Manipulating Files
Source repo: basic_skills | Branch:
hpc-training-doc| Last synced: 2026-04-24 10:27:17.425 UTC
Overview
This section will show you more ways to manipulate files: copying, listing, deleting and renaming, and examining contents
Creating files with touch
In the section above, we created files using the touch commmand, which will create a file with no contents. First we'll return to the first testdir using the full directory path:
[username@login01 testdir2]$ cd /home/username/testdir
[username@login02 testdir]$ touch myfile1.txt
[username@login02 testdir]$ touch myfile2.txt
[username@login02 testdir]$ ls -l
total 21
drwxr-xr-x 2 username abc123 4 Jul 17 20:53 .
drwxr-x--- 9 username abc123 25 Jul 17 20:49 ..
-rw-r--r-- 1 username abc123 0 Jul 17 20:53 myfile1.txt
-rw-r--r-- 1 username abc123 0 Jul 17 20:53 myfile2.txt
Copying files with cp
To copy a file from another directory to the current directory, use the full path. In this example, we will copy the filelisting.txt file from the directory above, using the .. ("dot-dot") variable for the directory location:
[username@login02 testdir]$ cp ../filelisting.txt .
[username@login02 testdir]$ ls -l
total 11
-rw-r--r-- 1 username abc123 322 Jul 17 21:09 filelisting.txt
-rw-r--r-- 1 username abc123 0 Jul 17 20:53 myfile1.txt
-rw-r--r-- 1 username abc123 0 Jul 17 20:53 myfile2.txt
Renaming files with mv
To rename a file, use the mv (move) command:
[username@login02 testdir]$ mv myfile2.txt newfile.txt
[username@login02 testdir]$ ls -l
total 11
-rw-r--r-- 1 username abc123 1543 Jul 17 21:09 filelisting.txt
-rw-r--r-- 1 username abc123 0 Jul 17 20:53 myfile1.txt
-rw-r--r-- 1 username abc123 0 Jul 17 20:53 newfile.txt
Deleting files with rm
To delete a file, use the rm (remove command):
[username@login02 testdir]$ rm myfile1.txt
[username@login02 testdir]$ ls -l
total 10
-rw-r--r-- 1 username abc123 1543 Jul 17 21:09 filelisting.txt
-rw-r--r-- 1 username abc123 0 Jul 17 20:53 newfile.txt
-rw-r--r-- 1 username use300 1410 Jan 18 00:00 sdsc.txt
Examining file contents
You can examine the contents of a file by using several Linux commands. First, we'll create a small file for testing:
[username@login01 testdir]$ ls -al > dirlist.txt
[username@login01 testdir]$ ls -al
total 88
drwxr-xr-x 2 username use300 5 Jan 17 23:49 .
drwxr-x--- 51 username use300 93 Jan 17 23:46 ..
-rw-r--r-- 1 username use300 284 Jan 17 23:49 dirlist.txt
-rw-r--r-- 1 username use300 322 Jan 17 23:42 filelisting.txt
-rw-r--r-- 1 username use300 0 Jan 17 23:42 newfile.txt
-rw-r--r-- 1 username use300 1410 Jan 18 00:00 sdsc.txt
To print out the contents of the entire file, use the cat command (cat - concatenate files and print on the standard output):
[username@login01 testdir]$ cat sdsc.txt
The San Diego Supercomputer Center (SDSC) was established as one of the nation’s first supercomputer centers under a cooperative agreement by the National Science Foundation (NSF) in collaboration with UC San Diego and General Atomics (GA) Technologies. SDSC first opened its doors on November 14, 1985.
For more than 35 years, it has grown and stewarded its national reputation as a pioneer and leader in high-performance and data-intensive computing and cyberinfrastructure. Located on the campus of UC San Diego, SDSC provides resources, services and expertise to the national research community including industry and academia.
