Daily Bulletin Archive

Sep. 9, 2012

With Yellowstone soon to enter its acceptance testing period, CISL will no longer be accepting new project requests for the Bluefire environment from university PIs or NCAR labs. CISL will use the opportunity to help ensure a smooth transition to the new accounting system for Yellowstone, migrate all recently created projects to Yellowstone, and focus on setting up users and projects for the new environment.

After Sept. 7, a project lead may still add users to existing projects, and most other updates to existing projects will be accommodated.

Starting Monday, Sept. 10, university users will be able to submit small allocation requests for the Yellowstone system. New project requests will be queued and prepared for Yellowstone.

We apologize for any inconvenience.

Sep. 8, 2012

The upcoming transition to the new Yellowstone environment is an opportunity to implement CISL best practices if you haven’t already done so. Consider this one in particular as you prepare for the new system:

Organize your files and keep them that way. Arrange them in same-purpose trees, for example. Say you have 20 TB of Mount Pinatubo volcanic aerosols data. Keep the files in a subdirectory such as /glade/home/username/pinatubo rather than scattered among unrelated files or in multiple directories. Specialized trees are easier to share with other users and to transfer to other users or projects as necessary.

Getting organized will also help you transition smoothly to the new Yellowstone system and bring along only the files you need. Once Yellowstone is generally available, users will have an opportunity to migrate essential files to the new GLADE environment as described on our Transition from Bluefire page.

Sep. 5, 2012

The Yellowstone timeline has continued to slip despite long hours put in by CISL, IBM and Mellanox staff. At this writing, the most optimistic timeline has the three-week acceptance test period beginning late this week (the tail end of August), which pushes first user access at least to late September.

While the compute and storage hardware looks good and has demonstrated itself to be more stable than anticipated, with little “infant mortality” observed so far, IBM and Mellanox are continuing to address challenges to achieving the expected performance of 90 GB/s between the compute and storage systems.

The performance tuning involves complex hardware, software, and firmware interactions among the more than 4,500 compute nodes on Yellowstone; the 4,500 disk drives, 76 disk controllers, and 20 GPFS servers of the GLADE resource; and the InfiniBand interconnect comprised of nine core switches, 250 leaf switches, and more than 9,500 copper and fibre cables.

CISL is monitoring the deployment process closely, with ongoing interactions with and updates from the IBM team. Given the extent of the delays thus far, CISL is watching the system's stability and performance results and looking for the earliest possible opportunity to move into acceptance testing. If IBM's performance results are not quite at the promised levels, CISL may elect to pursue acceptance despite the shortfall and discuss alternate methods of later achieving performance targets with IBM.

When the Yellowstone timeline solidifies, CISL will also re-evaluate the schedule for Bluefire. With any Yellowstone delays, users can expect Bluefire’s decommissioning date to be extended accordingly.

Aug. 30, 2012

Registration is now open for “Linux/Unix Basics,” a webcast training course presented by XSEDE. The class, for beginners and intermediate users, will cover the basic Linux/Unix command line environment and feature hands-on exercises. It will emphasize common strategies for interacting with clusters and HPC resources. There are no prerequisites. Participants must register here by Sept. 18.

Aug. 21, 2012

The CISL User Services Section has published additional documentation to help users prepare for computing with the Yellowstone, Geyser, and Caldera resources that are being tested at the NCAR-Wyoming Supercomputing Center.

The documentation includes compilation commands for the Intel, PGI, PathScale, and GNU compilers to be used in the new system. It also describes the Yellowstone environment’s file format and mathematical libraries.

Feel free to use the Feedback link on our Support & Training menu to let us know what you think.

Aug. 16, 2012
Date and Time: 
Aug 16th, 2012, 10:00

Who should attend:

  • UCAR users who move big data…
    lots of small files, very large files,
    or anywhere in between
  • Users that access NCAR data nodes
    on XSEDE, DOE, or U.Colorado endpoints
  • Campus computing resource admins
  • When: Thursday, August 16, 10:00AM MT
  • Location: Webinar URL will be provided after registration
  • Presenter: Steve Tuecke, Deputy Director of the Computation Institute, University of Chicago and Argonne National Laboratory

Globus Online is a convenient interface for transferring files between two endpoints – for example, between NCAR resources, the University of Colorado, and XSEDE facilities or other sites. Globus Online also offers a feature called Globus Connect, which enables you to move files easily to and from your laptop or desktop computer and other endpoints.

The Consulting Services Group at NCAR will host a two-hour online workshop to help UCAR users set up and work with Globus Online. You are encouraged to use your own laptop and follow along with the presenter.

Click here to register for this workshop. Please contact Si Liu (siliu_at_mail_dot_ucar_dot_edu) if you have any questions or concerns.

Aug. 10, 2012

The NCAR-Wyoming Supercomputing Center (NWSC) has been the site of a flurry of activity in July, with IBM and CISL making significant progress on the complex installation of the Yellowstone environment. As of July 30, most hardware installation issues have been resolved, IBM has run performance tests on the full 11-PB GLADE system, and IBM and CISL have installed most key software and configured the administrative and user environments.

