GEOS-Chem High Performance (GCHP v11-02c):  a next-generation implementation of the GEOS-Chem chemical transport model for massively  parallel applications

Eastham, Sebastian D.; Long, M. S.; Keller, Christoph A.; Lundgren, Elizabeth W.; Yantosca, Robert M.; Zhuang, Jiawei; Li, Chi; Lee, Colin J.; Yannetti, Matthew; Auer, Benjamin M.; Clune, Thomas; Kouatchou, Jules; Putman, William M.; Thompson, Matthew A.; Trayanov, Atanas; Molod, Andrea; Martin, Randall V.; Jacob, Daniel

doi:10.5194/gmd-11-2941-2018

Cited by 87 publications

(102 citation statements)

References 20 publications

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“…A comparison of modeled versus observed PBL:FT VOC concentration ratios over the southeastern US suggests that inadequate PBL ventilation in the model may play a role in driving the observed FT biases. Recent work has sought to improve CTM transport performance through improved spatial resolution (e.g., (Zhuang et al, 2018;Yu et al, 2016)), through use of a cubed-sphere rather than regular Cartesian grid (e.g., (Eastham et al, 2018;Yu et al, 2018)), and by integration into Atmos. Chem.…”

Section: Discussionmentioning

confidence: 99%

On the sources and sinks of atmospheric VOCs: An integrated analysis of recent aircraft campaigns over North America

Chen¹,

Millet²,

Singh³

et al. 2019

Preprint

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Abstract. We apply a high-resolution chemical transport model (GEOS-Chem CTM) with updated treatment of volatile organic compounds (VOCs) and a comprehensive suite of airborne datasets over North America to i) characterize the VOC budget, and ii) test the ability of current models to capture the distribution and reactivity of atmospheric VOCs, over this region. Biogenic emissions dominate the North American VOC budget in the model, accounting for 70&#8201;% and 95&#8201;% of annually emitted VOC-carbon and reactivity, respectively. Based on current inventories anthropogenic emissions have declined to the point where biogenic emissions are the dominant summertime source of VOC reactivity even in most major North American cities. Methane oxidation is a 2&#215; larger source of non-methane VOCs (via production of formaldehyde and methyl hydroperoxide) over North America in the model than are anthropogenic emissions. However, anthropogenic VOCs account for over half the ambient VOC loading over the majority of the region owing to their longer aggregate lifetime. Fires can be a significant VOC source episodically but are small on average. In the planetary boundary layer (PBL), the model exhibits skill in capturing observed variability in total VOC-abundance (R2&#8201;=&#8201;0.36) and reactivity (R2&#8201;=&#8201;0.54). The same is not true in the free troposphere (FT), where skill is low and there is a persistent low model bias (~&#8201;60&#8201;%), with most (27 of 34) model VOCs underestimated by more than a factor of 2. A comparison of PBL&#8201;:&#8201;FT concentration ratios over the southeastern US points to a misrepresentation of PBL ventilation as a contributor to these model FT biases. We also find that a relatively small number of VOCs (acetone, methanol, ethane, acetaldehyde, formaldehyde, isoprene&#8201;+&#8201;oxidation products, methyl hydroperoxide) drive a large fraction of total ambient VOC reactivity and associated model biases; research to improve understanding of their budgets is thus warranted. A source tracer analysis suggests a current overestimate of biogenic sources for hydroxyacetone, methyl ethyl ketone and glyoxal, an underestimate of biogenic formic acid sources, and an underestimate of peroxyacetic acid production across biogenic and anthropogenic precursors. Future work to improve model representations of vertical transport and to address the VOC biases discussed are needed to advance predictions of ozone and SOA formation.

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Section: Discussionmentioning

confidence: 99%

On the sources and sinks of atmospheric VOCs: An integrated analysis of recent aircraft campaigns over North America

Chen¹,

Millet²,

Singh³

et al. 2019

Preprint

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“…It includes detailed HO x −NO x -VOC-ozone-BrO x -aerosol tropospheric chemistry with 158 species and 412 reactions, following Jet Propulsion Laboratory (JPL) and International Union of Pure and Applied Chemistry (IU-PAC) recommendations for chemical kinetics (Sander et al, 2011) and updates for BrO x and isoprene chemistry (Parrella et al, 2012;Mao et al, 2013). The default GEOS-Chem bulk aerosol scheme is used to simulate major components for dust, sea salt, black carbon, organic carbon, sulfate, nitrate, and ammonium aerosols (Park et al, 2004;Fairlie et al, 2007;Jaeglé et al, 2011;Wang et al, 2014;Kim et al, 2015). The Fast-JX scheme with approximate randomized cloud overlap method and taking aerosol loading into account is used to calculate photolysis frequencies (Bian and Prather, 2002), as implemented by Mao et al (2010).…”

Section: General Descriptionmentioning

confidence: 99%

Global simulation of tropospheric chemistry at 12.5 km resolution: performance and evaluation of the GEOS-Chem chemical module (v10-1) within the NASA GEOS Earth system model (GEOS-5 ESM)

Keller

Long

et al. 2018

Geosci. Model Dev.

