MSI Users Bulletin – September 2021

The Users Bulletin provides a summary of new policies, procedures, and events of interest to MSI users. It is published quarterly.

MSI Users pipeline information

1. MSI Operations:

MSI staff are now working under a hybrid model; not all staff are working on-site. The Help Desk is staffed Monday - Friday, 9 a.m. - 4 p.m. Tutorials continue to be held remotely (see below for details).

All MSI systems are operational and can be accessed remotely. To request technical assistance with your MSI account, contact the Help Desk:

  • In-person visit: 587 Walter Library
  • Email:
  • Phone: 612-626-0802
  • Online Support Request Form
  • Video consultation

2. Agate Update:

a. An article about Agate appeared on the OVPR’s Inquiry blog in late July: Revealing the Invisible: New Supercomputer Equipped to Find Meaning in Data.

b. Agate is undergoing burn-in testing and benchmarking by the manufacturer. Construction in the data center is underway. We expect delivery by mid-October, with initial production capability by the end of 2021. We will update the Agate page on the MSI website with information as it becomes available. 

Initial data test groups are currently onboarding, and the report from the third-party audit is being prepared.

4. Core Dumps:

The ability for users to create “core dumps” has been re-enabled; they remain off by default. A core dump is essentially a snapshot of what was in computer memory when a running program was halted by an interrupt. They are mostly used by people who are writing their own code, using these files as input to advanced tools like debuggers. Core dumps can be quite large in size, so if you don’t have a need for them, we recommend you not enable their creation.

Instructions for enabling core dumps can be found on our website.

5. Scratch Storage:

We have had performance problems with the Panasas scratch storage. The problems have also been found at other customers, and Panasas will be issuing a fix in their next release. We are working with the users who are experiencing problems; anyone having issues should contact

6. Planet Labs:

The University of Minnesota recently signed a deal with the commercial satellite data company Planet Labs for an Enterprise Account to access their data. This account gives the users at the U of M access to a substantial part of Planet's data holdings. U-Spatial is administering the account for the U of M; more information is available on their website.

MSI is developing training materials for MSI users who want to use their data within MSI’s HPC environment. If you’re interested in using this resource, see the following:

7. Fall Tutorials:

The Fall 2021 tutorial schedule is posted on our website.

Some tutorials will be held live online via Zoom classrooms. For others, we will host Q&A sessions (held on Zoom) to discuss questions about video tutorials on our YouTube channel. The procedures for each tutorial are posted on the individual tutorial pages.

8. Software Carpentry:

Registration is now open for four free Software Carpentry workshops this fall. Software Carpentry workshops are hands-on events that cover core computational research skills to be productive as an individual scientist or in small research teams. These workshops offer graduate students, staff, and faculty practical exercises on basic computational research skills. No previous experience is needed and each workshop is taught by experienced researchers who use these tools in their own work. This is an excellent opportunity to learn about tools that will help your research process become more efficient, rigorous, and reproducible.

The Fall 2021 workshops are being held via Zoom.

9. UMII-MnDRIVE PhD Graduate Student Assistantships:

The application period for the 2022 UMII-MnDRIVE PhD Graduate Assistantship Program is open. This program supports U of M PhD candidates pursuing research at the intersection of informatics and any of the five MnDRIVE areas: Robotics, Sensors and Advanced Manufacturing; Global Food Ventures; Advancing Industry, Conserving Our Environment; Discoveries and Treatments for Brain Conditions; and Cancer Clinical Trials.

PhD candidates are eligible to apply. Graduate students are expected to have successfully completed their preliminary oral exam by the start of the appointment. The application deadline is October 1, 2021, at 5:00 pm CDT. To submit an application and see complete program information, visit the MnDRIVE-UMII Informatics PhD Graduate Assistantship Program on the UMII Research Funding Portal. Log in with your U of M credentials (preferred) by selecting “UMN Login” from the Login dropdown, or create a SM Apply account to access the application. 

10. noRth 2021 Conference:

Intermediate and advanced users of R are invited to attend the virtual noRth 2021 Conference on September 29 and 30. R is a multifunctional, open source tool used to do data visualization, statistical analysis, and data science across diverse sectors, fields, and industries. Getting the most out of R requires constant learning and skill development because it is always changing. The noRth Conference brings R users from the Upper Midwest together to share expertise, develop skills, and connect with one another. The conference is sponsored by the Institute for Research in Statistics and Its Applications and the School of Statistics in the College of Liberal Arts. Information and registration can be found on the conference website.

11. Oklahoma Supercomputing Symposium 2021:

The 20th annual Oklahoma Supercomputing Symposium will be held online on Wednesday, September 29, 2021, 8:00 a.m. - 5 p.m. CDT. This symposium is free. Complete information and registration are available on the symposium website.

12. Programming and Pizza:

Experienced programmers from Libraries, Liberal Arts Technology and Innovation Services, and Research Computing are available to help you out with your programming issues. Sessions are 30 minutes long and will continue to be virtual through the fall semester. See the schedule and sign up.

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