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 - TY - CHAP A1 - Fajerski, J. A1 - Noack, Matthias A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - Schütt, Thorsten A1 - Steinke, Thomas T1 - Fast In-Memory Checkpointing with POSIX API for Legacy Exascale-Applications T2 - SPPEXA Symposium 2016 Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-40528-5_19 ER - TY - GEN A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko N2 - Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term obser- vations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial dis- tribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending. T3 - ZIB-Report - 17-78 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66338 SN - 1438-0064 ER - TY - CHAP A1 - Noack, Matthias T1 - OpenCL in Scientific High Performance Computing: The Good, the Bad, and the Ugly T2 - Proceedings of the 5th International Workshop on OpenCL N2 - For writing a new scientific application, portability across existing and future hardware should be the major design goal, as there is a multitude of different compute devices, and programme codes typically outlive systems by far. Unlike other programming models that address parallelism or heterogeneity, OpenCL does provide practical portability across a wide range of HPC-relevant architectures. Other than that, it has a range of further advantages like being a library-only implementation, and using runtime kernel-compilation. We present experiences with utilising OpenCL alongside C++, MPI, and CMake in two real-world scientific codes. Our targets are a Cray XC40 supercomputer with multi- and many-core (Xeon Phi) CPUs, as well as multiple smaller systems with Nvidia and AMD GPUs. We shed light on practical issues arising in such a scenario, like the interaction between OpenCL and MPI, discuss solutions, and point out current limitations of OpenCL in the domain of scientific HPC from an application developer's and user's point of view. Y1 - 2017 U6 - https://doi.org/10.1145/3078155.3078170 SP - 12:1 EP - 12:3 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Dust and gas emission from cometary nuclei: the case of comet 67P/Churyumov-Gerasimenko JF - Advances in Physics: X N2 - Comets display with decreasing solar distance an increased emission of gas and dust particles, leading to the formation of the coma and tail. Spacecraft missions provide insight in the temporal and spatial variations of the dust and gas sources located on the cometary nucleus. For the case of comet 67P/Churyumov-Gerasimenko (67P/C-G), the long-term obser- vations from the Rosetta mission point to a homogeneous dust emission across the entire illuminated surface. Despite the homogeneous initial dis- tribution, a collimation in jet-like structures becomes visible. We propose that this observation is linked directly to the complex shape of the nucleus and projects concave topographical features into the dust coma. To test this hypothesis, we put forward a gas-dust description of 67P/C-G, where gravitational and gas forces are accurately determined from the surface mesh and the rotation of the nucleus is fully incorporated. The emerging jet-like structures persist for a wide range of gas-dust interactions and show a dust velocity dependent bending. Y1 - 2018 U6 - https://doi.org/10.1080/23746149.2017.1404436 VL - 3 IS - 1 SP - 1404436 ER - TY - GEN A1 - Kramer, Tobias A1 - Noack, Matthias T1 - On the origin of inner coma structures observed by Rosetta during a diurnal rotation of comet 67P/Churyumov-Gerasimenko. N2 - The Rosetta probe around comet 67P/Churyumov-Gerasimenko (67P) reveals an anisotropic dust distribution of the inner coma with jet-like structures. The physical processes leading to jet formation are under debate, with most models for cometary activity focusing on localised emission sources, such as cliffs or terraced regions. Here we suggest, by correlating high-resolution simulations of the dust environment around 67P with observations, that the anisotropy and the background dust density of 67P originate from dust released across the entire sunlit surface of the nucleus rather than from few isolated sources. We trace back trajectories from coma regions with high local dust density in space to the non-spherical nucleus and identify two mechanisms of jet formation: areas with local concavity in either two dimensions or only one. Pits and craters are examples of the first case, the neck region of the bilobed nucleus of 67P for the latter one. The conjunction of multiple sources in addition to dust released from all other sunlit areas results in a high correlation coefficient (∼0.8) of the predictions with observations during a complete diurnal rotation period of 67P. T3 - ZIB-Report - 16-26 KW - comet KW - 67p Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59225 SN - 1438-0064 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias A1 - Baum, Daniel A1 - Hege, Hans-Christian A1 - Heller, Eric J. T1 - Homogeneous dust emission and jet structure near active cometary nuclei: the case of 67P/Churyumov-Gerasimenko N2 - We compute trajectories of dust grains starting from a homogeneous surface activity-profile on a irregularly shaped cometary nucleus. Despite the initially homogeneous dust distribution a collimation in jet-like structures becomes visible. The fine structure is caused by concave topographical features with similar bundles of normal vectors. The model incorporates accurately determined gravitational forces, rotation of the nucleus, and gas-dust interaction. Jet-like dust structures are obtained for a wide range of gas-dust interactions. For the comet 67P/Churyumov-Gerasimenko, we derive the global dust distribution around the nucleus and find several areas of agreement between the homogeneous dust emission model and the Rosetta observation of dust jets, including velocity-dependent bending of trajectories. Y1 - 2015 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias T1 - On the origin of inner coma structures observed by Rosetta during a diurnal rotation of comet 67P/Churyumov-Gerasimenko JF - The Astrophysical Journal Letters N2 - The Rosetta probe around comet 67P/Churyumov–Gerasimenko (67P) reveals an anisotropic dust distribution of the inner coma with jet-like structures. The physical processes leading to jet formation are under debate, with most models for cometary activity focusing on localized emission sources, such as cliffs or terraced regions. Here we suggest, by correlating high-resolution simulations of the dust environment around 67P with observations, that the anisotropy and the background dust density of 67P originate from dust released across the entire sunlit surface of the nucleus rather than from few isolated sources. We trace back trajectories from coma regions with high local dust density in space to the non-spherical nucleus and identify two mechanisms of jet formation: areas with local concavity in either two dimensions or only one. Pits and craters are examples of the first case; the neck region of the bi-lobed nucleus of 67P is an example of the latter case. The conjunction of multiple sources, in addition to dust released from all other sunlit areas, results in a high correlation coefficient (~0.8) of the predictions with observations during a complete diurnal rotation period of 67P. Y1 - 2016 U6 - https://doi.org/10.3847/2041-8205/823/1/L11 VL - 823 IS - 1 SP - L11 ER - TY - JOUR A1 - Kramer, Tobias A1 - Noack, Matthias T1 - Prevailing Dust-transport Directions on Comet 67P/Churyumov–Gerasimenko JF - The Astrophysical Journal Letters N2 - Dust transport and deposition behind larger boulders on the comet 67P/Churyumov–Gerasimenko (67P/C–G) have been observed by the Rosetta mission. We present a mechanism for dust-transport vectors based on a homogeneous surface activity model incorporating in detail the topography of 67P/C–G. The combination of gravitation, gas drag, and Coriolis force leads to specific dust transfer pathways, which for higher dust velocities fuel the near-nucleus coma. By distributing dust sources homogeneously across the whole cometary surface, we derive a global dust-transport map of 67P/C–G. The transport vectors are in agreement with the reported wind-tail directions in the Philae descent area. Y1 - 2015 U6 - https://doi.org/10.1088/2041-8205/813/2/L33 VL - 813 IS - 2 SP - L33 ER - TY - CHAP A1 - Noack, Matthias A1 - Focht, Erich A1 - Steinke, Thomas T1 - Heterogeneous Active Messages for Offloading on the NEC SX-Aurora TSUBASA T2 - 2019 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Heterogeneity in Computing Workshop (HCW 2019) N2 - The NEC SX-Aurora TSUBASA is a new generation of vector processing architectures that combines a standard Intel Xeon host with the newly developed NEC Vector Engine co-processor cards. One way to use these co-processors is offloading suitable parts of the program from the host to the Vector Engines. Currently, the only vendor-provided offloading solutions are the low-level Vector Engine Offloading (VEO) library, and a builtin reverse-offloading mechanism named VHcall. In this work, we extend the portable Heterogeneous Active Messages (HAM) based HAM-Offload framework with support for the NEC SX-Aurora TSUBASA. Therefore, we design, implement, and evaluate two messaging protocols aimed at minimising offloading cost. This sheds some light on how to achieve fast communication between host CPU and the Vector Engines of the NEC SX-Aurora TSUBASA. Compared with VEO, the DMA-based protocol reduces offloading overhead by a factor of 13×. The resulting framework enables users to write portable offload applications with low overhead, that do neither require a language extension like OpenMP, nor a special language like OpenCL. Existing HAM-Offload applications are now ready to run on the NEC SX-Aurora TSUBASA. Y1 - 2019 ER -