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Abstract. We present a full-year online global simulation of tropospheric chemistry (158 coupled species) at cubed-sphere c720 (∼12.5×12.5km2) resolution in the NASA Goddard Earth Observing System Model version 5 Earth system model (GEOS-5 ESM) with GEOS-Chem as a chemical module (G5NR-chem). The GEOS-Chem module within GEOS uses the exact same code as the offline GEOS-Chem chemical transport model (CTM) developed by a large atmospheric chemistry research community. In this way, continual updates to the GEOS-Chem CTM by that community can be seamlessly passed on to the GEOS chemical module, which remains state of the science and referenceable to the latest version of GEOS-Chem. The 1-year G5NR-chem simulation was conducted to serve as the Nature Run for observing system simulation experiments (OSSEs) in support of the future geostationary satellite constellation for tropospheric chemistry. It required 31 wall-time days on 4707 compute cores with only 24 % of the time spent on the GEOS-Chem chemical module. Results from the GEOS-5 Nature Run with GEOS-Chem chemistry were shown to be consistent to the offline GEOS-Chem CTM and were further compared to global and regional observations. The simulation shows no significant global bias for tropospheric ozone relative to the Ozone Monitoring Instrument (OMI) satellite and is highly correlated with observations spatially and seasonally. It successfully captures the ozone vertical distributions measured by ozonesondes over different regions of the world, as well as observations for ozone and its precursors from the August–September 2013 Studies of Emissions, Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) aircraft campaign over the southeast US. It systematically overestimates surface ozone concentrations by 10 ppbv at sites in the US and Europe, a problem currently being addressed by the GEOS-Chem CTM community and from which the GEOS ESM will benefit through the seamless update of the online code.

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“…We use GEOS‐Chem Version 12.3.2 in its high‐performance implementation (Eastham et al, 2018). GEOS‐Chem simulates tropospheric‐stratospheric chemistry by solving the 3‐D chemical continuity equations in an Eulerian framework for over 200 chemical species.…”

Section: Application To Massively Parallel Geos‐chem Simulations On Tmentioning

confidence: 99%

“…The GFDL‐FV3 model involves intensive internode communication and is designed to achieve high scalability using the cubed‐sphere grid (Chapter 5 of Putman, 2007). The MAPL I/O component in GEOS‐Chem Version 12.3.2 reads most data in serial, rather than parallelized across cores, which may become a bottleneck for a large number of cores (Figure 4 in Eastham et al, 2018). More recent GEOS‐Chem versions (12.5.0 and beyond) allow parallel I/O via the “GMAO_pFIO” module (ESMF, 2018).…”

Section: Application To Massively Parallel Geos‐chem Simulations On Tmentioning

confidence: 99%

“…Here we show that new technology makes it possible to conduct computationally and cost‐efficient simulations with over a thousand cores on cloud platforms. We apply this new capability to the GEOS‐Chem chemical transport model (Eastham et al, 2018) and present an easy‐to‐follow research workflow for GEOS‐Chem users on the Amazon Web Services (AWS) cloud that can also serve as template for other Earth science models.…”

Section: Introductionmentioning

confidence: 99%

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Enabling High‐Performance Cloud Computing for Earth Science Modeling on Over a Thousand Cores: Application to the GEOS‐Chem Atmospheric Chemistry Model

Zhuang

Jacob

Lin

et al. 2020

J Adv Model Earth Syst

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Cloud computing platforms can facilitate the use of Earth science models by providing immediate access to fully configured software, massive computing power, and large input data sets. However, slow internode communication performance has previously discouraged the use of cloud platforms for massively parallel simulations. Here we show that recent advances in the network performance on the Amazon Web Services cloud enable efficient model simulations with over a thousand cores. The choices of Message Passing Interface library configuration and internode communication protocol are critical to this success. Application to the Goddard Earth Observing System (GEOS)-Chem global 3-D chemical transport model at 50-km horizontal resolution shows efficient scaling up to at least 1,152 cores, with performance and cost comparable to the National Aeronautics and Space Administration Pleiades supercomputing cluster.Plain Language Summary Earth science model simulations are computationally expensive, typically requiring the use of high-end supercomputing clusters that are managed by universities or national laboratories. Commercial cloud computing offers an alternative. However, past work found that cloud computing platforms were not efficient for large-scale simulations on over 100 CPU cores, because the network communication performance on the cloud was slow compared to local clusters. Here we show that recent advances in the cloud network performance enable efficient model simulations with over a thousand cores, and cloud platforms can now serve as a viable alternative to local clusters for simulations at large scale. Computing on the cloud has extensive advantages, such as providing immediate access to fully configured model code and large data sets for any users, allowing full reproducibility of model simulation results, offering quick access to novel hardware that might not be available on local clusters, and being able to scale to virtually unlimited amounts of compute and storage resources. Those benefits will help advance Earth science modeling research.

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GEOS-Chem High Performance (GCHP v11-02c): a next-generation implementation of the GEOS-Chem chemical transport model for massively parallel applications

Cited by 87 publications

References 20 publications

On the sources and sinks of atmospheric VOCs: An integrated analysis of recent aircraft campaigns over North America

On the sources and sinks of atmospheric VOCs: An integrated analysis of recent aircraft campaigns over North America

Global simulation of tropospheric chemistry at 12.5 km resolution: performance and evaluation of the GEOS-Chem chemical module (v10-1) within the NASA GEOS Earth system model (GEOS-5 ESM)

Enabling High‐Performance Cloud Computing for Earth Science Modeling on Over a Thousand Cores: Application to the GEOS‐Chem Atmospheric Chemistry Model

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