At this time, we estimate that Yellowstone will be ready for the first users in early September, at which point the Accelerated Scientific Discovery (ASD) projects will begin. The rest of the user community will have access as soon as practical after the ASD projects have started.

In addition, because the Yellowstone schedule has slipped, CISL has reviewed the plan for Bluefire. Barring further delays, CISL will extend Bluefire's lifetime at least through the end of October 2012. CISL intends to operate Bluefire through November, but in the event of a major system failure during the month, the system may not be returned to service. Bluefire users should plan their work accordingly.

Between now and the beginning of September, Yellowstone will be subjected to a battery of tests. The system is now entering the "functional testing" period during which IBM will begin to put Yellowstone through a series of tests designed to confirm that all components are functioning as an integrated system and delivering the expected performance.

Following functional testing and after resolving any remaining hardware issues, Yellowstone will enter the three-week Acceptance Testing Period, during which IBM and CISL will jointly conduct benchmarks and run the system with a simulated workload around the clock. When Yellowstone successfully passes the acceptance tests, CISL will take over the system from IBM, and we are allowing a few days for NCAR-specific configuration and customization.

We will keep you posted as we proceed, particularly about significant changes in this schedule. Please contact cislhelp@ucar.edu with any questions.

Aug. 9, 2012
Date and Time: 
Aug 8th - 10th, 2012, 9:00-12:00, 13:00-16:00
ML Damon Room
Damian Rouson, Karla Morris, and Salvatore Filippone

Workshop Introduction:

Modern Fortran explicitly supports object-oriented programming (OOP). OOP aims to increase a program's maintainability in part by reducing cross-module data dependencies and to increase a program's reusability in part by providing for extensible derived types. Emerging compiler support for Fortran 2003/2008 inspires a more modern program design and implementation style. This course provides the requisite skills.

  • Day 1 introduces OOP in Fortran 2003.
  • Day 2 introduces patterns of best practice in program organization.
  • Day 3 explores several paths toward parallel OOP, including parallel numerical libraries and Fortran 2008 coarray programming.

Examples will utilize introductory-level numerical algorithms from linear algebra and differential equations inspired by multiphysics modeling that is coupled field problems common to many interdisciplinary, engineering, and physical science simulations.
Additional information, including a syllabus and schedule from the NERSC URL for previous offerings of the course can be found here:


If you are interested in purchasing the reference book Scientific Software Design - The Object-Oriented Way written by Damian Rouson(Sandia National Laboratories), Jim Xia(IBM Canada Lab, Markham), and Xiaofeng Xu(General Motors Corp.), here is a discount coupon.


Please register for the workshop from the link here.

Speaker Description: 

Damian is the manager of the Reacting Flow Research Department and a Visiting Assistant Professor at the University of Cyprus. His research interests focus on scalable scientific software design. He has recently written a book on the subject, Scientific Software Design: The Object Oriented Way . He is also the software architect of the object oriented Fortran interface to Trilinos, ForTrilinos. ForTrilinos provides Fortran applications direct access to capabilities in the Trilinos project.

Karla is a senior member of technical staff in the Reacting Flow Research Department at Sandia. She is the lead developer of ForTrilinos. Her research interests include computational fluid dynamics to multiphysics flows and scientific software architecture.

Salvatore Filippone graduated from the University of Rome "Tor Vergata" where he is currently with the Dep. of Industrial Engineering. His main research interests are in algorithms for numerical linear algebra, their implementation on high performance computers and their application to engineering domains such as fluid dynamics and electromagnetism. From 1990 to 2001 he has been with IBM Corp. where he was one of the lead developers of the numerical libraries ESSL and PESSL. He evaluates scientific projects in HPC for both the European Commission and the National Science Foundation.

Aug. 8, 2012

"ISTeC at CSU is hosting the Front Range Consortium for Research Computing's (FRCRC's) Second Annual Front Range High Performance Computing Symposium, August 13-14, 2012, at Colorado State University, Fort Collins, CO 


The program is available on the above website. 

The FRCRC membership includes CSU, CU, Boulder, University of Wyoming, the Colorado School of Mines, NCAR, NREL, and NOAA. It includes HPC tutorials, birds of a feather, student presentations and more! This is a great opportunity to network with your colleagues in computational science on the Front Range and learn new skills.

Advance Registration is due by August 6th, 2012 at 12:00 noon. Registration at the door is not accepted. 

We hope you will attend. Please feel free to contact Rich Loft at loft@ucar.edu for more information."

Aug. 6, 2012

The CISL User Services Section has published additional documentation to help users prepare for computing with the Yellowstone, Geyser, and Caldera resources that are being installed and tested at the NCAR-Wyoming Supercomputing Center.

The information deals with scheduling, queue selection, and running jobs in the new environment. It includes a sample batch script and points out notable differences from scripts used with the Bluefire system.

More Yellowstone documentation will be provided soon.

Feel free to use the Feedback link on our Support & Training menu to let us know what you think.