OpenMOLE Crazy Coconut

‘He’s a nut! He’s crazy as a coconut!’

What is definitely crazy is the number of unused computers, left lying around by the march of progress, but with few simple ways to harness their power. And power means prizes, or in the world of science, papers. And possibly patents (if you’re lucky).

The opening quote, by the way (a sample featured in the the Avalanches’ Frontier Psychiatrist), is a reference to the new version of OpenMOLE, called Crazy Coconut. OpenMOLE – Open MOdeL Experiment – is  a generic workflow engine for experimenting on simulation models; in their own words, a solution to “use spare computers for model exploration”. OpenMOLE makes no distinction between a federal grid, such as EGI in Europe, or a desktop grid – it just has to be able to connect to a computer running the workflow. 

As you might expect for a technical tool, it gets quite technical, but in their own lingo a Mole is a workflow containing a succession of tasks connected by transitions. Essentially, it allows a number of variables to be explored in simulations in a wide number of disciplines.

In developmental biology, for example, OpenMOLE is being used to explore how 3D organisation of genetic material affects its transcription to make proteins, so that different genes are active in cells at different times. This kind of computation “cannot be realized on single computers because the space to be explored is too large,” says Ivan Junier, Researcher at the Center for Genomic Regulation in Barcelona. OpenMOLE is also being used for Neuronal computation, for modelling the Paris Public Transport System, to modelling the emergence of hierarchical structured populations centres in Neolithic societies and those from antiquity.

The new release has support for PBS and SSH, has an improved GUI and an inbuilt builder for distributed genetic algorithms. You can find OpenMOLE (distributed under AGPLv3) here.

...why not take a look and put those unused computers to good use? Much better than burying them in the ground, where they'll just give real moles a headache!

CloudScape II

Day one of CloudScape II in Brussels, organised by OGF-Europe, was filled with much discussion. Following the first CloudScape, held last year, the afternoon was dedicated to use case scenarios for cloud computing featuring speakers from industry and research.
It kicked off with a talk from Paul Strong of eBay who championed the idea of companies being able to 'run their business from a cellphone'. In the long term, cloud could enable us to do this, allowing businesses to focus on their ideas (their major asset) rather than the technologies that implement them. But so far clouds are being leveraged mainly in small and medium enterprises - integrating clouds into large enterprises is a non-trivial task. This is something that the RESERVOIR project are looking at, giving a large-scale perspective of cloud technologies.

In science, clouds are being used by enterprising individuals to reduce the time from idea to realisation. Paul Watson gave a great example of a PhD student at his university who independently ran his experiment on cloud rather than using university resources. Paul described a collaboration between chemists and computational scientists at Newcastle University, UK who are using the cloud to aid drug discovery. In this area of research researchers often want to answer the question 'What is the activity of a given molecule?' While this can be determined through experimentation, it takes a long time, so scientists would like to be able to predict the answer. Chemists use a method called QSAR (Quantitative Structure Activity Relationship) to do so, using the properties of other molecules to make predictions for unknown molecules. However integrating new data into these models is computationally intensive – it could take 5 years to introduce a large data set into the model. The collaboration are seeing if they can speed this up by moving the models onto the Azure cloud, and using it to split and queue tasks before returning the results.

CloudScape is an opportunity for the community to discuss the challenges we face when trying to implement clouds in research and business. Although they can offer a number of benefits, clouds do not make it easier to build complex scalable dependable distributed systems. Davide Solomon from INFN stressed the importance of leveraging on the successes we've already achieved with grid. Grids have a long history with multi-domain large scale resource sharing and using the know-how and infrastructure we've created in grids could help with issues such as interoperability, open standards and privacy in clouds. This sentiment has been echoed by the Commission who stress the importance of protecting the investment we've made in grids so far while ensuring we have enough space to innovate with other technologies. INFN are working on the coexistance of grids and clouds together with a project called WNoDes. WNoDes is reusing existing know-how to integrate cloud services through grid. For example they are giving alternative access to their service (e.g. through Shibboleth) so cloud and grid services can all be accessed in the same way.

At the networking drinks after day one of the conference, I asked delegates how they thought this event compared to last year's. While one participant thought there was not much progress from last year, others though that we've moved from asking 'are clouds useful?' to 'how can we use them?' What everyone does seem to agree on is that the development of clouds is going to be hard work. The community will have to use all the skills they've learnt so far in areas such as grid and HPC. As Kyriakos Baxevanidis said in his presentation this morning it's likely that the strong interactions between EGI, which will soon begin, and cloud initiatives in the coming months will define cloud development in the future.

