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This paper addresses the challenge of providing portable and highly efficient code structures for CPU and GPU architectures. We choose the assembly of the right-hand term in the incompressible flow module of the High-Performance Computational Mechanics code Alya, which is one of the two CFD codes in the Unified European Benchmark Suite. Starting from an efficient CPU-code and a related OpenACC-port for GPUs we successively investigate performance potentials arising from code specialization, algorithmic restructuring and low-level optimizations. We demonstrate that only the combination of these different dimensions of runtime optimization unveils the full performance potential on the GPU and CPU. Roofline-based performance modelling is applied in this process and we demonstrate the need to investigate new optimization strategies if a classical roofline limit such as memory bandwidth utilization is achieved, rather than stopping the process. The final unified OpenACC-based implementation boosts performance by more than 50x on an NVIDIA A100 GPU (achieving approximately 2.5 TF/s FP64) and a further factor of 5x for an Intel Icelake based CPU-node (achieving approximately 1.0 TF/s FP64). The insights gained in our manual approach lays ground implementing unified but still highly efficient code structures for related kernels in Alya and other applications. These can be realized by manual coding or automatic code generation frameworks.

The complexity of combustion simulations demands the latest high-performance computing tools to accelerate its time-to-solution results. A current trend on HPC systems is the utilization of CPUs with SIMD or vector extensions to exploit data parallelism. Our work proposes a strategy to improve the automatic vectorization of finite element-based scientific codes. The approach applies a parametric configuration to the data structures to help the compiler detect the block of codes that can take advantage of vector computation while maintaining the code portable. A detailed analysis of the computational impact of this methodology on the different stages of a CFD solver is studied on the PRECCINSTA burner simulation. Our parametric implementation has proven to help the compiler generate more vector instructions in the assembly operation: this results in a reduction of up to 9.3 times of the total executed instruction maintaining constant the Instructions Per Cycle and the CPU frequency. The proposed strategy improves the performance of the CFD case under study up to 4.67 times on the MareNostrum 4 supercomputer.

This paper presents a load balancing strategy for reaction rate evaluation and chemistry integration in reacting flow simulations. The large disparity in scales during combustion introduces stiffness in the numerical integration of the PDEs and generates load imbalance during the parallel execution. The strategy is based on the use of the DLB library to redistribute the computing resources at node level, lending additional CPU-cores to higher loaded MPI processes. This approach does not require explicit data transfer and is activated automatically at runtime. Two chemistry descriptions, detailed and reduced, are evaluated on two different configurations: laminar counterflow flame and a turbulent swirl-stabilized flame. For single-node calculations, speedups of 2.3x and 7x are obtained for the detailed and reduced chemistry, respectively. Results on multi-node runs also show that DLB improves the performance of the pure-MPI code similar to single node runs. It is shown DLB can get performance improvements in both detailed and reduced chemistry calculations., Comment: 32 pages, 18 figures, Submitted to Computer & Fluids

Communities around the world are increasingly interested in nature-based solutions to mitigation of coastal risks like coastal forests, but it remains unclear how much protective benefits vegetation provides, particularly in the limit of highly energetic flows after tsunami impact. The current study, using a three-dimensional incompressible computational fluid dynamics model with a fluid-structure interaction approach, aims to quantify how energy reflection and dissipation vary with different degrees of rigidity and vegetation density of a coastal forest. We represent tree trunks as cylinders and use the elastic modulus of hardwood trees such as pine or oak to characterize the rigidity of these cylinders. The numerical results show that energy reflection increases with rigidity only for a single cylinder. In the presence of multiple cylinders, the difference in energy reflection created by varying rigidity diminishes as the number of cylinders increases. Instead of rigidity, we find that the blockage area created by the presence of multiple tree trunks dominates energy reflection. As tree trunks are deformed by the hydrodynamic forces, they alter the flow field around them, causing turbulent kinetic energy generation in the wake region. As a consequence, trees dissipate flow energy, highlighting coastal forests reducing the onshore energy flux of tsunamis by means of both reflection and dissipation.

GPUs have climbed up to the top of supercomputer systems making life harder to many legacy scientific codes. Nowadays, many recipes are being used in such code's portability, without any clarity of which is the best option. We present a comparative analysis of the two most common approaches, CUDA and OpenACC, into the multi-physics CFD code Alya. Our focus is the combustion problems which are one of the most computing demanding CFD simulations. The most computing-intensive parts of the code were analyzed in detail. New data structures for the matrix assembly step have been created to facilitate a SIMD execution that benefits vectorization in the CPU and stream processing in the GPU. As a result, the CPU code has improved its performance by up to 25%. In GPU execution, CUDA has proven to be up to 2 times faster than OpenACC for the assembly of the matrix. On the contrary, similar performance has been obtained in the kernels related to vector operations used in the linear solver, where there is minimal memory reuse.

