Towards convection-resolving, global atmospheric simulations with the Model for Prediction Across Scales (MPAS) v3.1: an extreme scaling experiment, links to sourcecode of model and grides

The Model for Prediction Across Scales (MPAS) is a novel set of Earth system simulation components and consists of an atmospheric model, an ocean model and a land-ice model. Its distinct features are the use of unstructured Voronoi meshes and C-grid discretisation to address shortcomings of global models on regular grids and the use of limited area models nested in a forcing data set, with respect to parallel scalability, numerical accuracy and physical consistency. This concept allows one to include the feedback of regional land use information on weather and climate at local and global scales in a consistent way, which is impossible to achieve with traditional limited area modelling approaches. Here, we present an in-depth evaluation of MPAS with regards to technical aspects of performing model runs and scalability for three medium-size meshes on four different high-performance computing (HPC) sites with different architectures and compilers. We uncover model limitations and identify new aspects for the model optimisation that are introduced by the use of unstructured Voronoi meshes. We further demonstrate the model performance of MPAS in terms of its capability to reproduce the dynamics of the West African monsoon (WAM) and its associated precipitation in a pilot study. Constrained by available computational resources, we compare 11-month runs for two meshes with observations and a reference simulation from the Weather Research and Forecasting (WRF) model. We show that MPAS can reproduce the atmospheric dynamics on global and local scales in this experiment, but identify a precipitation excess for the West African region. Finally, we conduct extreme scaling tests on a global 3?km mesh with more than 65 million horizontal grid cells on up to half a million cores. We discuss necessary modifications of the model code to improve its parallel performance in general and specific to the HPC environment. We confirm good scaling (70?% parallel efficiency or better) of the MPAS model and provide numbers on the computational requirements for experiments with the 3?km mesh. In doing so, we show that global, convection-resolving atmospheric simulations with MPAS are within reach of current and next generations of high-end computing facilities.

Solar irradiance over and under seasonal land-fast sea ice off Barrow, Alaska, in 2010

The amount of solar radiation transmitted through Arctic sea ice is determined by the thickness and physical properties of snow and sea ice. Light transmittance is highly variable in space and time since thickness and physical properties of snow and sea ice are highly heterogeneous on variable time and length scales. We present field measurements of under-ice irradiance along transects under undeformed land-fast sea ice at Barrow, Alaska (March, May, and June 2010). The measurements were performed with a spectral radiometer mounted on a floating under-ice sled. The objective was to quantify the spatial variability of light transmittance through snow and sea ice, and to compare this variability along its seasonal evolution. Along with optical measurements, snow depth, sea ice thickness, and freeboard were recorded, and ice cores were analyzed for chlorophyll a and particulate matter. Our results show that snow cover variability prior to onset of snow melt causes as much relative spatial variability of light transmittance as the contrast of ponded and white ice during summer. Both before and after melt onset, measured transmittances fell in a range from one third to three times the mean value. In addition, we found a twentyfold increase of light transmittance as a result of partial snowmelt, showing the seasonal evolution of transmittance through sea ice far exceeds the spatial variability. However, prior melt onset, light transmittance was time invariant and differences in under-ice irradiance were directly related to the spatial variability of the snow cover.

Revised age models and foraminiferal records obtained for the Last Interglacial period in six marine sediment cores

The dataset contains the revised age models and foraminiferal records obtained for the Last Interglacial period in six marine sediment cores: - the Southern Ocean core MD02-2488 (age model, sea surface temperatures, benthic d18O and d13C for the period 136-108 ka), - the North Atlantic core MD95-2042 (age model, planktic d18O, benthic d18O and d13C for the period 135-110 ka), - the North Atlantic core ODP 980 (age model, planktic d18O, sea surface temperatures, seawater d18O, benthic d18O and d13C, ice-rafted detritus for the period 135-110 ka), - the North Atlantic core CH69-K09 (age model, planktic d18O, sea surface temperatures, seawater d18O, benthic d18O and d13C, ice-rafted detritus for the period 135-110 ka), - the Norwegian Sea core MD95-2010 (age model, percentage of Neogloboquadrina pachyderma sinistral, sea surface temperatures, benthic d18O, ice-rafted detritus for the period 134-110 ka), - the Labrador Sea core EW9302-JPC2 (age model, percentage of Neogloboquadrina pachyderma sinistral, sea surface temperatures, benthic d18O for the period 134-110 ka).

