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In this paper, several blocking techniques are applied to matrices that do not have a strong blocked structure. The aim is to efficiently use vectorization with current CPUs, even for matrices without an explicit block structure on nonzero elements. Different approaches are known to find fixed or variable sized blocks of nonzero elements in a matrix. We present a new matrix format for 2D rectangular blocks of variable size, allowing fill-ins per block of explicit zero values up to a user definable threshold. We give a heuristic to detect such 2D blocks in a sparse matrix. The performance of a Sparse Matrix Vector Multiplication for chosen block formats is measured and compared. Results show that the benefit of blocking formats depend – as to be expected – on the structure of the matrix and that variable sized block formats can have advantages over fixed size formats.

In this paper, a set of micro-benchmarks is proposed to determine basic performance parameters of single-node mainstream hardware architectures for High Performance Computing. Performance parameters of recent processors, including those of accelerators, are determined. The investigated systems are Intel server processor architectures as well as the two accelerator lines Intel Xeon Phi and Nvidia graphic processors. Results show similarities for some parameters between all architectures, but significant differences for others.

In this paper, a set of micro-benchmarks is proposed to determine basic performance parameters of single-node mainstream hardware architectures for High Performance Computing. Performance parameters of recent processors, including those of accelerators, are determined. The investigated systems are Intel server processor architectures and the two accelerator lines Intel Xeon Phi and Nvidia graphic processors. Additionally, the performance impact of thread mapping on multiprocessors and Intel Xeon Phi is shown. The results show similarities for some parameters between all architectures, but significant differences for others.

The Sparse Matrix Vector Multiplication is an important operation on sparse matrices. This operation is the most time consuming operation in iterative solvers and therefore an efficient execution of that operation is of great importance for many applications. Numerous different storage formats that store sparse matrices efficiently have already been established. Often, these storage formats utilize the sparsity pattern of a matrix in an appropiate manner. For one class of sparse matrices the nonzero values occur in small dense blocks and appropriate block storage formats are well suited for such patterns. But on the other side, these formats perform often poor on general matrices without an explicit / regular block structure. In this paper, the newly developed sparse matrix format DynB is introduced. The aim is to efficiently use several optimization approaches and vectorization with current processors, even for matrices without an explicit block structure of nonzero elements. The DynB matrix format uses 2D rectangular blocks of variable size, allowing fill-ins per block of explicit zero values up to a user controllable threshold. We give a simple and fast heuristic to detect such 2D blocks in a sparse matrix. The performance of the Sparse Matrix Vector Multiplication for a selection of different block formats and matrices with different sparsity structures is compared. Results show that the benefit of blocking formats depend – as to be expected – on the structure of the matrix and that variable sized block formats like DynB can have advantages over fixed size formats and deliver good performance results even for general sparse matrices.

There exist various different high- and low-level approaches for GPU programming. These include the newer directive based OpenACC programming model, Nvidia’s programming platform CUDA and existing libraries like cuSPARSE with a fixed functionality. This work compares the attained performance and development effort of different approaches based on the example of implementing the SpMV operation, which is an important and performance critical building block in many application fields. We show that the main differences in development effort using CUDA and OpenACC are related to the memory management and the thread mapping.

Quantum mechanical theories are used to search and optimized the conformations of proposed small molecule candidates for treatment of SARS-CoV-2. These candidate compounds are taken from what is reported in the news and in other pre-peer-reviewed literature (e.g. ChemRxiv, bioRxiv). The goal herein is to provided predicted structures and relative conformational stabilities for selected drug and ligand candidates, in the hopes that other research groups can make use of them for developing a treatment.