Here we present a generic system for utilization of application programs in the EGEE Grid environ... more Here we present a generic system for utilization of application programs in the EGEE Grid environment - the CHARON system. Charon was developed by computational chemistry community in the Czech republic to provide easy manageable, comfortable and modular environment to fulfill specific requirements of computational chemistry application users. It currently offers an alternative to standard LCG/EGEE environment in application-generic Virtual Organization for Central Europe (VOCE). Present-day implementation of Charon system is completely compatible with scripting roots of the EGEE Grid environment, provides comfort computational jobs management by encapsulation of available LCG/EGEE middleware enviroment, support for smooth administration of large amount of computational jobs and enables easy retracing of already finished calculations. Compared to widely-spread graphical user interfaces (i.e. portals) Charon is oriented towards users requiring simple but feature-rich and powerful command line and scripting interface that offers support for tens and hundreds of jobs withing a single research project. Taking into account the cornerstones on which the system is built up - modularity and generality - it is not targeted only for molecular modelling purposes but represents a generic application framework easily adoptable for broad set of generic application areas and their specific programs. Moreover Charon also permits to utilize resources from non-EGEE Grids as well. Therefore Charon is expected to be one of useful tools available for promoting utilization of Grid environment for general public purposes.
Presentation describes Graphical User Interface for Charon Extension Layer System and Application... more Presentation describes Graphical User Interface for Charon Extension Layer System and Application Dashboards.
This contribution describes accomplishments achieved by the computational chemistry community uti... more This contribution describes accomplishments achieved by the computational chemistry community utilizing computational resources and corresponding applications within a grid environment of the Virtual Organization for Central Europe (VOCE). VOCE infrastructure, part of the EGEE II Grid, currently consists of computational resources and storage capacities provided by the Central European resource owners. VOCE currently provides a complete grid infrastructure running all necessary grid services helping thus scientists to solve their research projects and problems. One of the currently intensively studied areas of modern material design and drug discovery is chemistry of interlocked supramolecules and their mutual interactions. In the presented work, we investigate rotaxane, a supramolecular complex. Rotaxanes are interlocked molecules in which macrocycle (the 'wheel') is threaded by a long 'axle' component. Our system consists of a molecule cucurbit[7]uril (CB7) and a 4,4'-bipyridinium derivate. Experiments show a switch-like movements along the axle in this supramolecular complex. To give a detailed insight to the switch-mechanism we calculated the free energy profile along reaction coordinate related to this movement. The evaluation of the free energy is a computationally demanding task requiring extensive computational resources due to necessity to properly sample large phase-space. Currently used methods for the free energy estimations (such as umbrella, bluemoon or adaptive biassing force method) require a calculation of a huge amount of middle-length molecular dynamic simulations which can run independently in parallel. Therefore, these types of computational tasks are very well suited to exploit large grid environments like the VOCE. The complete solving of described research problem comprises approximately hundreds thousands of CPU hours at 1.6 GHz CPU with 1 GB RAM. Our results clearly demonstrate that the VOCE Grid is the place where challenging applications requiring advanced computational chemistry techniques can be easily utilized and corresponding research problems successfully solved.
Knowledge of conformational space is essential in assessment of dynamical behaviour of biomolecul... more Knowledge of conformational space is essential in assessment of dynamical behaviour of biomolecules, which is important, for example, in drug design and folding studies. Unfortunately, systematic exploration of conformational space is impossible due to its high complexity. To circumvent this problem, we have developed the program CICADA that tries to rationalize the search in such a space. In this work, we will demonstrate utilization of innovated version of CICADA in the grid environment during the study of selected middle size biomolecules.
The Charon Extension Layer (CEL) is a unique generic sys tem for computational jobs and applicati... more The Charon Extension Layer (CEL) is a unique generic sys tem for computational jobs and applications management within grid environments. It provides a sophisticated command-line interface that encapsulates all operations required to control a computational job lifetime - it allows users to submit their jobs, check jobs’ statuses and get results using only three basic commands. In this paper we present CharonGUI - a graphical user interface built over the original CEL. CharonGUI adopts all advantages of the CEL with their benefits and turns them into a graphical representation. Moreover, CharonGUI simultaneously brings a set of new interesting features that offers additional comfort for the grid end users. CharonGUI is expected to complement the command-line version of CEL allowing users to have both approaches available in parallel.
In biochemical or chemical disciplines, the free energy forms a basis for the assessment of theor... more In biochemical or chemical disciplines, the free energy forms a basis for the assessment of theoretical models towards experimental data. Unfortunately, its calculation is still very time consuming task. Recently, we have implemented and tested the multiple walker approach, which significantly accelerates such kind of calculations, in a cluster environment. Since this approach requires only small communication overhead, we would like to extend and test it in a grid environment too.
Propagacni poster MetaCentra, prezentovaný na konferenci v Nových Hradech "8th Discussions i... more Propagacni poster MetaCentra, prezentovaný na konferenci v Nových Hradech "8th Discussions in Structural Molecular Biology".
