Upcoming Maintenance for Summer 2023

The RCD team has planned a scheduled maintenance window for the Palmetto Cluster between Monday, July 10th and Friday, July 14th, 2023. Users should expect the cluster to be unavailable during this time, and any jobs running when maintenance begins will be cancelled.

We’ll be working on:

• Introducing a new mini-cluster as a test for the SLURM scheduler, which will replace PBS on Palmetto during a future maintenance window.
• Updating configuration on compute nodes to improve I/O performance to the Indigo data lake.
• Preparing for the end-of-life for /scratch1 and /fastscratch, which is planned for July of 2024.
• Upgrading infiniband drivers to improve stability and NVIDIA drivers to support newer versions of CUDA.

New Senior Research Facilitator Joins RCDE

Fanchen Meng, PhD joins the Research Computing and Data, Engagement (RCDE) team as a Senior Research Facilitator.

RCDE Announces Summer 2023 Workshop Series

The RCDE team is excited to announce our Summer 2023 workshop series! We have 12 workshopsplanned, which are offered for free to any interested Clemson University students, faculty, or staff members.

Our series will cover various high-performance computing, machine learning, and software development topics. Here’s a summary of what we’ll cover:

• Introduction to Linux
• Introduction to Research Computing on Palmetto
• Advanced Research Computing on Palmetto
• Introduction to Python Programming
• Data Processing and Visualization in Python
• Introduction to R Programming
• Introduction to Big Data Analytics using Spark and Python
• Introduction to Git Version Control with GitLab
• Machine learning in Python (sklearn)
• Machine learning in R (caret)
• Introduction to Deep Learning in PyTorch
• Advanced Deep Learning in PyTorch

You can learn more about the details of each workshop, the schedule, and registration links on the upcoming live training sessions page of our documentation site.

Register today through our online system to secure your spot!

You may register up to three weeks in advance, but we ask that you cancel your registration if you can’t attend since space is limited. We also encourage you to join us in person for the best interactive experience, but some workshops have virtual attendance options if you need to join us remotely.

New Executive Director for RCD Infrastructure

Scott Groel was named the new Executive Director for Research Computing and Data, Infrastructure (RCDI) on May 1st, 2023. This follows the retirement of Corey Ferrier, who served at Clemson for 25 years, and operated the Palmetto Cluster since its inception in 2008.

New Associate Vice President for RCD

Jill Gemmill, PhD was named the new Associate Vice President for Research Computing and Data (RCD) on April 1st, 2023.

Scratch Storage Update

An issue with the metadata servers caused an outage for /scratch1 and /fastscratch, starting on March 16th, 2023. Our storage architects have worked diligently this afternoon to re-initialize the /scratch1 and /fastscratch file systems.

While working on this issue, we have also brought our new /scratch storage system online. This is a new all-flash storage system that will be the new primary scratch storage space for Palmetto for the forseeable future.

All scratch file systems are now back online and available for use across the cluster.

However, we encourage users to continue using /scratch for their temporary storage needs. We plan to retire /scratch1 and /fastscratch during a future maintenance period, but no definitive retirement date has been set.

New GitLab Service

We have created a new GitLab instance at git.rcd.clemson.edu. This service will help researchers with code storage, version control, continuous integration, and continuous delivery needs.

If you want to learn more and get started, review our GitLab documentation.

RCD Invites Users to Join Our Mattermost Chat Server

We welcome users to our new Mattermost chat server at chat.rcd.clemson.edu. This server operates similarly to Slack and provides a way to collaborate with other researchers to share ideas and best practices. Various channels already exist to help us start the conversation.

If you’d like to join, please follow our Mattermost sign-in instructions on the documentation.

New RCD Documentation

On Mach 8th, 2023, the RCDE team deployed our new documentation site is hosted at docs.rcd.clemson.edu. This site will permanently replace the old documentation at palmetto.clemson.edu.

The new site was developed to make information easier to find and keep the information accurate. We hope you enjoy the modern appearance and vastly improved documentation search.

Palmetto Now Benchmarks at 3 Petaflops!

During the winter maintenance, our infrastructure team ran the HPL linpack benchmark to ensure proper operation of the cluster after the maintenance on compute nodes was performed, and also to verify the hardware stability of compute nodes. The team was able to achieve a score of 3.01 PetaFLOPS during this testing.

Cluster Maintenance for Winter 2022

The RCD team performed scheduled maintenance on the Palmetto Cluster between December 21st and 23rd, 2022. The following changes were made:

• We have patched and rebooted all compute nodes; firmware has been updated.
• We have updated firmware and OS versions on all network switches.
• We have updated BeeGFS.
• We have installed new optimized versions of OpenMPI and new versions of software that depend on OpenMPI. The old versions were not modified and will remain installed until everyone can migrate to the new optimized versions.

New Nodes Added to Palmetto

Clemson University has funded the purchase of additional compute resources for the Palmetto Cluster. The infrastructure team has added 40 new nodes with 2x 32-core CPUs, 256GB of RAM, and 2x NVIDIA A100 GPUs to the cluster. These resources will be for shared use by the Clemson research community.

RCD Town Hall on December 15, 2022

The Research Computing and Data (RCD) group held a town hall on Thursday, December 15, 2022 from 2-3 p.m via Zoom. We shared with the community our new team structure, new node additions to Palmetto, new flash storage system, and our future goals.

Resulting from the community’s input, we have made the following changes:

• The units named “CITI” (user support) and “ACI” (infrastructure support) have been eliminated.
• The newly formed “Research Computing and Data” (RCD) division in CCIT combines RCD Engagement (formerly CITI) and RCD Infrastructure (formerly ACI) into one group to better serve the research community and to streamline operations.
• RCD Infrastructure (RCDI) is led by Corey Ferrier and is responsible for installing, operating, and maintaining the research computing hardware infrastructure, including the Palmetto HPC cluster and data storage.
• RCD Engagement (RCDE) is led by Jill Gemmill and is responsible for research computing user support including training, application installation, and one-on-one help with using the research computing facilities. RCDE also includes the Center for Geospatial Technologies.
• RCD is expanding the Palmetto HPC support team and adding new support services for Cloud Computing, Machine Learning, Data Science, and regulated data such as PHI and CUI.
• Clemson has invested $6M for a new data lake storage system, new Palmetto nodes, improved hardware for ArcGIS software, specialized machine learning nodes, and systems for secure use and analysis of regulated research data (such as PHI/HIPAA and Controlled Unclassified Information).

For more details, please review the slide deck and webinar recording of the town hall (Clemson login required).