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This paper presents the design, implementation, and application of TALP, a lightweight, portable, extensible, and scalable tool for online parallel performance measurement. The efficiency metrics reported by TALP allow HPC users to evaluate the parallel efficiency of their executions, both post-mortem and at runtime. The API that TALP provides allows the running application or resource managers to collect performance metrics at runtime. This enables the opportunity to adapt the execution based on the metrics collected dynamically. The set of metrics collected by TALP are well defined, independent of the tool, and consolidated. We extend the collection of metrics with two additional ones that can differentiate between the load imbalance originated from the intranode or internode imbalance. We evaluate the potential of TALP with three parallel applications that present various parallel issues and carefully analyze the overhead introduced to determine its limitations. ; This work is partially supported by the Spanish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), and by the European POP CoE (GA n. 824080). ; Peer Reviewed ; Postprint (author's final draft)

Computational fluid and particle dynamics simulations (CFPD) are of paramount importance for studying and improving drug effectiveness. Computational requirements of CFPD codes involves high-performance computing (HPC) resources. For these reasons we introduce and evaluate in this paper system software techniques for improving performance and tolerate load imbalance on a state-of-the-art production CFPD code. We demonstrate benefits of these techniques on both Intel- and Arm-based HPC clusters showing the importance of using mechanisms applied at runtime to improve the performance independently of the underlying architecture. We run a real CFPD simulation of particle tracking on the human respiratory system, showing performance improvements of up to 2X, keeping the computational resources constant. ; This work is partially supported by the Spanish Government (SEV-2015-0493), by the Spanish Ministry of Science and Technology project (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), and by the European Mont-Blanc projects (288777, 610402 and 671697). ; Peer Reviewed ; Postprint (author's final draft)

Computational fluid and particle dynamics simulations (CFPD) are of paramount importance for studying and improving drug effectiveness. Computational requirements of CFPD codes involves high-performance computing (HPC) resources. For these reasons we introduce and evaluate in this paper system software techniques for improving performance and tolerate load imbalance on a state-of-the-art production CFPD code. We demonstrate benefits of these techniques on both Intel- and Arm-based HPC clusters showing the importance of using mechanisms applied at runtime to improve the performance independently of the underlying architecture. We run a real CFPD simulation of particle tracking on the human respiratory system, showing performance improvements of up to 2X, keeping the computational resources constant. ; This work is partially supported by the Spanish Government (SEV-2015-0493), by the Spanish Ministry of Science and Technology project (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), and by the European Mont-Blanc projects (288777, 610402 and 671697). ; Peer Reviewed ; Postprint (author's final draft)

Computational Fluid and Particle Dynamics (CFPD) simulations are of paramount importance for studying and improving drug effectiveness. Computational requirements of CFPD codes demand high-performance computing (HPC) resources. For these reasons we introduce and evaluate in this paper system software techniques for improving performance and tolerate load imbalance on a state-of-the-art production CFPD code. We demonstrate benefits of these techniques on Intel-, IBM-, and Arm-based HPC technologies ranked in the Top500 supercomputers, showing the importance of using mechanisms applied at runtime to improve the performance independently of the underlying architecture. We run a real CFPD simulation of particle tracking on the human respiratory system, showing performance improvements of up to 2x, across different architectures, while applying runtime techniques and keeping constant the computational resources. ; This work is partially supported by the Spanish Government (SEV-2015-0493), by the Spanish Ministry of Science and Technology project (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), and by the European Mont-Blanc projects (288777, 610402 and 671697). ; Peer Reviewed ; Preprint

Computational Fluid and Particle Dynamics (CFPD) simulations are of paramount importance for studying and improving drug effectiveness. Computational requirements of CFPD codes demand high-performance computing (HPC) resources. For these reasons we introduce and evaluate in this paper system software techniques for improving performance and tolerate load imbalance on a state-of-the-art production CFPD code. We demonstrate benefits of these techniques on Intel-, IBM-, and Arm-based HPC technologies ranked in the Top500 supercomputers, showing the importance of using mechanisms applied at runtime to improve the performance independently of the underlying architecture. We run a real CFPD simulation of particle tracking on the human respiratory system, showing performance improvements of up to 2x, across different architectures, while applying runtime techniques and keeping constant the computational resources. ; This work is partially supported by the Spanish Government (SEV-2015-0493), by the Spanish Ministry of Science and Technology project (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), and by the European Mont-Blanc projects (288777, 610402 and 671697). ; Peer Reviewed ; Preprint

