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posted on September 17, 2013
The Department of Biomedical Engineering, in the College of Science and Engineering, announced recently that they had a “Summer of Grants” in their department – several of their faculty were awarded grants from various funding agencies. Some of these faculty are MSI Principal Investigators and the grants will support research that they are performing at MSI.
Professor Victor Barocas (MSI Fellow) was awarded three grants. One, from the National Institutes of Health (NIH), funds a collaborative project with the University of Pennsylvania (Philadelphia, Pennsylvania) and Rensselaer Polytechnic Institute (Troy, New York). The Barocas group will study how certain ligaments in the spine respond to normal and abnormal loads, which could eventually help us understand spinal injuries and pain. The second grant, this one from the National Science Foundation (NSF), will fund a project to determine how different structural proteins contribute to the function and dysfunction of the filtration apparatus in the kidney and could contribute to our knowledge of kidney disease. Finally, Professor Barocas received a four-year extension of NIH funding for his long-term research into the mechanical behavior of bio-artificial tissues.
Professor Barocas and his group use MSI resources for their computer models of tissues. Systems they have studied and continue to study include a collagen gel model system and co-gels of collagen with fibrin, agarose, and hyaluronic acid. The computer models are also being applied to tissues such as ligaments and blood vessels.
Assistant Professor Shai Ashkenazi received two grants this summer. The first, a grant from NIH, will fund a collaborative project with faculty from the Department of Chemical Engineering (College of Science and Engineering) and Department of Laboratory Medicine and Pathology (Medical School). This project will develop a new method for non-invasive, photoacoustic imaging of Maxtrix Metalloproteinases (MMPs) activity in tissue. MMPs are linked to cancer metastatsis, among other diseases. This method might lead to better, more individualized diagnoses and treatments for cancer patients. The second award, from NSF, will develop Optical Micromachined Ultrasound Transducers (OMUT) technology. The researchers are developing ultrasound probes for high-resolution imaging that can be mounted on the tip of a needle.
Professor Ashkenazi uses MSI resources to run molecular dynamics simulations. These simulations help the research group in their work to design molecular probes.
Assistant Professor Pat Alford received funding from NIH to study whether the changes in vascular smooth muscle cells, caused by disease or vascular stents, can result in degraded ability of those muscles to contract. Professor Alford’s group uses software available through MSI as part of their research into the mechanical properties of tissues.
Professor Dave Odde received a new grant from the National Cancer Institute, a part of NIH, for a collaborative project with the Cleveland Clinic in Cleveland, Ohio. The researchers will develop a computer simulator to show how brain cancer cells invade tissue, which may result in the creation of new therapies. Professor Odde uses MSI resources for Monte Carlo simulations of various cytoskeletal and signaling processes involved in cell division and growth.
posted on September 12, 2013
As part of the ongoing selection process for the next HPC system at MSI, MSI has invited top high performance computing vendors to present their high performance computing portfolios and roadmaps to users in a Town Hall setting.
IBM will be on-site Friday, September 20, 2013, 10:00 a.m. - 1:00 p.m., to provide presentations and have interactive discussions with MSI users. The meeting will take place in Walter Library, Room 402. The agenda is provided below:
Introductions
- Presented by Todd Heiman, IBM Client Executive
HPC/Research Computing and IBM
- Presented by Kent Winchell, IBM Deep Computing Chief Technology Officer
HPC in Industrial Engineering
- Presented by Dr. Martin Feyereisen
HPC in Life Sciences/Genomic Processing and Research
- speaker TBA
Platform Software in HPC Environments
- Presented by Marc West, World Wide Platform Computing Synergy Manager
Intelligent Cluster Solutions, Computer/Storage
- Presented by Steve Chase, HPC Lead, and Josh Babcock, Intel Servers and CPFS Storage
We look forward to seeing all interested MSI users at this Town Hall meeting.
posted on September 12, 2013
As part of the ongoing selection process for the next HPC system at MSI, MSI has invited top high performance computing vendors to present their high performance computing portfolios and roadmaps to users in a Town Hall setting.