Pigment data set from the SeaWiFS Bio-optical Archive and Storage System (1961-1996)

The oceans play a critical role in the Earth's climate, but unfortunately, the extent of this role is only partially understood. One major obstacle is the difficulty associated with making high-quality, globally distributed observations, a feat that is nearly impossible using only ships and other ocean-based platforms. The data collected by satellite-borne ocean color instruments, however, provide environmental scientists a synoptic look at the productivity and variability of the Earth's oceans and atmosphere, respectively, on high-resolution temporal and spatial scales. Three such instruments, the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) onboard ORBIMAGE's OrbView-2 satellite, and two Moderate Resolution Imaging Spectroradiometers (MODIS) onboard the National Aeronautic and Space Administration's (NASA) Terra and Aqua satellites, have been in continuous operation since September 1997, February 2000, and June 2002, respectively. To facilitate the assembly of a suitably accurate data set for climate research, members of the NASA Sensor Intercomparison and Merger for Biological and Interdisciplinary Oceanic Studies (SIMBIOS) Project and SeaWiFS Project Offices devote significant attention to the calibration and validation of these and other ocean color instruments. This article briefly presents results from the SIMBIOS and SeaWiFS Project Office's (SSPO) satellite ocean color validation activities and describes the SeaWiFS Bio-optical Archive and Storage System (SeaBASS), a state-of-the-art system for archiving, cataloging, and distributing the in situ data used in these activities.

Lead 210 and silicate profiles from sediments of the equatorial Pacific and South Atlantic

Particle mixing rates have been determined for 5 South Atlantic/Antarctic and 3 equatorial Pacific deep-sea cores using excess 210Pb and 32Si measurements. Radionuclide profiles from these siliceous, calcareous, and clay-rich sediments have been evaluated using a steady state vertical advection diffusion model. In Antarctic siliceous sediments210Pb mixing coefficients (0.04-0.16 cm**2/y) are in reasonable agreement with the 32Si mixing coefficient (0.2 or 0.4 cm**2/y, depending on 32Si half-life). In an equatorial Pacific sediment core, however, the 210Pb mixing coefficient (0.22 cm**2/y) is 3-7 times greater than the 32Si mixing coefficient (0.03 or 0.07 cm**2/y). The difference in 210Pb and 32Si mixing rates in the Pacific sediments results from: (1) non-steady state mixing and differences in characteristic time and depth scales of the two radionuclides, (2) preferential mixing of fine-grained clay particles containing most of the 210Pb activity relative to coarser particles (large radiolaria) containing the 32Si activity, or (3) the supply of 222Rn from the bottom of manganese nodules which increases the measured excess 210Pb activity (relative to 226Ra) at depth and artificially increases the 210Pb mixing coefficient. Based on 32Si data and pore water silica profiles, dissolution of biogenic silica in the sediment column appears to have a minor effect on the 32Si profile in the mixed layer. Deep-sea particle mixing rates reported in this study and the literature do not correlate with sediment type, sediment accumulation rate, or surface productivity. Based on differences in mixing rate among three Antarctic cores collected within 50 km of each other, local variability in the intensity of deep-sea mixing appears to be as important as regional differences in sediment properties.

Gas emissions and ROV survey tracks of the Regab pockmark (Northern Congo Fan)

Pockmarks are seafloor depressions commonly associated with fluid escape from the seabed and are believed to contribute noticeably to the transfer of methane into the ocean and ultimately into the atmosphere. They occur in many different areas and geological contexts, and vary greatly in size and shape. Nevertheless, the mechanisms of pockmark growth are still largely unclear. Still, seabed methane emissions contribute to the global carbon budget, and understanding such processes is critical to constrain future quantifications of seabed methane release at local and global scales. The giant Regab pockmark (9°42.6' E, 5°47.8' S), located at 3160 m water depth near the Congo deep-sea channel (offshore southwestern Africa), was investigated with state-of-the-art mapping devices mounted on IFREMER's (French Research Institute for Exploitation of the Sea) remotely operated vehicle (ROV) Victor 6000. ROV-borne micro-bathymetry and backscatter data of the entire structure, a high-resolution photo-mosaic covering 105,000 m2 of the most active area, sidescan mapping of gas emissions, and maps of faunal distribution as well as of carbonate crust occurrence are combined to provide an unprecedented detailed view of a giant pockmark. All data sets suggest that the pockmark is composed of two very distinctive zones in terms of seepage intensity. We postulate that these zones are the surface expression of two fluid flow regimes in the subsurface: focused flow through a fractured medium and diffuse flow through a porous medium. We conclude that the growth of giant pockmarks is controlled by self-sealing processes and lateral spreading of rising fluids. In particular, partial redirection of fluids through fractures in the sediments can drive the pockmark growth in preferential directions.

Molecular dissolved organic matter composition in lakes across Sweden as relative intensities of FT-ICR-MS peaks and PARAFAC components and optical indices

Whether intrinsic molecular properties or extrinsic factors such as environmental conditions control the decomposition of natural organic matter across soil, marine and freshwater systems has been subject to debate. Comprehensive evaluations of the controls that molecular structure exerts on organic matter's persistence in the environment have been precluded by organic matter's extreme complexity. Here we examine dissolved organic matter from 109 Swedish lakes using ultrahigh-resolution mass spectrometry and optical spectroscopy to investigate the constraints on its persistence in the environment. We find that degradation processes preferentially remove oxidized, aromatic compounds, whereas reduced, aliphatic and N-containing compounds are either resistant to degradation or tightly cycled and thus persist in aquatic systems. The patterns we observe for individual molecules are consistent with our measurements of emergent bulk characteristics of organic matter at wide geographic and temporal scales, as reflected by optical properties. We conclude that intrinsic molecular properties are an important control of overall organic matter reactivity.

