More Terminal Schooling

You are probably asking yourself “and why do I need more terminal schooling?”. The short answer is: to not have to spend as much time as you do on the terminal, most of which spent (1) pushing arrow keys thousands of times per afternoon to move through a command or history of commands, (2) waiting for a command that takes forever to be done running before you can run anything else, (3) clicking all over the place on MobaXTerm and still feeling lost, (4) manually running the same command multiple times with different inputs, (5) typing the two-step verification token every time you want to change a “+” to a “-” on a file on a supercomputer, (6) waiting forever for a time-consuming run done in serial on a single core, and (7, 8, …) other useless and horribly frustrating chores. Below are some tricks to make your Linux work more efficient and reduce the time you spend on the terminal. From now on, I will use a “$” sign to indicate that what follows is a command typed in the terminal.

The tab autocomple is your best friend

When trying to do something with that file whose name is 5480458 characters long, be smart and don’t type the whole thing. Just type the first few letters and hit tab. If it doesn’t complete all the way it’s because there are multiple files whose names begin with the sequence of characters. In this case, hitting tab twice will return the names of all such files. The tab autocomplete works for commands as well.

Ctrl+r for search through previous commands

When on the terminal, hit ctrl+r to switch to reverse search mode. This works like a simple search function o a text document, but instead looking in your bash history file for commands you used over the last weeks or months. For example, if you hit ctrl+r and type sbatch it will fill the line with the last command you ran that contained the word sbatch. If you hit ctrl+r again, it will find the second last used command, and so on.

Vim basics to edit files on a system that requires two-step authentication

Vim is one the most useful things I have came across when it comes to working on supercomputers with two-step identity verification, in which case using MobaXTerm of VS Code requires typing a difference security code all the time. Instead of uploading a new version of a code file every time you want to make a simple change, just edit the file on the computer itself using Vim. To make simple edits on your files, there are very few commands you need to know.

To open a file with Vim from the terminal: $ vim <file name> or $ vim +10 <file name>, if you want to open the file and go straight to line 10.

Vim has two modes of operation: text-edit (for you to type whatever you want in the file) and command (replacement to clicking on file, edit, view, etc. on the top bar of notepad). When you open Vim, it will be in command mode.

To switch to text-edit mode, just hit either “a” or “i” (you should then see “– INSERT –” at the bottom of the screen). To return to command mode, hit escape (Esc). When in text-edit more, the keys “Home,” “End,” “Pg Up,” “Pg Dn,” “Backspace,” and “Delete” work just like on Notepad and MS Word.

When in command mode, save your file by typing :w + Enter, save and quite with :wq, and quit without saving with :q!. Commands for selecting, copying and pasting, finding and replacing, replacing just one character, deleting a line, and other more advanced tasks can be found here. There’s also a great cheatsheet for Vim here. Hint: once you learn some more five to ten commands, making complex edits on your file with Vim becomes blazingly fast.

Perform repetitive tasks on the terminal using one-line Bash for-loops.

Instead of manually typing a command for each operation you want to perform on a subset of files in a directory (“e.g., cp file<i>.csv directory300-400 for i from 300 to 399 , tar -xzvf myfile<i>.tar.gz, etc.), you can use a Bash for-loop if using the is not possible.

Consider a situation in which you have 10,000 files and want to move files number 200 to 299 to a certain directory. Using the wildcard “*” in this case wouldn’t be possible, as result_2<i>.csv would return result_2.csv, result_20.csv to result_29.csv, and result_2000.csv to result_2999.csv as well–sometimes you may be able to use Regex, but that’s another story. To move a subset of result files to a directory using a Bash for-loop, you can use the following syntax:

$ for i in {0..99}; do cp result_2$i results_200s/; done

Keep in mind that you can have multiple commands inside a for-loop by separating them with “;” and also nest for-loops.

Run a time-intensive command on the background with an “&” and keep doing your terminal work

Some commands may take a long time to run and render the terminal unusable until it’s complete. Instead of opening another instance of the terminal and login in again, you can send a command to the background by adding “&” at the end of it. For example, if you want to extract a tar file with dozens of thousands of files in it and keep doing your work as the files are extracted, just run:

$ tar -xzf my_large_file.tar.gz &

If you have a directory with several tar files and want to extract a few of them in parallel while doing your work, you can use the for-loop described above and add “&” to the end of the tar command inside the loop. BE CAREFUL, if your for-loop iterates over dozens or more files, you may end up with your terminal trying to run dozens or more tasks at once. I accidentally crashed the Cube once doing this.

