New campus-wide access to MATLAB

By | Educational, General Interest, News

U-M is offering a new, campus-wide license for MATLAB, Simulink, and companion products. All faculty, researchers, and students are eligible to download and install these products, including toolboxes such as:

  • Bioinformatics Toolbox
  • Control System Toolbox
  • Curve Fitting Toolbox
  • Data Acquisition Toolbox
  • Image Processing Toolbox
  • Instrument Control Toolbox
  • Optimization Toolbox
  • Parallel Computing Toolbox
  • Signal Processing Toolbox
  • Simscape
  • Simscape Multibody
  • Simulink Control Design
  • Stateflow
  • Statistics and Machine Learning Toolbox
  • Symbolic Math Toolbox.

Access free, self-paced training to get started in less than 2 hours:  MATLAB Onramp.

Commercial use of MathWorks products is not covered by our TAH license, so if you are using a commercial license, please continue to do so. 

Read more…

U-M part of new software institute on high-energy physics

By | General Interest, Happenings, News, Research

The University of Michigan is part of an NSF-supported 17-university coalition dedicated to creating next-generation computing power to support high-energy physics research.

Led by Princeton University, the Institute for Research and Innovation in Software for High Energy Physics (IRIS-HEP) will focus on developing software and expertise to enable a new era of discovery at the Large Hadron Collider (LHC) at CERN in Geneva, Switzerland.

Shawn McKee, Research Scientist in the U-M Department of Physics, is a co-PI of the institute. His His work will focus on integrating and extending the Open Storage Grid networking activities with similar efforts at the LHC.

For more information, see Princeton’s press release, and the NSF’s announcement.

ARC-TS contributes to successful fNIRS workshop

By | General Interest, Happenings, HPC, News

The Center for Human Growth and Development (CHGD) held a workshop on functional near-infrared spectroscopy (fNIRS), a form of neuroimaging, with a special focus on pediatric applications. The workshop was sponsored by units at U-M, as well as units from Eastern Michigan University and Gallaudet University. It was attended by 50 people from as far away as Texas, and included research talks, instructional sessions, and hands-on experience with fNIRS data processing. The workshop was the first of its kind at U-M.

CHGD, ARC-TS, and LSA IT staff collaborated to provide a remote neuroimaging computing environment, which included a graphical interface, access to Matlab, and a suite of fNIRS software, that was accessed from participants’s laptops during the workshop. The attendees rated the practice exercises done via the computing environment one of the most important components of the workshop.

ARC-TS was pleased to be able to contribute to training in computational tools needed for emerging methods in neuroimaging. For more information about the fNIRS workshop, please see http://chgd.umich.edu/facilities-resources/developmental-neuroscience-laboratories/fnirs/fnirs-workshop/

Application container software installed on Flux and Armis

By | General Interest, News

Singularity, which is new “application container” software, has been installed on the Flux and Armis HPC clusters. An application container is a program — a single file — that can be used to combine an application with the system software it needs to run. This enables applications to run on the clusters even if the system software is different. For example, an older application that is needed to finish a project can continue to be used even if it is incompatible with the updated cluster. An application that needs a different Linux distribution can be containerized to run on the cluster.

Singularity containers cannot be created on Flux or Armis, but they can be created and brought to the clusters to run.  Singularity provides tools to convert Docker containers for use on Flux and Armis. Please contact hpc-support@umich.edu if you are interested in using Singularity and would like more information about how to create and run Singularity containers or would like a referral to unit support who can help.

Information about Singularity on Flux and Armis can be found at http://arc-ts.umich.edu/software/singularity and about Singularity itself at http://singularity.lbl.gov/

Dr. Greg Wilson, founder of Software Carpentry, to speak on U-M campus Oct. 12-13

By | Educational, Events, General Interest, Happenings

The founder of Software Carpentry, Dr. Greg Wilson, will be on the U-M campus to give two public talks. Over the past 18 years, The Software and Data Carpentry organizations have sought to improve the data analysis and computing skills of researchers around the world. The organizations’ materials are developed collaboratively under the Creative Commons-Attribution license and taught by hundreds of trained volunteer instructors. Dr. Wilson will present two talks that you are invited to attend. Both talks will be in the Clark Library presentation space on the second floor of Hatcher South:

“Software Carpentry: Lessons Learned”
1:00 pm on Wednesday, 10/12, Clark Library
Since its start in 1998, Software Carpentry has evolved from a week-long training course at the US national laboratories into aworldwide volunteer effort to improve researchers’ computing skills. This talk will explore the lessons we’ve learned along the way about applying open source software development techniques to teaching at scale, and about getting people and institutions to change the way they work.

