Application: VEPPAR Application short description & Main features VEPPAR is a Grid Service Library Applications Framework for scientific visualisations. It's main idea is to provide a (more or less) generic tool(chain) which would enable scientists, researchers, artists and other users a system in which it is reasonable easy to make computer supported experiments (e.g. simulations) and visualise the results. Computer modelling and simulation now plays a very important role in development of new processes, structural modelling and technical systems in order to make them as safe, efficient and reliable as possible. As science and systems increase in complexity, so does the amount of computation required to model them effectively. The scientists should be able to use the ICST (Information Communication Scientific Technology) infrastructure, computing power and visualization to further their research. Scientific visualization is an interdisciplinary field, which can only flourish when computer graphics experts cooperate with specialists from application areas, and providers of computing, visualization, and data management facilities. Promotion of e-Science infrastructure usage can allow all researchers to attain a new level of scientific understanding and presentation, thus enabling to further their scientific endeavours. Image programming for scientific visualization by cluster and Grid computing is a prospective roadmap. See: http://veppar.irb.hr/. VEPPAR primarily integrates several Grid Service Library Applications:
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Experimental data acquired from NMR, X-ray diffraction and other experimental methods are usually stored into formatted files called PDB files that can be found at www.pdb.org. Searching through PDB files and extracting or visually representing the results, usually requires a lot of programming or using a variety of software. To make these tasks easier we created the relational model of a database, and our web interface, which enables the user to send queries to database, retrieve the results, export them into ASCII text format or POV-Ray format and send them to a computer grid for rendering the animation. |
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The work on QRBG Service has been motivated by scientific necessity (primarily of local scientific community) of running various simulations (in cluster/Grid environments), whose results are often greatly affected by quality (distribution, nondeterminism, entropy, etc.) of used random numbers. Since true random numbers are impossible to generate with a finite state machine (such as today's computers), scientists are forced to either use specialized expensive hardware number generators, or, more frequently, to content themselves with suboptimal solutions (like pseudo-random numbers generators). |
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Virtue is a Grid Service Library Application Mathematical Processor. It is a “very low level” (actually Reversed Polish Notation stack based language and its processor) mathematical processor developed for parallel execution (on SMP, cluster(s) and Grid(s)) of complex mathematical, statistical and general algorithms. |
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The Persistence of Vision Raytracer is a cross-platform application that implements the raytracing algorithm for simulating the physical behaviour of light utilizing software based mathematical models. It can be used to generate photorealistic images that resemble objects as results of simulations. PovRay is, in the framework of VEPPAR, used as a Grid Service Library Application. See: http://www.povray.org/. |
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In addition to the abovementioned Grid Service Library Applications, the VEPPAR framework consists of a Web interface and a “glue” enabling different computation elements to interwork. |
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Visualization on cluster is simpler than visualization on grid. Command qsub is used to job submission, and qstat to veiw the status of the job. Communication between nodes is much faster, so there is no need for downloading results. All results are being automaticly downloaded to your home directory or to directory where they were run from. That depends of server configuration, but the path can be set up. |
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All pictures in this gallery are used for testing infrastructure of grid, and clusters.
The first picture represents light harvesting complex which was get from PDB database with code 1RZG found at the Protein Data Bank web pages. Every atom from database file is represented as sphere (spacefill method), and uses unique color which makes it different from other atoms. H uses light blue color, C uses white color, O uses red color, N is blue. Yellow colour represents sulphur. Every atom has it's own radius. All mentioned atom atributes were get from Damir Zucic's molecular visualization software named Garlic. All PDB data was exported to relational database (developed at Unveirsity of Split, Faculty of Natural Sciences, at the Department of Physics) specially designed for easier and faster visualization and analysis of membrane proteins, or other molecules. Data salected from databse is exported into povray, and rendered on grid or clusters, depending on it's complexity.
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If you don't have enough local resources, grid is ideal solution for you. As mentioned in the distributive visualization article your input has to be split into parts and sent to grid by using the scripts.
Veppar project uses SEEgrid infrastructure where every job must be submitted with special scripts.Here is one example of those JDL scripts which are used for submission. |
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