MSI Users Bulletin – December 2019

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

To request technical assistance with your MSI account, please contact contact the Help Desk via email at, by phone at 612-626-0802, or using the online Support Request Form.

1. Mangi: Mangi, the expansion to Mesabi, is currently in pre-production and is being tested by MSI staff. The projected go-live date is Wednesday, January 8, 2020.

  • Mangi Hardware Overview: Mangi will add 164 AMD EPYC nodes, doubling the number of cores in Mesabi. The majority of the new nodes will have 256 GB of memory and 128 cores, and a smaller subset (10) will have 2 TB of memory. In addition to these nodes, MSI has also installed 15 nodes with a total of 40 NVIDIA V100 GPUs. More hardware information can be found on the Mangi webpage.
  • Mangi Queue Configuration: Mangi will be split into eight different queues. The full specifications of the Mangi Queues can be found on the MSI Queues webpage. Mangi jobs will use PBS scripts similar to Mesabi but may require different modules loaded. 
  • Software on Mangi: Most of the software that is currently used on Mesabi will work on Mangi. Software compiled with Intel, IMPI, or MKL may break or have performance issues. If you have software built against Intel, IMPI, or MKL, please rebuild the software against the GNU or AMD toolchain. Also, software packages developed for Mesabi's K40 GPU queue will need to be rebuilt for Mangi's V100 GPU queue.

If you have questions, need assistance preparing your research software, or need help with other tasks related to onboarding to Mangi, please contact the Help Desk via email at, by phone at 612-626-0802, or using the online Support Request Form. Also, once Mangi is live, if you find broken modules, please email

2. Interactive Queue: MSI has created and released a Mesabi Interactive Queue. The purpose of this queue is to increase the availability of nodes for interactive use and to replace the interactive resources available in the LabQi Cluster. The queue can be used in real-time for tasks such as interactive data exploration, creating plots or images, visualizations, or testing sections of code that will be used on other MSI queues.

Several basic examples of how to request an interactive HPC job of the Mesabi Interactive Queue can be found in the news story about the queue release.

Full specifications of the Mesabi Interactive Queue, including those for Mangi, are found on the MSI Queues webpage.

More examples on how to use qsub -1 for interactive use can be found on the Interactive queue use with qsub page.

3. Decommissioning of Itasca and Lab: With the activation of Mangi and the interactive queue, MSI will soon be decommissioning older assets:

  • Itasca will be taken offline on Wednesday, January 8, 2020.
  • The LabQi Cluster will be shut down and decommissioned on Wednesday, February 5, 2020.

If you have any questions about how your work will be affected, contact the Help Desk via email at, by phone at 612-626-0802, or using the online Support Request Form.

4. Research Exhibition 2020: Save the date! The annual MSI Research Exhibition will be held on April 28, 2020. This event will include a poster competition, a panel discussion on careers in high-performance computing, industry presentations, visualization demos, and tours.

The Call for Posters will be sent out in early February. The event webpage will be updated as information becomes available.

5. Visualization Lab: The LCSE-MSI Visualization Lab (LMVL) is available to all MSI users. It is set up for high definition presentations and interactive graphical analyses of very large or complex systems and data through the use of high performance networking, storage, and computational resources. It is designed to be used in the following modes:

  • Data Exploration: Interactive exploration of very large and complex volumes of data using HPC resources together with very high-end graphical analyses.
  • Beta-testing: Development and demonstration of novel software, hardware, and networking applications.
  • Presentation: Pre-generated high resolution slides and movies to be viewed by groups of up to 40 people.

More information can be found on the LMVL webpage. You can reserve the LMVL using the web form linked from the webpage.

6. U-Spatial Mapping Prize: The U-Spatial Mapping Prize celebrates great design and cartography through maps. There are cash prizes awarded in several categories. The submission deadline for the 2020 prizes is May 15, 2020. Complete information and links to previous winners can be found at the U-Spatial website.

7. Grant Opportunity Available: The Consortium on Law and Values in Health, Environment & the Life Sciences is issuing a call for proposals addressing the societal implications of problems in health, environment, or the life sciences to law, graduate, and professional students for work during the upcoming summer (2020) and/or academic year (2020-21). 

A total of $35,000 is available for these grants with a maximum award of $7,000. Proposals for student-initiated programs or colloquia will also be accepted. Proposals are due by February 10, 2020.  

Please see the Consortium website for further information, deadlines, and application instructions. This funding opportunity is open to all law, graduate, and professional students. Reports on completed projects can be found on the Research Awards webpage. Topics vary widely. 

8. University of Minnesota Day of Data: Many people and groups across the University of Minnesota are developing interesting approaches to data, methods, and workflows, but don’t always get a chance to share work across departments and units. The U of M Day of Data helps you connect with other data enthusiasts to share and learn from each other. All experience levels are welcome.

Morning coffee and lunch will be provided. Free, but registration is required. Live-streaming will also be available. More information and registration can be found on the event website.

9. 2020 DMD Conference: Registration for the 2020 Design of Medical Devices Conference opens in January 2020. The conference will be held at the Graduate Hotel on the University of Minnesota Twin Cities campus in Minneapolis on April 6-9, 2020. Complete information can be found on the conference website.

10. Spring Tutorials: The spring tutorial schedule will be posted on the Events Calendar on the MSI website in January 2020.

Tutorials are also live-streamed on the MSI YouTube channel. Tutorials can also be viewed on the channel afterwards.

11. 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. Programming and Pizza sessions are held monthly at the Wilson Research Collaboration Studio (first floor, Wilson Library). Sessions are free, but you must sign up. The schedule for the spring semester will be available on the DASH website in January 2020.

12. Jobs at MSI:

a. Bioinformatics Analyst

b. Scientific Computing Consultant

c. Systems Administrator (multiple positions available)

13. Useful Webpages: Looking for help with using MSI? One of these pages may have the information you need:

a. Services available at MSI

b. Getting Started (includes Quickstart Guides)

c. MSI Systems

d. Systems Status

e. Software at MSI

f. Software License Reservations

g. Help and Documentation

h. MSI Glossary

i. Staff Listing and Areas of Expertise

j. Upcoming Events and Tutorials

k. Proposal Support