Parallel Simulation of a Fluid Flow by Means of the SPH Method: OpenMP vs. MPI Comparison

The SPH method for simulating incompressible fluids is presented in this article. The background and principles of the SPH method are explained and its application to incompressible fluids simulations is discussed. The parallel implementation of the SPH simulation with OpenMP and MPI environments are demonstrated. Both models of parallel implementation are analyzed and discussed. The comparison of both models is performed and discussed, as well as their results

Propagation-Based Biclustering Algorithm for Extracting Inclusion-Maximal Motifs

Biclustering, which is simultaneous clustering of columns and rows in data matrix, became an issue when classical clustering algorithms proved not to be good enough to detect similar expressions of genes under subset of conditions. Biclustering algorithms may be also applied to different datasets, such as medical, economical, social networks etc. In this article we explain the concept beneath hybrid biclustering algorithms and present details of propagation-based biclustering, a novel approach for extracting inclusion-maximal gene expression motifs conserved in gene microarray data. We prove that this approach may successfully compete with other well-recognized biclustering algorithms

Procrustes Analysis of Truncated Least Squares Multidimensional Scaling

Multidimensional Scaling (MDS) is an important class of techniques for embedding sets of patterns in Euclidean space. Most often it is used to visualize in mathbbR3 multidimensional data sets or data sets given by dissimilarity measures that are not distance metrics. Unfortunately, embedding n patterns with MDS involves processing O(n2) pairwise pattern dissimilarities, making MDS computationally demanding for large data sets. Especially in Least Squares MDS (LS-MDS) methods, that proceed by finding a minimum of a multimodal stress function, computational cost is a limiting factor. Several works therefore explored approximate MDS techniques that are less computationally expensive. These approximate methods were evaluated in terms of correlation between Euclidean distances in the embedding and the pattern dissimilarities or value of the stress function. We employ Procrustes Analysis to directly quantify differences between embeddings constructed with an approximate LS-MDS method and embeddings constructed with exact LS-MDS. We then compare our findings to the results of classical analysis, i.e. that based on stress value and correlation between Euclidean distances and pattern dissimilarities. Our results demonstrate that small changes in stress value or correlation coefficient can translate to large differences between embeddings. The differences can be attributed not only to the inevitable variability resulting from the multimodality of the stress function but also to the approximation errors. These results show that approximation may have larger impact on MDS than what was thus far revealed by analyses of stress value and correlation between Euclidean distances and pattern dissimilarities

Portable Userspace Virtual Filesystem Switch

Multiple different filesystems — including disk-based, network, distributed, abstract — arean integral part of every operating system. They are usually written as kernel modules and abstracted to the user via a virtual filesystem switch. In this paper we analyse the feasibility of reimplementing the virtual filesystem switch as a userspace daemon and applicability of this approach in real-life usage. Such reimplementation will require a way to virtualise processes behaviour related to filesystem operations. The problem is non-trivial, as we assume limited capabilities of the VFS switch implemented in userspace. We present a layered architecture comprising of a monitoring process, the VFS abstraction and real filesystem implementations. All working in userspace. Then, we evaluate this solution in four areas: portability, feasibility, usability and performance. Our results demonstrate possible gains in using the userspace-based approach with monolithic kernels, but also underline problems that are encountered in this approach

Past strong experiences determine acute cardiovascular autonomic responses to acoustic stress

Background: Stress is a major risk factor for cardiovascular (CV) disease. We hypothesized that past strong experiences might modulate acute CV autonomic responses to an unexpected acoustic stimulus. A i m: The study’s aim was to compare acute CV autonomic responses to acoustic stress between students with and without a past strong experience associated with the acoustic stimulus. Materials and Methods: Twenty five healthy young volunteers - medical and non-medical students - were included in the study. CV hemodynamic parameters, heart rate (HR), and blood pressure (BP) variability were assessed for 10 min at rest and for 10 min after two different acoustic stimuli: a standard sound signal and a specific sound signal used during a practical anatomy exam (so-called "pins"). Results: Both sounds stimulated the autonomic nervous system. The "pins" signal caused a stronger increase in HR in medical students (69 ± 10 vs. 73 ± 13 bpm, p = 0.004) when compared to non-medical students (69 ± 6 vs. 70 ± 10, p = 0.695). Rises in diastolic BP, observed 15 seconds after sound stressors, were more pronounced after the "pins" sound than after the standard sound signal only in medical students (3.1% and 1.4% vs. 3% and 4.4%), which was also reflected by low-frequency diastolic BP variability (medical students: 6.2 ± 1.6 vs. 4.1 ± 0.8 ms2, p = 0.04; non-medical students: 6.0 ± 4.3 vs. 4.1 ± 2.6 ms2, p = 0.06). Conclusions: The "pins" sound, which medical students remembered from their anatomy practical exam, provoked greater sympathetic activity in the medical student group than in their non-medical peers. Thus, past strong experiences modulate CV autonomic responses to acute acoustic stress

Parallel Approach for Visual Clustering of Protein Databases

Visualization of a large-scale protein databases may help biologists in discovering similarity between sequences of different organisms. In this article we present a complex approach for visually representing relations between proteins in large scale databases. Our approach includes sequence alignment, mutual distance measurement, clustering and classification of protein sequences. We propose a visual representation method for considered as well-established Pfam 4.0 proteins database. Our objective is to visually reflect the similarity of protein sequences in three dimensional space using non-standard approach

The Use of a Fault Tree Analysis (FTA) in the Operator Reliability Assessment of the Critical Infrastructure on the Example of Water Supply System

Background: Specialist literature indicates a large share of the human factor among the causes of failure of technical systems at the level of 70 to 90%, which depends on the sector studied. The collective water supply system is an anthropotechnical system, i.e., it is a complex connection between man and the technical system resulting from the deliberate influence of man on the technical system. Methods: The work presents an assessment of operator reliability of a selected water treatment process based on the fault tree analysis (FTA). Elementary events are determined by the operator’s error probability. Results: A failure tree was prepared for the peak event of the filter station failure, resulting from an operator’s error during the filter washing procedure. The probability of a peak event occurring is 0.0580. Conclusions: The developed fault tree allows for the identification of elementary events leading to an emergency event. The operator fulfills its task of maintaining the continuity of water treatment

Analysis of selected aspects of collective water supply system operation in the selected municipality

The purpose of the work was to analyze the exploitation of the collective water supply system (CWSS), on the example of Czudec, Podkarpackie CWSS. The water balance was prepared. The system operation was simulated using the Epanet software. The obtained data was presented in graphical form of pressure distribution on the network during the minimum and maximum demand. Water age simulations were also prepared, that is, the period of water residence in water distribution subsystem

Forecasting water use in selected water supply system

The study analyzed data on water consumption in selected municipal water supply system. The forecast was made based on daily water consumption from the period of five years (2012 ÷ 2016). The results are a valuable information source for municipal water supply system operator. Water consumption forecast allows to schedule the amount of water that should be produced e.g., taking into account day of the week, month, and the least onerous terms for water consumers to make repair or modernization of water supply system elements