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Showing posts with label HPC. Show all posts
Showing posts with label HPC. Show all posts

Thursday, August 29, 2013

A Latin America Collage in High Performance and Large Scale Computing

Speakers and Contributions in CLCAR 2013
CLCAR 2013 in San José Costa Rica, shown an interesting "collage" of the High Performance and Large Scale Computing activity in the continent. Diversity of users, important scientific contributions and one thing in common: collaboration.

Collaboration among all scientific and academic institutions allows to develop new ideas and proposals. More and more the interaction Europe-LatinAmerica and North America-LatinAmerica is open. 

Some of the contributions in this version of CLCAR are addressed to global interests and to resolve some technical problems and open questions in related areas. In Costa Rica, this year, inspired by the most green country in the continent, Bioinformatics and biodiversity are the common subjects in the most part of the projects.

On the other hand, researchers and HPC Latin American community have meet supported by RedCLARA and some european institutions as CETA CIEMAT and Barcelona Supercomputing Center (BSC) to continue with the development of the Advanced Computing Service for Latin America and Caribbean, SCALAC (from spanish/portuguese acronym). This important meeting is the second face to face journey to address a large scale -advanced computing facility today, with the experience of the past projects EELA, EELA-2 and GISELA.

CLCAR 2013 continues until tomorrow. GridCast and ISGTW are from 2007 media partners of this important activity in Latin America.

Sunday, July 21, 2013

High Performance Computing, e-Science and Scalable Architectures Next a Volcano


36 Students from Mexico and some countries of central america have begun the participation in the 2013 version of the Supercomputing and Distributed Systems Camp. This year, the SCCAMP is conducted at the Instituto Tecnológico de Colima, in the beautiful town of Villa de Alvarez in the Colima State, México. As in 2011, the SCCamp is developed near of a volcano: the Colima Volcano.

SCCamp is an initiative of researchers to offer to undergraduate and master students a state-of-the-art knowledge upon High Performance and Distributed Computing topics. In 2013 version, students will learn topics in 7 days summer school, starting from large-scale infrastructures (Cluster, Grid, Cloud) to CUDA Programming.  Instructors are from several countries in the world: Brazil, Colombia, France, Germany, Greece, Mexico and Venezuela.

Past SC-CAMP were made in Colombia (2010), Costa Rica (2011) and Venezuela (2012). Every year an interesting special topic is proposed and selected. The special topic of this year is the use of reconfigurable architectures to scientific applications. 

The SCCAMP 2013  is supported by some international partners.  GridTalk and iSTGW are media partners of SCCAMP.

Monday, June 17, 2013

Latinamerican High Performance and Grid Computing Community calls for contributions to CLCAR 2013 in San José Costa Rica

The Latinamerican Conference on High Performance Computing (CLCAR, from spanish acronym) 2013 will be held this year in San José, Costa Rica. Since 2007, the Latin-American Conference on High Performance Computing (CLCAR) is an event for students, scientists and researchers in the areas of high performance computing, high throughput computing, parallel and distributed systems, e-science and applications, in a global context, but with special scope in latinoamerican propositions. GridCast is media-partner of this latinamerican activity.

The program and scientific committees are formed by experts and researchers from different countries and related domains. Competent people from various countries and institutes will carry out the process of evaluating the proposals. CLCAR 2013 to be held in San José,  Costa Rica, in August 26-30. 

CLCAR 2013 official languages are English, Portuguese and Spanish. People willing to present their proposals can present them mainly in two forms: Oral Presentations (Full Paper) and Posters (Extended abstract) until Sunday, June 23.

This year there are two activities proposed inside the conference: the first one, the bioinformatic and biochemistry researchers propose the bio-CLCAR, and the second, the CLCAR scientific visualization challenge. 

Different Proposals can be  submitted in  ENGLISH, PORTUGUESE or SPANISH only (full papers and extended abstracts).  Papers written in Spanish or Portuguese should have the title and its abstract in english too. The oral presentation may be in any CLCAR official language, but the slides will be in English anyway.  Selected posters from extended abstracts must be show in English.

For more information about CLCAR 2013, please visit the official site: www.clcar.org

Thursday, August 30, 2012

CLCAR 2012 hosts Parallel Workshops to L. A. Needs Using HPC and Grid Computing

Prof. Mateo Valero (BSC-Spain) during the MesoAmerica Project Workshop
CLCAR 2012 hosts parallel workshops to treat Regional Interests and project future interactions using high performance computing resources linked by Grid Computing.