This poster describes a grid environment of the Virtual Organization for Central Europe (VOCE). V... more This poster describes a grid environment of the Virtual Organization for Central Europe (VOCE). VOCE infrastructure currently consists of computational resources and storage capacities provided by Central European resource owners. Unlike majority of other virtual organizations VOCE tends to be generic VO providing application neutral environment especially suitable for Grid newcomers allowing them to get quickly first experience with Grid computing and to test and evaluate Grid environment towards their specific application needs. VOCE facilities currently provide base for Central European t-infrastructure. The main goal of VOCE is to assist in adapting a software for use on a fully production Grid, not within a closed teaching environment, even for applications that do not have any Grid / cluster /remote computing experience. The VOCE application neutrality can be seen as an important feature that allows to provide an environment where different application requirements meet and expectations are to be fulfilled. All technical aspects related to the supported middleware (LCG, gLite), computing environments (MPI support), specific user interface support (Charon and P-GRADE portal) will be discussed and preliminary users experiences evaluated.
2] [1] CESNET z. s. p. o., Zikova 4, CZ-16000 Praha 6, Czech Republic; [2] National Abstract This... more 2] [1] CESNET z. s. p. o., Zikova 4, CZ-16000 Praha 6, Czech Republic; [2] National Abstract This article describes Charon Extension Layer (CEL) system – a uni-versal framework creating a layer upon the basic Grid middleware en-vironment and making an access to the complex Grid infrastructures much easier compared to the native middleware systems. The CEL sys-tem unifies the variability in Grid middleware (PBS, OpenPBS, LCG, gLite, etc.) allowing transparent access to distinct Grids. Moreover, the CEL system offers easy access and utilization of heterogeneous Grids in a unique, easy and smoothly integrated way. Here we present a new implementation of the high-level middleware core services provided by CEL. Specific parts of the system were rewritten to enable new set of features to be available for end users utilization. First of all, present version of CEL is capable to provide multi-Grid approach (through so-called "sites") that makes everyday CEL utilization much more c...
Managed Grids and Cloud Systems in the Asia-Pacific Research Community, 2010
The virtual organizations form a key concept for seamless utilization of all advanced features of... more The virtual organizations form a key concept for seamless utilization of all advanced features of available worldwide grid environments, the EGEE Grid in particular. However, apart from large, well organized user communities there is a substantial, non-trivial activation barrier in adopting grid concept and creating a new VO for small research groups. To minimize this barrier, a so-called “catch-all” virtual
Here we present a generic system for utilization of application programs in the EGEE Grid environ... more Here we present a generic system for utilization of application programs in the EGEE Grid environment - the CHARON system. Charon was developed by computational chemistry community in the Czech republic to provide easy manageable, comfortable and modular environment to fulfill specific requirements of computational chemistry application users. It currently offers an alternative to standard LCG/EGEE environment in application-generic Virtual Organization for Central Europe (VOCE). Present-day implementation of Charon system is completely compatible with scripting roots of the EGEE Grid environment, provides comfort computational jobs management by encapsulation of available LCG/EGEE middleware enviroment, support for smooth administration of large amount of computational jobs and enables easy retracing of already finished calculations. Compared to widely-spread graphical user interfaces (i.e. portals) Charon is oriented towards users requiring simple but feature-rich and powerful command line and scripting interface that offers support for tens and hundreds of jobs withing a single research project. Taking into account the cornerstones on which the system is built up - modularity and generality - it is not targeted only for molecular modelling purposes but represents a generic application framework easily adoptable for broad set of generic application areas and their specific programs. Moreover Charon also permits to utilize resources from non-EGEE Grids as well. Therefore Charon is expected to be one of useful tools available for promoting utilization of Grid environment for general public purposes.
Presentation describes Graphical User Interface for Charon Extension Layer System and Application... more Presentation describes Graphical User Interface for Charon Extension Layer System and Application Dashboards.
This contribution describes accomplishments achieved by the computational chemistry community uti... more This contribution describes accomplishments achieved by the computational chemistry community utilizing computational resources and corresponding applications within a grid environment of the Virtual Organization for Central Europe (VOCE). VOCE infrastructure, part of the EGEE II Grid, currently consists of computational resources and storage capacities provided by the Central European resource owners. VOCE currently provides a complete grid infrastructure running all necessary grid services helping thus scientists to solve their research projects and problems. One of the currently intensively studied areas of modern material design and drug discovery is chemistry of interlocked supramolecules and their mutual interactions. In the presented work, we investigate rotaxane, a supramolecular complex. Rotaxanes are interlocked molecules in which macrocycle (the 'wheel') is threaded by a long 'axle' component. Our system consists of a molecule cucurbit[7]uril (CB7) and a 4,4'-bipyridinium derivate. Experiments show a switch-like movements along the axle in this supramolecular complex. To give a detailed insight to the switch-mechanism we calculated the free energy profile along reaction coordinate related to this movement. The evaluation of the free energy is a computationally demanding task requiring extensive computational resources due to necessity to properly sample large phase-space. Currently used methods for the free energy estimations (such as umbrella, bluemoon or adaptive biassing force method) require a calculation of a huge amount of middle-length molecular dynamic simulations which can run independently in parallel. Therefore, these types of computational tasks are very well suited to exploit large grid environments like the VOCE. The complete solving of described research problem comprises approximately hundreds thousands of CPU hours at 1.6 GHz CPU with 1 GB RAM. Our results clearly demonstrate that the VOCE Grid is the place where challenging applications requiring advanced computational chemistry techniques can be easily utilized and corresponding research problems successfully solved.