The simulation of detailed neuronal circuits is based on computationally expensive software simulations and requires access to a large computing cluster. The appearance of new Instruction Set Architectures (ISAs) in most recent High-Performance Computing (HPC) systems, together with the layers of system software and complex scientific applications running on top of them, makes the performance and power figures challenging to evaluate. In this paper, we focus on evaluating CoreNEURON on two HPC systems powered by Intel and Arm architectures. CoreNEURON is a computational engine of the widely used NEURON simulator adapted to run on emerging architectures while maintaining compatibility with existing NEURON models developed by the neuroscience community. The evaluation is based on the analysis of the dynamic instruction mix on two versions of CoreNEURON. It focuses on the performance gain obtained by exploiting the Single Instruction Multiple Data (SIMD) unit and includes energy measurements. Our results show that using a tool for increasing data-level parallelism (ISPC) boosts the performance up to 2× independently on the ISA. Its combination with vendor-specific compilers can further speed up the neural simulation time. Also, the performance/price ratio is higher for Arm-based systems than for Intel ones making them more cost-efficient keeping the same usability level of other HPC systems. ; This work is partially supported by the Spanish Government (SEV-2015-0493), by the Spanish Ministry of Science and Technology (TIN2015-65316-P), by the Generalitat de Catalunya (2017-SGR-1414), by the European Mont-Blanc 3 project (GA n. 671697), Human Brain Project SGA2 (GA n. 785907), and POP CoE (GA n. 824080). ; Peer Reviewed ; Postprint (author's final draft)

In the design of future HPC systems, research in resource management is showing an increasing interest in a more dynamic control of the available resources. It has been proven that enabling the jobs to change the number of computing resources at run time, i.e. their malleability, can significantly improve HPC system performance. However, job schedulers and applications typically do not support malleability due to the common belief that it introduces additional programming complexity and performance impact. This paper presents DROM, an interface that provides efficient malleability with no effort for program developers. The running application is enabled to adapt the number of threads to the number of assigned computing resources in a completely transparent way to the user through the integration of DROM with standard programming models, such as OpenMP/OmpSs, and MPI. We designed the APIs to be easily used by any programming model, application and job scheduler or resource manager. Our experimental results from two realistic use cases analysis, based on malleability by reducing the number of cores a job is using per node and jobs co-allocation, show the potential of DROM for improving the performance of HPC systems. In particular, the workload of two MPI+OpenMP neuro-simulators are tested, reporting improvement in system metrics, such as total run time and average response time, up to 8% and 48%, respectively. ; This work is partially supported by the Span- ish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology through TIN2015-65316-P project, by the Generalitat de Catalunya (contract 2017-SGR-1414) and from the European Union's Horizon 2020 under grant agreement No 785907 (HBP SGA2) ; Peer Reviewed ; Postprint (author's final draft)

In the design of future HPC systems, research in resource management is showing an increasing interest in a more dynamic control of the available resources. It has been proven that enabling the jobs to change the number of computing resources at run time, i.e. their malleability, can significantly improve HPC system performance. However, job schedulers and applications typically do not support malleability due to the common belief that it introduces additional programming complexity and performance impact. This paper presents DROM, an interface that provides efficient malleability with no effort for program developers. The running application is enabled to adapt the number of threads to the number of assigned computing resources in a completely transparent way to the user through the integration of DROM with standard programming models, such as OpenMP/OmpSs, and MPI. We designed the APIs to be easily used by any programming model, application and job scheduler or resource manager. Our experimental results from two realistic use cases analysis, based on malleability by reducing the number of cores a job is using per node and jobs co-allocation, show the potential of DROM for improving the performance of HPC systems. In particular, the workload of two MPI+OpenMP neuro-simulators are tested, reporting improvement in system metrics, such as total run time and average response time, up to 8% and 48%, respectively. ; This work is partially supported by the Span- ish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology through TIN2015-65316-P project, by the Generalitat de Catalunya (contract 2017-SGR-1414) and from the European Union's Horizon 2020 under grant agreement No 785907 (HBP SGA2) ; Peer Reviewed ; Postprint (author's final draft)

