Bulletin 179 - 2008 August 01

  1. CSIRO IBM Blade Cluster Upgrade
  2. CSIRO Altix upgrade
  3. CSIRO Data Store upgrade
  4. CSIRO - New ASC software
  5. CSIRO - Upgraded ASC Software
  6. ARCS Workshop on Video Collaboration Tools
  7. CSIRO ASC and HPCCC staff changes

Note: "CSIRO" items can apply to BoM users of cherax and burnet


1. CSIRO IBM Blade Cluster Upgrade

The upgrade of the CSIRO clusters burnet and nelson is nearly complete.

The two clusters will be merged, with a new systems management node, a new user head node, and two storage server nodes.

About 8 Tbyte of new disc is connected, distributed among:

  • /cs/home 500 Gbyte
  • /cs/data 2.6 Tbyte
  • /cs/flush 4.1 Tbyte
  • /tools 500 Gbyte

The file systems are managed by IBM's GPFS, which allows for scalable performance and resiliency. The two storage servers are configured using fail-over capabilities.

The first group of users will be migrated to the new cluster from Monday 4th August, with other groups to follow. Users will be contacted within a few weeks, to move over to using the new file systems and login nodes.

There will be one further downtime on the entire cluster, probably on Saturday 16th August, to re-cable the switch infrastructure in the cluster.

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2. CSIRO Altix upgrade

The new Altix 4700, temporarily called cherax-1, will be available for user testing from Monday 4th August.

However, there are some cautions, that will be displayed upon login.

The chief of these is the absence of a batch system, and the fact that all the user file systems are in fact the existing cherax ones, but cross-mounted using NFS. So any changes in those filesystems will affect both the new (test) Altix and the old (production) one.

There is potential for great confusion if you work on both machines, since cherax-1 gives its host name as "cherax" once you log in, which was done to make the transition easier in the long run.

Please test for the existence and correct running of your applications.

It will have the same Wednesday maintenance outages as the production Altix 3700, as we work towards the changeover. A date for that has yet to be chosen, as it depends on the results of testing beforehand.

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3. CSIRO Data Store upgrade

On 17th July, two new tape drives were configured on the CSIRO Data Store Data Migration Facility hosted on the Altix 3700, cherax. The StorageTek/Sun T10000A drives are currently attached to the Bureau's SL8500 tape library.

Already, the second copies of all newly migrated files in /cs/datastore are being written to the new tapes, which have greater capacity and higher speed than the older ones. Soon the first and only copies of files in the backup areas will be written to them as well.

After that, second copies of files on the T9840 and T9940 tapes will be copied to the new T10000 tapes.

This latter process, which will take months, will be done at quiet times, so we expect impact on retrieval of files by users to be low.

You can monitor the status of file retrievals through the DMF 'more' report from the traffic lights at http://intra.hpsc.csiro.au/traffic/servicestatus.xml or http://www.hpccc.gov.au/hpccc/system_status/ .

The dmget wrapper command has been recently enhanced to provide better grouping of files into batches for retrievals, and further enhancements are being addressed.

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4. CSIRO - New ASC software

  • MATLAB Distributed Compute Server (DCS) / Parallel Computing Toolbox (PCT)

    MATLAB DCS, used in conjunction with PCT, enables MATLAB users to execute applications on a computer cluster.

    The toolbox provides constructs for users to prototype and test applications that solve computationally and data-intensive problems. Once the application runs on the desktop, a user can submit it to the MATLAB DCS product to harness the resources available in a computer cluster.

    There are 2 PCT Licenses for development and front-end use. There are 32 DCS licenses are available for job execution.

    Note that all MATLAB toolboxes can potentially be installed and used with DCS. If you need a particular toolbox installed, please contact us.

    Matlab DCS and PCT is installed on burnet and can also be used on other platforms including your local workstation.

    Please see the APAC software map for usage instructions for Matlab DCS - http://nf.apac.edu.au/facilities/software/index.php?site=CSIRO

  • MATLAB Compiler

    The MATLAB compiler (mcc) can be used to create standalone applications that do not require access to MATLAB licenses. The applications use a MATLAB run-time environment that is freely distributable.

  • MATLAB Signal Processing Toolbox

    The Signal Processing Toolbox is a collection of industry-standard algorithms for analog and digital signal processing. It provides graphical user interfaces for interactive design and analysis and command-line functions for advanced algorithm development.

  • Tempest 6.4

    The Tempest suite of products provides a range of engineering solutions for reservoir simulation and visualisation.

