Table of Contents
CIRCE Tutorial: MUST WATCH THIS!!!
A new user should be able to establish herself/himself by following this tutorial video (https://youtu.be/5Bpk_vnxM60 ) and documentation (Using_CIRCE.pdf).
--Both files are produced by Matias Casas and Robert Moncrief
Information on CIRCE
CIRCE is the "Central Instructional and Research Computing Environment”. CIRCE is USF's on-campus research cloud computing cluster. A computing cluster is set of connected computers that work together. USF's Research computing maintains the CIRCE cluster. We use CIRCE to gain access to over 422 nodes (computers used as a server) with over 8,400 processor cores. CIRCE uses a Lustre parallel file system for fast I/O, and InfiniBand for a computational interconnect.
Why We Use CIRCE
We utilize the processing power of CIRCE to store data, run memory-intensive scripts, and schedule scripts to be ran automatically.
We deploy memory-intensive and time-dependent scripts that we would otherwise not run on our personal computers. These scripts include automatic data collection scripts, intermittent data cleaning procedures, and various forms of analysis (such as complex sentiment analysis, and OTHER EXAMPLES). CIRCE is capable of scheduling and deploying scripts written in various languages; these languages include R, Python, and BASH. When scheduling either a memory-intensive or time-dependent script, researchers must use BASH shell scripts to send scheduling instructions to Research Computing. Requests are put into a queue and the CIRCE Cluster executes those requests on a first-come-first-serve basis.
CIRCE is also home to our data, which is stored in a shared folder. After an approval process, all lab members have the authority to access this data. The shared folder contains our datasets and programming scripts.
Requesting Access
In general, Dr. Hagen will ask students to join CIRCE for specific project. If you want to work using CERCE, you MUST contact Dr. Hagen to receive a permission to apply to CERCE.
Once you've been granted permission, request access by sending an email from your official USF email address:
- TO: rc-help@usf.edu
- CC: Dr. Hagen
- SUBJECT: "CIRCE Account Request"
- BODY: Provide Dr. Hagen's name and email address.
Connection Methods
Once approved, you have many methods to connect with CIRCE. You can read about different methods to connect and access data here.
Linux -- Interactive Interface
If you have never remotely accessed another machine before, Research Computing recommends the free remote desktop called X2Go. It can be installed here. Instructions are located here. This linux-based remote desktop can run on Windows, MacOS, and Linux. It provides a virtual machine that runs on your computer where you can execute normal computer operations; these operations include using a file explorer, drag and drop, copy/paste, connecting to the internet with Firefox, and deploying programming scripts. The image to the right shows the X2Go client launched on a Windows 10 computer.
- Session Type: MATE
- Host: circe.rc.usf.edu
- Login: Your USF NetID
- SSH Port: 22
SSH -- Terminal or CMD
A Secure Shell (SSH) client allows you to access and run scripts on CIRCE without a remote desktop. These clients are an option if you need to schedule or run scripts and prefer not to rely on X2Go. If you are using macOS or Linux, you can SSH into CIRCE directly through the built-in Terminal. On Windows, you will need to use an SSH client (such as PuTtY) or a virtual machine (if you prefer to work in Linux). The image to the right shows the Ubuntu Linux Distribution loaded in Virtual Box on a Windows 10 computer.
- Credentials: Your USF NetID and Password
- Hostname: circe.rc.usf.edu
- SSH Port: 22 (This is the default)
- Example Command Line: ssh NetID@circe.rc.usf.edu
FTP -- Move data to/from local machine to CIRCE
A File Transfer Protocol (FTP) client allows you to access CIRCE without a remote desktop. These clients are an option if you only need to move data to/from your local machine. A FTP client will not allow you to run scripts. Cyberduck is an FTP client available for macOS. WinSCP (shown on the right) is a popular FTP client for Windows. This client displays your local machine on the left and your target machine (CIRCE) on the right. The FTP interface allows you to easily drag/drop files across computers.
- Protocol: SFTP
- Host: circe.rc.usf.edu
- Login: Your USF NetID
- SSH Port: 22
How to Use Storage on CIRCE
Once approved, you should gain access to atleast 2 partitions (home and work)
Home Directory (250 GB of storage):
- Path: home/first_initial/first_initial_last_name
- Example: home/d/ddyson
Work Directory (2 TB of storage):
- Path: work/first_initial/first_initial_last_name
- Example: work/d/ddyson
Shares Directory (shared cluster):
- Path: shares_bgfs/si_twitter
How to Use Scripts on CIRCE
Running jobs:
There are many ways to run scripts with linux. Here we will discuss three methods.
Requesting Resources
First you will need to request resources. DO NOT RUN SCRIPTS WITHOUT REQUESTING RESOURCES.
Demonstration: Inside X2Go
The following video launches X2Go on a macOS machine. The user connects with their usf credentials. Once connected (00:22 mark), he opens the MATE terminal on the X2Go virtual desktop. He then copy/pastes a saved SLURM request into the MATE terminal. After CIRCE allocates resources, he runs "hello world" in both R and Python.
https://youtu.be/0Q-8QFKbKdA
Demonstration: SSH through Terminal
The following video launches the native macOS Terminal. The user connects to CIRCE using SSH and their usf credentials. He then copy/pastes a saved SLURM request into the terminal, waits for CIRCE to allocate resources, then runs "hello world" in both R and Python.
https://youtu.be/g2ad1pbYk8s
- SLURM
- Batch scripts
Related
External Links
Comments (0)
You don't have permission to comment on this page.