This guide is designed for new users of the Levich Institute Linux servers who have no prior experience.
Linux file system and basic commands
Inquire system resources
Show operating system:
jmao@Jupiter:~$ cat /etc/issueUbuntu 22.04.1 LTS
Show kernel version:
jmao@Jupiter:~$ uname -aLinux Jupiter 4.19.128-microsoft-standard #1 SMP Tue Jun 23 12:58:10 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Show disk usage of mounted file systems:
jmao@Jupiter:~$ dfFilesystem 1K-blocks Used Available Use% Mounted on/dev/sdb 263174212 31208448 218527608 13% /tmpfs 6524932 0 6524932 0% /mnt/wsltools 511747028 506051256 5695772 99% /initnone 6524932 4 6524928 1% /runnone 6524932 0 6524932 0% /run/locknone 6524932 0 6524932 0% /run/shmnone 6524932 0 6524932 0% /run/usertmpfs 6524932 0 6524932 0% /sys/fs/cgroupdrivers 511747028 506051256 5695772 99% /usr/lib/wsl/driverslib 511747028 506051256 5695772 99% /usr/lib/wsl/libC:\ 511747028 506051256 5695772 99% /mnt/cD:\ 1953512444 863395912 1090116532 45% /mnt/dF:\ 5860487164 4247379760 1613107404 73% /mnt/fG:\ 104857600 99446620 5410980 95% /mnt/g
Show disk usage of mounted file systems in human readable unit:
jmao@Jupiter:~$ df -hFilesystem Size Used Avail Use% Mounted on/dev/sdb 251G 30G 209G 13% /tmpfs 6.3G 0 6.3G 0% /mnt/wsltools 489G 483G 5.5G 99% /initnone 6.3G 4.0K 6.3G 1% /runnone 6.3G 0 6.3G 0% /run/locknone 6.3G 0 6.3G 0% /run/shmnone 6.3G 0 6.3G 0% /run/usertmpfs 6.3G 0 6.3G 0% /sys/fs/cgroupdrivers 489G 483G 5.5G 99% /usr/lib/wsl/driverslib 489G 483G 5.5G 99% /usr/lib/wsl/libC:\ 489G 483G 5.5G 99% /mnt/cD:\ 1.9T 824G 1.1T 45% /mnt/dF:\ 5.5T 4.0T 1.6T 73% /mnt/fG:\ 100G 95G 5.2G 95% /mnt/g
Show disk usage of folders:
jmao@Jupiter:~$ du -hs *1.2M 1akk144K 1akk.pdb17.6M 1fue6.0M 4j8p116M 4lzt1.1M 4lzt_new25M 6nwa3.2G Downloads148K Figure_1.png4.0K LightsailDefaultKey-us-east-1.pem90M Miniconda3-latest-Linux-x86_64.sh8.0K Untitled.ipynb4.0K a32K batch-download-structures-1716948321485.zip4.0K bin4.0K chemsilo48K cve_list.json440M cves940K cyc
Show CPU and memory usage:
top
Press "q" to quit.
or
htop
Press F10 key to quit.
Show memory usage:
jmao@Jupiter:~$ free -h total used free shared buff/cache availableMem: 12Gi 66Mi 11Gi 0.0Ki 969Mi 12GiSwap: 4.0Gi 0B 4.0Gi
Show current users on the system:
who
Show recently logged in users:
last
Show user information:
finger username
Send a message to another user:
Syntax: write username [terminal]
write jmao pts/0
Use CTRL-D to end the message.
Display a command manual:
man last
Inquire current user name:
whoami
File system and related commands
List files:
Basic command: ls
jmao@Jupiter:~$ ls1akk bin java_error_in_pycharm_1372.log pcet1akk.pdb1 chemsilo java_error_in_pycharm_1425.log pcet_demo1fue cve_list.json java_error_in_pycharm_1470.log projects4j8p cves java_error_in_pycharm_1561.log pycharm4lzt cyc java_error_in_pycharm_1941.log scan.txt4lzt_new d java_error_in_pycharm_2031.log seaborn-data6nwa delphi java_error_in_pycharm_307.log testDownloads diprotic_demo java_error_in_pycharm_3624.log test.datFigure_1.png drobo java_error_in_pycharm_3687.log test.txtLightsailDefaultKey-us-east-1.pem fad java_error_in_pycharm_387.log uiucMiniconda3-latest-Linux-x86_64.sh fmn_Em_-520 java_error_in_pycharm_475.log user_paramUntitled.ipynb granepura java_error_in_pycharm_489.loga index.html josebatch-download-structures-1716948321485.zip ipscan miniconda3
Some useful options for command `ls`:
| Command | Function |
|---|---|
| ls -l | List details |
| ls -lh | list with human readable details units |
| ls -a | list hidden files * |
| ls -lt | list files in chronological order, newest first |
| ls -lrt | list files in chronological order, reversed order |
* Under Linux, hidden files are those files names tart with a "."
Navigate file system
Go to home directory:
cd or cd ~
Go to parent directory:
cd ..
In Unix, ". ." means parent directory, "." means current directory, and "~" means user's home directory.
Go to a directory:
cd Documents
or
cd /home/jmao/Documents
The first command uses relative path and the second uses absolute path.
Show current directory's absolute path:
pwd
Look for files
To locate a file by name:
jmao@ChemE:~$ locate Documents/Users/jmao/Documents/Users/jmao/Documents/MATLAB/Users/jmao/Documents/New Document.ott/Users/jmao/Documents/New Spreadsheet.otsjmao@ChemE:~$ locate -b '\Documents'/Users/jmao/Documents
The command "locate" searches folder name and file name that contains the specified string. If you want to search the exact file name, the option "-b" limits the scope to base name (excluding path name before the match, but still printed out), and the escape "\" removes the global name match. Be noted that `locate` command searches from a database refreshes daily, therefore new files may not show up in the search.
