Monday, October 27, 2014

On Campus Research Computing Symposium

Details and Registration Links November 6th, Rackham Building.

The Flux Staff attends these events so if you come say hello!

The ARC Research Computing Symposium is a twice-yearly conference conference held on-campus that brings together more than 200 U-M researchers who rely on large-scale computational tools and methods for research. Formerly known as Cyberinfrastructure (CI) Days, the symposium is an opportunity to learn more about advanced computing technologies that are helping to spur new discoveries and breakthroughs in a wide range of disciplines.

  • Edward Seidel, Director of the National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign
    The Data-Enabled Revolution in Science and Society: A Need for National Data Services and Policy
  • Marc Snir, Director of the Mathematics and Computer Science Division at Argonne National Laboratory
    High Performance Computing: Exascale and Beyond
  • Leslie Greengard, Director, Simons Center for Data Analysis, Simons Foundation; Professor, Courant Institute of Mathematical Sciences, New York University
    Fast, Accurate Tools for Physical Modeling in Complex Geometry
  • Gonçalo Abecasis, Chair of the Biostatistics Department and Felix E. Moore Collegiate Professor of Biostatistics, U-M
    Biostatistics: Bringing Big Data to Genetics, Biology and Medicine
  • Sharon Glotzer, Stuart W. Churchill Collegiate Professor of Chemical Engineering; Professor of Material Science and Engineering, Macromolecular Science and Engineering, and Physics, U-M
    Discovery and Design of Digital Matter
  • Scott Page, Leonid Hurwicz Collegiate Professor of Complex Systems and Political Science; Professor of Economics; and Director, Center for the Study of Complex Systems, U-M.
    Diversity + Ability

Wednesday, October 15, 2014

Running MATLAB on XSEDE Resources

MATLAB is one of the most popular prototyping systems available in research computing. It is a set of powerful tools all wrapped in a language similar to FORTRAN with object oriented features.

XSEDE is a set of national computing resources that researcher can apply for.  It is one in a set of national resources that powers a large share of national resources including DOE, Blue Waters, and others.

Currently it is very difficult to combine the two sets of resources. MATLAB is commercial and getting access to a license that you can use on XSEDE can be problematic due to license cost and technical complexity.

MCC - The MATLAB Compiler

MCC (Flux Docs) is a toolbox/add-on to MATLAB that allows the wrapping of mcode into a standalone executable. Features of this executable is that it can be ran anywhere using any functionality that was available at the site it was compiled at.  Thus MATLAB programs can be moved to a resource such as XSEDE within your license terms.

The downsides are you cannot modify your mcode on the XSEDE resource. You have to make any design changes where you have your MATLAB license and MCC license.  This limitation can be mitigated by the fact that MCC can compile functions and arguments can be passed on the command line.  Of course MCC compiled code can also read from files that regular MATLAB can.  So if your code is stable but you are running different inputs that is no problem.

The How-To

This is will be in two parts. What needs to be done on Flux or other machine with MATLAB and MCC installed, and what needs to be done to run the result on the XSEDE resource. In this example I am going to use Stampede at TACC.

The example code is implicitthreads.m which solves a system of equations using the \ operator in MATLAB.  It is implemented as a function, taking the number of unknowns. 

Compile on Flux

Setup MCR on Stampede

Run on Stampede

Wednesday, October 1, 2014

GLCPC Blue Waters Allocations Call Open

The Great Lake Consortium for Petascale Computation (GLCPC) is the easiest way to get access for moderate users of HPC CPU/GPU resources to gain access and use the Blue Waters super computer.

Proposals are due November 3rd, full details are available at the GLCPC website.

What is the difference between GLCPC Blue Waters allocations?
When there is the NSF Petascale Computing Resource Allocation (PRAC) program for Blue Waters?

The bar is higher for the NSF allocations, they expect users to have significant resource need and run at extreme scale.  If your work falls into this area please apply to the NSF program, which are due November 14th.  GLCPC is only granted a small portion of the Blue Waters system ~3.5 Million node hours. GLCPC is also only available to GLCPC members, which Michigan is one.

The availability of time on Blue Waters is broken down as:
  • 80% or more NSF Petascale Computing Resource Program (PRAC)
  • 7% University of Illinois at Urbana-Champaign
  • 2% Great Lake Consortium for Petascale Computation
  • 1% Teaching/Education
For most HPC users access via GLCPC is the most appropriate choice, and for a small subset the NSF Petascale program also applies.

How does GLCPC compare to XSEDE?
When should I pursue XSEDE or GLCPC?

GLCPC in the number of hours it can give away is about on par with medium to small XSEDE allocations.  Currently XSEDE also does not have a long lived large scale GPU/CUDA capable machine while Blue Waters is capable of that.

As always contact us at if you have questions.