Users have access to both a shared home directory as well as local scratch storage on each cluster node.

Note: Home directories and scratch space are not backed up.

Home Directory
Your home directory is stored on a central storage server and shared over the network to all cluster nodes. By default each home directory has a quota of 250GB storage. If you need more space, contact us and we will try to accommodate you.
Scratch directory
Each cluster node has a directory called /scratch which all users may write to. The scratch directory resides on a node’s local disk and ranges from 60GB to 130GB in size, depending on the node.
Transferring files
Files may be transferred to your home directory on the cluster via the scp command, various point-and-click apps, or by the following network path: \\\yourusername.
scp command
The scp command is available by default in Mac OS X and Linux. Windows users may transfer files using the network path described next. To transfer a file from your computer to your home directory on the cluster, run a command like the following from the Terminal application on your Mac or Linux PC.
scp file1.txt
Similarly, to copy a file from the cluster to your computer, run a command like the following from the Terminal application on your Mac or Linux PC.
Graphical file transfer apps
In addition to transferring files via the scp terminal command, a variety of graphical SCP/SFTP applications allow transferring files to and from the cluster.

File Naming

Avoid spaces and special characters in file names. While supported, they make dealing with file names from the command line more complicated. Naming your files with only alphanumeric characters, underscores ( _ ), and dashes ( - ) will ensure your file names are compatible and easy to manage.

Text File Formats

Text files, such as Perl, Python and job submission (qsub) scripts, must be formatted with Unix compatible line endings. Text files created on MS Windows platforms are not created in this format by default and may cause problems. When working in a MS Windows environment, do not create or edit scripts or other text files with MS Word, WordPad, or Notepad as these programs will not save files in the correct format.

How to determine and set a text file’s format

The free Notepad++ application for Windows, and TextWrangler for Mac will display a text file’s current format, and can easily switch from one format to another.

Notepad++ will display the format in the lower right as either “Dos\Windows” or “UNIX”.

To convert a text file to Unix format

  1. Select “Edit
  2. EOL Conversion”
  3. Choose “UNIX/OSX Format”
  4. Save the file.

Similarly, TextWrangler will display a text file’s current format as either “Unix (LF)” or “Windows (CRLF)” at the bottom of the screen. Clicking on the current format will allow you to convert to a different one.

From the command line

You can also convert a text file to Unix format from the HPC command line with the dos2unix command:

dos2unix my_qsub_file.txt