Check what is currently running on the terminal using ps

To make sure you are not overloading the terminal by throwing too many processes at it, you can check what it is currently running by running the command ps. For example, if I run an program with MPI creating two processes and run ps before my program is done, it will return the following:

bernardoct@DESKTOP-J6145HK /mnt/c/Users/Bernardo/CLionProjects/WaterPaths
$ mpirun -n 2 ./triangleSimulation -I Tests/test_input_file_borg.wp &
[1] 6129     <-- this is the process ID
bernardoct@DESKTOP-J6145HK /mnt/c/Users/Bernardo/CLionProjects/WaterPaths
 $ ps
 PID TTY TIME CMD
 8 tty1 00:00:00 bash
 6129 tty1 00:00:00 mpirun    <-- notice the process ID 6129 again
 6134 tty1 00:00:00 triangleSimulat
 6135 tty1 00:00:00 triangleSimulat
 6136 tty1 00:00:00 ps

Check the output of a command running on the background

If you run a program on the background its output will not be printed on the screen. To know what’s happening with your program, send (to pipe) its output to a text file using the “>” symbol, which will be updated continuously as your program is running, and check it with cat <file name>, less +F<file name>, tail -n<file name>, or something similar. For example, if test_for_background.sh is a script that will print a number on the screen every one second, you could do the following (note the “> pipe.csv” in the first command):

bernardoct@DESKTOP-J6145HK /mnt/c/Users/Bernardo/CLionProjects/WaterPaths
 $ ./test_for_background.sh > pipe.csv &
 [1] 6191

bernardoct@DESKTOP-J6145HK /mnt/c/Users/Bernardo/CLionProjects/WaterPaths
 $ cat pipe.csv
 1
 2

bernardoct@DESKTOP-J6145HK /mnt/c/Users/Bernardo/CLionProjects/WaterPaths
 $ cat pipe.csv
 1
 2
 3

bernardoct@DESKTOP-J6145HK /mnt/c/Users/Bernardo/CLionProjects/WaterPaths
 $ tail -3 pipe.csv
 8
 9
 10

This is also extremely useful in situations when you want to run a command that takes long to run but whose outputs are normally displayed one time on the screen. For example, if you want to check the contents of a directory with thousands of files to search for a few specific files, you can pipe the output of ls to a file and send it to the background with ls > directory_contents.txt & and search the resulting text file for the file of interest.

System monitor: check core and memory usage with htop, or top if htop is not available

If ps does not provide enough information given your needs, such as if you’re trying to check if your multi-thread application is using the number of cores it should, you can try running htop instead. This will show on your screen something along the lines of the Performance view  of Windows’ Task Manager, but without the time plot. It will also show how much memory is being used, so that you do not accidentally shut down a node on an HPC system. If htop is not available, you can try top.

Running make in parallel with make -j for much shorter compiling time

If a C++ code is properly modularized, make can compile certain source code files in parallel. To do that, run make -j<number of cores> <rule in makefile>. For example, the following command would compile WaterPaths in parallel over four cores:

$ make -j4 gcc

For WaterPaths, make gcc takes 54s on the Cube, make -j4 gcc takes 15s, make -j8 gcc takes 9s, so the time and patience savings are real if you have to compile the code various times per day. To make your life simpler, you can add an alias to bash_aliases such as alias make='make -j4' (see below in section about .bash_aliases file). DO NOT USE MAKE -J ON NSF HPC SYSTEMS: it is against the rules. On the cube keep it to four cores or less not to disturb other users, but use all cores available if on the cloud or iterative section.

Check the size of files and directories using du -hs

The title above is quite self-explanatory. Running du -hs <file name> will tell you its size.

Check the data and time a file was created or last modified using the stat command

Also rather self-explanatory. Running stat <file name> is really useful if you cannot remember on which file you saved the output last time you ran your program.

Split large files into smaller chunks with the split command and put them back together with cat

This works for splitting a large text file into files with fewer lines, as well as for splitting large binary files (such as large tar files) so that you can, for example, upload them to GitHub or e-mail them to someone. To split a text file with 10,000 into ten files with 1,000 lines each, use:

 $ split -l 1000 myfile myfile_part

This will result in ten files called myfile_part00, myfile_part01, and so on with 1,000 lines each. Similarly, the command below would break a binary file into parts with 50 MB each:

 $ split -b 50m myfile myfile_part

To put all files back together in either case, run:

$ cat myfile_part* myfile

More information about the split command can be found in Joe’s post about it.

