Improving the throughput of an atmospheric model using an asynchronous parallel I/O server

This master's thesis analyzes the I/O process of IFS. It is presented an easy-to-use development that integrates an asynchronous parallel I/O server called XIOS into IFS. Moreover, different optimization techniques are applied in the integration to minimize the I/O overhead in the IFS execution

Optimització de la cadena de processat de l'aplicació d'Earth Sciences NMMB/BSC-CTM

[CATALÀ] Aquest document explica les anàlisis i optimitzacions que s'han dut a terme per tal de millorar el temps d'execució de l'etapa de postprocés de l'aplicació NMMB/BSC-CTM. Els resultats obtinguts són favorables, ja que el temps d'execució de postprocés quasi bé es redueix a 0.[ANGLÈS] This paper explains the analysis and optimizations which have been done in order to improve execution time of postprocess stage of the NMMB/BSC-CTM application. The achieved results are favourable, because the execution time of postprocess is virtually reduced to 0

Evaluation and optimisation of the I/O scalability for the next generation of Earth system models: IFS CY43R3 and XIOS 2.0 integration as a case study

Earth system models have considerably increased their spatial resolution to solve more complex problems and achieve more realistic solutions. However, this generates an enormous amount of model data which requires proper management. Some Earth system models use inefficient sequential input/output (I/O) schemes that do not scale well when many parallel resources are used. In order to address this issue, the most commonly adopted approach is to use scalable parallel I/O solutions that offer both computational performance and efficiency. In this paper we analyse the I/O process of the European Centre for Medium-Range Weather Forecasts (ECMWF) operational Integrated Forecasting System (IFS) CY43R3. IFS can use two different output schemes: a parallel I/O server developed by Météo-France used operationally and an obsolete sequential I/O scheme. The latter is the only scheme that is being exposed by the OpenIFS variant of IFS. “Downstream” Earth system models that have adopted older versions of an IFS derivative as a component – such as the EC-Earth 3 climate model – also face a bottleneck due to the limited I/O capabilities and performance of the sequential output scheme. Moreover, it is often desirable to produce grid-point-space Network Common Data Format (NetCDF) files instead of the IFS native spectral and grid-point output fields in General Regularly-distributed Information in Binary form (GRIB), which requires the development of model-specific post-processing tools. We present the integration of the XML Input/Output Server (XIOS) 2.0 into IFS CY43R3. XIOS is an asynchronous Message Passing Interface (MPI) I/O server that offers features especially targeted at climate models: NetCDF output files, inline diagnostics, regridding, and, when properly configured, the capability to produce CMOR-compliant data. We therefore expect our work to reduce the computational cost of data-intensive (high-resolution) climate runs, thereby shortening the critical path of EC-Earth 4 experiments. The performance evaluation suggests that the use of XIOS 2.0 in IFS CY43R3 to output data achieves an adequate performance as well, outperforming the sequential I/O scheme. Furthermore, when we also take into account the post-processing task, which is needed to convert GRIB files to NetCDF files and also transform IFS spectral output fields to grid-point space, our integration not only surpasses the sequential output scheme but also the operational IFS I/O server.This research has been supported by Horizon 2020 (ESiWACE2 (grant no. 823988) and PRIMAVERA (grant no. 641727)).Peer ReviewedPostprint (published version

