News

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.

posted on September 3, 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 open discussion setting. 

Dell Computing will be at MSI on Wednesday, September 4, from 10 a.m. until 1 p.m. to provide presentations and have interactive discussions with users.

The meeting will take place in room 402 Walter Library. The agenda is provided below:

10 – 10:10 a.m.: Welcome and introductions

10:10 – 10:30 a.m.: Opportunity for users/staff to talk about what they want from program

10:30 – 10:40 a.m.: Dell in HPC today (why Dell for HPC)

10:40 a.m. – 12:50 p.m.: Dell’s HPC Solutions

• Our Commitment, Our Progress and Our Plans
- Michael Dell’s commitment
- Progress (Industry Analysts) and Examples (hints about our plans)

• The Dell Scalable Unit (DSU) Concept
-  Complete Solutions: 256-Node Example
-  Integrated and Supported Subsystems Within the DSU
-  DSU for Genomics (codenamed SANGER, launched 04-June-2013!)

• Technology Updates and Futures
- Intel processor futures (Xeon Sandy Bridge -> Ivy Bridge  -> )
- Accelerators: GPUs and Intel Xeon Phi Coprocessors
- Interconnects

• Near-Term Advancements (0-2 Years)
-  Dell Processor Accelerator Technology (Dell PAT); Green-MPI

• Longer Term (2015-2018)
- (at least) 5 things coming

• If Time: Need Your Help
-  3 future design options/considerations

•  Summary

12:50 – 1:00 p.m.: Closing and next steps

We look forward to seeing all interested MSI users at this Town Hall meeting. Please save the dates for these future meetings (agendas will be posted before the events):

September 17, HP, 9 a.m. – 12 p.m., room 402 Walter Library
September 20, IBM, 10 a.m. – 1 p.m., room 402 Walter Library

 

On Wednesday, September 4, 2013, from 04:00 – 15:00, MSI will perform scheduled maintenance and upgrades to the network and various systems.

During this maintenance period, we will be performing the following updates:

  • Network firmware updates and modifications will be performed affecting external connectivity for up to one hour.
  • Itasca will be offline for system updates.
  • Cascade will be briefly unavailable for Panasas client updates.
  • MSI Windows systems will be offline for system updates.

 

Systems status is always available on our Status page.

If you have any questions, please email help@msi.umn.edu.

 

 

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