Authors: SimonBenjaminssona, David Silversteina, PawelHermana, Paul Melisb, Vladimir Slavnićc,Marko
Spasojevićc, KirilAlexievd, Anders Lansnera,

a Dept of Computational Biology, CSC,KTH Royal institute of Technology
b Visualization Group, SARA, SciencePark 140, 1098 XG, Amsterdam, The Netherlands
c Scientific Computing Laboratory,Institute of Physics Belgrade, University of
Belgrade, Pregrevica 118, 1108,Belgrade, Serbia
d Department of Mathematical Methodsfor Sensor Information Processing, Institute of Information
and Communication Technologies, 25AAcad.G.Bonchev Str., Sofia 1113, Bulgaria

Abstract: This project concerned the development of tools for visualization of output from brain simulations performed on supercomputers. The project had two main parts: 1) creating visualizations using large-scale simulation output from existing neural simulation codes, and 2) making extensions to some of the existing codes to allow interactive runtime (in-situ) visualization. In 1) simulation data was converted to HDF5 format and split over multiple files. Visualization pipelines were created for different types of visualizations, e.g. voltage and calcium. In 2) by using the VisIt visualization application and its libsim library, simulation code was instrumented so that VisIt could access simulation data directly. The simulation code was instrumented and tested on different clusters where control of simulation was demonstrated and in-situ visualization of neural unit’s and population data was achieved.

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Authors: MarziaRivia, Luigi Caloria, Giuseppa Muscianisia,Vladimir Slavnicb
aCINECA, via Magnanelli 6/3,40033 Casalecchio di Reno, Italy
bScientific ComputingLaboratory, Institute of Physics Belgrade, University of Belgrade,Pregrevica 118, 1108, Belgrade, Serbia

Abstract: In this paper we present an investigation about techniques and frameworks supporting in situ-visualization. With this term we mean that visualization is coupled with simulation and it occurs whilst the simulation is running. By coupling these together we can utilize the high performance computing for post processing, and we can circumvent the bottlenecks associated with storing and retrieving data in disk storage. Moreover it allows monitoring the simulation in-situ, performing not only visualization, but analysis of the incoming data as it is generated so that the simulation may be stopped or modified, thereby conserving CPU resources. In particular we have tested two techniques, by exploiting different visualization tools on two applications. The first one is the astrophysics code Pluto instrumented by using a ParaView plug-in called ICARUS, the second one is the neural simulator code BrainCore instrumented by using a library of VisIt.

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Authors: Dr. ValentinPavlov, Dr. Miroslav Iliev, Anton Tomov, Veslin Slavchev, DimitarDimitrov, Nina Ilieva
NCSA, Acad. G. Bonchev str., bl. 25A,Sofia 1113, Bulgaria

Abstract: Visualization is a key post-processing activity for petaflops simulations. In this paper we have researched, identified and implemented a methodology suitable for carrying out this activity, based on the VisIt open-source visualization tool by LLNL. We have installed the toolkit on a specialized hardware in NCSA’s Tier-1 facilities in Sofia, integrating it with our primary Tier-1 system, an IBM Blue Gene/P. We have researched the possibility to support GROMACS, CP2K and NAMD data formats and proposed best practice procedures. The experience and methodology is documented and can be used to integrate the tools into other PRACE facilities.

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These whitepapers have been prepared by the PRACE Implementation Phase Projects and in accordance with the Consortium Agreements and Grant Agreements n° RI-261557, n°RI-283493, or n°RI-312763.

They solely reflect the opinion of the parties to such agreements on a collective basis in the context of the PRACE Implementation Phase Projects and to the extent foreseen in such agreements. Please note that even though all participants to the PRACE IP Projects are members of PRACE AISBL, these whitepapers have not been approved by the Council of PRACE AISBL and therefore do not emanate from it nor should be considered to reflect PRACE AISBL’s individual opinion.

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