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New Storage System on Itasca

The Minnesota Supercomputing Institute (MSI) is happy to announce that it has added 550 TB of usable disk space for its flagship Itasca system with the addition of a Dell | Terascala HPC Storage Solution (HSS). This is a complete Lustre appliance including hardware, file system and the Terascala...

What are some user-friendly ways to use Second Tier Storage via S3?

Before getting started, you will need to fetch your s3 credentials . The s3 credentials act like a username and password for graphical interfaces to There are several graphical clients that support S3 and that make transferring files as easy as dragging and dropping. These clients...

How can my programs interface with Second Tier Storage?

Application Programming Interface (API) Support for S3 Access For advanced tasks or in writing your own software, you may want to interact with Second Tier Storage directly through the S3 programming API. Libraries exist to do this from many programming languages. boto is a useful Python library...

Data-Storage Case Study

The Active Archive Alliance has released a case study about MSI’s Spectra Logic file archive system. The case study can be found on the linked page under the "University of Minnesota" header. The Active Archive Alliance is a collaborative industry association dedicated to educating users about...

Brain Imaging With Serial Optical Coherence Scanning


Brain Imaging With Serial Optical Coherence Scanning

These researchers are developing an optical imaging technique called serial optical coherence scanning (SOCS) that will be used for studying brain anatomy. The research will enable a comprehensive three-dimensional reconstruction of the brain and cerebellum, and support quantitative assessments on white matter content and organization.

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Facilities Overview (Full)

Established in 1983, the Minnesota Supercomputing Institute (MSI) is the University of Minnesota's principle center for computational research. MSI provides services to over 560 active groups that sponsor more than 3,300 unique users from 19 different university colleges, maintaining an array of...

PacBio SMRT Analysis Portal

The PacBio Single Molecule Real Time (SMRT) analysis portal is an easy-to-use web-based platform for analyzing 3rd generation sequencing data generated from the PacBio SMRT platform. Currently, workflows for microbial whole genome assembly, resequencing analysis, transcriptome analysis and various data processing steps are available through the portal. For more information on the analysis portal itself, see and the tutorial materials . The software must be run from a browser in the MSI network. This can be achieved via connection through the NICE interface , or by...

Gamma Ray Astrophysics; Zooniverse Crowdsourcing Science


Gamma Ray Astrophysics; Zooniverse Crowdsourcing Science

The Fortson research group is focused on two main research areas, each of which can require MSI resources.

  • Gamma Ray Astrophysics: VERITAS is an array of four imaging atmospheric Cherenkov telescopes (IACTs), located at the F. L. Whipple Observatory in southern Arizona. The array has been detecting extraterrestrial gamma rays since 2007. In order to properly calibrate the results, large amounts of simulation and data processing are required. In addition to VERITAS, the next-generation gamma-ray experiment CTA, with a factor of 10 improvement in sensitivity over existing arrays, is finalizing development of its low-level systems. One key system is the triggering and event building stage, which collects and associates information from telescopes spread over several square kilometers.  

    The Fortson group at UMN has responsibilities for both VERITAS and CTA development. For VERITAS, they produce a large fraction of the simulations necessary for calibrating the instrument and performing analysis on the data. More processing capability allows them to explore a larger parameter space of observational conditions. Different atmospheric humidity and aerosol content between summer and winter require them to repeat these simulations. Another important example of the importance of simulations is to track the performance as the array hardware is upgraded.

    For CTA, the group is developing a novel use of self-assembly algorithms to generate a self-annealing event building architecture. These algorithms are meant to better cope with the high data rate and correspondingly high failure rates. These failures include network errors, timing errors, and other hardware errors. The ability of the CTA event builder to correctly identify the information associated with a particular gamma-ray atmospheric shower is vital to the success of this large-scale project.

    Supercomputing resources are also required for running NASA Fermi LAT gamma-ray analysis. Typically this is run in several stages depending on the data products required such as counts maps, test statistic maps, spectra and light curves. For example, to perform a standard binned analysis on a single gamma-ray source (using all the photons collected by the Fermi satellite to date) this typically requires about 2GB of disk storage space with memory usage between 2 to 4GB using approximately 15 CPU hours. This example is for a Log Likelihood analysis of an object situated away from the Galactic plane where the relative number of nearby Fermi sources is smaller and the diffuse background emission low. For an object on or close to the Galactic plane the same analysis could easily take 30 CPU hours depending on the number of sources to be included in the Log Likelihood fit. For data products such as a test statistic map which can only be generated once the standard analysis is complete, this requires significantly longer CPU hour usage e.g. ~168 CPU hours. This is because a maximum likelihood computation is performed on each and every pixel in the requested map. Typically, computing jobs using the Fermi LAT analysis tools are submitted serially to a batch management system.  The group expects to analyze several dozen Fermi LAT sources this year.

  • The Zooniverse is the world’s largest online citizen science platform and several members of the Fortson group are involved in the development and analysis of Zooniverse project data. It is likely that the Fortson group will need to use MSI resources about two-three times during 2016 to batch process hundreds of thousands of images in preparation for their upload to the Zooniverse site.

This PI's work in translational informatics and the Zooniverse project was featured in an MSI Research Spotlight in November 2014.

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MSI Users Bulletin – March 2016

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 . 1. User Accounts: MSI is making changes that will consolidate user accounts and...