Abstract: Urban flooding resulting from a sudden release of
water due to dam-break or excessive rainfall is a serious threatening
environment hazard, which causes loss of human life and large
economic losses. Anticipating floods before they occur could
minimize human and economic losses through the implementation
of appropriate protection, provision, and rescue plans. This work
reports on the numerical modelling of flash flood propagation
in urban areas after an excessive rainfall event or dam-break.
A two-dimensional (2D) depth-averaged shallow water model is
used with a refined unstructured grid of triangles for representing
the urban area topography. The 2D shallow water equations are
solved using a second-order well-balanced discontinuous Galerkin
scheme. Theoretical test case and three flood events are described
to demonstrate the potential benefits of the scheme: (i) wetting and
drying in a parabolic basin (ii) flash flood over a physical model of
the urbanized Toce River valley in Italy; (iii) wave propagation on
the Reyran river valley in consequence of the Malpasset dam-break
in 1959 (France); and (iv) dam-break flood in October 1982 at the
town of Sumacarcel (Spain). The capability of the scheme is also
verified against alternative models. Computational results compare
well with recorded data and show that the scheme is at least as
efficient as comparable second-order finite volume schemes, with
notable efficiency speedup due to parallelization.
Abstract: The main goal of this article is to describe the online
flood monitoring and prediction system Floreon+ primarily developed
for the Moravian-Silesian region in the Czech Republic and the basic
process it uses for running automatic rainfall-runoff and
hydrodynamic simulations along with their calibration and
uncertainty modeling. It takes a long time to execute such process
sequentially, which is not acceptable in the online scenario, so the use
of a high performance computing environment is proposed for all
parts of the process to shorten their duration. Finally, a case study on
the Ostravice River catchment is presented that shows actual
durations and their gain from the parallel implementation.
Abstract: In a previous work, we presented the numerical
solution of the two dimensional second order telegraph partial
differential equation discretized by the centred and rotated five-point
finite difference discretizations, namely the explicit group (EG) and
explicit decoupled group (EDG) iterative methods, respectively. In
this paper, we utilize a domain decomposition algorithm on these
group schemes to divide the tasks involved in solving the same
equation. The objective of this study is to describe the development
of the parallel group iterative schemes under OpenMP programming
environment as a way to reduce the computational costs of the
solution processes using multicore technologies. A detailed
performance analysis of the parallel implementations of points and
group iterative schemes will be reported and discussed.
Abstract: Protein 3D structure prediction has always been an
important research area in bioinformatics. In particular, the
prediction of secondary structure has been a well-studied research
topic. Despite the recent breakthrough of combining multiple
sequence alignment information and artificial intelligence algorithms
to predict protein secondary structure, the Q3 accuracy of various
computational prediction algorithms rarely has exceeded 75%. In a
previous paper [1], this research team presented a rule-based method
called RT-RICO (Relaxed Threshold Rule Induction from Coverings)
to predict protein secondary structure. The average Q3 accuracy on
the sample datasets using RT-RICO was 80.3%, an improvement
over comparable computational methods. Although this demonstrated
that RT-RICO might be a promising approach for predicting
secondary structure, the algorithm-s computational complexity and
program running time limited its use. Herein a parallelized
implementation of a slightly modified RT-RICO approach is
presented. This new version of the algorithm facilitated the testing of
a much larger dataset of 396 protein domains [2]. Parallelized RTRICO
achieved a Q3 score of 74.6%, which is higher than the
consensus prediction accuracy of 72.9% that was achieved for the
same test dataset by a combination of four secondary structure
prediction methods [2].
Abstract: The deterministic quantum transfer-matrix (QTM)
technique and its mathematical background are presented. This
important tool in computational physics can be applied to a class of
the real physical low-dimensional magnetic systems described by the
Heisenberg hamiltonian which includes the macroscopic molecularbased
spin chains, small size magnetic clusters embedded in some
supramolecules and other interesting compounds. Using QTM, the
spin degrees of freedom are accurately taken into account, yielding
the thermodynamical functions at finite temperatures.
In order to test the application for the susceptibility calculations to
run in the parallel environment, the speed-up and efficiency of
parallelization are analyzed on our platform SGI Origin 3800 with
p = 128 processor units. Using Message Parallel Interface (MPI)
system libraries we find the efficiency of the code of 94% for
p = 128 that makes our application highly scalable.