Volume 10, Number 3, September 2013

University of Minnesota
Supercomputing Institute
Users Bulletin

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

1. Project Space Taken Offline, Sep 15: The old project space (/project) was taken offline on September 15. Users should have migrated their data to the new high-performance storage space. You can see more information on the Primary Storage Migration webpage, in the "Project Space" section. Please contact help@msi.umn.edu with any questions.

2. Bioinformatics - New Location for Genome Indices: To accommodate the retirement of the /project filesystem, genome indices for applications such as Bowtie and BWA and other reference data currently hosted at /project/db have been copied to /panfs/roc/rissdb. MSI users who use these datasets for command-line data analysis will need to update their PBS scripts to point to the new location. Galaxy users are not affected by this change. More details are available on the RISSdb page on the MSI website.

3. RISS to Present Services and Demos at UMGC GenoFest 2013: On September 19, the University of Minnesota Genomics Center will host a celebration of genomic technology at its new location, the Cancer and Cardiovascular Research Building, in the Biomedical Discovery District. The focus of the morning sessions will be on technology advances and the afternoon session will focus on informatics and analytical solutions. MSI-RISS will present  the analytical services and resources it offers to the research community. Analysts will also be at the MSI booth to answer questions and provide quick demos. The bioinformatics demo session will continue the next day on Friday, September 20, from 9:00 a.m. - 1:00 p.m. The schedule and registration information can be found on the GenoFest webpage.

4. Changes to MSI Account Information: As part of the IT alignment initiative at the University, MSI accounts will be changed to align with UMN accounts. During the upcoming renewal period, we will be asking all users to change their MSI account information to their UMN Internet ID (formerly known as X.500). Once we have activated this process, you will be able to make the update through your MyMSI Profile page. We will require that the profile update process be completed before January 1, 2014. Further information will be sent out during the renewal process.

5. Additional SU and Storage Allocations Due Oct 1: The deadline for submitting requests for additional SUs and storage for the remainder of 2013 is October 1. Email notifications for requesting additional SUs/storage have been sent out to PIs and Group Admins. If you would like to request additional SUs or storage space beyond your current allocations for the rest of the calendar year, please follow the instructions provided in the email. If you have not received the notification, please email the Research Programs Administrator at rpa@msi.umn.edu.

6. Annual Account Renewal Deadline, Nov 1: The deadline for annual MSI account renewals is November 1. PIs and Group Administrators will receive email notifications about the opening of the renewal process. Information about the process can be found on the Access Renewals page of the MSI website.

7. Intel Default Module Updates: Users interested in the planned updates to the Intel default modules can now find information about this topic on the Updating Intel Software page on the MSI website.

8. MSI User Forums: MSI now has, in additional to the main MSI User Forum, a specialized forum for Fluids, Structures, and Fields. This forum is a way for researchers to exchange ideas and ask questions on numerical modeling of a wide variety of physical and biological systems, including fluid dynamics, material and structural analysis, and calculation of thermal, concentration, and electromagnetic fields. Users can request membership to both this forum and the main forum through the Forums page of the MSI website or from the UMN Google Groups menu.

9. Vendor Town Hall Meetings: As part of the ongoing selection process for the next HPC system at MSI, we have been holding Town Hall-style meetings with a number of HPC vendors. The vendors give presentations about their systems and are available for questions from users. The final two Town Hall Meetings are shown below:

  • HP, September 17, 9-12, in 402 Walter (agenda)
  • IBM, September 20, 10-1, in 402 Walter (agenda)


10. Workshop on HPC Needs and Supercomputing Procurement: Itasca, MSI's flagship HPC system has finished its third year of service and planning has begun to purchase a new supercomputer. On October 1, MSI will hold a workshop where members of the MSI user community will give presentations about future HPC needs in their disciplines. Brief discussion will follow each presentation. The workshop will begin at 10:15 in 402 Walter Library and will run until 12:00. The agenda is:
10:15 - 10:25: Introduction (Jorge Vinals/Jeff McDonald, Minnesota Supercomputing Institute)
10:25 - 10:45: GPUs and related software (David Morse, Chemical Engineering and Materials Science)
10:45 - 11:05: Analysis Needs for Neuroimaging Research in Psychiatry (Kelvin Lim, Psychiatry)
11:05 - 11:25: presentation (Graham Candler, Aerospace Engineering and Mechanics)
11:25 - 11:45: Storage and Memory Requirements for Modern Applications of DNA Sequencing (Peter Morrell, Agronomy and Plant Genetics)
11:45 - 12:00: presentation (tentative) (Angus MacDonald, Psychology)

11. Upcoming Tutorials:
PETSc Tutorial: MSI will hold a tutorial about PETSc, a suite of data structures and routines for the scalable parallel solution of scientific applications, on September 30. The tutorial will be taught by one of the authors, Dr. Matthew G. Knepley of the University of Chicago. This is an all-day tutorial (9-4, with a break for lunch). A complete description of the tutorial and an instructor bio can be found on the MSI website. Registration instructions can be found on the tutorial webpage
b. Fall Tutorials: Upcoming tutorials for the fall are posted on the MSI website Tutorials page

12. Software Renewals and Discontinuations: In order to align software resources to the needs of researchers, MSI’s software working group regularly reviews software at MSI. The Software Renewal page contains information about which software packages are coming up for renewal and which ones will not be renewed. You can also provide feedback and requests for MSI software purchases.

13. Useful Email Addresses:
- For technical assistance with your account, please contact the Help Desk: help@msi.umn.edu
- Address for submitting citations for articles, papers, posters, book chapters, and other publications supported in whole or in part by MSI resources: submissions@msi.umn.edu
- Address for submitting videos of your research or suggestions for research articles: videoclips-articles@msi.umn.edu