ICTS staff members Timothy and Andrew assisted at a two week site admin and application porting school held at the University of Johannesburg.  The first week focused on lectures and hands-on practicals and covered in-depth the main topics of Grid technology as well as the gLite middleware.  The second week was spent working with researchers porting software to the Grid format.

Applications addressed in this course included HLT, Grass, NAMD, WCD and AutoDock

Application porting session

Albert van Eck joins us for lunch via video conference.

Stavros, Valeria, Tim, Andrew

The course was the second to be supported in Africa by the European Community framework project EPIKH; the Exchange Programme to advance e-Infrastructure Know-How.  Once again we were privileged to have 4 members of the INFN; Andrea Cort, Emidio Giorgio, Fabricio Pistagna and Valeria Ardezonne to assist us.

The course was followed up by workshop and report back in the coucil chambers at the university of JHB.  Thanks are due to Stavros Lambropolous from the University of Johannesburg for his institute's hospitality and hard work in setting up the venue.

Today we added srvslngrd013 to the cluster.  This is also a HPBL460, dual quad core CPU's but with 32 GB of RAM.  This brings our number of CPUs in the cluster to 16.

This weekend, Ake Fagereng from the UCT Geology department became the first UCT researcher to use the UCT High Performance Cluster in ICTS's data centre.  The HPC allowed him to run several jobs at once; with each job taking between 3 and 10 hours to complete.  Andrew Lewis, one of ICTS's two research support engineers,  says "While e-NMR have been using our hardware for some time, this is the first work submitted by a UCT researcher."

Figure:
Thermal structure of a theoretical subduction zone, in a 2d cross-section perpendicular to the trend of the margin, 100degC contour interval.

Figure:
Thermal structure of a theoretical subduction zone, in a 2d cross-section perpendicular to the trend of the margin, 100degC contour interval.  Mr Fagereng explains: "The model we tried calculates the thermal structure of an evolving subduction zone. It was published as applied to the New Zealand plate boundary by Fagereng & Ellis (Earth and Planetary Science Letters, 2009), and work on applying the model to other margins globally is ongoing as a collaboration between UCT and GNS Science (New Zealand).

I am currently also working on applying the model to predict what the thermal structure of an Archean subduction zone would have been, in collaboration with Gary Stevens' group at Stellenbosch, for use in their work on the Barberton Greenstone Belt. The data we just produced on the ICTS hardware is a first step towards the Barberton model, although more trial and failure is required before we get a model that matches observational data."

ICTS would like to take this opportunity to thank the EBE faculty for their assistance.  The jobs that Mr Fagereng ran required the use of Matlab, a software application for which ICTS doesn't own any licences. Erica le Roux, from EBE, kindly allowed ICTS to use their licence server so that a legitimate copy of Matlab could be used in the data centre.

Monday Paper recently reported on the success of the SAGrid core services team at UCT, who enabled the research activities of two very large and renowned projects. The article may have prompted readers to ask: How can my research project/experiment/collaboration obtain access to the grid?  Read more in the Monday Paper...

Andrew Lewis and Tim Carr presented a strategy for a sustainable HPC service at UCT to the ASAUDIT HPC Special Interest Group in Bloemfontein.  The talk focused on issues of attracting users, supporting applications as well as the life cycle of data center equipment.

Recent work by members of the university's Information and Communication Technology Services (ICTS) Technical Support Services team, which is part of the South African National Grid (SAGrid) national operations team, has advanced scientific collaboration between South African researchers and their international counterparts.

Read more in the Monday Paper...

UCT hosted a round table discussion for South African Bioinformatics Applications in the grid environment.  We will be investigating porting a number of bioinforatics applications to Grid format.

eNMR jobs have started running at UCT's cluster.

Andrew Lewis attended the CHPC National Meeting and 5th BELIEF Symposium in Sandton on behalf of Sakkie van Rensburg.  BELIEF (Bringing European eLectronic e-Infrastructures to Expanding Frontiers) is an EU FP7 project supporting the goals of e-Infrastructure projects.  Its objective is to coordinate the efficient & effective communication of results, networking and knowledge between e-Infrastructure projects and their users to promote worldwide development and exploitation.  The symposium was attended by over 250 delegates from South Africa and other countries.  This year's theme was “Advancing Research and Development through the National Cyberinfrastructure Initiatives”.

The CHPC put forward a proposal for a national Very Large Data Base (VLDB) which was workshopped by delegates from academic and research institutes country wide.  Other sessions included a discussion on SANReN's history, progress and future, Supercomputing for weather and climate modelling, parallel computing, development of EGEE into the sustainable EGI model as well as ICT support for HPC and grid.

UCT hosted a 1 week site administrator course followed by a 1 week application porting course.  The first week was spent demonstrating how to set up and run a basic Grid site.  The course was run by Dr Bruce Becker from the Meraka institute, Andrew Lewis and Timothy Carr from ICTS and Albert van Eck from the University of the Free State.  In essence it mimicked the course that the site operators attended in Catania in June.  However this was the first Grid course in South Africa to rely solely on South African infrastructure.  We were very fortunate to have several guests from the INFN in Catania assisting us; Emidio Giorgio, Valeria Ardizonne and Giuseppe Platania.

The second week was spent examining scientific packages selected by several South African researchers and attempting to convert them to Grid format.  While not entirely successful it gave the South African Grid team insight into the complexities of the work involved. The course relied heavily on a mini cluster supported by a 20 HP Elitebooks, generously donated by Hewlett Packard.

Many thanks to the department of Engineering as well as Erica Le Roux and her staff for the excellent venue.

The new Grid site at UCT is up and running.  It consists of a CE and a single worker node with 8 CPUs.

Andrew Lewis and Timothy Carr attended a 3 day course at the CHPC on Sun Hybrid System for storage and job submission followed by a course on parallel computing run by Dr James Wood.  The course focused on Lustre, a massively parallel distributed file system.

ICTS took delivery of 3 HP BL460G6 blade servers.  Each has 2 quad core processors (Intel Xeon 2400MHz) and 16GB of RAM.  Additionally they come with fibre channel cards to attach to the SAN.

Initially we will configure them as follows: CE, WMS and Worker node.

Timothy Carr and Andrew Lewis attended a 3 day parallel architecture course at the Center for High Perfoamce Computing in Mowbray.  The course covered new chip designs as well as programming methdology for OpenMP and MPI.  The course was run by Kunle Olukotun, a visiting Professor of Electrical Engineering and Computer Science at Stanford University.  Much of the course work was hands on programming, very challenging and thoroughly enjoyable.  Thanks also to CHPC for their hospitality.

Fixed a bandwidth problem with the Top BDII, ldap queries were taking too long.