Modern supercomputers allow the simulation of complex phenomena with increased accuracy. Eventually, this requires finer geometric discretizations with larger numbers of mesh elements. In this context, and extrapolating to the Exascale paradigm, meshing operations such as generation, adaptation or partition, become a critical bottleneck within the simulation workflow. In this paper, we focus on mesh partitioning. In particular, we present some improvements carried out on an in-house parallel mesh partitioner based on the Hilbert Space-Filling Curve. Additionally, taking advantage of its performance, we present the application of the SFC-based partitioning for dynamic load balancing. This method is based on the direct monitoring of the imbalance at runtime and the subsequent re-partitioning of the mesh. The target weights for the optimized partitions are evaluated using a least-squares approximation considering all measurements from previous iterations. In this way, the final partition corresponds to the average performance of the computing devices engaged., Comment: 10 pages, 9 figures. arXiv admin note: text overlap with arXiv:2005.05899

The main computing tasks of a finite element code(FE) for solving partial differential equations (PDE's) are the algebraic system assembly and the iterative solver. This work focuses on the first task, in the context of a hybrid MPI+X paradigm. Although we will describe algorithms in the FE context, a similar strategy can be straightforwardly applied to other discretization methods, like the finite volume method. The matrix assembly consists of a loop over the elements of the MPI partition to compute element matrices and right-hand sides and their assemblies in the local system to each MPI partition. In a MPI+X hybrid parallelism context, X has consisted traditionally of loop parallelism using OpenMP. Several strategies have been proposed in the literature to implement this loop parallelism, like coloring or substructuring techniques to circumvent the race condition that appears when assembling the element system into the local system. The main drawback of the first technique is the decrease of the IPC due to bad spatial locality. The second technique avoids this issue but requires extensive changes in the implementation, which can be cumbersome when several element loops should be treated. We propose an alternative, based on the task parallelism of the element loop using some extensions to the OpenMP programming model. The taskification of the assembly solves both aforementioned problems. In addition, dynamic load balance will be applied using the DLB library, especially efficient in the presence of hybrid meshes, where the relative costs of the different elements is impossible to estimate a priori. This paper presents the proposed methodology, its implementation and its validation through the solution of large computational mechanics problems up to 16k cores.

During a rapid inhalation, such as a sniff, the flow in the airways accelerates and decays quickly. The consequences for flow development and convective trans- port of an inhaled gas were investigated in a subject geometry extending from the nose to the bronchi. The progress of flow transition and the advance of an inhaled non-absorbed gas were determined using highly resolved simulations of a sniff 0.5 s long, 1 litre per second peak flow, 364 ml inhaled volume. In the nose, the distribution of airflow evolved through three phases: (i) an initial transient of about 50 ms, roughly the filling time for a nasal volume, (ii) quasi-equilibrium over the majority of the inhalation, and (iii) a terminating phase. Flow transition commenced in the supraglottic region within 20ms, resulting in large- amplitude fluctuations persisting throughout the inhalation; in the nose, fluctuations that arose nearer peak flow were of much reduced intensity and diminished in the flow decay phase. Measures of gas concentration showed non-uniform build-up and wash-out of the inhaled gas in the nose. At the carina, the form of the temporal concentration profile reflected both shear dispersion and airway filling defects owing to recirculation regions., Comment: 15 pages

Alya is the BSC in-house HPC-based multi-physics simulation code. It is designed from scratch to run efficiently in parallel supercomputers, solving coupled problems. The target domain is engineering, with all its particular features: complex geome- tries and unstructured meshes, coupled multi-physics with exotic coupling schemes and Physical models, ill-posed problems, flexibility needs for rapidly including new models, etc. Since its conception in 2004, Alya has shown scaling behaviour in an increasing number of cores. In this paper, we present its performance up to 100.000 cores in Blue Waters, the NCSA supercomputer. The selected tests are representative of the engineering world, all the problematic features included: incompressible flow in a hu- man respiratory system, low Mach combustion problem in a kiln furnace and coupled electro-mechanical problem in a heart. We show scalability plots for all cases, discussing all the aspects of such kind of simulations, including solvers convergence., Comment: Preprint. Paper submitted to International Supercomputing Conference 2014. Waiting for approval