Getting Started

Getting Started
Access to the LI-red cluster login node using the command-line from any modern workstation is available using secure shell (SSH). In Linux or MacOSX, simply ssh to the Handy login node by issuing the command:

ssh -X username@handy.iacs.stonybrook.edu

If you are using Windows, you will need to use a utility such as PuTTY.

The login node provides an external interface to the Handy compute cluster. The login node is for developing and compiling source code, preparing submission scripts for the batch queue, submitting and monitoring jobs in the batch queue, analyzing results, and moving data. It is NOT appropriate for running computational jobs - to do this use the batch queue. If necessary, interactive batch session can be requested via the "qsub -I" command. 

Storage
On the Handy cluster, data storage is a finite resource. Anticipating that people in the future will need space for their data, we will allot storage space as the demand arises, when requests for storage beyond the default amount are submitted through the OSTicket system: https://iacs.supportsystem.com.

Home Directory
Each user is given 20 GB of disk space for their home directory, which is only accessible by them. This space is backed up. The home directory for user jsmith is /gpfs/home/jsmith.

Scratch
In addition to the home directory, users have access to a scratch file space. This scratch file space is intended to be used when users need to run jobs that produce a large amount of temporary data. However, it is not intended for long-term data storage. For this reason, files older than 30 days will be automatically deleted. The scratch space for the user jsmith is /gpfs/scratch/jsmith. The limit is 20TB/user.

Project space
In addition to the user home space, projects can also request persistent storage which can be shared by all members of the project. Project space for the “Smith Project” can be found in /gpfs/projects/smith.

The default project space is 100GB. A project can ask for up to 5TB of space by submitting a request describing:

• The size of the data
• How it will be used/processed (e.g., software, how often it is accessed, bandwidth requirements, etc.)
• The duration of storage (the high-performance disk on the cluster is expensive and it is a waste of resources for it to be used as an archive)
• Confirmation that the user understands that this data is not backed up and therefore backing up data and the integrity of the data is the sole responsibility of the user

 Requests for more than 5TB will require more detail and if granted will likely only be satisfied for a specific period of time. 

HIPAA Policy
Handy has not been approved for HIPAA data or any data associated with privacy or liability concerns. Consequently, use of this system to process ePHI or other data that falls under the purview of HIPAA and privacy guidelines is in violation of the act.

Software environment

https://it.stonybrook.edu/help/kb/understanding-li-red-modules

Batch Queue System

https://it.stonybrook.edu/services/high-performance-computing#faq-section-related-9916

Queues