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Linux Commands
If you have not done yet, download Sample files by:
git clone https://hidekiCCS@bitbucket.org/hidekiCCS/hpc-workshop.git
Basic Linux Commands
Here is a curated list of the most common Linux commands you will use. This list is by no means extensive, but these commands will allow you to navigate the clusters as well as create, destroy, and manipulate files and directories.
man
Display online manual pages. Most Linux commands have a manual page with detailed instructions on use. Replace <command name> below with command you would like information on.
[tulaneID@cypress1 ~]$ man <command name>
pwd
On a *nix system, directories are containers for files and objects. The pwd command lists the present working directory. This is the "where am I?" command.
[tulaneID@cypress1 ~]$ pwd /home/tulaneID [tulaneID@cypress1 ~]$
cd
The cd command changes directory. (Observe the change of directory name in the resulting system prompt as well!)
[tulaneID@cypress1 ~]$ cd hpc-workshop [tulaneID@cypress1 hpc-workshop]$ pwd /home/tulaneID/hpc-workshop [tulaneID@cypress1 hpc-workshop]$
As you can see, workshop is a subdirectory of tulaneID. And tulaneID is itself a subdirectory of home, which is a subdirectory of the root directory (/). Thus, the directories form a downward facing tree with all directories stemming from the root directory. You can move one level up in the tree by typing cd ..
[tulaneID@cypress1 hpc-workshop]$ pwd /home/tulaneID/workshop [tulaneID@cypress1 hpc-workshop]$ cd .. [tulaneID@cypress1 ~]$ pwd /home/tulaneID [tulaneID@cypress1 ~]$
And you can navigate using either relative or absolute paths. That is, you can enter directory paths relative to your current location, or you can entire the entire path starting with the root directory.
[tulaneID@cypress1 ~]$ pwd /home [tulaneID@cypress1 ~]$ cd tulaneID/hpc-workshop [tulaneID@cypress1 hpc-workshop]$ pwd /home/tulaneID/hpc-workshop [tulaneID@cypress1 ~]$ cd /home [tulaneID@cypress1 ~]$ pwd /home [tulaneID@cypress1 ~]$
Lastly, if you ever get lost you can use the tilde (~ - or simply cd with no argument!) to return to your HOME directory.
[tulaneID@cypress1 ~]$ cd ~ [tulaneID@cypress1 ~]$ pwd /home/tulaneID [tulaneID@cypress1 ~]$
ls
The ls command will list files in the current directory.
[tulaneID@cypress1 ~]$ ls woekshop [tulaneID@cypress1 ~]$
If you would like to see if a directory contains a specific file, you can pass the directory path and file name to ls as an argument
[tulaneID@cypress1 ~]$ ls hpc-workshop BlasLapack Eigen3 HeatMass JobArray1 JobDependencies MPI PETSc precision Python ScaLapack SimpleExample TestCodes VTK CUDA FlowInCavity hybridTest JobArray2 Matlab OpenMP PI PSE R SerialJob SLU40 uBLAS [tulaneID@cypress1 ~]$
Setting the -l flag will display files along with their permissions and ownership.
[tulaneID@cypress1 ~]$ ls -l hpc-workshop total 100 drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 BlasLapack drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 CUDA drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 Eigen3 drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 FlowInCavity drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 HeatMass drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 hybridTest drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 14:23 JobArray1 drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 14:42 JobArray2 drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 15:20 JobDependencies drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 Matlab drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 MPI drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 OpenMP drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 PETSc drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 PI drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 precision drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 PSE drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:15 Python drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 R drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 ScaLapack drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:45 SerialJob drwxr-xr-x 9 fuji hpcstaff 4096 Aug 21 13:06 SimpleExample drwxr-xr-x 5 fuji hpcstaff 4096 Aug 21 13:06 SLU40 drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 TestCodes drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 uBLAS drwxr-xr-x 3 fuji hpcstaff 4096 Aug 21 13:06 VTK [tulaneID@cypress1 ~]$
mkdir
Create new directory.
[tulaneID@cypress1 ~]$ cd testdir -bash: cd: testdir: No such file or directory [tulaneID@cypress1 ~]$ mkdir testdir [tulaneID@cypress1 ~]$ cd testdir [tulaneID@cypress1 testdir]$ pwd /home/tulaneID/testdir [tulaneID@cypress1 testdir]$
rm
Remove files and directories. CAUTION: THERE IS NO UNDOING THIS COMMAND.