Cyberinfrastructure refers to an accessible, integrated network of computer-based resources and expertise, focused on accelerating scientific inquiry and discovery. With Voyager and Expanse, SDSC’s latest supercomputing resources, the center supports hundreds of multidisciplinary programs spanning a wide range of science themes—from earth sciences and biology to astrophysics, bioinformatics and health IT.
SDSC participates in Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) and was a partner in eXtreme Science and Engineering Discovery Environment (XSEDE), two of the most advanced collections of integrated digital resources and services in the world.
For general inquiries and comments: info@sdsc.edu
SDSC website: www.sdsc.edu
note
The contents of a file may be too large to see at one time, to see how large it is we can run the wc, word count command:
[username@login01 testdir]$ wc ../README.md
644 4531 30519 ../README.md
The output says that README file has 644 lines, 4531 words, and 30519 characters.
We might want to look at the beginning (head) or end (tail):
[username@login01 testdir]$ head -n 1 sdsc.txt
The San Diego Supercomputer Center (SDSC) was established as one of the nation’s first supercomputer centers under a cooperative agreement by the National Science Foundation (NSF) in collaboration with UC San Diego and General Atomics (GA) Technologies. SDSC first opened its doors on November 14, 1985.
[username@login01 testdir]$
[username@login01 testdir]$ tail -n 2 sdsc.txt
For general inquiries and comments: info@sdsc.edu
SDSC website: www.sdsc.edu
Sorting and searching file contents
You can reorder the contents of a file using the sort command:
[mthomas@login01 testdir]$ sort sdsc.txt
Cyberinfrastructure refers to an accessible, integrated network of computer-based resources and expertise, focused on accelerating scientific inquiry and discovery. With Voyager and Expanse, SDSC’s latest supercomputing resources, the center supports hundreds of multidisciplinary programs spanning a wide range of science themes—from earth sciences and biology to astrophysics, bioinformatics and health IT.
For general inquiries and comments: info@sdsc.edu
For more than 35 years, it has grown and stewarded its national reputation as a pioneer and leader in high-performance and data-intensive computing and cyberinfrastructure. Located on the campus of UC San Diego, SDSC provides resources, services and expertise to the national research community including industry and academia.
SDSC participates in Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) and was a partner in eXtreme Science and Engineering Discovery Environment (XSEDE), two of the most advanced collections of integrated digital resources and services in the world.
SDSC website: www.sdsc.edu
The San Diego Supercomputer Center (SDSC) was established as one of the nation’s first supercomputer centers under a cooperative agreement by the National Science Foundation (NSF) in collaboration with UC San Diego and General Atomics (GA) Technologies. SDSC first opened its doors on November 14, 1985.
The sort command is useful for sorting through a long file and reording data.
To search a file for a string you can use the grep command:
[mthomas@login01 testdir]$ grep -ni SDSC sdsc.txt
1:The San Diego Supercomputer Center (SDSC) was established as one of the nation’s first supercomputer centers under a cooperative agreement by the National Science Foundation (NSF) in collaboration with UC San Diego and General Atomics (GA) Technologies. SDSC first opened its doors on November 14, 1985.
3:For more than 35 years, it has grown and stewarded its national reputation as a pioneer and leader in high-performance and data-intensive computing and cyberinfrastructure. Located on the campus of UC San Diego, SDSC provides resources, services and expertise to the national research community including industry and academia.
5:Cyberinfrastructure refers to an accessible, integrated network of computer-based resources and expertise, focused on accelerating scientific inquiry and discovery. With Voyager and Expanse, SDSC’s latest supercomputing resources, the center supports hundreds of multidisciplinary programs spanning a wide range of science themes—from earth sciences and biology to astrophysics, bioinformatics and health IT.
7:SDSC participates in Advanced Cyberinfrastructure Coordination Ecosystem: Services & Support (ACCESS) and was a partner in eXtreme Science and Engineering Discovery Environment (XSEDE), two of the most advanced collections of integrated digital resources and services in the world.
9:For general inquiries and comments: info@sdsc.edu
10:SDSC website: www.sdsc.edu
In the command above, we used the grep -ni argument to get the line number, and to ignore case.