Bioinformatics Service Platform Sub-committees: Education and Training, Services and Support
The Bioinfomatics Service Platform would like to call for nominations for members of the following sub-committees: Education and Training, Services and Support.
The Department of Science and Technology (DST) has invested in a national Bioinformatics Service Platform (BSP) with the aim of providing a range of user-centred and well-coordinated computational bioinformatics services to the South African biotechnology industry and life science researchers. The BSP service shall encompass access to bioinformatics expertise, computational infrastructure, human capital development activities and research partnership opportunities. DST has appointed a BSP steering committee, based on a nomination process, to oversee the high level strategy or business plan of the BSP.
The sub-committees will focus on advocacy, consultation and outreach projects, as well as propose plans to address the high-level strategy areas proposed by the steering committee. The Services and Support sub-committee will review requests for hosting BSP staff and the Education and Training sub-committee will review requests for specialised courses and trainings. These committees will meet regularly to develop the strategic direction of the platform under these two activities. The BSP manager will be involved in these meetings and will be responsible for implementing these strategies. The chairpersons for these sub-committees will be appointed from the steering committee. The members of each of the sub-committees will be five, including the chairperson.
Education and Training committee will provide:
Services and Support Committee will provide:
Guidance on service models,
Guidance on support needs; and
Advice on infrastructure development (equipment).
The candidate must exhibit a firm understanding of the needs of bioinformatics services and/or training to non-bioinformaticists and clearly demonstrate at least five years of experience in one or more of the following criteria:
The committees’ composition will take into consideration ethnicity, gender and geographical representation.
The closing date for nominations of all above committees is 31October 2014.
Last Updated on Friday, 10 October 2014 11:26
South Africa has successfully defended its championship of the International Student Cluster Competition, winning the overall prize in Leipzig, Germany.
The announcement made on 25 June 2014, shocked many attendees of the International Supercomputing Conference since it is the first time a team wins the competition two years in a row. The South African Team of six was also the youngest as it was made up of undergraduate students only.
The High Performance Computing (HPC) Advisory Council Student Cluster Challenge is an opportunity to showcase the world's brightest computer science students' expertise in a friendly, yet spirited competition. Team preparations prior to the competition includes working with supervisors and vendor partners to design and build a winning cluster from commercially available components without exceeding the set power limitations, and to learn the predetermined HPC applications. The Dell computing company was the vendor partner behind the South African Team, proving all equipment. Dell also sponsored a trip to its headquarters in Austin, Texas and to the Texas Advanced Computing Center where the team received a tour of the facilities and mentoring from technicians that manage the centres. NVIDIA sponsored Graphics Processing Unit (GPU) accelerators for the team and Mellanox sponsored the interconnect.
South African team members:
· Eugene de Beste - University of the Western Cape
· Nicole Thomas - University of the Western Cape
· Saeed Natha - University of the Western Cape
· Warren Jacobus - University of the Western Cape
· Pieter Malan - University of Stellenbosch
· Ellen Nxala - University of Fort Hare
David Macleod – CHPC
Vernon Nichols – DELL
Nicholas Thorne – CHPC
Head Node (Dell R320):
· Intel E5 v2 Processor
· 8GB RAM
· 400GB RAID1 Array
· 2.4TB RAID0 Array
· Infiniband FDR
8x Compute Nodes (Dell R720):
· 2x Intel E5-2660v2 Processors
· 64GB RAM
· NVIDIA 40m GPU
· Infiniband FDR
High Performance Computing Challenge
High Performance Conjugate Gradient (a surprise application)
Lowest power consumption to complete a task (Surprise Task)
The challenge also featured High Performance LINPACK (HPL) as a side competition. The HPL score does not count towards the overall competition. To win HPL teams have to build a cluster specifically for it by using more GPUs per node and fewer nodes. This however, has a negative impact for the main competition because the team would have fewer CPU cores.
The team that won HPL had two GPUs per node and only 4 nodes. This means they had enough power to use all their GPUs and some of their CPU cores to run LINPACK. Team SA also had 8 GPUs but double the nodes. This means the team only had enough power to run LINPACK on the GPUs. All the CPU cores sat idle.
The South African cluster was deemed better balanced than those of other teams.