Benthic and fish community composition as well as water quality along the Thousand Islands north of the megacity Jakarta, Indonesia

Worldwide, coral reefs are challenged by multiple stressors due to growing urbanization, industrialization and coastal development. Coral reefs along the Thousand Islands off Jakarta, one of the largest megacities worldwide, have degraded dramatically over recent decades. The shift and decline in coral cover and composition has been extensively studied with a focus on large-scale gradients (i.e. regional drivers), however special focus on local drivers in shaping spatial community composition is still lacking. Here, the spatial impact of anthropogenic stressors on local and regional scales on coral reefs north of Jakarta was investigated. Results indicate that the direct impact of Jakarta is mainly restricted to inshore reefs, separating reefs in Jakarta Bay from reefs along the Thousand Islands further north. A spatial patchwork of differentially degraded reefs is present along the islands as a result of localized anthropogenic effects rather than regional gradients. Pollution is the main anthropogenic stressor, with over 80 % of variation in benthic community composition driven by sedimentation rate, NO2, PO4 and Chlorophyll a. Thus, the spatial structure of reefs is directly related to intense anthropogenic pressure from local as well as regional sources. Therefore, improved spatial management that accounts for both local and regional stressors is needed for effective marine conservation.

Index properties, consolidation characteristics and sediment rebound of ODP Sites 167-1020 and 167-1021 sediments

Drilling during Leg 167 at the California margin was scheduled to recover continuous sedimentary sections. Multiple advanced piston core (APC) holes drilled at different depth offsets provided core overlap in successive APCs. Correlation of high-resolution laboratory physical properties data from adjacent APC holes was used to compile composite depth sections for each site. The composite depth sections were used to confirm continuous recovery and enable high-resolution sampling. The meters composite depth (mcd) scale differs from the shipboard meters below seafloor (mbsf) scale because of (1) core expansion following recovery (MacKillop et al., 1995, doi:10.2973/odp.proc.sr.138.118.1995), (2) coring gaps, and (3) stretching/compression of sediment during coring (Lyle, Koizumi, Richter, et al., 1997, doi:10.2973/odp.proc.ir.167.1997). Moran (1997, doi:10.2973/odp.proc.sr.154.132.1997) calculated that sediment expansion accounted for 90%-95% of the Leg 154 depth offset between shipboard mbsf and the mcd scales. Terzaghi's one-dimensional theory of consolidation (Terzaghi, 1943) describes the response of sediments to stress loading and release. Mechanical loading in marine environments is provided by the buoyant weight of the overlying sediments. The load increases with depth below seabed, resulting in sediment volume reduction as water is "squeezed" out of the voids in the sediment. Stress release during core recovery results in expansion of the sediment and volume increase as water returns to the sediment. The sediment expansion or rebound defines the elastic properties of the sediment. In this study we examine the elastic deformation properties of sediments recovered from Sites 1020 and 1021. These results are used to (1) correct the laboratory index properties measurements to in situ values and (2) determine the contribution of sediment rebound to the depth offset between the mbsf and mcd scales.

Global and Regional Sea level budget components from GRACE and radar altimetry (2002-2014)

This dataset contains the result of a joint least squares inversion of GRACE and altimetry data. The results are evaluated in terms of sea level change for the global ocean as well as dedicated areas. In addition, some auxiliary data is provided to enable reproducibility of the results in Rietbroek et al. 2016, and a google Earth kmz file is provided which visualizes the trends derived from the inversion results.

Anthropogenic aerosol emissions and rainfall decline in South-West Australia - accompanying model results in NetCDF format

It is commonly understood that the observed decline in precipitation in South-West Australia during the 20th century is caused by anthropogenic factors. Candidates therefore are changes to large-scale atmospheric circulations due to global warming, extensive deforestation and anthropogenic aerosol emissions - all of which are effective on different spatial and temporal scales. This contribution focusses on the role of rapidly rising aerosol emissions from anthropogenic sources in South-West Australia around 1970. An analysis of historical longterm rainfall data of the Bureau of Meteorology shows that South-West Australia as a whole experienced a gradual decline in precipitation over the 20th century. However, on smaller scales and for the particular example of the Perth catchment area, a sudden drop in precipitation around 1970 is apparent. Modelling experiments at a convection-resolving resolution of 3.3km using the Weather and Research Forecasting (WRF) model version 3.6.1 with the aerosol-aware Thompson-Eidhammer microphysics scheme are conducted for the period 1970-1974. A comparison of four runs with different prescribed aerosol emissions and without aerosol effects demonstrates that tripling the pre-1960s atmospheric CCN and IN concentrations can suppress precipitation by 2-9%, depending on the area and the season. This suggests that a combination of all three processes is required to account for the gradual decline in rainfall seen for greater South-West Australia and for the sudden drop observed in areas along the West Coast in the 1970s: changing atmospheric circulations, deforestation and anthropogenic aerosol emissions.