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CSC and Unix cheatsheet

adapted from https://docs.csc.fi/img/csc-quick-reference/csc-quick-reference.pdf Note that this is simplified for beginners usage, once you get more experienced, you'll notice that there is more (and better) options for everything, and that not everything written here is "the whole truth".

Service names

  • Puhti, Mahti, LUMI - supercomputers
  • Pouta, Rahti - cloud services
  • Allas - object storage

Unix commands and hints

(all text within <> is replaced with real names, e.g. cp /home/user/my-file.txt scratch/project_200xxxx/new-directory) Check out all options of the commands with man <command> (for manual), exit with q.

File system exploration

  • ls - list current directory contents
  • cd <directory-to-change-to> - change the current directory
    • cd .. - change to "one level higher" in directory tree
    • cd - (without argument) change to $HOME
  • pwd - print full path of the current directory

File manipulation

  • cp <file-to-copy> <destination> - copy a file
  • mv <file-to-move> <destination/new-file-name> - move or rename a file
  • rm <file-to-remove> - delete a file
  • mkdir <new-directory-name> - create a directory
  • touch <new-file-name> - create an empty new file

Permissions

  • chmod <whowhatwhich> <file-name> - change file permissions
    • who -> u: user , g: group , o: others, a: all
    • what -> -:remove permission, +: add permission
    • which -> r: read, w: write, x: execute
    • example chmod u+x my-batch-job-script.sh adds execution rights for current user to the file
  • chgrp - change file/folder owner

Check file contents

  • less <text-file> - see text file (exit with q)
  • cat <file-name> - see file content
  • head <file-name> - list ten first lines of the file
  • tail -100 <file-name> - show the last 100 lines

Other

  • history - show history of commands run
  • grep - find rows containing a string
    • example: history | grep "some strings" would show you all commands in your history that contain "some string" (| is called a pipe)
  • echo "some text" - prints some text to terminal
  • exit - quit the session on commandline
  • <some command> > <file-name> - output of a command to a file
  • <some command> >> <file-name> - append output of a command to a file
  • which <application-name> - shows path to the executable of an application

Variables

Defining a variable: MYPATH=/home/user/something Using a defined or environment (predefined!) variable: $MYPATH, e.g. to print its content: echo $MYVAR Some environment variables:

  • $HOME : users home directory
  • $PATH : path where executables are looked for
  • $USERNAME: current username
  • $HOSTNAME: current host system name

Command line editors

Nano

Process to edit a file in nano:

  • nano <file-name> - (create and) open file with nano
    • edit your file
    • when done, use CTRL + o key combination
    • (edit the filename and) press enter
    • use CTRL + x key combination to exit the editor

Vi

Process to edit a file in vi:

  • vi <file-name> - (create and) open file with vi
    • press i to switch to "edit mode"
    • edit your file
    • when done, press esc to switch to "normal mode"
    • press :wq to save (write) the file and exit (quit) the editor

File transfer

  • scp <file name> <username@puhti.csc.fi:/scratch/project_200xxxx/dir_name> - copy a file from current computer to Puhti
  • wget <some-url> or curl <some-url> - get a file from the internet

CSC modules

  • Geoinformatics applications and how to use them: https://docs.csc.fi/apps/by_discipline/#geosciences
  • module load <application-name> - initialize the environment of an application
  • module list - list loaded applications
  • module purge - remove application environments

CSC batch jobs

  • sbatch <batch-job-file> - submit a job
  • sacct - info about job status
  • squeue - see the job status in the queue
  • scancel <jobid> - cancel a job
  • seff <jobid> - info about completed jobs

Support and links

Git "the way you need it"

Cheatsheet by Aalto Scientific Computing