“Not on the Shelves: What Nonexistent Books, Tools, and Courses Can Tell Us About Ourselves”
11 am on Thursday, 10/13, Clark Library
Hundreds of books about writing compilers are currently on the market, but there are only three about writing debuggers. Spreadsheets are used to do calculations more often than every other kind of tool combined, but thirty-five years after their invention, version control systems still can’t handle them. Everyone thinks we should teach children how to program, but undergraduate courses on computing education are practically nonexistent.  This talk will explore what
these gaps in our books, tools, and courses tell us about the state of computing today, and about what it could look like tomorrow.

For more information: pschloss@umich.edu

Cluster upgrades completed

By | Flux, General Interest, News

Several key systems were updated and improved during the ARC-TS HPC summer maintenance from July 16 – 23, 2016.

Among other improvements, the updates provide access to more current versions of popular software and libraries, allow new features and more consistent runtimes for job scheduling, and migrate two-factor authentication for the login servers to a new system.

The improvements included:

  • Upgrades to the operating OS and supporting software for the cluster. This was a major update to the previously installed RedHat version (RHEL 6.6) up to CentOS 7.1. This provides newer versions of commonly used software and libraries, and will help us deliver more user-facing features in the coming months.
  • Cluster management software updates and reconfiguration. This includes Torque 6, which has a new set of resource options. The new Torque version will give better language for defining tasks, more consistent runtimes, and a platform for new  features.
  • The Flux Hadoop environment upgrade to Cloudera 5.7, which now includes Hive-On-Spark (the Hadoop cluster will return to service later this week).
  • /scratch on Flux updates.
  • Transition of the software modules environment to a system called Lmod. For more information, see our Lmod transition page. The complete Lmod User Guide can be found here: https://www.tacc.utexas.edu/research-development/tacc-projects/lmod/user-guide.

An HPC 2016 Upgrade Frequently Asked Questions page is available documenting a variety of issues related to the upgrades. Please direct any questions to hpc-support@umich.edu.

New ARC Connect service provides desktop graphical interface for HPC resources

By | Educational, Flux, General Interest, News

Users of ARC-TS computing resources can now use desktop versions of popular software packages like Matlab and R while accessing the Flux shared computing cluster. The new service, called ARC Connect, provides an easily accessible graphical user interface that simplifies doing interactive, graphical work backed by the high performance and large memory capabilities of the Flux cluster.

Using ARC Connect may benefit you if you need to:

  • Very easily interactively use graphical software on HPC clusters (Flux, Armis).
  • Do high performance, interactive visualizations.
  • Share and collaborate with colleagues on HPC-driven research.
  • Use HPC in teaching.

Features:

  • Remote desktop sessions (VNC) for using Flux graphically and interactively.
  • Jupyter notebooks for Python and R (other languages coming soon).
  • RStudio interactive development environment for R.

Users can run desktop applications such as MATLAB or RStudio as if running on a laptop, but with all the power of Flux, as opposed to using them in batch mode or via text-only interactive sessions. Users can also use notebooks which require more processing power or memory than are available on their local computer or tablet (currently, Python and R notebooks are available).

ARC Connect is an enhanced version of the TACC / XSEDE Visualization Portal, and has been made possible at the University of Michigan through a collaboration between ARC Technical Services and the Texas Advanced Computing Center at the University of Texas.

For information on how to use ARC Connect, visit arc-ts.umich.edu/arc-connect. If you need further help, contact hpc-support@umich.edu.

Software Carpentry workshop at U-M — May 2-3

By | Educational, Events

A Software Carpentry workshop will be held at the U-M Medical School May 2 and 3. These workshops are free and open to anyone on campus; the sessions are suitable for researchers in the humanities and social sciences. Register here.

This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems.

Who: The course is aimed at graduate students, postdocs, and other researchers across the University of Michigan. You don’t need to have any previous knowledge of the tools that will be presented at the workshop.

Where: Furstenberg 2710 (2nd floor of Med Sci II).