TY - JOUR A1 - Wende, Florian A1 - Marsman, Martijn A1 - Kim, Jeongnim A1 - Vasilev, Fedor A1 - Zhao, Zhengji A1 - Steinke, Thomas T1 - OpenMP in VASP: Threading and SIMD JF - International Journal of Quantum Chemistry N2 - The Vienna Ab initio Simulation Package (VASP) is a widely used electronic structure code that originally exploits process-level parallelism through the Message Passing Interface (MPI) for work distribution within and across nodes. Architectural changes of modern parallel processors urge programmers to address thread- and data-level parallelism as well to benefit most from the available compute resources within a node. We describe for VASP how to approach for an MPI + OpenMP parallelization including data-level parallelism through OpenMP SIMD constructs together with a generic high-level vector coding scheme. We can demonstrate an improved scalability of VASP and more than 20% gain over the MPI-only version, as well as a 2x increased performance of collective operations using the multiple-endpoint MPI feature. The high-level vector coding scheme applied to VASP's general gradient approximation routine gives up 9x performance gain on AVX512 platforms with the Intel compiler. Y1 - 2018 U6 - https://doi.org/10.1002/qua.25851 IS - Emerging Architectures in Computational Chemistry SP - e25851 PB - Wiley Online Library ER - TY - JOUR A1 - Knoop, Helge A1 - Gronemeier, Tobias A1 - Sühring, Matthias A1 - Steinbach, Peter A1 - Noack, Matthias A1 - Wende, Florian A1 - Steinke, Thomas A1 - Knigge, Christoph A1 - Raasch, Siegfried A1 - Ketelsen, Klaus T1 - Porting the MPI-parallelized LES model PALM to multi-GPU systems and many integrated core processors: an experience report JF - International Journal of Computational Science and Engineering. Special Issue on: Novel Strategies for Programming Accelerators N2 - The computational power and availability of graphics processing units (GPUs), such as the Nvidia Tesla, and Many Integrated Core (MIC) processors, such as the Intel Xeon Phi, on high performance computing (HPC) systems is rapidly evolving. However, HPC applications need to be ported to take advantage of such hardware. This paper is a report on our experience of porting the MPI+OpenMP parallelised large-eddy simulation model (PALM) to multi-GPU as well as to MIC processor environments using the directive-based high level programming paradigm OpenACC and OpenMP, respectively. PALM is a Fortran-based computational fluid dynamics software package, used for the simulation of atmospheric and oceanic boundary layers to answer questions linked to fundamental atmospheric turbulence research, urban modelling, aircraft safety and cloud physics. Development of PALM started in 1997, the project currently entails 140 kLOC and is used on HPC farms of up to 43,200 cores. The main challenges we faced during the porting process are the size and complexity of the PALM code base, its inconsistent modularisation and the complete lack of a unit-test suite. We report the methods used to identify performance issues as well as our experiences with state-of-the-art profiling tools. Moreover, we outline the required porting steps in order to properly execute our code on GPUs and MIC processors, describe the problems and bottlenecks that we encountered during the porting process, and present separate performance tests for both architectures. These performance tests, however, do not provide any benchmark information that compares the performance of the ported code between the two architectures. Y1 - 2017 PB - Inderscience ET - Special Issue on: Novel Strategies for Programming Accelerators ER -