You have a limited amount of space in your home directory (/home) of only 10 GB. You will get a warning when you reach 9 GB, and will not be able to write any more files after 10 GB.

Your home directory is to be used only for storing your software, analysis scripts etc.

To store the output of simulations, please use one of the /projects directories. There are 12 /projects directories, one for each of the BrisSynBio projects;

• /projects/s11 : Space for the S1.1 project
• /projects/s12 : Space for the S1.2 project
• /projects/s13 : Space for the S1.3 project
• /projects/s21 : Space for the S2.1 project
• /projects/s22 : Space for the S2.2 project
• /projects/s23 : Space for the S2.3 project
• /projects/s31 : Space for the S3.1 project
• /projects/s32 : Space for the S3.2 project
• /projects/s33 : Space for the S3.3 project
• /projects/t1 : Space for the T1 project
• /projects/t2 : Space for the T2 project
• /projects/t3 : Space for the T3 project

Each project has 3.5 TB of total space. There will be a warning at 3.0 TB, and then no more files can be written once 3.5 TB has been reached.

You can check how much space has been used and your remaining quota by typing

• pan_df -h /directory e.g.
• pan_df -h /projects/s11

In addition to the project space, there is 9 TB available in /scratch. This is for use only by running jobs, and old files in /scratch will be deleted. This is shared by everyone using BlueGem, so please make sure that you don't fill it up! Note that you have to have a user account that is in the  "synbio" group to be able to use /scratch (this should be nearly everyone who has a BlueGem account). If you cannot write to /scratch and think you should be allowed, please email Christopher.Woods and ask to be added to the "synbio" group. To check if you are a member of the "synbio" group type "groups" to list all of your group memberships.

Every node in the cluster has a local disk, that is mounted on /local. This provides about 800 GB of space. This is only to be used by jobs that are running on that node, and any data will be deleted after the job has finished.

Finally, all of the disks that are available to BlueCrystal Phase 3 are also available on BlueGem. These are mounted on

• /panfs/panasas01

e.g. /panfs/panasas01/chem/chzcjw is the home directory  on BlueCrystal Phase 3 of the chemistry user chzcjw. You can read and write to the BlueCrystal Phase 3 disks,  so if your work does not fit into any of the synbio projects, then feel free to use your BlueCrystal Phase 3 home directory.

Also, all of the BlueGem disks are mounted and available on BlueCrystal Phase 3. These are also mounted on /panfs/panasas01, and are called "bluegem-SOMETHING", e.g. "bluegem-home" contains all of the home directories, "bluegem-s11" contains the S1.1 project directory and "bluegem-scratch" contains the /scratch directory. You can read and write to these directories from BlueCrystal Phase 3, and are welcome to run jobs on BC3 that write to these disks.