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International HPC Summer School 2015

The sixth International Summer School on HPC Challenges in Computational Sciences is now accepting applications for this summer’s session, which will be held June 21-26, 2015, in Toronto, Canada. Graduate students and post-docs from Canada, Europe, Japan, and the U.S. are invited to apply. The...

This two part tutorial will first introduce you to the concept of interactive high performance computing, as distinct from batch computing. We will cover the Citrix (Windows) and NICE EnginFrame (Linux) interactive computing environments hosted by MSI.

New Director for MSI

MSI is very happy to report that Jorge Vinals has accepted the offer to become the next MSI Director. He will also become a professor of physics. Jorge will assume the directorship on August 1, 2010. Jorge is currently the director of CLUMEQ, a Canadian Supercomputing Center led by McGill...

Modeling Efficient Organic Photovoltaic Cells

Abstract: 
<h4>Modeling Efficient Organic Photovoltaic Cells</h4><p>The quest for higher efficiency organic photovoltaic cells (OPVs) is dependent on furthering the current understanding of fundamental device physics. At the heart of OPV operation is the diffusion of bound electron-hole pairs, or excitons, and their dissociation into free charge carriers at a donor-acceptor interface. The characteristic length an exciton can diffuse is called the diffusion length (LD). Knowledge of LD for OPV active materials of interest allows for intelligent device design where no excitons are generated more than a diffusion length away from a donor-acceptor interface. There are currently no methods available for the direct measurement of LD, instead one-dimensional models describing exciton motion with the diffusion equation are used to connect a value of LD to experimental data. Further complicating matters, not all device designs can be understood by the simple 1-D diffusion equation. This project seeks to create three-dimensional models of exciton diffusion at the molecular instead of device level. By employing the Monte Carlo method, exciton diffusion at the molecular level can be modeled by a series of energy transfer events between molecules instead of as diffusion across an active layer. The rates of energy transfer events are described by photophysical parameters which are easily obtainable for the OPV active materials of interest. The better understanding of exciton diffusion enabled by this work will guide the development of future high-efficiency OPVs.</p>
Group name: 
holmesr

Critical Phenomena in Topologically Ordered Systems

Abstract: 
<h3 class="red">Critical Phenomena in Topologically Ordered Systems</h3><p>The aim of this research project is to improve understanding of certain types of phase transitions that cannot be described by the standard (Landau) paradigm typically used to study phase transitions across which a symmetry is broken. Specifically, these researchers are studying a family of lattice Hamiltonians which can realize transitions between phases of differing topological order. Since topological order is not described by any local order parameter, the analytical techniques applicable in the symmetry-breaking case fail, and numerical studies are crucial in understanding these systems&#39; behaviors. Simultaneously, they are exploring the (often complex) phase diagrams of these systems. The primary tools currently employed for these studies are high-order perturbative series expansion methods, and Lanczos exact diagonalization.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/1cc2e28f3824d6f817830c6f988700a7/10685">main page</a>.</p>
Group name: 
burnellf

September 2011

A "jet in cross-flow" is a jet of fluid that exits an orifice to interact with the surrounding fluid that is flowing "across" the orifice. The term "high-speed jets in crossflow" implies that either the jet or the crossflow is supersonic. These are very complex flows, as shown in the image above...

High-Performance and Big Data Research

Abstract: 
<h3 class="red">High-Performance and Big Data Research</h3><p>This group&#39;s research during 2015 focused on the development of parallel shared-memory graph partitioning, ordering, and clustering algorithms that use the multilevel paradigm. Graph partitioning is used widely for parallel task scheduling and data distribution. Graph ordering is used reducing the amount of computation and memory required for sparse direct numerical methods. Graph clustering is a widely used technique for discovering relationships between data points by creating groups of unconstrained size with high internal connectivity. Access to MSI&#39;s HPC resources has been critical in the development of these algorithms as evaluating the scalability of the algorithms requires machines with a large number of compute cores, and many of the graphs/matrices in these domains reach massive size, requiring large amounts of memory.</p><p>The group&#39;s work in 2016 focuses on developing hybrid shared/distributed memory codes that can effectively utilize compute architectures composed of many multicore nodes. This work will be an extension of the researchers&#39; past work on shared and distributed memory graph partitioning, ordering, and clustering. Part of this will include ensuring their methods scale to very large numbers of processing cores. These methods will be required for partitioning, ordering, and clustering problems on the next generation of large petascale and exascale machines, which will have millions of processing cores.</p><p>Return to this PI&#39;s <a href="https://www.msi.umn.edu/pi/589311b8db5db9b82645320a8036047e/16200">main page</a>.</p><p>&nbsp;</p>
Group name: 
karypisg

Simulation modeling in HIV prevention intervention research

Abstract: 
<h4>Simulation Modeling in HIV Prevention Intervention Research</h4><p>This researcher is involved in two simulation-intensive projects in the area of HIV prevention intervention research.</p><p>Project one is a benchmarking analysis that is investigating optimal ways of using data from HIV seroconverter panels to estimate Mean Duration of Recent Infection (MDRI). The benchmarking exercise is simulating large numbers of datasets to run under various models to compute MDRI. This modeling exercise requires both MATLAB and R to execute the simulation code. Computing MDRI is critical in the development of assays for determining recency of infection, and therefore to have implementable ways for assessing HIV incidence without using logistically difficult and costly longitudinal cohort recruitment in resource poor settings where HIV prevalence is high.</p><p>Project two involves a simulation investigation of predicting, using longitudinal CD4 measurements, time to reaching a treatable CD4 threshold level (i.e. a CD4 measurement at which antiretroviral treatment can be initiated). The data are from a large household survey conducted in Botswana. The researcher is generating simulated datasets to investigate the performance of the prediction methods when time of seroconversion of the HIV infected person is unknown. These investigations make use of Bayesian inferential methods which are computationally intensive, and would be assisted by computational resources capable of quickly executing a large-scale simulation exercise.</p>
Group name: 
lynchm

MSI PIs on Team Winning Breast Cancer Challenge Award

MSI PIs Chad Myers , an associate professor in the Department of Computer Science and Engineering , and Carol Lange , a professor at the Masonic Cancer Center , are on the interdisciplinary team that has won one of the two Grand Prizes in the National Cancer Institute ’s Up for a Challenge (U4C)...

IGV

Software Description: 

The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.

Software Support Level: 
Secondary Support
Software Access Level: 
Open Access
Software Categories: 
Software Interactive/GUI: 
No
General Linux Documentation: 

To run this software interactively in a Linux environment use the commands:

module load igv
igv.sh

You can also launch IGV, a Java application, on your own computer by visiting the IGV homepage (user registration is required.

IGV has a selection of genomes pre-loaded.  If you are using your own computer you will need to move your bam file(s) to your own computer too.  An alternative method is to login to a MSI computer with NX client and enter the following command in a terminal: 

isub -q lab

Then, start a web browser, log in to Galaxy, and save your bam file(s) into a scratch folder if you just need them temporarily, or save them to your project space folder if you want to save them long term.  Files left in scratch folder will be deleted automatically after two weeks.

 
Additional Information

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