In an attempt to advance the understanding of the Earth's weather and climate by representing deep convection explicitly, we present a global, four‐month simulation (November 2018 to February 2019) ...with ECMWF's hydrostatic Integrated Forecasting System (IFS) at an average grid spacing of 1.4 km. The impact of explicitly simulating deep convection on the atmospheric circulation and its variability is assessed by comparing the 1.4 km simulation to the equivalent well‐tested and calibrated global simulations at 9 km grid spacing with and without parametrized deep convection. The explicit simulation of deep convection at 1.4 km results in a realistic large‐scale circulation, better representation of convective storm activity, and stronger convective gravity wave activity when compared to the 9 km simulation with parametrized deep convection. Comparison of the 1.4 km simulation to the 9 km simulation without parametrized deep convection shows that switching off deep convection parametrization at a too coarse resolution (i.e., 9 km) generates too strong convective gravity waves. Based on the limited statistics available, improvements to the Madden‐Julian Oscillation or tropical precipitation are not observed at 1.4 km, suggesting that other Earth system model components and/or their interaction are important for an accurate representation of these processes and may well need adjusting at deep convection resolving resolutions. Overall, the good agreement of the 1.4 km simulation with the 9 km simulation with parametrized deep convection is remarkable, despite one of the most fundamental parametrizations being turned off at 1.4 km resolution and despite no adjustments being made to the remaining parametrizations.
Plain Language Summary
We present the world's first global simulation of an entire season of the Earth's atmosphere with 1.4 km average grid spacing and the top of the modeled atmosphere as high as 80 km. Albeit only a single realization due to its considerable computational cost, the resulting model output provides a reference and guidance for future simulations. For illustration we compare to simulations at 9 km grid spacing that represent the state of the art in numerical weather prediction and are still considerably finer when compared to models that are used for climate projections today. Thanks to its unprecedented detail, the simulation output will support future model development and satellite mission planning and may be seen as a prototype contribution to a future digital twin of our Earth.
Key Points
A unique simulation with 1.4 km average grid spacing is presented for model development and process evaluation
The 1.4 km simulation shows remarkable fidelity with respect to the well‐calibrated simulation at 9 km with parametrized deep convection
Switching off deep convection at a too coarse resolution (9 km) generates too strong convective gravity waves
The land-surface developments of the European Centre for Medium-range Weather Forecasts (ECMWF) are based on the Carbon-Hydrology Tiled Scheme for Surface Exchanges over Land (CHTESSEL) and form an ...integral part of the Integrated Forecasting System (IFS), supporting a wide range of global weather, climate and environmental applications. In order to structure, coordinate and focus future developments and benefit from international collaboration in new areas, a flexible system named ECLand, which would facilitate modular extensions to support numerical weather prediction (NWP) and society-relevant operational services, for example, Copernicus, is presented. This paper introduces recent examples of novel ECLand developments on (i) vegetation; (ii) snow; (iii) soil; (iv) open water/lake; (v) river/inundation; and (vi) urban areas. The developments are evaluated separately with long-range, atmosphere-forced surface offline simulations and coupled land-atmosphere-ocean experiments. This illustrates the benchmark criteria for assessing both process fidelity with regards to land surface fluxes and reservoirs of the water-energy-carbon exchange on the one hand, and on the other hand the requirements of ECMWF’s NWP, climate and atmospheric composition monitoring services using an Earth system assimilation and prediction framework.
Modern multicore and manycore processors exhibit multiple levels of parallelism through a wide range of architectural features such as SIMD for data parallel execution or threads for core ...parallelism. The exploitation of multi-level parallelism is therefore crucial for achieving superior performance on current and future processors. This paper presents the performance tuning of a multiblock CFD solver on Intel SandyBridge and Haswell multicore CPUs and the Intel Xeon Phi Knights Corner coprocessor. Code optimisations have been applied on two computational kernels exhibiting different computational patterns: the update of flow variables and the evaluation of the Roe numerical fluxes. We discuss at great length the code transformations required for achieving efficient SIMD computations for both kernels across the selected devices including SIMD shuffles and transpositions for flux stencil computations and global memory transformations. Core parallelism is expressed through threading based on a number of domain decomposition techniques together with optimisations pertaining to alleviating NUMA effects found in multi-socket compute nodes. Results are correlated with the Roofline performance model in order to assert their efficiency for each distinct architecture. We report significant speedups for single thread execution across both kernels: 2-5X on the multicore CPUs and 14-23X on the Xeon Phi coprocessor. Computations at full node and chip concurrency deliver a factor of three speedup on the multicore processors and up to 24X on the Xeon Phi manycore coprocessor.
This paper presents a number of optimisations for improving the performance of unstructured computational fluid dynamics codes on multicore and manycore architectures such as the Intel Sandy Bridge, ...Broadwell and Skylake CPUs and the Intel Xeon Phi Knights Corner and Knights Landing manycore processors. We discuss and demonstrate their implementation in two distinct classes of computational kernels: face-based loops represented by the computation of fluxes and cell-based loops representing updates to state vectors. We present the importance of making efficient use of the underlying vector units in both classes of computational kernels with special emphasis on the changes required for vectorising face-based loops and their intrinsic indirect and irregular access patterns. We demonstrate the advantage of different data layouts for cell-centred as well as face data structures and architectural specific optimisations for improving the performance of gather and scatter operations which are prevalent in unstructured mesh applications. The implementation of a software prefetching strategy based on auto-tuning is also shown along with an empirical evaluation on the importance of multithreading for in-order architectures such as Knights Corner. We explore the various memory modes available on the Intel Xeon Phi Knights Landing architecture and present an approach whereby both traditional DRAM as well as MCDRAM interfaces are exploited for maximum performance. We obtain significant full application speed-ups between 2.8 and 3X across the multicore CPUs in two-socket node configurations, 8.6X on the Intel Xeon Phi Knights Corner coprocessor and 5.6X on the Intel Xeon Phi Knights Landing processor in an unstructured finite volume CFD code representative in size and complexity to an industrial application.
