Research Computing

Research Computing at South Dakota State University

Jeffrey Doom, ME, Turbulent impinging jet in crossflow performed on RT (600 cores)
Jeffrey Doom, ME, Turbulent impinging jet in crossflow performed on Roaring Thunder (600 cores)

About SDSU Research Computing

South Dakota State University offers support for research computing through Research Computing, part of the Division of Technology and Security.  

Research Computing (RC) currently manages the fastest High Performance Computing (HPC) cluster in the state of South Dakota.  The current cluster, Roaring Thunder, or Thunder for short, currently provides HPC resources across 65 nodes and 2800 cores.  Thunder runs on the CentOS operating system and supports over 300 open-source computational applications and frameworks such as R, Python, C/C++ code with MPI, and a multitude of bioinformatics applications.  SDSU also holds a campus site license for MATLAB. The research computing support staff, including domain specialists, can assist users in configuring and running their jobs on the clusters.

Roaring Thunders' login node, rt.sdstate.edu, is the main development and job submission node of the cluster.  From this system, one can run small test jobs and develop the submission script files necessary to run on the worker nodes of the cluster.  Thunder resources are managed by SLURM, an open source simple Linux utility for resource management.

A job is run on a worker node by submitting the script file to SLURM scheduler, where the job is queued for the next available node(s) necessary to run the job.  Two common scenarios for cluster use are high-throughput, where different data sets are run on many nodes or processors at once, with each job processing different data, and parallel computing, where a single job is split up and run on many nodes at once.

"Roaring Thunder" Linux Cluster

In fall of 2018, the new SDSU Linux cluster, "thunder", became operational. The system is housed in the Admin building (Morrill hall) data center and consists of 56 compute nodes, 5 big memory nodes, 4 NVIDIA GPU nodes (V100/P100), and a 1.2 PB high performance GPFS parallel file system.

Roaring Thunder Linux cluster
Roaring Thunder cluster. photo: SDSU Collegian/Brookings Register

In the picture shown, the 1.2 PB DDN GPFS parallel file system is at the top of the rack on the left. The larger nodes are the specialty nodes (gpu or high memory), the main enclosures for the compute nodes (4 nodes per enclosure) are near the bottom of both racks.

Single Node HPC Compute Resources

Research computing supports over 100 Linux and Windows servers in additional to the Thunder cluster.  These servers provide access to resources that span all disciplines across campus.  

Most recently, two servers were added to provide access to bioinformatics applications and GPU applications.  Prairie Thunder (PT) is a 160 core (with HT), 3TB of memory system that supports non-cluster applications like CLC Genomics Workbench.  Iris is another 160 core (with HT), 3TB of memory with 4 NVIDIA V100 GPU's connected via NVLink that supports our Artificial Intelligence and other GPU workloads.  

Prairie Thunder and Iris are two additional standalone nodes which use the same storage as "Thunder" so moving between the two is seamless.

Access to the research nodes requires a cluster account. 

Please see Getting Connected for connection instructions.

Data Storage Services

Storage solutions are available to enable researchers to securely store and share data in a collaborative environment. Faculty can purchase multiple terabytes of space, as needed, and can utilize Globus Online, a fast and powerful file transfer service, for moving large files to and from the HPC systems.

Support