One of the parallel workshops is the MesoAmerica Project workshop. The meeting is led by Luis Nuñez, responsible of Academic Communities of the RedCLARA, the Latinamerican advanced and academic network consortium.

The project, from the high performance and Grid Computing point of view, reach to provide infrastructure and computer resources to receive, transfer, treat and store climatological and geophysics data to use for early warning systems, national weather systems, from Mexico to Ecuador. 

Some Latin American supercomputer and research centres from Mexico, Costa Rica, Guatemala, Honduras, Panama, Colombia, Venezuela, Peru, Ecuador and Argentina participate in the project. But also, European partners from France and Spain, as is the case of the Barcelona Supercomputing Center directed by Prof. Mateo Valero.

Sunday, June 17, 2012

PRACE at International SuperComputing’12 – a game of two halves

Travelling round Europe during Euro 2012 can be a lively experience – in Amsterdam the orange bunting is fluttering in abundance in the streets; in Hamburg this weekend the cars all seem to have sprouted flags from their bonnets and an overactive set of car horns. I’m here for this year’s International SuperComputing event, kicking off with the PRACE workshop on Sunday. The second half will be on Tuesday with the announcement of the Future Technologies Evaluation results. Hopefully with no own goals or questions lobbed in from offside in the meantime….

Maria Ramalha, Chair of the Board of Directors for PRACE, introduced us to PRACE (Partnership for Advanced Computing in Europe), which since 2010 has worked to create a persistent pan-European Research Infrastructure, providing High Performance Computing services for researchers and industry. The infrastructure provides peer reviewed access to HPC resources in France, Germany, Italy and Spain.

Kostas Glinos, Head of the European Commission’s GÉANT and e-Infrastructures Unit outlined the importance of HPC across the world. The US believes being able to out-compute competitors equals out-competing them. Japan already has the largest HPC system in the world, the K computer and China is making multi-billion dollar investments in this area. India also announced a one billion dollar programme for its own supercomputing machine in March 2012. Meanwhile, Europe has lost 10% of its HPC capabilities since 2007, while both Asia and the US have increased. At the moment, Europe takes a fragmented approach across its different member states, relies heavily on foreign components and is not capitalising on its IPR fully, leaving others to reap the benefits. Europe represents 24% of HPC usage, for example in academia, biosciences, engineering, government and defence, but provides only 4% of the systems supply.

However, Europe does have strong potential in the areas of applications and codes, offers deep and diverse HPC user experience and has leading capabilities in certain areas, such as power efficient microelectronics. In April this year, the European Commission published a strategy communication advising member states on the way forward for HPC. This covered a number of key policy actions, looking at improving governance at a European level and issuing a recommendation to double investment nationally in HPC, as well as at European level and in industry. Kostas welcomed PRACE’s proposal to extend services for industry and urges PRACE, and others, to develop the EU’s native capacity via pre-commercial tendering and by pooling resources. HPC Consultant, Wolfgang Gentzsch pointed out that industry needs help to use HPC resources effectively, and the EC strategy also recommends training, workshops and competency centres aimed at industry. Similarly, the EC is looking to provide a level playing field for the European HPC supply industry.

The next EC funding framework programme, Horizon2020, will include funding actions to set up HPC centres of excellence, perhaps targeted to particular research communities such as the life sciences, as well as hardware and software design centres. Richard Kenway, Chair of the PRACE Scientific Steering Committee stressed that the aim is to be user-driven. Some scientific communities are more structured than others – but everyone seems to be concerned about how to move large quantities of data around. Interoperability will also be important – depending on their application, users don’t necessarily care whether their resources are from HPC or grids such as the European Grid Infrastructure at the end of the day… but they urgently need tools and professional software that can give them access to the resources they need to solve their own particular computational problems.

“Europe is ready to run the HPC race,” summarised Glinos. Europe has expertise across the full supply chain that it can build on and the race to solve the challenges of exascale computing provides a particular window of opportunity – but a joint European effort is needed. To push the football metaphor a bit further, HPC has to be a team game if we want to reach our goal of achieving a world-beating result.

Just don’t ask me to explain the offside rule.

Monday, April 30, 2012

What are Computers For?


What are computers for?

Such a big question calls for a very long answer. Hence the delay (about a month) in posting this answer, which cuts out most of my original draft. Hopefully it gets to the point.

