This page describes the filesystem structure on the SCC as well as commands for basic navigation and file manipulation on the system. We also have a Getting Started Reference Sheet (PDF) which we recommend you print out, look over, and keep available as a reference. This has a variety of information that will likely be useful to all new SCC users, whether experienced with Linux or not. More detailed information about the cluster is available on our System Usage page.

Filesystem Structure

The Linux filesystem starts at the “root” (/) and extends forward into directories that can contain both subdirectories and files. A series of decending directories can be strung together separated by slash characters (“/”) to indicate a location on the filesystem. This string of folders is called a “path” and will look like /project/projectname/subfolder/file.  This structure is much like that on other common operating systems. More detailed information about the filesystem on the SCC can be found here, but an overview of the most common locations is detailed below.

Location Description
/usr#/university_status/username Each user has a “home directory,” this is the directory you are put in when you first log in each session.
/project/projectname Backed up Project Disk Space is backed up to another location each night.
/projectnb/projectname Not backed up (“nb”) Project Disk Space.
Note: For BUMC users with dbGaP restricted datasets, the /project/ and /projectnb/ shares are located in /restricted/project/project_name/ and /restricted/projectnb/project_name/.

Working with Files/Directories

Below are some simple examples of basic Linux commands for accessing and changing your files and directories. For all of these commands, you can run man command_name to see the manual page (system documentation) on the command, including explanation of available command line options.

  • Show the current “full path”, the directory you are in with its parent and all levels of grandparents up to the root directory (/):
    scc1% pwd
  • Create a file:
    scc1% touch myfile
    This command will create a blank file named myfile. You will also want to be able to use an editor to create or modify an existing text file. A simple graphical editor to use is gedit, but more complex editors like emacs and vi are also available.
  • Create a new directory:
    scc1% mkdir newdir
  • List the files, including other directories, in the current directory:
    scc1% ls newdir

    There are many options to the ls command such as ls -l to list the files in the current directory in “long” (verbose) format such as:

    scc1% ls -l newdir
    total 0
    drwxr-xr-x 3 adftest2 adftest 512 Oct 28 16:03 newdir

    The letters on the left (“drwxr-xr-x”) indicate the “permissions” of this file/directory. The “d” indicates that it is a directory. The next 9 characters indicate that is is “readable”, “writable”, and “executable” by you and “readable” and “executable” by both the members of your project group and the world. The commands you can use to change these “permissions” are chmod and umask.

  • Move and/or rename a File
    scc1% mv myfile newdir/newfilename

    This command will move the file myfile into the directory newdir and simultaneously rename it to be called newfilename.

  • Move to a different directory:
    scc1% cd newdir

    Move to the newly created newdir directory. You can also specify a “full path” (a path that starts with a /) such as cd /usr/local/bin. Typing just cd (or cd .) by itself will always take you to your home directory.

  • Copy a file
    scc1% cp newfilename filecopy

    This command will make a copy of newfilename in the file filecopy. You can copy entire directories by using the -r (recursive) option.

  • Delete a file
    scc1% rm filecopy
    rm: remove regular empty file `filecopy'? y

    By default you will be asked to confirm that you want to remove a file by typing y when asked. You could avoid this by using the command line option -f but then you must be much more careful. Empty directories are removed using the command rmdir directory_name. Full directories can be removed by again using the -r (recursive) option to rm.

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