10  Using Linux

10.1 General Short Cuts

  • super+tab switches between windows
  • super+left/right arrow fits active window to left or right of screen
  • ctrl+alt+t opens a new terminal window
  • ctrl+d closes a terminal window

10.2 Terminal Short Cuts

  • tab autocompletes from what you have started to type
  • ctrl+c breaks out of a command or process
  • ctrl+d logs out of current terminal
  • `ctrl+l clears screen
  • ctrl+a moves cursor to beginnng of line
  • ctrl+e moves cursor to the end of line
  • ctrl+u clears the current line
  • ctrl+p or up arrow scrolls through previous commands
  • ctrl_n or down arrow scrolls forward through commands
  • ctrl+shift+c copies highlighted text
  • ctrl+shift+v pastes copied text

10.3 control processes

  • command & to launch program in background of terminal
  • fg %1 to move program to foreground
  • bg %1 to move to background
  • kill %1 (see chap 10 in linux book)

10.4 Pdf manipulation

We use evince [filename.pdf] to view pdfs

we use qpdf --empty --pages infile.pdf 1-5 -- outfile.pdf to extract pages from a pdf

10.5 Quarto

10.6 Markdown

You will need to install pandoc to render markdown to pdf: sudo apt-get install pandoc texlive-latex-base texlive-fonts-recommended texlive-extra-utils texlive-latex-extra.

Use pandoc [infile.md] -o [outfile.pdf] to render infile.md to outfile.pdf.

Note also that the ReText app can render markdown to pdf (and html) as well if you don’t want to use the terminal.

10.7 Firefox

You can view an html file in firefox from terminal using firefox [filename]

10.8 Common Commands

  • wc, uniq, head, tail, |, >, >>, less, sort, grep, cat, man, help, –help, type, which, echo

  • ls -lSr to list files sorted by size (with larger sizes later: r). Useful to find the non-zero error files. Can have issues when applied to large numbers of files (> 60K). See use of find and xargs below if needed.

  • cd - changes tio previous directory

  • mv to move files between directories. can use .. as target to move file to home directory. e.g., mv results_* ..

  • > redirect standard output to a new file (creates file if does not exist; writes over file contents if it does exist). >> redirect standard output to append to a file

  • rm to remove file(s). rm -r to remove non-empty directory

  • cat filename_* > all_files.csv to concatenate all files into one file.

  • less views file contents

  • | is pipe operator

  • wc is word count. wc -l counts lines

  • chmod +x get_missing_jobs.sh to change permissions on get_missing_jobs.sh to run it. ./get_missing_jobs.sh to run it.

  • find -maxdepth 1 -name "results_*.csv" | wc -l will find results_*.csv in local folder (maxdepth 1) and pipe them into a word count that counts lines (-l)

  • cat job_nums.csv | wc -l reads contents of job_nums.csv and pipes to a word count that counts lines (-l)

  • find -maxdepth 1 -name "results_*.csv" | ls -lSr gets around the too many arguments issue. Find searches recursively by default (override with maxdepth if needed), whereas ls searches just . or the specified directory (e.g., ./results)

  • See tutorial on awk to understand its use for simple programming. See a tutorial on the use of xargs.

  • printf to send formatted text to standard output or to a file

    • printf "John is %s\n" "nice"
    • printf "John is %d years old" 54
    • printf "hello world\nIt is John!" > out.txt)

  • man [command] to open manual for command

  • sdiff file1 file2 - Compare two files side by side.

  • vimdiff file1 file2 - Highlight the differences between two files in the vim editor.

  • tar [-] c|x|t f tarfile [pattern] - Create, extract or list contents of a tar archive using pattern, if supplied.

  • du -h - Display sizes in human readable format. For example, 1.2M, 3.7G, etc.

  • head, tail, and sort work as expected. Remember to use -n with sort if you want to do a numeric (rather than text) sort. Sort also takes -r for reverse. Use pipe to pipe in a vector of numbers or text. Use -1 with head or tail to get the first (or last) value in series.

10.9 Compressing and archiving files

  • `gzip foo.txt - Compress foo.txt. The resulting compressed file is named file.txt.gz. -r to compress subdirectories when compressing a directory rather than file.
  • gunzip foo.txt - Uncompress foo.txt.gz (no need to append .gz).
  • gunzip foo.txt -c | less to view contents of foo.txt without decompressing it
  • tar cf playground.tar playground make archive of playground directory. r rather than c to append rather than create new archive.
  • tar czf playground.tgz playground to archive and compress (could also name playground.tar.gz)
  • tar xf playground2.tar to extract files from archive
  • see linux book, chapter 18 for more details

10.10 FTP

  • use sftp at command line. e.g., sftp submit-1.chtc.wisc.edu
  • can use command line to review local and remote computers.
  • For local lls, lcd, lpwd are the three most useful commands
  • For remote ls, cd, pwd
  • Use get foo.txt to copy foo.txt from remote to local director
  • Use put foo.txt to copy foo.txt from local directory to remote directory
  • exit when done
  • Can set up a ssh key to log in without credentials to CHTC.

10.11 SSH

  • use ssh at command line. e.g., ssh submit-1.chtc.wisc.edu
  • Can set up a ssh key to log in without credentials to CHTC, Github, etc.

10.12 Kill a frozen app

Press Alt + F2 . Type xkill and hit Enter. The cursor will turn into a small ‘x’. Left click any window to kill the process associated with that window.