Program Title: some_opt_for_unstructured_cfd
Program Files doi:http://dx.doi.org/10.17632/zyh2zkf3jw.1
Licensing provisions: GNU General Public License 3 (GPL)
Programming language: C/C++
Nature of problem: The solution of fluid flow problems in the vicinity of complex geometries mandates the utilisation of unstructured grids. However, this flexibility of unstructured mesh methods in dealing with complicated geometries comes at a cost of increased difficulty in extracting high performance out of modern processors. We provide implementations for a number of optimisations useful for improving the performance of unstructured CFD codes on modern multicore and manycore architectures.
Solution method: grid renumbering via Reverse Cuthill–Mckee, code transformations necessary for enabling vectorisation, face colouring/reordering for removing dependencies at the face end-points when accumulating residuals, data layout transformations for reducing cache misses, hand-tuned gather and scatter primitives for in-register transpositions, software prefetching via auto-tuning and multithreading for exploiting SMT features of modern processors.
This thesis presents a number of optimisations used for mapping the underlying computational patterns of finite volume CFD applications onto the architectural features of modern multicore and ...manycore processors. Their effectiveness and impact is demonstrated in a block-structured and an unstructured code of representative size to industrial applications and across a variety of processor architectures that make up contemporary high-performance computing systems. The importance of vectorization and the ways through which this can be achieved is demonstrated in both structured and unstructured solvers together with the impact that the underlying data layout can have on performance. The utility of auto-tuning for ensuring performance portability across multiple architectures is demonstrated and used for selecting optimal parameters such as prefetch distances for software prefetching or tile sizes for strip mining/loop tiling. On the manycore architectures, running more than one thread per physical core is found to be crucial for good performance on processors with in-order core designs but not required on out-of-order architectures. For architectures with high-bandwidth memory packages, their exploitation, whether explicitly or implicitly, is shown to be imperative for best performance. The implementation of all of these optimisations led to application speed-ups ranging between 2.7X and 3X on the multicore CPUs and 5.7X to 24X on the manycore processors.
The synthesis of some novel donor-acceptor and acceptor-donor-acceptor systems containing a 2,2'-bi3,2-
thienothiophene donor block and various electron-accepting units is described alongside their ...photophysical properties studied using electrochemistry, optical spectroscopy and theoretical calculations. The obtained results show that the energy levels can be modulated by changing the strength of the acceptor unit. Among the three investigated end-groups, 1,1-dicyanomethylene-3-indanone exhibited the largest bathochromic shift and the lowest band gap suggesting the strongest electron-withdrawing character. Moreover, the emissive properties of the investigated systems vary greatly with the nature of the terminal group and are generally lower compared to their precursor aldehyde derivatives.
High antimicrobial efficacy of short tryptophan-and arginine-rich peptides makes them good candidates in the fight against pathogens. Substitution of tryptophan and arginine by histidine could be ...used to modulate the peptides efficacy by optimizing their structures.
The peptide (RRWWRWWRR), reported to showed good antimicrobial efficacy, was used as template, seven new analogs being designed substituting tryptophan or arginine with histidine. The peptides' efficacy was tested against E. coli, B. subtilis and S. aureus. The cytotoxicity and hemolytic effect were evaluated and the therapeutic index was inferred for each peptide. Atomic force microscopy and molecular simulation were used to analyze the effects of peptides on bacterial membrane.
The substitution of tryptophan by histidine proved to strongly modulate the antimicrobial activity, mainly by changing the peptide-to-membrane binding energy. The substitution of arginine has low effect on the antimicrobial efficacy. The presence of histidine residue reduced the cytotoxic and hemolytic activity of the peptides in some cases maintaining the same efficacy against bacteria. The peptides' antimicrobial activity was correlated to the 3D-hydrophobic moment and to a simple structure-based packing parameter.
The results show that some of these peptides have the potential to become good candidates to fight against bacteria. The substitution by histidine proved to fine tune the therapeutic index allowing the optimization of the peptide structure mainly by changing its binding energy and 3D-hydrophobic moment.
The short tryptophan reach peptides therapeutic index can be maximized using the histidine substitution to optimize their structure.
•The short Trp-Arg peptides proposed here have MIC in micromolar range concentration.•Mutation of Trp to His strongly modulates the peptides MIC.•Mutation of Arg to His improves the therapeutic index reducing peptide cytotoxicity•Peptides effects correlate with binding energy, 3D-hydrophobic moment and packing
We describe the synthesis of a novel polyamino polycarboxylic ligand, its ability to coordinate metal-ions and attachment to a solid support designed for protein purification through Immobilised ...Metal-ion Affinity Chromatography (IMAC). The resin was found to be highly efficient for purification of His-tagged HCV E2 glycoproteins expressed in 293T mammalian cells.
We describe the synthesis of a novel polyamino polycarboxylic ligand, its ability to coordinate metal-ions and attachment to a solid support designed for protein purification through Immobilised Metal-ion Affinity Chromatography (IMAC).
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