SUMMARY: The UNited RESisdue (UNRES) package for coarse-grained simulations, which has recently been optimized to treat large protein systems, has been implemented on Graphical Processor Units (GPUs). An over 100-time speed-up of the GPU code (run on an NVIDIA A100) with respect to the sequential code and an 8.5 speed-up with respect to the parallel Open Multi-Processing (OpenMP) code (run on 32 cores of 2 AMD EPYC 7313 Central Processor Units (CPUs)) has been achieved for large proteins (with size over 10 000 residues). Due to the averaging over the fine-grain degrees of freedom, 1 time unit of UNRES simulations is equivalent to about 1000 time units of laboratory time; therefore, millisecond time scale of large protein systems can be reached with the UNRES-GPU code. AVAILABILITY AND IMPLEMENTATION: The source code of UNRES-GPU along with the benchmarks used for tests is available at https://projects.task.gda.pl/eurohpcpl-public/unres.

An edge coloring of a graph G is called interval edge coloring if for each v ∈ V(G) the set of colors on edges incident to v forms an interval of integers. A graph G is interval colorable if there is an interval coloring of G. For an interval colorable graph G, by the interval chromatic index of G, denoted by χ'_i(G), we mean the smallest number k such that G is interval colorable with k colors. A bipartite graph G is called (α,β)-biregular if each vertex in one part has degree α and each vertex in the other part has degree β. A graph G is called (α*,β*)-bipartite if G is a subgraph of an (α,β)-biregular graph and the maximum degree in one part is α and the maximum degree in the other part is β. In the paper we study the problem of interval edge colorings of (k*,2*)-bipartite graphs, for k ∈ {3,4,5}, and of (5*,3*)-bipartite graphs. We prove that every (5*,2*)-bipartite graph admits an interval edge coloring using at most 6 colors, which can be found in O(n^{3/2}) time, and we prove that an interval edge 5-coloring of a (5*,2*)-bipartite graph can be found in O(n^{3/2}) time, if it exists. We show that every (4^*,2^*)-bipartite graph admits an interval edge 4-coloring, which can be found in O(n) time. The two following problems of interval edge coloring are known to be NP-complete: 6-coloring of (6,3)-biregular graphs (Asratian and Casselgren (2006)) and 5-coloring of (5*,5*)-bipartite graphs (Giaro (1997)). In the paper we prove NP-completeness of 5-coloring of (5*,3*)-bipartite graphs.

Abstract The Clairvoyant algorithm proposed in “A novel MPI reduction algorithm resilient to imbalances in process arrival times” was analyzed, commented and improved. The comments concern handling certain edge cases in the original pseudocode and description, i.e., adding another state of a process, improved cache friendliness more precise complexity estimations and some other issues improving the robustness of the algorithm implementation. The proposed improvements include skipping of idle loop rounds, simplifying generation of the ready set and management of the state array and an about 90-fold reduction in memory usage. Finally an extension enabling process arrival times (PATs) prediction was added: an additional background thread used to exchange the data with the PAT estimations. The performed tests, with a dedicated mini-benchmark executed in an HPC environment, showed correctness and improved performance of the solution, with comparison to the original or other state-of-the-art algorithms.