Teams entered into the competition included:
· Ulsan National Institute of Science and Technology (UNIST), South Korea
· A combined team of students from Massachusetts Institute of Technology (MIT), Bentley University, Northeastern University (NEU), United States
· The University of Edinburgh (EPCC), United Kingdom
· Chemnitz University of Technology, Germany
· University of Hamburg, Germany
· University of São Paulo, Brazil
· University of Colorado at Boulder, United States
· University of Science and Technology of China (USTC), China
· Two additional university teams from China
CHPC begins its Winter School next week where the selection for the 2015 team will begin.
Last Updated on Monday, 30 June 2014 10:14
Tianhe-2, a supercomputer developed by China's National University of Defense Technology has retained its position as the world's No.1 system for the third consecutive time. Tianhe-2 has performance of 33.86 petaflop/s (quadrillions of calculations per second) on the Linpack benchmark, according to the 43rd edition of the twice-yearly TOP500 list of the world’s most powerful supercomputers.
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Last Updated on Monday, 23 June 2014 14:28
CHPC has made significant progress in ensuring world-class computing services to its user-base, affiliated with international science and technology projects and put human capital development in the fore-front of its planning in the 2013-14 financial year.
CHPC has joined the Square Kilometre Array (SKA) project and forms part of the Science Data Processing (SDP) Consortium of SKA together with Cambridge University, SKA-SA and Daresbury Laboratories.
Organsations wishing to affiliate with the global project sent proposals to the SKA Office for participation. This was followed by SKA presentations of Work Package Consortia that showcased an overview of the composition, people, work concepts and approach to each particular work package. In the SDP Consortium, centre is set to contribute towards three full-time equivalent work packages: exascale prototypes, tiered data delivery and science support. In the financial year ended, CHPC participated in a number these SKA meetings. At the January 2014 meeting, held at the Juelich Supercomputing Center, final prototypes were discussed. The current heterogeneous architecture test-bed provided by CHPC, with a mixture of accelerators, will form part of the prototypes. The drive to enhance HPC astronomy competence in the centre has resulted in significant progress in the building the relationships with the MeerKAT and SKA teams.
Team South Africa scooped overall top honours on 19 June 2013 at the international Student Cluster Challenge in Leipzig, Germany, achieving the highest aggregate points total for all the benchmarks included in the competition (Linpack and the chosen applications) and acing the interview with the judges. South Africa’s resounding success was unsuspected since the country was a first time entrant. The team won over seasoned competitors from USA, China, Germany, UK and Costa Rica.
The Student Cluster Challenge is hosted by the International Supercomputing Conference (ISC) and is an opportunity to showcase student expertise in a friendly yet spirited competition. The Centre for High Performance Computing was the organizer of South African competition. In the challenge, students have a unique opportunity to learn, experience and demonstrate how high-performance computing influences our world and day-to-day learning. Held in collaboration with the High Performance Computing Advisory Council and ISC, the Student Cluster Challenge is designed to introduce the next generation of students to the high performance computing world and community.
One of the students who participated in the national competition, Mathew Cawood, completed his honours degree utilising CHPC resources. He has now been awarded a Master’s studentship and placed in the centre’s the Advance Computer Engineering Lab. The experience in the competition will assist South Africa grow a generation of high performance computing expertise for national economic development and for large projects such as SKA. South Africa will enter as defending champions in June 2014 and hopes to continue flying the flag.
The centre’s computational resources enabled about 60 peer-reviewed publications by users and 55 completions of postgraduate theses in the year. The centre is acknowledged in the published work.
After the successful completion of the pilot Bio-Informatics Service Platform (BSP), an extension of this project was granted by the Department of Science and Technology to increase the level of support for this community.
The centre received 171 new users registration in the year, 1197 helpdesk calls, a system utilization of over 91% was realised, were 22.6 million total CPU hours was provided to 537 active users with 172713 running jobs. The centre achieved a system uptime of approximately 83.8% where 5.2% was scheduled downtime for maintenance.
After the implementation of the new workload manager in the third quarter, there was significant improvement of the resource allocation to the research community. The cluster utilisation now averages about 75% with significant improvement of applications’ efficiency, where all CPU reserved for jobs are utilised.
Last Updated on Friday, 06 June 2014 13:46