Thursday, July 29, 2010

Ikerchem: Pharmacy, Chemical and Computational Design

Extremely good and important news:

"IkerChem specializes in the computational design and synthesis of Novel Chemical Entities (NCEs) with therapeutic applications in oncology."

They have recently won a National entrepreneurship award, prestigious emprendedorxxi sponsored by la Caixa.

Surfing the web I found this interesting interview in English. I would like to highlight the following part:

"Computing greatly facilitates laboratory work, is that right?

Yes, undoubtedly; and even more so being a small enterprise. One of the approaches of the multinationals is to take a group of compounds and subject them to massive trials to see which are the four or five molecules that might function. We do not have the wherewithal to carry out this in such a wide-scale manner. This is why our approach is based on analysing the biological system on the computer and undertaking amore selective search."

Finally a video from the contest -in spanish, though:

And this is what I call multidisciplinary and success. A group that emerged from the basque university, that probably used its computing and modest resources and that has such a promising future ahead. These are the people to help.

Saturday, July 24, 2010

ESS-Bilbao q&a proposal mentioned national computing centres

Locally we could not mention any. Even if we had them, we would and we will need to send data away, process it and bring it back. But what is worse, access to the resources is not guaranteed because we depend on external scientific review panels.

Saturday, July 17, 2010

Ikerlan and Simulation

The IKERLAN Technology research centre is a private non-profit making entity with a public service vocation, created in 1974 at the initiative of a group of companies and entities which today form part of the MONDRAGON Corporation.

Within their extensive and excel career we can identify at least the use of CFD simulation softwares for the Microsystems laboratory. Concretely the following softwares:

Design and simulation: Multiphysics finite elements simulation with:
  • Ansys Multiphysics.
  • CFD-ACE+
  • Fluid simulation with Fluent.
  • Optical simulation with Alcatel OlympiOs
  • Mask design with Alcatel Odin.
  • Encapsulation design with ProEngineer.
The following video explains and shows the centre, and it is in English.

Perhaps more computing resources, coordinated would let them scale and do fine grain simulations, and obtain more accurate resources. But for that we need to coordinate our computing resources.

Friday, July 16, 2010

Gaiker uses simulation to get a patent

Gaiker-IK4 research centre patented after running ANSYS simulations and deciding design parameters with the use of computers.

This is indeed good news and a very good reason. We need to organise our computing infrastructure, it is becoming more and more important.

Wednesday, July 14, 2010

Angel Rubio goes away to compute

Professor Angel Rubio has been actively using resources from the Spanish Supercomputing Network. His group activities are "focused on the field of theory and modelling of electronic and structural properties in condensed matter and on developing novel theoretical tools and computational codes to investigate the electronic response of solids and nanostructures to external electromagnetic fields."

Some numbers:

-In 2006: at least 40k hours
-In 2007: at least 90k hours
-In 2008: at least 150k hours
-In 2009: at least 600k + (450k + 450k) hours
-In 2010: at least 400k + 180k hours

Total of 2360k cpu / hours only in this network.

We could easily assume that he will mostly run jobs of 128 cores size (to develop and use advance computational codes).

That is to say, Angel Rubio used 18437 hours in the last three years for his average job size. 768 days or 2 complete years.

This is indeed a lot.

Seeing this, seeing the importance on his work and how well he does it, perhaps we should consider upgrade our resources, and again, as I always say, build and manage a shared infrastructure with all the basque science network members: why do it separately ? It is more expensive, it does not scale well and the data centres are under several risks due to their size and sometimes quality.

What is more, our business could improve their products significantly if they shared such facility.

INASMET-Tecnalia and casting processes simulation

The slides, distributed by INASMET tecnalia show the centre's works on simulation. As I explained INASMET is soon going to be Tecnalia. They are a relevant Materials research centre, so I assume simulation is quite important. However it is unknown whether they own a parallel computer.

These slides were found here, a blog about this topic.

Tuesday, July 13, 2010

Labein-Tecnalia goes away to compute

Labein Tecnalia, very soon Tecnalia, created not long ago NANOC the centre for Nanomaterials Applications in construction. Here they work with CSIC the Spanish National Research Council.

It is very interesting that these guys are working on high performance materials for construction. However they need to use other people's high performance computing resources to do so.

Having a look at CESGA's annual report, these partners have been calculating on the Galician centre's resources for the 2007-2009 period and I believe that possible during 2010 as well.

Some quick numbers:

-They used 673,861 cpu hours (2007-2009 period)
-Assuming their codes used around 128 cpus (lets say SIESTA code, but I do not know them so I have to pick one :) )
-This means 219 days in 3 years or 73 days per year.

Now, my opinion: I do not know these guys, but I wonder, having as we have resources here and probably sometimes misused, and assuming the Tecnalia and the local universities work together in certain projects: why dont they finally team up to excel in the hardware/software management (at least) ?