Checking your HPC submission history with `sacct`

Another quite sulf-explanatory tile. If you want to remember when you submitted something, such as to check if an output file resulted from this or that submission (see stat command), just run the command below in one line:

$ sacct -S 2019-09-18 -u bct52 --format=User,JobID,Jobname,start,end,elapsed,nnodes,nodelist,state

This will result in an output similar to the one below:

bct52 979 my_job 2019-09-10T21:48:30 2019-09-10T21:55:08 00:06:38 1 c0001 COMPLETED
bct52 980 skx_test_1 2019-09-11T01:44:08 2019-09-11T01:44:09 00:00:01 1 c0001 FAILED
bct52 981 skx_test_1 2019-09-11T01:44:33 2019-09-11T01:56:45 00:12:12 1 c0001 CANCELLED
bct52 1080 skx_test_4 2019-09-11T22:07:03 2019-09-11T22:08:39 00:01:36 4 c[0001-0004] COMPLETED
1080.0 orted 2019-09-11T22:08:38 2019-09-11T22:08:38 00:00:00 3 c[0002-0004] COMPLETED

Compare files with meld, fldiff, or diff

There are several programs to show the differences between text files. This is particularly useful when you want to see what the changes between different versions of the same file, normally a source code file. If you are on a computer running a Linux OS or have an X server like Xming installed, you can use meld and kdiff3 for pretty outputs on a nice GUI or fldiff to quickly handle a files with huge number of difference. Otherwise, diff will show you the differences in a cruder pure-terminal but still very much functional manner. The syntax for all of them is:

$ <command> <file1> <file2>

Except for diff, for which it is worth calling with the --color option:

$ diff --color <file1> <file2>

If cannot run a graphical user interface but is feeling fancy today, you can install the ydiff Python extension with (done just once):

$ python3 -m pip install --user ydiff 

and pipe diff’s output to it with the following:

$diff -u <file1> <file2> | python3 -m ydiff -s

This will show you the differences between two versions of a code file in a crystal clear, side by side, and colorized way.

Creating a .bashrc file for a terminal that’s easy to work with and good (or better) to look at

When we first login to several Linux systems the terminal is all black with white characters, in which it’s difficult find the commands you typed amidst all the output printed on the screen, and with limited autocomplete and history search. In short, it’s a real pain and you makes you long for Windows as much as for you long for your mother’s weekend dinner. There is, however, a way of making the terminal less of a pain to work with, which is by creating a file called .bashrc with the right contents in your home directory. Below is an example of a .bashrc file with the following features for you to just copy and paste in your home directory (e.g., /home/username/, or ~/ for short):

  • Colorize your username and show the directory you’re currently in, so that it’s easy to see when the output of a command ends and the next one begins–as in section “Checking the output of a command running on the background.”
  • Allow for a search function with the up and down arrow keys. This way, if you’re looking for all the times you typed a command starting with sbatch, you can just type “sba” and hit up arrow until you find the call you’re looking for.
  • A function that allows you to call extract and the compressed file will be extracted. No more need to tar with a bunch of options, unzip, unrar, etc. so long as you have all of them installed.
  • Colored man pages. This means that when you look for the documentation of a program using man, such as man cat to see all available options for the cat command, the output will be colorized.
  • A function called pretty_csv to let you see csv files in a convenient, organized and clean way from the terminal, without having to download it to your computer.
# .bashrc

# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi

# Load aliases
if [ -f ~/.bash_aliases ]; then
. ~/.bash_aliases
fi

# Automatically added by module
shopt -s expand_aliases

if [ ! -z "$PS1" ]; then
PS1='\[\033[G\]\[\e]0;\w\a\]\n\[\e[1;32m\]\u@\h \[\e[33m\]\w\[\e[0m\]\n\$ '
bind '"\e[A":history-search-backward'
bind '"\e[B":history-search-forward'
fi

set show-all-if-ambiguous on
set completion-ignore-case on
export PATH=/usr/local/gcc-7.1/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/gcc-7.1/lib64:$LD_LIBRARY_PATH

history -a
export DISPLAY=localhost:0.0

sshd_status=$(service ssh status)
if [[ $sshd_status = *"is not running"* ]]; then
sudo service ssh --full-restart
fi