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 strate- gies 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 task- ification 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. ; The use of large part of a supercomputer, even more in normal conditions of use, is never an innocuous exercise. The research leading to these results has received funding from: the European Union's Horizon 2020 Programme (2014–2020) and from Brazilian Ministry of Science, Technology and Innovation through Rede Nacional de Pesquisa (RNP), HPC4E Project, grant agreement 689772; the Energy oriented Centre of Excellence (EoCoE), grant agreement number 676629, funded within the Horizon2020 framework of the European Union; The Spanish Government (grant SEV2015-0493 of the Severo Ochoa Program); the Spanish Ministry of Science and Innovation (contract TIN2015-65316-P); the Generalitat de Catalunya (contract 2014-SGR-1051); the Intel-BSC Exascale Lab collaboration project. Comissió Interdepartamental de Recerca i Innovació Tecnológica(Interdepartmental Commission for Research and Technological Innovation) ; Sí ; Post-print (author's final draft)

High-performance computing (HPC) systems are very big and powerful systems, with the main goal of achieving maximum performance of parallel jobs. Many dynamic factors influence the performance which makes this goal a non-trivial task. According to our knowledge, there is no standard tool to automatize performance evaluation through comparing different configurations and helping system administrators to select the best scheduling policy or the best job scheduler. This paper presents the Dynamic Job Scheduler Benchmark (DJSB). It is a configurable tool that compares performance metrics for different scenarios. DJSB receives a workload description and some general arguments such as job submission commands and generates performance metrics and performance plots. To test and present DJSB, we have compared three different scenarios with dynamic resource management strategies using DJSB experiment-driven tool. Results show that just changing some DJSB arguments we can set up and execute quite different experiments, making easy the comparison. In this particular case, a cooperative-dynamic resource management is evaluated compared with other resource management approaches. ; This work is supported by the Spanish Government through Programa Severo Ochoa (SEV-2015-0493), by the Spanish Ministry of Science and Technology (project TIN2015-65316-P), by the Generalitat de Catalunya (grant 2014-SGR-1051), by the European Union's Horizon 2020 research and innovation program under grant agreement No. 720270 (HBP SGA1). ; Peer Reviewed ; Postprint (author's final draft)

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 strate- gies 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 task- ification 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. ; The use of large part of a supercomputer, even more in normal conditions of use, is never an innocuous exercise. The research leading to these results has received funding from: the European Union's Horizon 2020 Programme (2014–2020) and from Brazilian Ministry of Science, Technology and Innovation through Rede Nacional de Pesquisa (RNP), HPC4E Project, grant agreement 689772; the Energy oriented Centre of Excellence (EoCoE), grant agreement number 676629, funded within the Horizon2020 framework of the European Union; The Spanish Government (grant SEV2015-0493 of the Severo Ochoa Program); the Spanish Ministry of Science and Innovation (contract TIN2015-65316-P); the Generalitat de Catalunya (contract 2014-SGR-1051); the Intel-BSC Exascale Lab collaboration project. Comissió Interdepartamental de Recerca i Innovació Tecnológica(Interdepartmental Commission for Research and Technological Innovation) ; Sí ; Post-print (author's final draft)

In this paper, we analyze the performance and energy consumption of an Arm-based high-performance computing (HPC) system developed within the European project Mont-Blanc 3. This system, called Dibona, has been integrated by ATOS/Bull, and it is powered by the latest Marvell's CPU, ThunderX2. This CPU is the same one that powers the Astra supercomputer, the first Arm-based supercomputer entering the Top500 in November 2018. We study from micro-benchmarks up to large production codes. We include an interdisciplinary evaluation of three scientific applications (a finite-element fluid dynamics code, a smoothed particle hydrodynamics code, and a lattice Boltzmann code) and the Graph 500 benchmark, focusing on parallel and energy efficiency as well as studying their scalability up to thousands of Armv8 cores. For comparison, we run the same tests on state-of-the-art x86 nodes included in Dibona and the Tier-0 supercomputer MareNostrum4. Our experiments show that the ThunderX2 has a 25% lower performance on average, mainly due to its small vector unit yet somewhat compensated by its 30% wider links between the CPU and the main memory. We found that the software ecosystem of the Armv8 architecture is comparable to the one available for Intel. Our results also show that ThunderX2 delivers similar or better energy-to-solution and scalability, proving that Arm-based chips are legitimate contenders in the market of next-generation HPC systems. ; The authors thank the support team of Dibona operating at ATOS/Bull. This work is partially supported by the Spanish Government through Programa Severo Ochoa (SEV-2015-0493), the Spanish Ministry of Science and Technology project (TIN2015-65316-P), the Generalitat de Catalunya (2017-SGR-1414), the European Community's Seventh Framework Programme [FP7/2007-2013] and Horizon 2020 under the Mont-Blanc projects (grant agreements n. 288777, 610402 and 671697), the European POP2 Center of Excellence (grant agreement n. 824080), and the Human Brain Project SGA2 (grant agreement n. 785907). ...