The EC-Earth3 Earth system model for the Coupled Model Intercomparison Project 6

The Earth system model EC-Earth3 for contributions to CMIP6 is documented here, with its flexible coupling framework, major model configurations, a methodology for ensuring the simulations are comparable across different high-performance computing (HPC) systems, and with the physical performance of base configurations over the historical period. The variety of possible configurations and sub-models reflects the broad interests in the EC-Earth community. EC-Earth3 key performance metrics demonstrate physical behavior and biases well within the frame known from recent CMIP models. With improved physical and dynamic features, new Earth system model (ESM) components, community tools, and largely improved physical performance compared to the CMIP5 version, EC-Earth3 represents a clear step forward for the only European community ESM. We demonstrate here that EC-Earth3 is suited for a range of tasks in CMIP6 and beyond.The development of EC-Earth3 was supported by the European Union's Horizon 2020 research and innovation program under project IS-ENES3, the third phase of the distributed e-infrastructure of the European Network for Earth System Modelling (ENES) (grant agreement no. 824084, PRIMAVERA grant no. 641727, and CRESCENDO grant no. 641816). Etienne Tourigny and Raffaele Bernardello have received funding from the European Union’s Horizon 2020 research and innovation program under Marie Skłodowska-Curie grant agreement nos. 748750 (SPFireSD project) and 708063 (NeTNPPAO project). Ivana Cvijanovic was supported by Generalitat de Catalunya (Secretaria d'Universitats i Recerca del Departament d’Empresa i Coneixement) through the Beatriu de Pinós program. Yohan Ruprich-Robert was funded by the European Union's Horizon 2020 research and innovation program in the framework of Marie Skłodowska-Curie grant INADEC (grant agreement 800154). Paul A. Miller, Lars Nieradzik, David Wårlind, Roland Schrödner, and Benjamin Smith acknowledge financial support from the strategic research area “Modeling the Regional and Global Earth System” (MERGE) and the Lund University Centre for Studies of Carbon Cycle and Climate Interactions (LUCCI). Paul A. Miller, David Wårlind, and Benjamin Smith acknowledge financial support from the Swedish national strategic e-science research program eSSENCE. Paul A. Miller further acknowledges financial support from the Swedish Research Council (Vetenskapsrådet) under project no. 621-2013-5487. Shuting Yang acknowledges financial support from a Synergy Grant from the European Research Council under the European Community's Seventh Framework Programme (FP7/2007-2013)/ERC (grant agreement 610055) as part of the ice2ice project and the NordForsk-funded Nordic Centre of Excellence project (award 76654) ARCPATH. Marianne Sloth Madsen acknowledges financial support from the Danish National Center for Climate Research (NCKF). Andrea Alessandri and Peter Anthoni acknowledge funding from the Helmholtz Association in its ATMO program. Thomas Arsouze, Arthur Ramos, and Valentina Sicardi received funding from the Ministerio de Ciencia, Innovación y Universidades as part of the DeCUSO project (CGL2017-84493-R).​​​​​​​Peer Reviewed"Article signat per 61 autors/es: Ralf Döscher, Mario Acosta, Andrea Alessandri, Peter Anthoni, Thomas Arsouze, Tommi Bergman, Raffaele Bernardello, Souhail Boussetta, Louis-Philippe Caron, Glenn Carver, Miguel Castrillo, Franco Catalano, Ivana Cvijanovic, Paolo Davini, Evelien Dekker, Francisco J. Doblas-Reyes, David Docquier, Pablo Echevarria, Uwe Fladrich, Ramon Fuentes-Franco, Matthias Gröger, Jost v. Hardenberg, Jenny Hieronymus, M. Pasha Karami, Jukka-Pekka Keskinen, Torben Koenigk, Risto Makkonen, François Massonnet, Martin Ménégoz, Paul A. Miller, Eduardo Moreno-Chamarro, Lars Nieradzik, Twan van Noije, Paul Nolan, Declan O'Donnell, Pirkka Ollinaho11, Gijs van den Oord, Pablo Ortega, Oriol Tintó Prims, Arthur Ramos, Thomas Reerink, Clement Rousset, Yohan Ruprich-Robert, Philippe Le Sager, Torben Schmith, Roland Schrödner, Federico Serva, Valentina Sicardi, Marianne Sloth Madsen, Benjamin Smith, Tian Tian, Etienne Tourigny, Petteri Uotila, Martin Vancoppenolle, Shiyu Wang, David Wårlind, Ulrika Willén, Klaus Wyser, Shuting Yang, Xavier Yepes-Arbós, and Qiong Zhang"Postprint (author's final draft

The EC-Earth3 Earth system model for the Coupled Model Intercomparison Project 6

The Earth system model EC-Earth3 for contributions to CMIP6 is documented here, with its flexible coupling framework, major model configurations, a methodology for ensuring the simulations are comparable across different high-performance computing (HPC) systems, and with the physical performance of base configurations over the historical period. The variety of possible configurations and sub-models reflects the broad interests in the EC-Earth community. EC-Earth3 key performance metrics demonstrate physical behavior and biases well within the frame known from recent CMIP models. With improved physical and dynamic features, new Earth system model (ESM) components, community tools, and largely improved physical performance compared to the CMIP5 version, EC-Earth3 represents a clear step forward for the only European community ESM. We demonstrate here that EC-Earth3 is suited for a range of tasks in CMIP6 and beyond.Peer reviewe

