From nothing to more than nothing Carlo Nardone's Weblog

The ClusterTools 7 (CT7) Revenue Release is now available at
http://www.sun.com/software/products/clustertools/ct7.html

The CT7 user documentation is available at
http://www.sun.com/products-n-solutions/hardware/docs/Software/Sun_HPC_ClusterTools_Software/

The CT7 software is a set of MPI libraries and tools for launching parallel MPI jobs on Solaris (Sparc and x64). CT7 includes support for IB networks via a uDAPL Byte-Transfer Layer (BTL) and support for launching jobs with N1 Grid Engine (N1GE). Other interconnects supported are TCP, shared memory, and Myrinet MX.

CT7 is the first Sun release based on the Open MPI open source software. More information about Open MPI can be found at
http://www.open-mpi.org

Any user feedback and suggestions for features to be supported in future releases: use CT7-feedback@sun.com alias.

from Len Wisniewski, Manager of ClusterTools Team at Sun.

Try the Thread Analyzer tool in Sun Studio 12 Express / Early Access program.

Sun Studio 12 Express (February 2007) can be downloaded from: http://developers.sun.com/sunstudio/downloads/express.jsp

The Thread Analyzer tool detects data races and deadlocks in multi-threaded programs written using POSIX threads, Solaris threads, and OpenMP. More information can be found in the Thread Analyzer README: http://developers.sun.com/sunstudio/downloads/ssx/tha/index.html

In addition to the README, there is the following documentation:

• * Getting Started Guide http://developers.sun.com/sunstudio/downloads/ssx/tha/tha_getting_started.html
• * FAQ http://developers.sun.com/sunstudio/downloads/ssx/tha/tha_faq.html
• * Data Race Tutorial http://developers.sun.com/sunstudio/downloads/ssx/tha/tha_using.html
• * Deadlock Tutorial http://developers.sun.com/sunstudio/downloads/ssx/tha/tha_using_deadlock.html

The experimental programming language for supercomputing coming from Sun Labs is out! Fortress started as a key component of Sun effort funded by the HPCS (High Productivity Computing Systems) US DARPA program.

The first set of Fortress source code has been posted to SunSource.net and is available now for download by the Open Source Community. This reference implementation runs on the JVM, requiring Java 1.5 (or better) to run and Ant 1.6.5 (or better) to build. The majority of Fortress' implementation is BSD-licensed but some components are released under other licenses, all listed on the download site: http://fortress.sunsource.net/. Press release and other info at http://research.sun.com/spotlight/2007/2007-01-10_fortress.html

CNET article about this.

Server Virtualization News has an interview with Don Becker, a co-founder of the original Beowulf project:
Provisioning, booting, driver troubles virtually unfixable.

HPCWire has a feature article by Bob Monkman (Penguin Computing, which acquired Scyld):
Cluster Virtualization

Report Predicts Growth of Bioinformatics Market

The market research report on bioinformatics industry, "Bioinformatics Market Update (2006)" by RNCOS finds that in 2005 the bioinformatics industry worldwide reached $1,435 million with a growth of 17 percent from $1,235 million.

RNCOS' analysts predict that the bioinformatics market size is expected to grow at an average annual growth rate of 16 percent to hit $3 billion by 2010 with phenomenal growth in its offshoots like cheminformatics and pharmacogenomics.

NPACI Rocks

Rapid Cluster Deployment. From delivery to production in hours by Steve Jones (Maggio 2006).

Sun Microsystems a SC03 (SuperComputing 2003), dimostrazione con SDSC di installazione di un cluster da 128 x86 server in 2 ore.

[Technorati Tag: HPC]

Commom wisdom dictates the equation HPC = floating point. However, many high-performance scientific and technical tasks require almost integer-only number-crunching. For example, in the Bioinformatics realm BLAST, FAST, HMMER and other codes spring to mind.

Well, Sun recently launched the SMP-on-a-chip "Niagara servers". They are perfect for multithreaded, multiprocess, parallel applications and workloads, as long as floating point fraction is below 3%.

A nice survey of architecture, microbenchmarks and other technical stuff has been released by Aachen University, a competence center in CFD and MCAE.
www.rz.rwth-aachen.de/computing/hpc/hw/niagara.php
For example, they tested the Sun Fire T2000 on ParMETIS, a Finite Elements mesh partitioner.

With regard to BLAST, see the tuning tips in http://www.sun.com/servers/coolthreads/tnb/applications_blast.jsp.