High fidelity Computational Fluid Dynamics simulations are generally associated with large computing requirements, which are progressively acute with each new generation of supercomputers. However, significant research efforts are required to unlock the computing power of leading-edge systems, currently referred to as pre-Exascale systems, based on increasingly complex architectures. In this paper, we present the approach implemented in the computational mechanics code Alya. We describe in detail the parallelization strategy implemented to fully exploit the different levels of parallelism, together with a novel co-execution method for the efficient utilization of heterogeneous CPU/GPU architectures. The latter is based on a multi-code co-execution approach with a dynamic load balancing mechanism. The assessment of the performance of all the proposed strategies has been carried out for airplane simulations on the POWER9 architecture accelerated with NVIDIA Volta V100 GPUs. ; This work is partially supported by the BSC-IBM Deep Learning Research Agreement, under JSA \Application porting, analysis and optimization for POWER and POWER AI". It has also been partially supported by the EX-CELLERAT project funded by the European Commission's ICT activity of the H2020 Programme under grant agreement number: 823691. It has also received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement number: 846139 (Exa-FireFlows). This paper expresses the opinions of the authors and not necessarily those of the European Commission. The European Commission is not liable for any use that may be made of the information contained in this paper. This work has also been nan- cially supported by the Ministerio de Economia, Industria y Competitividad, of Spain (TRA2017-88508-R). The computing experiments of this paper have been performed on the resources of the Barcelona Supercomputing Center. ; Peer Reviewed ; Postprint (author's final draft)

Computational fluid dynamics (CFD) is the main field of computational mechanics that has historically benefited from advances in high-performance computing. High-performance computing involves several techniques to make a simulation efficient and fast, such as distributed memory parallelism, shared memory parallelism, vectorization, memory access optimizations, etc. As an introduction, we present the anatomy of supercomputers, with special emphasis on HPC aspects relevant to CFD. Then, we develop some of the HPC concepts and numerical techniques applied to the complete CFD simulation framework: from preprocess (meshing) to postprocess (visualization) through the simulation itself (assembly and iterative solvers). ; Part of the research developments and results presented in this chapter were funded by: the European Union's Horizon 2020 Programme (2014–2020) and from Brazilian Ministry of Science, Technology and Innovation through Rede Nacional de Pesquisa (RNP) under the HPC4E Project, grant agreement 689772; EoCoE, a project funded by the European Union Contract H2020-EINFRA-2015-1-676629; PRACE Type C and Type A projects. ; Peer Reviewed ; Postprint (published version)

Computational fluid dynamics (CFD) is the main field of computational mechanics that has historically benefited from advances in high-performance computing. High-performance computing involves several techniques to make a simulation efficient and fast, such as distributed memory parallelism, shared memory parallelism, vectorization, memory access optimizations, etc. As an introduction, we present the anatomy of supercomputers, with special emphasis on HPC aspects relevant to CFD. Then, we develop some of the HPC concepts and numerical techniques applied to the complete CFD simulation framework: from preprocess (meshing) to postprocess (visualization) through the simulation itself (assembly and iterative solvers). ; Part of the research developments and results presented in this chapter were funded by: the European Union's Horizon 2020 Programme (2014–2020) and from Brazilian Ministry of Science, Technology and Innovation through Rede Nacional de Pesquisa (RNP) under the HPC4E Project, grant agreement 689772; EoCoE, a project funded by the European Union Contract H2020-EINFRA-2015-1-676629; PRACE Type C and Type A projects. ; Peer Reviewed ; Postprint (published version)