Research Computing and Data

The RCD team has scheduled a change window to perform work on the Palmetto Cluster and Indigo Data Lake on August 15th, 2025.

All services will remain online during this time and no impact to jobs is expected.

We plan on making the following changes:

• Disable AD Lockout checking on Indigo
• Removal of legacy PBS/Torque commands – users will need to switch to native Slurm commands.
  • For assistance, users should review the PBS to Slurm migration guide.
  • List of commands that will be removed:
    • mpiexec
    • pbsnodes
    • qalter
    • qdel
    • qhold
    • qrerun
    • qrls
    • qstat
    • qsub
• The default CRAN and Bioconductor location for the R modules will be set to a private mirror hosted by RCD

Please reach out to the RCD team if you have any questions or concerns.

During the week of July 21^st, several members of Clemson’s Research Computing and Data team will be attending the PEARC’25 conference.

This year, our team has four accepted publications that we will be presenting at the conference. Below are the details for each and links to helpful resources.

Update (7/15/2025 4:18PM): The necessary changes to secure the network were made with no incident.

On Monday, July 14th, the RCDI team became aware of a Palmetto related network security vulnerability that needed to be patched.  Palmetto admins made the necessary changes around 10:50 AM after a successful test.  After this change went live, connectivity between the core Ethernet network devices dropped, causing Palmetto systems and services to go offline. Administrators worked quickly to revert the changes and systems and services started to restore by 11:45. 

The RCD team apologizes for this unanticipated service interruption.

Administrators are evaluating the changes to determine why this connectivity issue occurred, and will be scheduling a time in the future to retry the necessary changes.

Interactive jobs were terminated during this outage. Some batch jobs would have also failed during this time. Users should double-check the output of their completed jobs and resubmit if necessary.

We are excited to announce that the Spring 2025 maintenance work was completed successfully. 

All RCD services have been restored and are ready for users to access.

During the maintenance period, we completed the following:

• Critical updates to network and storage infrastructure were completed.
  • These improvements have improved performance and stability for all users of the cluster.
• Three large-memory nodes were added to the cluster. Two nodes have 3TB of memory and one node has 6TB of memory.
• More AMD Genoa nodes were added to the cluster.
• Slurm was updated to 24.11.5
• Installed AMD-optimized Compiler 5.0.0 and the following dependent modules:
  • amdblis/5.0
  • amdlibflame/5.0
  • amdlibm/5.0
  • openmpi/5.0.5
    • amdscalapack/5.0
    • lammps/20240829.1
    • osu-mircro-benchmarks/7.5
• Installed the following software:
  • gcc/14.2.0
  • intel-oneapi-compilers/2025.1.1
  • cmake/3.30.5
  • intel-oneapi-mkl/2025.1.0
  • perl/5.40.0
  • r/4.5.0
  • gromacs/gromacs-2025.1-cpu
  • gromacs/gromacs-2025.1-gpu
  • comsol/6.3
  • matlab/2025a
• Spack was upgraded to v0.23.1.
  • Users of spack will be able to install newer packages provided with this update.
  • After loading the spack module, make sure to run spack clean -a to remove old temporary build files.
• Open OnDemand was upgraded to 4.0.3
  • MATLAB application was added. This will launch a native web version of MATLAB.
  • PyMOL was added as a GUI application.
• GitLab was upgraded to v17.11.3
• ColdFront was updated to v1.15

This changelog may continue to be updated as our staff finishes their release notes.

We appreciate your patience during the maintenance period and hope that these changes will improve the user experience.

If you have any questions or have encountered post-maintenance issues, please let us know by submitting a support ticket.

The Research Computing and Data (RCD) team plans to host a Town Hall event on April 23rd, 2025 at 3 PM to share some imporant updates with the community.

Below is a summary of what we will cover:

• changes to RCD personnel
• plans for the Spring 2025 maintenance window
• new compute nodes added to Palmetto 2
• upcoming Granite environment for CUI, PHI, and NIST 800-171 (NIH) research
• updates to ReDCAT leadership
• updates to Indigo storage expiration notifications
• rollout of new Job Defense Shield tool

This event is open to all Clemson University students, faculty, and staff. Please register online if you plan to attend.

For those unable to join us, we will post the slide deck and recording here after the event. Come back for updates!

The Research Computing and Data (RCD) group in Clemson Computing and Information Technology (CCIT) is seeking interns to support Clemson’s goal to increase research capacity. Interns in this position will learn the basics of high-performance computing and will support researchers making use of advanced cyber infrastructure including the Palmetto 2 Cluster and Indigo Data Lake.

As an RCD intern, you will be responsible for supporting the RCD staff in several areas, including:

• User Support. You will provide the first line of support for researchers, triaging requests, answering the ones you are able to, and assigning others to the subject matter expert within the RCD staff.
• Documentation Updates. You will help review and test RCD user facing documentation and make updates as needed.
• Hardware Operations. When large cluster hardware changes are needed (installation or removal), you will assist the infrastructure team in the data center. This may involve lifting heavy equipment.

As interns gain more knowledge, in addition to the main support role, they will have the opportunity to work on advanced projects. The RCD staff will help match you with project topics areas such as AI/ML, software engineering, HPC software management, bioinformatics, or computational material science.

Ideal candidates should:

• have experience with Linux operating systems
• enjoy technical challenges
• have a strong work ethic
• be punctilious
• have an aptitude to learn

For more details on the position, please review our Position Description.

To apply, please use the CCIT Student Employment Application and select “RCD Intern” as the preferred position.