At the EGI Community Forum, many – if not most – people were familiar with a nowadays novel application of computers: computing things. More specifically, computing things for science and engineering. So it made sense that the final plenary of the week should be given by Horst Zuse, son of the Father of the Modern computer, Konrad Zuse. He talked about the development of the computer from a unique perspective; one that reminds us that the origins of the computer are not solely placed in sunny California.
The Zuse Z3 Control Unit

Konrad Zuse is not a widely-known name, and possibly this is true for much of the world outside Germany. The unfortunate circumstances of the Second World War tended to muffle the echoes of German innovation during that time, and Zuse’s contribution to computing is no exception. In the UK, the accolade ‘Parent of the Computer’ (I’m being non-gender specific; bear with me) most often goes to Alan Turing, an incredibly gifted mathematician specialising in theories of computability and computation. If it goes to an engineer in the traditional sense, it goes to the Victorian era’s Charles Babbage, who built a machine that could be programmed to perform calculations mechanically (though latterly some credit has duly been given to Ada Lovelace, genius mathematician and Lord Byron’s daughter, for aiding Babbage in his work). Those emphasising the importance of electrical engineering would cite American Claude E Shannon, whose Master’s thesis described how to build what Turing had in his head: electrical equivalents of logic gates that together could perform any mathematical operation, given enough time. They might also recall William Shockley, another American, for inventing the transistor that made Shannon’s electrical logic gates possible. Back in England, they could look to Tommy Flowers, the (London) East End electrical engineer who built Colossus alongside Turing at Bletchley Park. Despite all these giants of history, however, it was Konrad Zuse – a civil engineer – who was the first person to build an electrically-driven program-operated floating point digital computer that counted in binary. This makes his claim of parenthood of the modern computer extremely strong.

As 1990s UK indie-dance band Jesus Jones sang, “Zeros and Ones will take you there.” But when Konrad Zuse started on his quest to build a digital computer, no-one had figured out that binary would be an efficient and error-minimising means of holding numbers. Engineers had a hard job maintaining early prototype computers, such as the Harvard Mark I, as they were constantly having to replace unwieldy digit holders, each having with a different state for each of the 10 decimal digits. If a connection in one of these numerical states was faulty, it meant the whole digit placeholder failed to work. It’s not clear whether this would cause a program to fail or just deliver an incorrect answer (if anyone knows, please feel free to comment).  This meant that decimal computers were not only unreliable, but also unwieldy. Large. Very, very big indeed. Holding a big number in binary, however, is easier than in decimal, and performing computations with it is simpler. More importantly, the physical space needed is reduced, and the computer becomes more reliable.

Zuse was an engineer but foremost he was a Creative; an Artist. The fact is, he built his early computers with the same earnestness as he produced his fine paintings and drawings, and most importantly his woodcut prints, where the mechanical process of printing is integral to the artwork. The controller for the Z3 is a beautifully-designed object, but behind the scenes the computer is pragmatism itself: mechanical relays – slower than valves in the pre-transistor era in which it arose – are nevertheless assuredly more reliable, each operation heralded by a clatter of metal on metal as the contact is made. One can’t help thinking that the mechanical act of printing, with wood pressed onto paper, had some influence on his design choice.

The 'CPU', with Control Unit at right
The Z3 was an electromechanical device, but it was a digital computer and it was Turing-complete. Given enough time, it was capable of carrying out any computation that is theoretically computable. That was a milestone by any measure; Turing’s own Colossus would take three more years to reach this marker. But it also operated in binary floating point, something later machines missed out on (and something even some electronic home computers failed to achieve in high-level interpreters decades later, the most notable being the Apple II BASIC, which was fixed point). Being able to perform calculations in floating point would have been crucial for an engineer, and – as we were told by Professor Horst Zuse – it was the laboriousness of performing repeated calculations that inspired his father to build computers. By freeing up valuable brain-time, engineers could concentrate on solving problems rather than performing calculations. It is testament to the usefulness of computers in accurately performing the intense, repetitive work of engineering problems that such problems feature heavily in grid and supercomputer workloads, alongside particle physics and molecular dynamics simulations. And so computers, for Konrad Zuse, allowed people to be creative.

This is a million miles from Douglas Engelbart’s ‘augmented human intellect’, however, let alone Steve Jobs/Alan Kay's’ ‘bicycle for the mind’. The graphical user interface did not feature in Konrad’s Zuse’s vision for the computer. As the story goes, when he met the man responsible for popularising the graphical user interface for the masses, Bill Gates, he kindly presented him with his own portrait, which Zuse had painted himself. But a photograph of that time showed him as being almost antipathetic towards a GUI-based personal computer running – or perhaps crashing – on Windows. Zuse’s artwork remained quite apart from the digital realm, perhaps closer to an idea of human-made craft from a bygone world that was disappearing around him.

