Storage/Data

You can store your files on your home, work, and/or scratch directory. All directories are mounted on both submit nodes and all compute nodes. Each directory is assigned a variable when you log in that you can use for quicker access to that space and reference in your scripts.

NOT BACKED UP: No data, anywhere, is backed up. We recommend using the Research File Storage for those purposes.

To see any of the information below, run the command mystats

  • Home Directory ($HOME): Your home directory is a place only you have access to. If you wish to share your data, see $WORK directory below. You have a 100 GB disk quota.

    The path to your home directory is (replace username with your KU Online ID):

    /home/username
    
  • Work Directory ($WORK): Your work directory is a shared space for you to collaborate with your group. The quota is based off how much storage the owner of the group has purchased directory or indirectly from purchasing nodes.

    To find your $WORK directory, run the command.

    /panfs/pfs.local/work/groupname/username
    

    If you do not see a $WORK, then your owner group has not bought any, and/or bought nodes in 2013, which did not have storage included:

  • Scratch Directory ($SCRATCH): Your scratch directory is a place for you to use as a temporary space for your data processing. The quota for scratch is a finite amount, but is set for the whole volume, which CRC staff will maintain.

    Files equal to or greater than 60 days old will be deleted

    To find your $SCRATCH directory, run the command.

    /panfs/pfs.local/scratch/groupname/username
    

You can use $HOME, $WORK, and $SCRATCH in you submit scripts and make it easier to get around the file systems.

cd $WORK
#MSUB -o $SCRATCH/job12/out.txt

Quota

To determine how much of your quota you are using on the Panasas file system, login and run mystats

This will produce output similar to the following:

$HOME = /home/username
<GB> <soft> <hard> : <files> <soft> <hard> : <path to volume> <pan_identity(name)>
63.63  85.00 100.00 :    3949  85000 100000 : /home/username uid:100000000(username)

$WORK = /panfs/pfs.local/work/groupname/username
Filesystem            Size  Used Avail Use% Mounted on
panfs://pfs.local/work
                      2.8T  1.7T  1.1T  61% /panfs/pfs.local/work/groupname/username

$SCRATCH = /panfs/pfs.local/scratch/groupname/username
Filesystem            Size  Used Avail Use% Mounted on
panfs://pfs.local/scratch
                       55T   37T   18T  68% /panfs/pfs.local/groupname/username

Transferring your files

There are many ways to transfer files in and out of the cluster. CRC recommends using either Globus or rsync.

  • Globus: Globus works through your internet browser, so therefore works on Windows, Linux, and MacOS.

To start using Globus, navigate to https://www.globus.org/app/transfer in your browser. From there, choose University of Kansas as your institution. You will be redirected to login with your KU ID.

You should then see a screen with two panels, if this is your first time using Globus, you'll need to set up your personal computer as a Globus endpoint.


To do this, click the link on the bottom right of the screen that says "Get Globus Connect Personal". Then follow the prompts, naming your computer, generating a key, downloading the client, and then entering the previously generated key into the client. Your computer is now an endpoint.

Back on the page with the two panels, you need to choose the two endpoints you'd like to copy between. The cluster endpoint is named KU CRC Data Transfer Node. The other endpoint will be whatever you named your computer in the previous step.

Now you should be able to see the files both on your computer as well as your cluster home directory. From here transferring is just a simple click and drag from source to destination.

 

  • rsync: rsync is a command for Linux and Mac only. It is used to transfer files back and forth using the Terminal and comes with no GUI.

You must be on KU's network or connected to KU Anywhere to access the Data Transfer Node (DTN).

The KU Community Cluster supports SCP, SFTP and Rsync for transferring files:

Host: transfer.crc.ku.edu
Port: 22

rsync -avP username@host1:~/file1 username@host2:~/file1_copy

For example, to copy a file from your home directory on your local computer (e.g., ~/foo.txt) to your home directory on the HPC, on the command line, enter (replace username with your KU Online ID username):

rsync -avP ~/foo.txt username@transfer.hpc.crc.ku.edu:~/foo.txt

 

  • SCP: Similar to rsync above, this is a command to be run in the Linux or Mac terminal. This command-line utility is included with OpenSSH.

You must be on KU's network or connected to KU Anywhere to access the Data Transfer Node (DTN).

The KU Community Cluster supports SCP, SFTP and Rsync for transferring files:

Host: transfer.crc.ku.edu
Port: 22

scp username@host1:~/file1 username@host2:~/file1_copy

For example, to copy a file from your home directory on your local computer (e.g., ~/foo.txt) to your home directory on the HPC, on the command line, enter (replace username with your KU Online ID username):

scp ~/foo.txt username@transfer.hpc.crc.ku.edu:~/foo.txt

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