Data needs in the Social Sciences and Humanities

(Submitted on behalf of Bob Jones, Enabling Grids for E-sciencE project director)

Many large-scale European research projects are currently in their planning stages, in particular those on the ESFRI roadmap (see posts tagged “ESFRI”). Now is a busy time as they outline their data management needs. For organisations like EGEE and EGI, being involved in these phases can ensure that the grid infrastructure that has been developed during the last decade will serve the needs of these scientists for many years to come.

Last week I was in Brussels at a workshop, “Common Needs and Common Solutions for the ESFRI research infrastructures for the Social Sciences and Humanities (SSH)”. This meeting was very similar to the “Workshop on ICT and e-infrastructure needs for European Research Infrastructures in Biological and Medical Sciences” held in Brussels in the middle of last month (see my blog post of December 17).

The workshop had about 30 participants with a large number of representatives from the European Commission Research & Technical Development section, a few national groups and reps from DEISA, GÉANT /DANTE, EGEE DRIVE/OpenAIRE, CLARIN, ESS (European Social Survey), DARIAH, SHARE and CESSDA.

The key points I took away from this meeting were that:

• While there is not a clear, leading SSH ESFRI project (i.e. the equivalent of ELIXIR in life science) with which e-infrastructures can interact, the SSH projects do have a subset of common needs,
• Tighter integration of SSH projects would help ensure participation from more member states,
• The quantities of data concerned by the SSH projects is not exceptional but it is dispersed across many datasets that cannot be migrated and combined into a single source
• EGI/PRACE/GÉANT3 should offer a common Authorisation & Authentication infrastructure, The support for registered, Persistent Identifiers is essential.
• The long-terms stewardship of data is a key issue that not many centres understand
• The EC itself is a source of important data, e.g. eurostat statistics, and the workshop participants would like to see more harmonization between European researchers and EC directorates and more willingness of the EC to share its own data with researchers.

Amsterdam to host EGI.org !

Amsterdam has been chosen to host EGI.org, the coordinating organization responsible for managing the European Grid Initiative (EGI).

Amsterdam was selected as the host city at the last EGI policy board meeting in Catania on Monday 2 March 2009, ahead of seven other European cities that also expressed their interest in hosting the EGI Organization.

“The choice of the location of the EGI.org headquarters is a further and decisive step towards the implementation of a sustainable European grid infrastructure”, said Gaspar Barreira, chairman of the EGI Policy Board. “From now on we will be all mobilised for the real establishment of a new international research infrastructure in Europe, where a large number of countries will put together and operate the world’s largest grid computing facility.”

"We are very honoured that the European grid community has chosen Amsterdam to host EGI.org”, said Patrick Aerts, Director of the National Compute Facility (NCF), the Netherlands, after the announcement of the decision. “We thank all EGI-Policy Board members, and especially our runners-up for the trust that they have placed in the Netherlands. This is of course a very positive result for the Science Park Amsterdam, The City of Amsterdam and NWO/NCF, which together represent the Netherlands Grid Initiative (NGI), but it is above all a shared EGI achievement.”

“The decision on the EGI.org location is another major milestone for the establishment of the EGI”, said Ludek Matyska, the EGI_DS Project Director. “With this decision, the European grid community, represented by the EGI Policy Board, confirmed once again its commitment to the EGI model as the future for grid infrastructure in Europe.”

“This decision comes just after the approval of the EGI Blueprint in Prague, on the 20th of January 2009”, added Jürgen Knobloch, the EGI_DS Technical Director. “We can now proceed with the transition strategy from EGEE and other Grid infrastructures in Europe to EGI”.

Within the EGI partnership, EGI.org and National Grid Initiatives (NGIs) will work together to operate and further develop a sustainable, long-term grid infrastructure, enabling optimal sharing of computing and data resources.

The main role of EGI.org will be to facilitate the interaction and collaboration between the different NGIs, and to provide a common managerial and operational framework for the pan-European grid infrastructure. Full operation of the organization will begin in 2010.

EGI.org, as the coordinating body, will be funded through membership fees paid by NGIs, with an expected contribution from the European Commission (EC).


More information:

www.eu-egi.eu
www.eu-egi.eu/blueprint.pdf
press@eu-egi.eu


The EGI Design Study (EGI_DS) project was launched in September 2007 with the support of the European Commission’s 7th Framework Programme. The project will continue until the end of November 2009. According to current plans, the EGI Organization will begin its functions in early 2010. The EGI_DS has nine principal partners: CESNET, CERN, CNRS, CSC, DFN, GRNET, LMU, INFN and STFC, and is already endorsed by 39 National Grid Initiatives.

Virtual Tour : European Grid Initiative

Virtual Tour : this is the turn of European Grid Initiative :



Want more on EGI? Check out the GridTalk EGI GridBriefing, the third in our fabulous fantastic informative series.

Check out http://www.gridtalk-project.eu/GT-Documents.htm to see it online soon!