

make a copy of a file

cp file1.txt file2.txt

copy a file to the current directory (. means current directory)

cp /full/path/to/other/file.txt .

make a copy of a directory

cp -r directory1 directory2

mv (rename) a file

mv oldname.txt newname.txt

see how large files are

du -hs *

edit a file (exit with ctrl-x)

nano somefile.txt

kill a command that is running

<ctrl>-c

search a file for a string or word. e.g. print out all lines that have a ">" character:

grep ">" input.fna

print out all lines that DO NOT have a ">" character:

grep -v ">" input.fna

count all lines that have a ">" character:

grep -c ">" input.fna

Using "Screen" to keep a session open

If you need to run something that will take a while, there are ways to keep an interactive computing session open on MSI. One way is to log in to a specific login node (e.g. ahl01), open a "screen" session, and then start your interactive session. The screen session will stay open on the login node if you disconnect and connect again later. Here are the steps:

1. When you first connect to MSI, connect to a specific login node:

ssh username@ahl01.msi.umn.edu

2. Start a "screen" session (like opening a browser window, conceptually)

screen

3. Launch your compute node

srun ...

4. When you need to log off temporarily, detach from the screen session (don't hold ctrl after the a)

<ctrl>-a d

Then exit the login node with <ctrl>-d or exit. 5. When ready to log back on, connect to the same login node:

ssh username@ahl01.msi.umn.edu

6. Re-attach to the screen session

screen -Dr

Now you are back on the compute node, right where you left off. If you had a command running, it will have continued running in the background.

Other helpful screen commands

start another screen "window" (like opening another tab in a browser)

<ctrl>-a c

move to the next screen "tab"

<ctrl>-a n

move to the previous screen "tab"

<ctrl>-a p

terminate/permanently close a commandline session or screen session

<ctrl>-d