Knowledge of conformational space is essential in assessment of dynamical behaviour of biomolecul... more Knowledge of conformational space is essential in assessment of dynamical behaviour of biomolecules, which is important, for example, in drug design and folding studies. Unfortunately, systematic exploration of conformational space is impossible due to its high complexity. To circumvent this problem, we have developed the program CICADA that tries to rationalize the search in such a space. In this work, we will demonstrate utilization of innovated version of CICADA in the grid environment during the study of selected middle size biomolecules.
The Charon Extension Layer (CEL) is a unique generic sys tem for computational jobs and applicati... more The Charon Extension Layer (CEL) is a unique generic sys tem for computational jobs and applications management within grid environments. It provides a sophisticated command-line interface that encapsulates all operations required to control a computational job lifetime - it allows users to submit their jobs, check jobs’ statuses and get results using only three basic commands. In this paper we present CharonGUI - a graphical user interface built over the original CEL. CharonGUI adopts all advantages of the CEL with their benefits and turns them into a graphical representation. Moreover, CharonGUI simultaneously brings a set of new interesting features that offers additional comfort for the grid end users. CharonGUI is expected to complement the command-line version of CEL allowing users to have both approaches available in parallel.
In biochemical or chemical disciplines, the free energy forms a basis for the assessment of theor... more In biochemical or chemical disciplines, the free energy forms a basis for the assessment of theoretical models towards experimental data. Unfortunately, its calculation is still very time consuming task. Recently, we have implemented and tested the multiple walker approach, which significantly accelerates such kind of calculations, in a cluster environment. Since this approach requires only small communication overhead, we would like to extend and test it in a grid environment too.
Propagacni poster MetaCentra, prezentovaný na konferenci v Nových Hradech "8th Discussions i... more Propagacni poster MetaCentra, prezentovaný na konferenci v Nových Hradech "8th Discussions in Structural Molecular Biology".
This poster describes a grid environment of the Virtual Organization for Central Europe (VOCE). V... more This poster describes a grid environment of the Virtual Organization for Central Europe (VOCE). VOCE infrastructure currently consists of computational resources and storage capacities provided by Central European resource owners. Unlike majority of other virtual organizations VOCE tends to be generic VO providing application neutral environment especially suitable for Grid newcomers allowing them to get quickly first experience with Grid computing and to test and evaluate Grid environment towards their specific application needs. VOCE facilities currently provide base for Central European t-infrastructure. The main goal of VOCE is to assist in adapting a software for use on a fully production Grid, not within a closed teaching environment, even for applications that do not have any Grid / cluster /remote computing experience. The VOCE application neutrality can be seen as an important feature that allows to provide an environment where different application requirements meet and expectations are to be fulfilled. All technical aspects related to the supported middleware (LCG, gLite), computing environments (MPI support), specific user interface support (Charon and P-GRADE portal) will be discussed and preliminary users experiences evaluated.
2] [1] CESNET z. s. p. o., Zikova 4, CZ-16000 Praha 6, Czech Republic; [2] National Abstract This... more 2] [1] CESNET z. s. p. o., Zikova 4, CZ-16000 Praha 6, Czech Republic; [2] National Abstract This article describes Charon Extension Layer (CEL) system – a uni-versal framework creating a layer upon the basic Grid middleware en-vironment and making an access to the complex Grid infrastructures much easier compared to the native middleware systems. The CEL sys-tem unifies the variability in Grid middleware (PBS, OpenPBS, LCG, gLite, etc.) allowing transparent access to distinct Grids. Moreover, the CEL system offers easy access and utilization of heterogeneous Grids in a unique, easy and smoothly integrated way. Here we present a new implementation of the high-level middleware core services provided by CEL. Specific parts of the system were rewritten to enable new set of features to be available for end users utilization. First of all, present version of CEL is capable to provide multi-Grid approach (through so-called "sites") that makes everyday CEL utilization much more c...
Managed Grids and Cloud Systems in the Asia-Pacific Research Community, 2010
The virtual organizations form a key concept for seamless utilization of all advanced features of... more The virtual organizations form a key concept for seamless utilization of all advanced features of available worldwide grid environments, the EGEE Grid in particular. However, apart from large, well organized user communities there is a substantial, non-trivial activation barrier in adopting grid concept and creating a new VO for small research groups. To minimize this barrier, a so-called “catch-all” virtual
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Papers by Jan Kmunicek