    Tempest is installed on cherax. Please see the APAC software map for usage instructions. http://nf.apac.edu.au/facilities/software/index.php?site=CSIRO under 'Geophysics'

  • COMSOL

    COMSOL is a multiphysics simulation environment that facilitates all of the steps in the modeling process defining your geometry, specifying your physics, meshing, solving and then post-processing your results.

    For more information about COMSOL visit http://www.comsol.com/products/multiphysics/

    COMSOL is installed on cherax. Please see the APAC software map for usage instructions http://nf.apac.edu.au/facilities/software/index.php?site=CSIRO under 'CFD & Engineering'

  • POV-Ray

    The Persistence of Vision Raytracer is a high-quality, totally free tool for creating stunning three-dimensional graphics.

    For more information about POV-Ray See more on http://www.povray.org/

  • Accelrys Materials Studio

    Materials Studio is a software environment for materials simulation technology, solving key problems throughout the R&D process. It offers advanced visualization tools and access to the complete range of computational materials science methods. Materials Studio is designed for structural and computational researchers in chemicals and materials R&D who need to perform expert-level modelling and simulations tasks in an easy-to-learn yet powerful environment.

    See more at http://accelrys.com/products/materials-studio/

    Materials Studio 4.3 is available on burnet and can be used on your local workstation.

    Please note that in order to run remote Materials Studio jobs on burnet, users must be registered. Request registration for Materials Studio via hpchelp@csiro.au

    Please see the APAC software map for usage instructions. http://nf.apac.edu.au/facilities/software/index.php?site=CSIRO under 'Computational Chemistry'

  • gOpenMol

    OpenMol is a tool for the visualization and analysis of molecular structures and their chemical properties.

    For more information about gOpenMol visit http://www.csc.fi/english/pages/g0penMol/Introduction

    gOpenMol 3.00 is available on burnet. Please see the APAC software map for usage instructions. http://nf.apac.edu.au/facilities/software/index.php?site=CSIRO under 'Bioinformatics'

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5. CSIRO - Upgraded ASC Software

  • Subversion 1.5.0

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6. ARCS Workshop on Video Collaboration Tools

ARCS (Australian Research Collaboration Service) will be presenting two workshops on video-collaboration tools (Access Grid and EVO). There are two main sections to these three-day workshops

  • Day One : a general overview of two video-collaboration tools, and how they can be used to aid and enhance collaborative research.
  • Days 2 and 3 : in-depth technical information on installing, configuring and using the Access Grid Toolkit in particular, and other information relevant to setting-up collaborative information relevant to setting-up collaborative video-conference facilities in general

Day one is highly recommended for any researchers who want to collaborate, not just technical people. The workshop is suited for those who wish to find out what video collaboration is and what it can do for them.

The dates for the workshops are:

  • Adelaide: August 6th (7,8th for the second part.)
  • Melbourne: August 13th (14,15th for the second part.)

More information about start times, venues and a detailed schedule are available on the website: http://www.arcs.org.au/videoworkshops. Also attached is a flyer promoting the workshop.

Places are limited, so please RSVP. http://www.arcs.org.au/videoworkshops

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7. CSIRO ASC and HPCCC staff changes

CSIRO ASC and the HPCCC welcome:

Joel Ludbey-Bruhwel, who commenced with CSIRO ASC at Docklands on the 2nd of June. His role is GRID systems administration.

Peter Edwards, who commenced with CSIRO ASC at Docklands on the 10th of June. His role will be Senior Systems Administrator. Peter formerly worked with NEC, and prior to that with SGI and Cray Research. In the mid 1990s, he was the Cray Site Analyst for the CSIRO Supercomputing Facility.

Tim Ho, who commenced with CSIRO ASC at Docklands on the 23rd of June. His role will be User and Application Support Specialist.

Steve Fraser, who commenced with CSIRO ASC at Clayton on the 1st of July. His role will be HPC Systems Administration. Steve been working with CSIRO IM&T Business Support for many years and has a wealth of experience in server management, data storage and networking.

HPCCC farewells:

Polly Morgan, who has taken up the position Senior Systems Administrator in the ASC Cluster Services group at Clayton.

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BoM Solar Help:

CSIRO ASC Help:

For urgent help at all times:
  • CSIRO users 0428 108 333
  • Bureau out of hours emergencies are managed through internal policy
HPCCC WWW Site: http://www.hpccc.gov.au/
CSIRO External ASC Site: http://www.hpsc.csiro.au/
CSIRO ASC Users' Site: http://intra.hpsc.csiro.au/

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