To search a file:
jmao@ChemE:~$ find ./ -name Documents./Documents
The locate command searches a pre-updated database (usually refreshed everyday) and the find command searches the actual file system.
jmao@ChemE:~$ touch myfilejmao@ChemE:~$ locate -b '\myfile'jmao@ChemE:~$ find ~/ -name myfile/home/jmao/myfile
Find an executable
"whereis" finds the command location and the same command name may appear in multiple places. "which" finds the location of command that will be called. You can always specify the full path to call the desired command.
jmao@ChemE:~$ whereis python python: /usr/bin/python3.6 /usr/bin/python2.7 /usr/bin/python3.6m /usr/bin/python3.5m /usr/bin/python3.5 /usr/bin/python /usr/lib/python3.6 /usr/lib/python2.7 /usr/lib/python3.5 /usr/lib/python3.7 /etc/python3.6 /etc/python2.7 /etc/python3.5 /etc/python /usr/local/lib/python3.6 /usr/local/lib/python2.7 /usr/local/lib/python3.5 /usr/include/python2.7 /usr/include/python3.6m /usr/share/python /Users/jmao/miniconda3/bin/python /Users/jmao/miniconda3/bin/python3.6m-config /Users/jmao/miniconda3/bin/python3.6m /Users/jmao/miniconda3/bin/python3.6-config /Users/jmao/miniconda3/bin/python3.6 /usr/share/man/man1/python.1.gz jmao@ChemE:~$ which python /home/jmao/miniconda3/bin/python
Find current directory:
pwd
Unix file permissions
If you list files in details, you see some strings like this:
jmao@ChemE:~$ ls -ltotal 84drwxr-xr-x 2 jmao jmao 4096 Feb 7 14:35 Desktop-rwxrwxr-x 1 jmao jmao 45 Jan 25 07:21 test3.py-rw-r--r-- 1 jmao jmao 87 Jan 25 07:49 test.pydrwxr-xr-x 2 jmao jmao 4096 Mar 27 2018 Videosd: directoryr: read permissionw: write permissionx:execute permission
The first character is reserved for directory. Other 9 characters are divided into three rwx fields. They are for owner, group, and others. The permission bits control how these files are read, wriitten, and determine if they can be run as a program.
To change permission, use
chmod
command.
Word mode of chmod command
One way to edit the file permission bits is through the word mode. Example:
chmod a+w file
In above example, "a" is reference, "+" is operator, and "w" is mode. It means, all three permission fields turn on write permission. Other references, operators and modes are:
| Reference | Meaning |
|---|---|
| u | User (Owner) |
| g | Group |
| o | Others |
| a | All, same as "ugo" |
| Operator | Meaning |
|---|---|
| + | Turn on |
| - | Turn off |
| = | Set to be |
| Mode | Meaning |
|---|---|
| r | Readable |
| w | Writable |
| x | Executable, or allow to enter when being adirectory |
Example:
"chmod a+x file" turns a file to be executable by all users.
"chmod go-rwx file" makes a file not accessible by group and other users.
Binary mode of command chmod
Alternatively, you can set a file permission with a binary string.
rwx fields can be viewed as a binary number. When set, the value is 1, otherwise is 0. For example, rw_rw_rw is 110,110,110 in binary, and 666 in octal. So
chmod 666 file
means to set file to permission ```rw_rw_rw```.
This is a very straight forward way to set permission.
Handle files
Here are some commonly used commands to handle files:
| Command | Example | Meaning |
|---|---|---|
| cp | cp file file.bak | copy file to file.bak |
| cp -r run01 run02 | recursicely copy directory run01 to directory run02 | |
| cp -a file1 file2 | copy file and preserve file properties (permission, time etc) | |
| rm | rm file | delete file |
| rm -rf folder | recursively and silently delete directory named folder | |
| mv | mv file1 file2 | rename (move) file1 to file2 |
| file | file filename | determine file type, text or binary or compressed, etc |
| cat | cat text_file | print text file contents |
| less | less text_file | navigate text file content, "q" to exit |
| more | more text-file | same as "less" command |
| mkdir | mkdir dirname | make a directory |
| rmdir | rmdir dirname | delete an empty directory, see "rm -rf" |
| touch | touch file | update file time stamp or create an empty file |
| wc | wc -l text_file | count number of lines |
Special commands
There are some commands to handle odd situations in a terminal, for example, a terminal may hang, or print unrecognizable characters. These command may help.
CTRL-D
Send an EOF signal to the terminal. Some commands like mail and talk let you type text in terminal as input, but needs a non-text to indicate the end of input. This key combination indicates the end of file (text).
If you press this key combination at the terminal prompt, it serves as log out command.
CTRL-C
Interrupt a command, not resumable. Example:
jmao@ChemE:~$ sleep 60^C
CTRL-Z
Interrupt a command, resumable with "fg" at foreground or "bg" at background.
jmao@jmao-desktop ~/projects/mcce-develop $ sleep 120 ^Z[1]+ Stopped sleep 120jmao@jmao-desktop ~/projects/mcce-develop $ fgsleep 120
&
Send a job to background. Background job runs at background and you have the control of terminal before command finishes.
sleep 10sleep 10 &"jobs"
Check jobs issued from this terminal.
CTRL-L or "clear"
Clear the termical window.
"reset"
Reset and clear terminal. In case you ran some program and turned your terminal unusable, type in reset may give you back the terminal.
"history"
Show command history of this terminal window.
"echo $?"
$? is a special environment variable, holding the return value of the previous command. Each command has an exit code. Normally 0 means successful exit.
