Mariusz Sterzel

InSilicoLab --- managing complexity of chemistry computations

InSilicoLab is an application portal designed to support in silico experiments by easily running computational software on Grids. Unlike manual job submission or grid portals, InSilicoLab enables its users to run complex computations without technical knowledge of how to operate the grid resources. Instead, the users may focus only on the information and activities relevant to their research. This paper is a result of a feasibility study of applying the InSilicoLab concept to the domain of computational chemistry. It, therefore, includes a study of chemistry computations and their realisation in InSilicoLab, as well as a description of the generic architecture of the environment.

Comprehensive Support for Chemistry Computations in PL-Grid Infrastructure

InSilicoLab for Chemistry with its experiments and QC Advisor are the tools assisting PL-Grid users in chemistry computations on grid infrastructure. The tools are designed to help the user at all stages of calculations --- from the software choice and input data preparation, through job submission and monitoring to the retrieval of output files and analysis of results. General Quantum Chemistry experiment helps in launching QC computations on PL-Grid. A specialized tool --- Trajectory Sculptor --- is designed for manipulations with Molecular Dynamics trajectories and large sets of molecular structures in sequential computational experiments. QC Advisor collects information about availability of different computational methods in quantum-chemical programs and supports preparation of input files for the most popular software. The main idea behind the tools described in the paper is to reduce the effort needed to set-up the calculations, allowing users to focus on scientific content of their work.

Polish computational research space for international scientific collaborations

The Polish Grid Initiative commenced in 2009 as part of the PL-Grid project funded under the framework of the Innovative Economy Operational Programme [1]. The main purpose of this Project is to provide the Polish scientific community with an IT basic platform making use of Grid computer clusters, enabling e-science research in various fields. The Project is establishing a country-wide computing platform, which supports scientific research through integration of experimental data and results of advanced computer simulations carried out by geographically-dispersed teams. The solutions applied in setting up this e-infrastructure will ensure integration with other, similar platforms around the world. In the paper some basic facts concerning the Project history are given, PL-Grid goals are described and several examples of innovative grid services and software as well as support procedures developed to-date are presented.

Development of Polish Infrastructure for Advanced Scientific Research - Status and Current Achievements

Big science needs synergistic approach from theory, experiment and computations. Significance of the computational science is still on its way up due to the importance of results concerning features of extreme time and space scales as well as of multiscale phenomena being a subject of current research. These needs have been recognized internationally and one of the activities undertaken in the last decade is the European Grid Infrastructure, consolidating national efforts on computational infrastructures developed under National Grid Initiatives (NGI). In the paper we present the way of building Polish NGI established for Polish scientists, allowing them to conduct interdisciplinary research on a national scale, and giving them transparent access to international grid resources via affiliated international grid infrastructures. The approach applied in setting up this e-infrastructure ensured integration with other similar platforms around the world, recently with special focus on domain specific solutions.

Distributed Computing Instrastructure as a Tool for e-Science

It is now several years since scientists in Poland can use the resources of the distributed computing infrastructure – PLGrid. It is a flexible, large-scale e-infrastructure, which offers a homogeneous, easy to use access to organizationally distributed, heterogeneous hardware and software resources. It is built in accordance with good organizational and engineering practices, taking advantage of international experience in this field. Since the scientists need assistance and close collaboration with service providers, the e-infrastructure is relied on users’ requirements and needs coming from different scientific disciplines, being equipped with specific environments, solutions and services, suitable for various disciplines. All these tools help to lowering the barriers that hinder researchers to use the infrastructure.

Development of Domain-Specific Solutions Within the Polish Infrastructure for Advanced Scientific Research

The Polish Grid computing infrastructure was established during the PL-Grid project (2009–2012). The main purpose of this Project was to provide the Polish scientists with an IT basic platform, allowing them to conduct interdisciplinary research on a national scale, and giving them transparent access to international grid resources via international grid infrastructures. Currently, the infrastructure is maintained and extended within a follow-up PLGrid Plus project (2011–2014). Its main objective is to increase the potential of the Polish Science by providing necessary IT services for research teams in Poland, in line with European solutions. The paper presents several examples of the domain-specific computational environments, developed within the Project. For particular environments, specialized IT solutions are prepared, i.e. dedicated software implementation and infrastructure adaptation, suited for particular researchers groups’ demands.

IS-EPOS: a platform for anthropogenic seismicity research

Research in the field of anthropogenic seismicity (AS) requires not only seismicity data but also data regarding the progress of the technological/production activities which is the origin of the induced or triggered seismic events. Such data are typically restricted and proprietary, and therefore, usually not available for independent researchers who wish to develop, perform and verify scientific research. The induced seismicity-European plate observing system (IS-EPOS) web portal offers to its user’s access to data, applications and documents in order to facilitate AS research. IS-EPOS web portal has been designed to serve as one of the main pillars of the Thematic Core Service—-Anthropogenic Hazards belonging to pan-European multidisciplinary research infrastructure created within the EPOS program. IS-EPOS platform is open for research community and general public according to its rules of access. The platform is operating since January 2016 and is now integrated in the EPOS Integrated Core Services. IS-EPOS e-platform promotes new opportunities to study and comprehend the dynamic and complex solid earth system by integrating the use of multidisciplinary data, data products, analysis models and online applications. The integration of existing and new national and transnational Research Infrastructures increases the access and use of multidisciplinary data recorded by the solid earth observing systems, acquired in laboratory experiments and/or produced by computational simulations. In this paper, we describe the structure and the main innovative characteristics implemented in IS-EPOS. The platform is open to accommodate data integrated within other research projects, and it is continuously being updated with improvements in existing features and implementations of new ones. An appendix at the end of the article provides a summary of acronyms and abbreviations in order to make the reader familiar with the terms used throughout the manuscript.