Sunday, August 23, 2009

BioInformatics using OpenSolaris

Doing Bio-Informatics using OpenSolaris. Nice blog by Bruce Rothermal.

Wednesday, August 12, 2009

Sun’s Virtual HPC conference

Sun logo The only virtual conference dedicated to the best in high performance computing. During this virtual event, you will have an opportunity to hear from compute and HPC guru Andy Bechtolsheim and leading industry analysts discussing the trends and issues facing the computational ecosystem. In addition, industry and technology exhibits provide virtual opportunities to discuss technologies, accomplishments, and collaborations in HPC, networking, storage, software, and data management software.

Date: Thursday, September 17, 2009
Time: 8:00 AM Pacific / 11:00 AM Eastern / 3:00 PM Greenwich Mean Time

And you can register here.

Sun HPC Software Workshop '09 and Seminars

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The Sun Grid Engine, OpenStorage (Lustre and SAM-QFS) and HPC Developer Tools (HPC Cluster tools and SunStudio) teams are pleased to invite you to the Sun HPC Software Workshop '09

About the Workshop (Sep. 8th-10th)

This three-day workshop (Sep 8-10) contains three parallel tracks with presentation from Sun engineers, customers, community members, and partners about the Grid Engine open source project, Open Storage (including Lustre and SAM-QFS), and software tools such as Sun Studio and Sun HPC ClusterTools.

About the Seminars (Sep. 7th)

On Monday, Sep 7, three advanced seminars will be offered.

  • A special Lustre Advanced Technical Seminar is offered with senior Lustre engineers. They will discuss areas of the product they are working in and take questions and provide answers around tuning, configuration, and debugging.
  • An HPC Parallel Programming Seminar will teach aspects of parallel computing as well as provide a good understanding of the basics of the MPI and OpenMP programming models. Some basic understanding of C or Fortran will be helpful, but it is not a requirement.
  • The Grid Engine Administration Seminar will be a training class for Sun Grid Engine administrators who want to learn about administration facilities, expert configurations and best practices for complex use case scenarios. The class will be conducted by Sun Grid Engine experts and engineers.

These seminars are offered at an unbeatable fee and complement the following days of the workshop. Only limited seating is available for these classes.

Location, Agenda and Contact Information

The Sun HPC Software Workshop and Seminars will be held in the UNESCO World Heritage listed medieval city of Regensburg. Hotel reservations should be made directly with the workshop hotel.

Information about the draft agenda, hotel and transportation can be found at the registration web site:

Please check the website again for regular updates of the agenda. If you are interested in delivering a talk, please email a short abstract to:

Please send general questions about the event to:

We are looking forward to seeing you in Regensburg in September!

Thank you,
Sun Microsystems, Inc.

PS: Also, check out our HPC Reference Architecture, an integrated end-to-end approach to help you scale as demand for compute power, storage and interconnect bandwidth grows.

Wednesday, August 5, 2009

How to remove a compute host forcibly from Grid Engine cluster

Now it may so happen that you want to remove a node from your Sun Grid Engine cluster but the node is no longer accessible. It may be because,
  • You are running a HPC cluster in Amazon EC2 with SGE Service Domain Manager with Cloud Adapter
  • The node simply crashed and you don't have a budget to replace it
  • You may think of any scenario where you want remove a SGE execution host, but the execution host has gone down and is never going to come up.
So here the usual way of removing an execution host from SGE master is not going to work as uninstallation of exec daemon on execution host is not possible. So will keep getting those annoying entries in qstat -f about non accessible execution hosts. Unfortunately SGE doesn't provide a clean mechanism by which you can get rid of such hosts.

But that's not the of the story. You can simply hammer SGE by cleaning the entries of such hosts by following method. Lets assume the host you want to remove is, HOST_GO_AWAY

  1. qconf -dattr hostgroup hostlist HOST_GO_AWAY@cloud_hosts >/dev/null
  2. qconf -dattr hostgroup hostlist HOST_GO_AWAY@allhosts >/dev/null
  3. qconf -dh HOST_GO_AWAY >/dev/null
  4. qconf -ds HOST_GO_AWAY >/dev/null
  5. qconf -de HOST_GO_AWAY >/dev/null
  6. rm -f /opt/sge/default/common/local_conf/HOST_GO_AWAY
That's all!

Tuesday, August 4, 2009

Google App Engine as a Proxy Server

While browsing the Google App Engine application gallery , accidentally I came across one interesting app. Its called Calyphrox WebProxy. It a proxy server hosted on Google App Engine. Since this app is hosted on Google App Engine, it can take advantage of Google's enormous bandwidth and scaling capabilities.

I only wish if this app would have been open sourced then anyone could have built an proxy server within minutes. May be someone would do it someday. Let's hope so.

Sunday, August 2, 2009

General Purpose, Low Power Supercomputing - Google Talk

Google TechTalks
February 28, 2006

Prof. Bob Brodersen

ABSTRACT: The ability of FPGA technology to exploit the advances in IC fabrication technology has resulted in the present situation in which a FPGA computing fabric is the most power and area efficient approach for general purpose parallel computing. This has occurred because the Von-Neumann processor architectures are now power limited and can no longer fully exploit the technology advances (thus the move to multi-cores). Hardware composed of arrays of FPGA's and memory has been design that achieves a TeraOp/second of performance per board with over an order of magnitude higher efficiency for the computation per unit power over conventional microprocessors.