[tulaneID@cypress1 ~]$ rm hpc-workshop
If you would like to remove a directory and all of its contents use the following command:
[tulaneID@cypress1 ~]$ rm -ri hpc-workshop rm: descend into directory `hpc-workshop'? y rm: descend into directory `hpc-workshop/PI'? n rm: descend into directory `hpc-workshop/uBLAS'? ^C [tulaneID@cypress1 ~]$
ctrl+c to exit.
The r flag specifies to remove files/directories recursively. i specifies to prompt before deleting each file.
If you are confident with the command line and your understanding of file locations you can use the f flag instead of i to force deletion of all files without prompting:
[tulaneID@cypress1 ~]$ rm -rf hpc-workshop [tulaneID@cypress1 ~]$ ls hpc-workshop ls: cannot access workshop: No such file or directory [tulaneID@cypress1 ~]$
Do this again to download sample files:
git clone https://hidekiCCS@bitbucket.org/hidekiCCS/hpc-workshop.git
rmdir
Removes directories. CAUTION: THERE IS NO UNDOING THIS COMMAND AS WELL.
The rmdir is a safer approach than using rm -r as it will only act on empty directories.
[tulaneID@cypress1 ~]$ ls NextDirectoryDown/ file.txt [tulaneID@cypress1 ~]$ rmdir NextDirectoryDown/ rmdir: failed to remove `NextDirectoryDown/': Directory not empty [tulaneID@cypress1 ~]$ rm NextDirectoryDown/file.txt [tulaneID@cypress1 ~]$ rmdir NextDirectoryDown/ [tulaneID@cypress1 ~]$ ls [tulaneID@cypress1 ~]$
cp
Copy file to new location. CAUTION: THERE IS NO UNDOING THIS COMMAND AS WELL - SEE ALSO OPTIONS -i and -n.
In the example below sourcefile already exists, and destinationfile may or may not exist and will become a copy of sourcefile.
[tulaneID@cypress1 ~]$ cp sourcefile destinationfile
To copy a directory and all of its contents we use the recursive flag -r:
[tulaneID@cypress1 ~]$ cp -r sourcedir destinationdir
Take note of the order here: source first, destination second. This is the standard order across most *nix commands.
mv
Move a file to a new location. CAUTION: THERE IS NO UNDOING THIS COMMAND AS WELL - SEE ALSO OPTIONS -i and -n.
[tulaneID@cypress1 ~]$ mv file1 file2 [tulaneID@cypress1 ~]$ ls file1 ls: cannot access file1: No such file or directory [tulaneID@cypress1 ~]$ ls file2 file2 [tulaneID@cypress1 ~]$
Unlike cp, the mv command does not create a second instance of the file or directory.
cat
Print the entire contents of a file (short for conCATenate).
[tulaneID@cypress1 ~]$ cat daysofweek.txt monday tuesday wednesday thursday friday saturday sunday [tulaneID@cypress1 ~]$
tail
Displays lines from the end of a file. Useful for viewing recent results in an output file.
[tulaneID@cypress1 ~]$ cat animals dog Dog cat Racoon DOG bullfrog Little Doggie [tulaneID@cypress1 ~]$ tail -3 animals DOG bullfrog Little Doggie [tulaneID@cypress1 ~]$
The -f flag can be used to tail a file interactively. New additions to the end of the file will be printed to your screen.
head
head is much like tail, except it prints from the top of a file.
[tulaneID@cypress1 ~]$ head -2 animals dog Dog [tulaneID@cypress1 ~]$
more
more is like cat, except it prints the file one page at a time. The spacebar is used to continue on to the next page.
less
less is like more, except it handles large files more efficiently in memory and supports a bit more flexibility in file navigation.
zmore, zless
zmore and zless are the counterparts of more and less, respectively, for viewing files (with extension .gz) compressed via gzip.
(See also man gzip.)
which
which <command name> tells the location of the named command.
