High Performance Computing conferences in Galicia - May 2010

Next week there will be two meetings here in Galicia on HPC (that I am aware of, at least). The first is Tuesday, on Santiago the Compostela:

Título: Open Cirrus Cloud Computing Testbed
Ponente: Dejan Miljicic, Senior Researcher at HP and Managing Director OPEN CIRRUS
Data: 18 de Maio do 2010
Hora: 11:30h.
Lugar: Sala de Presentaciones do CESGA (Avda. de Vigo s/n)

ABSTRACT:
There are a number of important and useful testbeds, such as PlanetLab, EmuLab, IBM/Google cluster, and Amazon EC2/S3, that enable researchers to study different aspects of distributed computing. However, no single testbed supports research spanning systems, applications, services, open-source development, and datacenters. Towards this end, we have developed Open Cirrus, a cloud computing testbed for the research community that federates heterogeneous distributed data centers. Open Cirrus offers a cloud stack consisting of physical and virtual machines, and global services, such as sign-on, monitoring, storage, and job submission. By developing the testbed and making it available to the research community, we hope to help spur innovation in cloud computing and catalyze the  development of an open source stack for the cloud. In addition to presenting Open Cirrus, this talk will also include a number of important research effort currently undergoing in Open Cirrus, such as Cloud Sustainability Dashboard, OpenNet, ExaScale Data Center, Mercado (Cloud Services market Places), Federation of Open Cirrus and Planet Lab/GENI, etc.

And the second is the Workshop of the Galician Network of HPC, here in Vigo, on Friday:

Aplicaciones de la Supercomputación

Programa

Fecha: 21 de Mayo de 2010
Lugar: Salón de Actos del Edificio de Ciencias Experimentales, Campus Universitario, Universidad de Vigo, Vigo

Horarios

09:50 Apertura y presentación del WorkShop e invitados

10:00 Iain S. Duff - STFC Rutherford Appleton Laboratory, Oxfordshire, UK and CERFACS, Toulouse, France
Título: The solution of really large linear systems arising from discretizations of three-dimensional problems

10:45 Alexandros Stamatakis - Technische Universität München, Germany
Título: Orchestrating Phylogenetic Likelihood Computations on Parallel Architectures

11:30 Coffee Break

12:00 Andrew Gettelman - National Center for Atmospheric Research, Boulder, CO, USA
Título: Simulating Earth's Climate and Chemistry with the Earth's Biggest Computers

12:45 Clausura del WorkShop

Modeller 9v8 release

I just received this e-mail about the modeller software for protein structure comparative modeling and alignment. It's not open source, but I remember that many people depended on it. How is the situation now?

The new version of Modeller, 9v8, is now available for download! Please see the download page at http://salilab.org/modeller/ for more information.

If you have a license key for Modeller 8 or 9, there is no need to reregister for Modeller 9v8 - the same license key will work. (It won't do any harm to reregister if you want to, though!)

9v8 is primarily a bugfix release relative to the last public release (9v7). Major user-visible changes include:Silicon Graphics (IRIX) binaries are no longer provided. If you wish to use Modeller on an IRIX machine, please use the older 9v7 version.

• Residues treated as BLK no longer have to be HETATM residues; they will be marked as ATOM if so defined in restyp.lib or in the template  PDB (for example, DNA or RNA residues). automodel.nonstd_restraints()  now builds restraints on both HETATM and BLK residues.
• Bonds between BLK residues are now detected by a simple distance criterion and are restrained more strongly than other distances by automodel.nonstd_restraints().
• A new method Chain.join() allows chain breaks between chains to be removed.
• Files compressed with 'xz' can now be read, provided that the 'xz' binary is available on your system.
• The allow_alternates option to alignment.append() will now allow G in the alignment sequence to match any non-standard residue type in the PDB file which maps to G. This is useful if the alignment sequence is 'cleaned' as by sequence_db.read().

See the Modeller manual for a full change log: http://salilab.org/modeller/9v8/manual/node38.html

If you encounter bugs in Modeller 9v8, please see http://salilab.org/modeller/9v8/manual/node10.html for information on how to report them.

Recent CUDA applications

Taking a look at Nvidia's CUDA zone I found some recent additions - besides important ones that I already knew like the Smith-Waterman and the phylogenetic likelihood algoritihms. Here is a list of these new programs and libraries that take advantage of GPUs:

1. Expectation Maximization algorithm for Gaussian Mixture Models
2. Multilevel algorithm for MDS (multidimensional scaling)
3. Multiclass classifier based on SVMs (support vector machines)
4. GPU computing in the R statistical environment (BLAS lowlevel routines and dist(), hclust(), cor(), and granger.test() functions)
5. Smith-Waterman algorithm for sequence database search
6. Quicksort library
7. Feature finding algorithm for mass spectrometry
8. Smith-Waterman algorithm for sequence alignment
9. MDR (multifactor dimensionality reduction) algorithm for detecting genetic epistatic interactions (white paper)
   

The last reference is just a two-page summary, and the 8th reference is behind a paywall - I couldn't access it myself - but the slides are available here.

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