HP will be on-site Tuesday, September 17, 2013, 9:00 a.m. - 12:00 p.m., to provide presentations and have interactive discussions with MSI users. The meeting will take place in Walter Library, Room 402. The agenda is provided below:
Introductions
HP Eagle – next-generation multi-node servers (30 min)
- Presented by Marc Hamilton
HP Moonshot and Apollo (30 min)
- Presented by Marc Hamilton
Mellanox networking features (15 min)
- Presented by Peter Waxman
Application performance (45 min)
- Presented by Dave Mullally
Data Analytics – reference architure for Hadoop/SL4500 (30 min)
- Presented by Marc Hamilton
Q & A (30 min)
We look forward to seeing all interested MSI users at this Town Hall meeting. The final meeting in this series will be the IBM Town Hall Meeting, September 20, 10 a.m. – 1 p.m., 402 Walter Library.
posted on September 9, 2013
Researchers at the University of Minnesota recently developed a new delivery system for drugs that could be effective treatments for HIV (human immunodeficiency virus, which causes AIDS). MSI PI Professor Louis Mansky (Institute for Molecular Virology) is one of the co-authors on the study, which combines two FDA-approved drugs in pill form. Using pills is an improvement for the patient over most anti-HIV drugs, which must be injected.
This study was published on August 30, 2013 in the journal Antiviral Chemistry and Chemotherapy.The Minnesota Daily published an article about the research on September 9, 2013. It was also reported online in Science World Report and Daily News and Analysis.
Professor Mansky studies HIV mutation and how it affects the development of effective drug therapies. It is also thought that the mutation and evolution of HIV is responsible for the gradual breakdown of the immune system and the disease progression to AIDS. Professor Mansky and his group use MSI resources for several projects in this area.
posted on September 4, 2013
Dr. Matthew G. Knepley, University of Chicago, will present a hands-on tutorial for PETSc at MSI on September 30. Dr. Knepley is one of the authors of the widely used PETSc library for scientific computing from Argonne National Laboratory, and is a principal designer of the PyLith library for the solution of dynamic and quasi-static tectonic deformation problems.
PETSc is a suite of data structures and routines for the scalable parallel solution of scientific applications, often modeled by partial differential equations. It supports MPI, shared memory pthreads, and GPUs, as well as hybrid MPI-shared memory pthreads or MPI-GPU parallelism.
The tutorial will be held on Monday, September 30, from 9 a.m. – 4 p.m. There will be an hour for lunch (12 – 1 p.m.). The tutorial will be held in room 575 Walter. Register on the Tutorial page.
As workstations are limited, participants are invited to bring their own laptops to use during the tutorial. Please visit the PETSc website and install the program. You can install the latest release, but the most up-to-date snapshot is preferred, which uses the “git checkout next” branch; download it on the developers site.
You can also view prior tutorials and a User’s Manual plus extensive additional documentation.
Tutorial Description
This tutorial will cover basic sparse parallel linear algebra, as well as linear and nonlinear algebraic solvers, and timestepping. Students will learn to use the dynamic configuration object system in PETSc, and use it to assemble hierarchical, multilevel solvers for multiphysics problems. The tutorial also includes how to debug and profile the resulting applications.
The morning session will cover basic usage:
- Vectors and Matrices
- Generic Solver Setup
- Dynamic Object Configuration
- Debugging and Profiling
The afternoon session will cover advanced usage:
- Structured Meshes Using DMDA
- Linear Preconditioning
- Structured Linear Multigrid
- Block Preconditioners
- Nonlinear Solvers
- Nonlinear Preconditioners
- Timestepping
Instructor Biography
Matthew G. Knepley received a B.S. in Physics from Case Western Reserve University in 1994, an M.S. in Computer Science from the University of Minnesota in 1996, and a Ph.D. in Computer Science from Purdue University in 2000. He was a Research Scientist at Akamai Technologies in 2000 and 2001. Afterwards, he joined the Mathematics and Computer Science department at Argonne National Laboratory (ANL), where he was an Assistant Computational Mathematician, and a Fellow in the Computation Institute at University of Chicago. In 2009, he joined the Computation Institute as a Senior Research Associate. His research focuses on scientific computation, including fast methods, parallel computing, software development, numerical analysis, and multicore architectures. He is an author of the widely used PETSc library for scientific computing from ANL, and is a principal designer of the PyLith library for the solution of dynamic and quasi-static tectonic deformation problems. He developed the PETSc scalable unstructured mesh support based upon ideas from combinatorial topology. He was a J.T. Oden Faculty Research Fellow at the Institute for Computation Engineering and Sciences, University of Texas (Austin, TX), in 2008, and won the R&D 100 Award in 2009 as part of the PETSc team.