[tulaneID@cypress1 ~]$ which zless /usr/bin/zless [tulaneID@cypress1 ~]$
Basic Linux Commands Exercise
Lets take a break from lecture to practice some of the commands we've just learned
Not So Basic Linux Commands
Star Wildcard
Shell commands can often make use of the wildcard characters. The most universal of these is the asterisk or star wildcard, *. This acts as a stand-in for any and all strings.
ls again
Suppose we have a directory containing many files, but we only want to list files ending with the .txt extension. We can use the * wildcard to request a list of any file ending in .txt
[tulaneID@cypress1 ~]$ ls a.out NextDirectoryDown helloworld.c textfile01.txt textfile02.txt [tulaneID@cypress1 ~]$ ls *.txt textfile01.txt textfile02.txt [tulaneID@cypress1 ~]$
Additionally, the behavior of the ls command can be modified by the addition of option flags. By default ls does not list any "hidden" files and subdirectories. To display all files and subdirectories one must add the -a flag.
[tulaneID@cypress1 ~]$ ls -l total 4 -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 a.out drwxr-xr-x 2 tulaneID workshop 4096 Aug 18 21:37 NextDirectoryDown -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 helloworld.c -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 textfile01.txt -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 textfile02.txt [tulaneID@cypress1 ~]$ ls -al total 56 drwx------ 6 tulaneID workshop 4096 Aug 18 20:03 . drwxr-xr-x 5 root root 4096 Aug 12 13:00 .. -rw------- 1 tulaneID workshop 107 Aug 18 16:59 .bash_history -rw-r--r-- 1 tulaneID workshop 18 Jul 18 2013 .bash_logout -rw-r--r-- 1 tulaneID workshop 176 Jul 18 2013 .bash_profile -rw-r--r-- 1 tulaneID workshop 124 Sep 30 2014 .bashrc -rw-r--r-- 1 tulaneID workshop 500 May 7 2013 .emacs drwxr-xr-x 2 tulaneID workshop 4096 Nov 11 2010 .gnome2 -rw-r--r-- 1 tulaneID workshop 171 Aug 6 2014 .kshrc drwxr-xr-x 4 tulaneID workshop 4096 Aug 6 2014 .mozilla drwxr-xr-x 2 tulaneID workshop 4096 Aug 18 16:17 NextDirectoryDown drwx------ 2 tulaneID workshop 4096 Aug 13 16:18 .ssh -rw------- 1 tulaneID workshop 1786 Aug 18 20:03 .viminfo -rw------- 1 tulaneID workshop 54 Aug 13 16:18 .Xauthority [tulaneID@cypress1 ~]$
quota
Display disk quotas.
The '-s' flag translates the output into a readable format. If your blocks column is equal to or greater than the quota column, you have exceeded your available disk space.
[tulaneID@cypress1 ~]$quota -s
Disk quotas for user tulaneID (uid 12345):
Filesystem blocks quota limit grace files quota limit grace
master.10ge.cluster:/home
6459M 10000M 10000M 23260 250k 250k
master.10ge.cluster:/share/apps
6459M 10000M 10000M 23260 250k 250k
[tulaneID@cypress1 ~]$
There are two storage spaces for users on cypress, home directory and Lustre group project directory.
grep
Find text in a file. grep will return every line in the file that matches your search term.
[tulaneID@cypress1 ~]$ cat animals dog Dog cat Racoon DOG bullfrog Little Doggie [tulaneID@cypress1 ~]$ grep dog animals dog [tulaneID@cypress1 ~]$
Use the -v flag to print out every line excluding those containing the search term. Notice that "dog" (lowercase) is missing from the results.
[tulaneID@cypress1 ~]$ grep -v dog animals Dog cat Racoon DOG bullfrog Little Doggie [tulaneID@cypress1 ~]$
The -i flag will search without case-sensitivity.
[tulaneID@cypress1 ~]$ grep -i dog animals dog Dog DOG Little Doggie [tulaneID@cypress1 ~]$
The -i and -v flag can be combined to exclude all lines containing the search term regardless of capitalization.
[tulaneID@cypress1 ~]$ grep -iv dog animals cat Racoon bullfrog [tulaneID@cypress1 ~]$
find
Searches for files in a directory hierarchy. The find takes a directory as an argument and will search in that directory and all of it's subdirectories for files that match the search criteria. If no directory is specified, the current directory is used.
