Page Comparison

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There are two sub-directories under the /stor/work/CBRS_unix directory: fastq and unix, each with their own sub-directories and files. Again, notice how tree colors file with the extension .gz differently. These are FASTQ files produced by a Next Generation Sequencing (NGS) run in our Genome Sequencing and Analysis (GSAF) core facility.

Note that in Unix, and on Macs, directories are separated by forward slash ( / ) characters, unlike Windows where the backslash ( \ ) is used. And the root of all the file systems is that 1st forward slash.

Finding file systems

So if you're on a new system, how do you know what file systems are available to you? The df (disk free) command will list all the available file systems. As its name suggests, it also shows file system sizes, so it's always good to use df -h (human readable) so we to see sizes in more readable form. Also, there can be many many file systems available on any given system, so always pipe the output to more.

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Fortunately, you can ignore most of it. Focus on the Mounted on and Size columns.

• Under / (forward slash), under the Mounted on column:
  • / (forward slash) is  is the root of the file system where the operating system is installed
  • Note its Size is 98G with 47G used
• Look for Mounted on entries with large Size numbers:
  • Gigabytes (10^{^9} bytes), Terabytes (10^{^12} bytes), Petabytes (10^{^15} bytes)
• Ignore file systems with names like /run, /dev, /snap, /sys, /boot, /tmp, /var – these are system related
• Here we see a number starting with /stor (/stor, /stor/home, /stor/work, etc.)
  • Note its large Size: 39T - a sign that it's a file system you want to know about.

Here's a similar listing from the Lonestar5 compute cluster at TACC:

Image Added

Here the big important file systems are /home1 (7.0T), /scratch (8.1P) and /work (6.8P). There's also /admin (3.5T) but its name suggests that normal users won't be able to access it.

Navigating the file system

Now that we know there are other places, how do we get there? Enter the cd (change directory) command:

• cd <optional directory_name>
  • with no argument, always changes to your Home directory.

There are also some "special" built-in directory names:

• ~ (tilde) means my Home directory
• . (single period) means the current directory
• .. (two periods) means the parent of the current directory (directory above it)
  
  • So ls .. means "list contents of the parent directory"

So these two expressions do the same thing – take you to your Home directory from wherever you are in the file system.

cd
cd ~

Pathname wildcards ("globbing")

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