40 research outputs found
High Performance Algorithms for Counting Collisions and Pairwise Interactions
The problem of counting collisions or interactions is common in areas as
computer graphics and scientific simulations. Since it is a major bottleneck in
applications of these areas, a lot of research has been carried out on such
subject, mainly focused on techniques that allow calculations to be performed
within pruned sets of objects. This paper focuses on how interaction
calculation (such as collisions) within these sets can be done more efficiently
than existing approaches. Two algorithms are proposed: a sequential algorithm
that has linear complexity at the cost of high memory usage; and a parallel
algorithm, mathematically proved to be correct, that manages to use GPU
resources more efficiently than existing approaches. The proposed and existing
algorithms were implemented, and experiments show a speedup of 21.7 for the
sequential algorithm (on small problem size), and 1.12 for the parallel
proposal (large problem size). By improving interaction calculation, this work
contributes to research areas that promote interconnection in the modern world,
such as computer graphics and robotics.Comment: Accepted in ICCS 2019 and published in Springer's LNCS series.
Supplementary content at https://mjsaldanha.com/articles/1-hpc-ssp
Parallel Unsmoothed Aggregation Algebraic Multigrid Algorithms on GPUs
We design and implement a parallel algebraic multigrid method for isotropic
graph Laplacian problems on multicore Graphical Processing Units (GPUs). The
proposed AMG method is based on the aggregation framework. The setup phase of
the algorithm uses a parallel maximal independent set algorithm in forming
aggregates and the resulting coarse level hierarchy is then used in a K-cycle
iteration solve phase with a -Jacobi smoother. Numerical tests of a
parallel implementation of the method for graphics processors are presented to
demonstrate its effectiveness.Comment: 18 pages, 3 figure
Parameterized Single-Exponential Time Polynomial Space Algorithm for Steiner Tree
"In the Steiner tree problem, we are given as input a connected n-vertex graph with edge weights in {1,2,...,W}, and a subset of k terminal vertices. Our task is to compute a minimum-weight tree that contains all the terminals. We give an algorithm for this problem with running time O(7.97^k n^4 log W) using O(n^3 log nW log k) space. This is the first single-exponential time, polynomial-space FPT algorithm for the weighted Steiner tree problem."
PLEASE NOTE:This is an author-created version that the author has self-archived to the "Aaltodoc" (aaltodoc.aalto.fi) faculty-level repository at Aalto University. The final publication is available at link.springer.com via the link http://dx.doi.org/10.1007/978-3-662-47672-7_40Peer reviewe
Collagen processing and cuticle formation is catalysed by the astacin metalloprotease DPY-31 in free-living and parasitic nematodes
The exoskeleton or cuticle performs many key roles in the development and survival of all nematodes. This structure is predominantly collagenous in nature and requires numerous enzymes to properly fold, modify, process and cross-link these essential structural proteins. The cuticle structure and its collagen components are conserved throughout the nematode phylum but differ from the collagenous matrices found in vertebrates. This structure, its formation and the enzymology of nematode cuticle collagen biogenesis have been elucidated in the free-living nematode Caenorhabditis elegans. The dpy-31 gene in C. elegans encodes a procollagen C-terminal processing enzyme of the astacin metalloprotease or bone morphogenetic protein class that, when mutated, results in a temperature-sensitive lethal phenotype associated with cuticle defects. In this study, orthologues of this essential gene have been identified in the phylogenetically diverse parasitic nematodes Haemonchus contortus and Brugia malayi. The DPY-31 protein is expressed in the gut and secretory system of C. elegans, a location also confirmed when a B. malayi transcriptional dpy-31 promoter-reporter gene fusion was expressed in C. elegans. Functional conservation between the nematode enzymes was supported by the fact that heterologous expression of the H. contortus dpy-31 orthologue in a C. elegans dpy-31 mutant resulted in the full rescue of the mutant body form. This interspecies conservation was further established when the recombinant nematode enzymes were found to have a similar range of inhibitable protease activities. In addition, the recombinant DPY-31 enzymes from both H. contortus and B. malayi were shown to efficiently process the C. elegans cuticle collagen SQT-3 at the correct C-terminal procollagen processing site
Parallel Tree Search in Volunteer Computing: a Case Study
International audienc