Marek Pogoda

Complex fluid-dynamical phenomena modeled by large-scale molecular-dynamics simulations

We carried out large-scale molecular-dynamics simulations of the classical Rayleigh–Taylor (RT) phenomenon in a Lennard-Jones molecular liquid. We have observed from these simulations, involving 106–107 particles, the development of hydrodynamic instabilities from two different kinds of interacting particles. A free surface is introduced by deploying an overlying void. For a box with a dimension up to about 1 μm and two layers having different particle sizes, the fingering type of instability is observed as a result of oscillations caused by the gravitational field. In this gridless scheme, surface waves can be captured self-consistently. For equally sized particles, a spontaneous “fluctuation driven” mixing with a long start-up time is observed. These molecular- dynamics results suggest the possibilities of upscaling the RT phenomenon. For conducting these numerical experiments, which require at least ∼105 time steps, a single simulation would require 100–200 Tflops of massively parallel computer power. ...

Transmission Rates and Performance of a Network of Computers

Transmission rates for two communication schemes: ping/pong and ring transfer have been measured on multiprocessors and clusters of workstations. Performance of a network of computers as a tool for numerically intensive computing has been evaluated on the basis of SLALOM and EP-NAS parallel benchmarks.

Molecular dynamics and lattice gas parallel algorithms for transputers and networked workstations

Abstract In this paper we present parallel algorithms for molecular dynamics and lattice gas simulations for hydrodynamics phenomena at the microscopic level. Characteristics of the algorithms (execution time, efficiency and speedup) are shown for the transputer networks and for the networks of SUN SPARC and IBM RS/6000 workstations. Some of the results are compared with those obtained on the iPSC/860 multiprocessor computer.

MANAGEMENT METHODS IN SLA-AWARE DISTRIBUTED STORAGE SYSTEMS

Traditional data storage systems provide access to user’s data on the “best effort” basis. While this paradigm is sufficient in many use cases it becomes an obstacle for applications with Quality of Service (QoS) constraints. Service Level Agreement (SLA) is a part of the contract agreed between the service provider and the client and contains a set of well defined QoS requirements regarding the provided service and the penalties applied in case of violations. In the paper we propose a set of SLA parameters and QoS metrics relevant to data storage processes and the management methods necessary for avoiding SLA violations. A key assumption in the proposed approach is that the underlying distributed storage system does not provide functionality for resource or bandwidth reservation for a given client request.

Storing Large Volumes of Structured Scientific Data on Tertiary Storage

As the scientific data become larger and larger, a method is needed to store and retrieve it in time- and cost-efficient way. NCSA HDF is a data/programming model widely used for storing and sharing scientific data. We present an approach to store large volumes of structured scientific data in HDF format on tertiary storage.

Parallel Distributed 2-D Short-Range Molecular Dynamics on Networked Workstations

In the paper we present efficient parallel algorithm for molecular dynamics simulation of 2-D Lennard-Jones systems with large number of particles (106+). Computational complexity is reduced by use of neighbour and link lists. The algorithm was implemented on networked workstations under PVM programming environment and optimized for the execution time and the memory requirements.

Model of QoS Management in a Distributed Data Sharing and Archiving System

Abstract The scientific applications of the fourth paradigm of science deal with large amounts of data stored in various storage devices or systems. Distributed storage systems are often chosen for storing these data. Some of the requirements posed to those storage systems may concern Quality of Service (QoS) aspects formally expressed in a Service Level Agreement. The QoS management in distributed storage systems is a challenging task given the possible storage device heterogeneity, the dynami- cally changing data access patterns, the clients concurrency and storage resource sharing. The problem becomes even more complicated when distributed computing environments with virtualized and shared resources like Clouds are considered. In this paper we present our research concerning the methods of storage performance management with respect of QoS in dis- tributed environments which has been done within the National Data Storage 2 (NDS2) project. A new model of storage QoS management is proposed and its implementation within NDS2 is described.

Replica management for national data storage

National Data Storage is a distributed data storage system intended to provide high quality backup, archiving and data access services. These services guarantee high level of data protection as well as high performance of data storing and retrieval by using replication techniques. In this paper some conceptual and implementation details on creating a Prediction and Load Balancing Subsystem for replica management are presented. Preliminary real system test results are also shown.

Large-Scale Molecular Dynamics Experiments on Cray T3E System

The latest results of large scale MD simulations of Rayleigh-Taylor instability on Cray T3E System are presented. It is shown that using large (106+) Lennard-Jones particles ensembles it is possible to investigate the spontaneous initialization of mixing, i.e., the process neglected by the standard finite elements hydrocodes.