Horst Zuse spoke of his father’s work with justified pride. I had a chance to talk to him afterwards about some of the science being presented in the booths that lined the conference atrium. He thought the work itself was impressive; that grid, and cloud, were both ideas worth exploring for scientific computation. But the pride with which he talked about his replica Z3, which he built himself in 1998; and the admiration he clearly had for the Barcelona Supercomputing Centre’s MareNostrum (a supercomputer in a church), made me realise that in the single machine, as a self-standing device, there is a level of artistry – that there will always be a place for these computational leviathans, the HPCs of whatever time period they represent. So, to the Antikythera Mechanism, to the Difference Engine, to Colossus, to the Z3, to MareNostrum, and to all the other supercomputers that take the grunt-work out of science in whatever age, we salute you!

Wednesday, March 28, 2012

One-stop-shop for the life sciences

The ScalaLife is a recent European Commission FP7 project that provides services, to connect researchers in the computational Life Sciences with software developers and experts, to enable faster research using high-performance computing.

Computing has become an indispensable tool for Life Science research, from protein dynamics and structure predictions, to bioinformatics and neuroinformatics.

“But, some Life Science researchers coming from a biology background, for example, are not very familiar with using powerful software and hardware resources at their disposal optimally and efficiently,” said Rossen Apostolov, the Technical Director of ScalaLife, during a presentation at the EGI Community Forum in Munich, Germany.

If a biologist wants to study a certain protein, there are many online tutorials advising the necessary software applications for parallel computing that can help him. To gain maximum performance of the available high-performance computers advice by application experts can significantly reduce the time for running these computations.

For example, simple optimisations and runtime settings of a popular application for Molecular Dynamics simulations called GROMACS can increase the speed of the simulations two or three times.

This is where ScalaLife comes in. “General users can find some of the applications very hard to understand in order to gain maximum performance. The goal of our project is to connect software users with the software developers,” said Apostolov.

“To help accelerate research, ScalaLife provides a ‘one-stop-shop’ knowledge base and expert support centre for the Life Science software communities. We provide experts who give advice on how to optimally use these codes. So much is lost when there is a lack of communication between life scientists and computer scientists,” he said.

“ScalaLife also helps users to get access to EU e-infrastructures such as EGI and PRACE, and collaborate with other researchers on improving their code bases,” said Apostolov. He explained that by giving users just a little help their software can be accelerated five times faster.

“Right now, we’re focusing on direct interaction with users and sharing knowledge of how efficiently to use applications on high-performance computers. If the project is successful, then we could develop similar centres for other communities as well,” said Apostolov.

Monday, May 10, 2010

First PRACE Petaflop System Ready for European Researchers

PRACE (the Partnership for Advanced Computing in Europe) allows researchers from across Europe to apply for time on the PRACE resources via a peer review process. This call marks the first opportunity for researchers to apply for PRACE resources. It is an early access call inviting applications for the first HPC system available to researchers through PRACE: the IBM BlueGene/P – JUGENE – hosted by the Gauss-Centre member site in Jülich, Germany.

JUGENE offers computation power of one Petaflop/s and is one of the fastest computers in the world (number 4 on the latest Top 500 list of world’s most powerful computers).

The deadline for submission of proposals is June 10th at 16.00 CEST. All proposals must be submitted via the PRACE website.

The Early access call is intended for large-scale projects that have reached a high level of scientific and technical maturity, and could benefit from a relatively small window of access (4 months) to achieve significant scientific results: results offered should lead to the anticipated publication of results in one or more high-quality journals. The projects must demonstrate scientific excellence and should cover topics of major relevance for European research and also demonstrate the need for Tier-0 resources.

Besides requesting computer time through project access, applicants may also request support from software experts for code scaling improvement and optimisation through preparatory access. Preparatory access must be followed by a project access proposal that it is linked to it.

All proposals will undergo PRACE technical and scientific assessment. The assessment procedure will adhere to the PRACE principles of peer review. For this call only proposals from academia are eligible and project leader must be homed in a European Union country or a PRACE initiative country. The JUGENE at GCS@Jülich also has further restrictions due to US export rules. All applicants should expect to be notified of the outcome by the end of July.

The first call for PRACE access with the standard allocation time of 1 year will open in June 2010. A continuous call for applications for preparatory access will be also announced in June 2010.

More information and application form: www.prace-project.eu/hpc-access, see also a related document on www.prace-project.eu/hpc-access/early_access_call.doc

More information: Prace-peer-review(at)fz-juelich.de