You can search for a file by name using the -name flag as your search criteria
[tulaneID@cypress1 ~]$ find /home/tulaneID/ -name file1.txt /home/tulaneID/dir1/file1.txt [tulaneID@cypress1 ~]$
One can also search for all files that have a string of text in any portion of their name by using the star wildcard, e.g. we can find all the .txt files in our HOME directory and it's subdirectories. Note that quotes are required around our criteria as we are now using a wildcard.
[tulaneID@cypress1 ~]$ find /home/tulaneID/ -name "*.txt" /home/tulaneID/textfile02.txt /home/tulaneID/dir1/file1.txt /home/tulaneID/examples/alphabet.txt /home/tulaneID/examples/numbers.txt /home/tulaneID/textfile01.txt [tulaneID@cypress1 ~]$
These are just a couple examples of the many ways find can be used. A nice short tutorial on find with a lot of examples can be found at http://alvinalexander.com/unix/edu/examples/find.shtml
Pipe ( | )
The pipe command, |, takes the output of one command and passes it to another. For example we could "pipe" the output of cat to grep in order to search a file for a particular string
[tulaneID@cypress1 examples]$ head -5 numbers.txt | grep 1 01 [tulaneID@cypress1 examples]$
I/O Redirection ( >, >> and < )
Redirect input or output. CAUTION: THERE IS NO UNDOING THE REDIRECT OVERWRITE > COMMAND.
The redirect output operator, >, takes the output (see man stdout) of a command and redirects it to a file. For example we could "redirect" the output of grep above to a file in order to capture the results of the above search
[tulaneID@cypress1 examples]$ head -5 numbers.txt | grep 1 > grep.out [tulaneID@cypress1 examples]$ cat grep.out 01
The redirect append output operator >> does the same as > except the former APPENDS whereas the latter OVERWRITES the output to the specified file.
The redirect input operator < is used for redirecting input
[tulaneID@cypress1 examples]$ cat < grep.out 01
history
Displays the command history list with line numbers. You can add an optional integer, n, argument to display only the last n commands
[tulaneID@cypress1 examples]$ history 2 299 cat numbers.txt | grep 1 300 history 2 [tulaneID@cypress1 examples]$
Note: history, |, and grep when used together are a powerful combination as they allow you to search for old commands that you may not remember the exact syntax for:
[tulaneID@cypress1 examples]$ history | grep chmod 153 chmod u+x myscript.sh 204 chmod +x myexecutable.sh 271 chmod +x myscript.sh 273 chmod -x myscript.sh 301 history | grep chmod [tulaneID@cypress1 examples]$
chmod
The chmod commands allow a user to modify the permissions of files and directories that they own. To see the permissions of a file/directory we can use the ls -l command
[tulaneID@cypress1 ~]$ ls -l total 4 -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 a.out -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 helloworld.c -rw-r--r-- 1 tulaneID workshop 0 Aug 19 07:15 myscript.sh drwxr-xr-x 2 tulaneID workshop 4096 Aug 18 21:37 NextDirectoryDown -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 textfile01.txt -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 textfile02.txt [tulaneID@cypress1 ~]$
The ten left most characters describe your permissions. The first character describes the file type (- for a file, d for a directory). The next three describe the permissions for the user who owns the file, the middle three describe the permissions for the group that owns the file, and the last three describe the permissions for "others". The "r" denotes permission to read, the "w" means permission to write, and the "x" indicates permission to execute the file/directory.
The change mode or chmod command allows us to alter those permissions. In the past one had to remember (or google) numeric codes that corresponded to permission states, but modern syntax allows for the addition and subtraction of permissions with greater ease. Now one needs only indicate whose permissions to change and what changes to make. For example, let's add executable permissions for the user to the file myscript.sh
[tulaneID@cypress1 ~]$ chmod u+x myscript.sh [tulaneID@cypress1 ~]$ ls -l total 4 -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 a.out -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 helloworld.c -rwxr--r-- 1 tulaneID workshop 0 Aug 19 07:15 myscript.sh drwxr-xr-x 2 tulaneID workshop 4096 Aug 18 21:37 NextDirectoryDown -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 textfile01.txt -rw-r--r-- 1 tulaneID workshop 0 Aug 18 21:50 textfile02.txt [tulaneID@cypress1 ~]$
The user (and only the user) can now run the script myscript.sh as an executable. For a more complete introduction see http://alvinalexander.com/linux-unix/linux-chmod-command-permissions-file-directories