HISTSIZE=-1
HISTFILESIZE=-1

extract () {
if [ -f $1 ] ; then
case $1 in
*.tar.bz2)   tar xvjf $1    ;;
*.tar.gz)    tar xvzf $1    ;;
*.bz2)       bunzip2 $1     ;;
*.rar)       unrar x $1       ;;
*.gz)        gunzip $1      ;;
*.tar)       tar xvf $1     ;;
*.tbz2)      tar xvjf $1    ;;
*.tgz)       tar xvzf $1    ;;
*.zip)       unzip $1       ;;
*.Z)         uncompress $1  ;;
*.7z)        7z x $1        ;;
*)           echo "don't know how to extract '$1'..." ;;
esac
else
echo "'$1' is not a valid file!"
fi
}

# Colored man pages
export LESS_TERMCAP_mb=$'\E[01;31m'
export LESS_TERMCAP_md=$'\E[01;31m'
export LESS_TERMCAP_me=$'\E[0m'
export LESS_TERMCAP_se=$'\E[0m'
export LESS_TERMCAP_so=$'\E[01;44;33m'
export LESS_TERMCAP_ue=$'\E[0m'
export LESS_TERMCAP_us=$'\E[01;32m'

# Combine multiline commands into one in history
shopt -s cmdhist

# Ignore duplicates, ls without options and builtin commands
HISTCONTROL=ignoredups
export HISTIGNORE="&:ls:[bf]g:exit"

pretty_csv () {
cat "$1" | column -t -s, | less -S
}

There are several .bashrc example files online with all sorts of functionalities. Believe me, a nice .bashrc will make your life A LOT BETTER. Just copy and paste the above into a text file called .bashrc and sent it to your home directory in your local or HPC system terminal.

Make the terminal far less user-friendly and less archane by setting up a .bash_aliases file

You should also have a .bash_aliases file to significantly reduce typing and colorizing the output of commands you often use for ease of navigation. Just copy all the below into a file called .bash_aliases and copy into your home directory (e.g., /home/username/, or ~/ for short). This way, every time you run the command between the word “alias” and the “=” sign, the command after the “=”sign will be run.

alias ls='ls --color=tty'
alias ll='ls -l --color=auto'
alias lh='ls -al --color=auto'
alias lt='ls -alt --color=auto'
alias uu='sudo apt-get update && sudo apt-get upgrade -y'
alias q='squeue -u '
alias qkill='scancel $(qselect -u bct52)'
alias csvd="awk -F, 'END {printf \"Number of Rows: %s\\nNumber of Columns: %s\\n\", NR, NF}'"
alias grep='grep --color=auto'                          #colorize grep output
alias gcc='gcc -fdiagnostics-color=always'                           #colorize gcc output
alias g++='g++ -fdiagnostics-color=always'                          #colorize g++ output
alias paper='cd /my/directory/with/my/beloved/paper/'
alias res='cd /my/directory/with/my/ok/results/'
alias diss='cd /my/directory/of/my/@#$%&/dissertation/'
alias aspell='aspell --lang=en --mode=tex check'
alias aspellall='find . -name "*.tex" -exec aspell --lang=en --mode=tex check "{}" \;'
alias make='make -j4'

Check for spelling mistakes in your Latex files using aspell

Command-line spell checker, you know what this is.

aspell --lang=en --mode=tex check'

To run aspell check on all the Latexfiles in a directory and its subdirectories, run:

find . -name "*.tex" -exec aspell --lang=en --mode=tex check "{}" \;

Easily share a directory on certain HPC systems with others working on the same project [Hint from Stampede 2]

Here’s a great way to set permissions recursively to share a directory named projdir with your research group:

$ lfs find projdir | xargs chmod g+rX

Using lfs is faster and less stressful on Lustre than a recursive chmod. The capital “X” assigns group execute permissions only to files and directories for which the owner has execute permissions.

Run find and replace in all files in a directory [Hint from Stampede 2]

Suppose you wish to remove all trailing blanks in your *.c and *.h files. You can use the find command with the sed command with in place editing and regular expressions to this. Starting in the current directory you can do:

$ find . -name *.[ch] -exec sed -i -e ‘s/ +$//’ {} \;

The find command locates all the *.c and *.h files in the current directory and below. The -exec option run the sed command replacing {} with the name of each file. The -i option tells sed to make the changes in place. The s/ +$// tells sed to replace one or blanks at the end of the line with nothing. The \; is required to let find know where the end of the text for the -exec option. Being an effective user of sed and find can make a great different in your productivity, so be sure to check Tina’s post about them.

Other post in this blog

Be sure to look at other posts in this blog, such as Jon Herman’s post about ssh, Bernardo’s post about other useful Linux commands organized by task to be performed, and Joe’s posts about grep (search inside multiple files) and cut.

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