Improving the throughput of an atmospheric model using an asynchronous parallel I/O server

This master's thesis analyzes the I/O process of IFS. It is presented an easy-to-use development that integrates an asynchronous parallel I/O server called XIOS into IFS. Moreover, different optimization techniques are applied in the integration to minimize the I/O overhead in the IFS execution

Improving the throughput of an atmospheric model using an asynchronous parallel I/O server

This master's thesis analyzes the I/O process of IFS. It is presented an easy-to-use development that integrates an asynchronous parallel I/O server called XIOS into IFS. Moreover, different optimization techniques are applied in the integration to minimize the I/O overhead in the IFS execution

Optimització de la cadena de processat de l'aplicació d'Earth Sciences NMMB/BSC-CTM

[CATALÀ] Aquest document explica les anàlisis i optimitzacions que s'han dut a terme per tal de millorar el temps d'execució de l'etapa de postprocés de l'aplicació NMMB/BSC-CTM. Els resultats obtinguts són favorables, ja que el temps d'execució de postprocés quasi bé es redueix a 0.[ANGLÈS] This paper explains the analysis and optimizations which have been done in order to improve execution time of postprocess stage of the NMMB/BSC-CTM application. The achieved results are favourable, because the execution time of postprocess is virtually reduced to 0

Reproducibility of an Earth System Model under a Change in Computing Environment

Most Earth System Models (ESMs) are running under different high performance computing (HPC) environments. This has several advantages, from allowing different groups to work with the same tool in parallel, to leveraging the burden of ensemble climate simulations but also offering alternative solutions in case of shutdown (expected or not) of any of the environments. However, for obvious scientific reasons, it is critical to ensure that ESMs provide reproducible results under changes in computing environment. While reproducibility in a strong sense (bit-for-bit) is in general unfeasible, it can be hoped that results obtained under one computing environment are statistically indistinguishable from those obtained under another environment (reproducibility in a weak sense). Here, we develop a protocol to assess the reproducibility (in a weak sense) of the EC-Earth ESM. Using two versions of that ESM, we present one case of non-reproducibility and one case of reproducibility. The non-reproducible case occurs with the older version of the model and likely finds its origin in the treatment of river runoffs along Antarctic coasts. However, it was not possible to nail the problem further down. By contrast, the more recent version of the model provides reproducible results. The protocol introduced in this note can help users of EC-Earth and, by extensión other ESMs, assessing whether their model can be ported from one HPC environment to another. Our results and experience in this work suggest that the default assumption should be that an ESM is not reproducible under changes in the HPC environment, until proven otherwise

Replicability of the EC-Earth3 Earth system model under a change in computing environment

International audienceCyanoacetylene molecules are widespread in the interstellar medium (ISM) and several of its isomers have been detected in cold molecular clouds and circumstellar gas. Accurate estimates of the abundance ratio of cyanoacetylene isomers may provide deep insight into their environment. Such knowledge requires rigorous modeling of the emission spectra based on non-Local Thermodynamic Equilibrium (LTE) radiative transfer calculations. To this end, we computed excitation cross sections of HC2NC and HNC3 induced by collision with para- and ortho-H2, using a quantum mechanical close-coupling method. Then, by thermally averaging these data, we derived rate coefficients for the first 31 low-lying rotational levels of each isomer for temperatures up to 80 K. For the para-H2 collider, the propensity rules are in favor of rotational transitions involving Δj1 = 2 for both isomers; while for the ortho-H2 collider, Δj1 = 2 and Δj1 = 1 rotational transitions are favored for HC2NC and HNC3, respectively. A comparison of rate coefficients for the HC3N isomers shows differences up to an order of magnitude, especially at low temperatures. Finally, we performed non-LTE radiative transfer calculations to assess the impact of such variations in the analysis of observations. Our simulation suggests that the lack of collisional data specific to each isomer could lead to errors up to a factor of 2–3 in the excitation temperatures. We expect that these data could help in better understanding the cyanoacetylene chemistry and constraining the nitrogen chemistry in the ISM