Performance improvements of an atmospheric radiative transfer model on GPU-based platform using CUDA

Classical applications of Atmospheric Radiative Transfer Model (ARTM) for modelization of absorption coefficient line-by-line on the atmosphere consume large computational time since seconds up to a few minutes depending on the atmospheric characterization chosen. ARTM is used together with Ground- Based or Satellite measurements to retrieve atmospheric parameters such as ozone, water vapour and temperature profiles. Nowadays in the Atmospheric Observatory of Southern Patagonia (OAPA) at the Patagonian City of Río Gallegos have been deployed a Spectral Millimeter Wave Radiometer belonging Nagoya Univ. (Japan) with the aim of retrieve stratospheric ozone profiles between 20-80 Km. Around 2 GBytes of data are recorder by the instrument per day and the ozone profiles are retrieving using one hour integration spectral data, resulting at 24 profiles per day. Actually the data reduction is performed by Laser and Application Research Center (CEILAP) group using the Matlab package ARTS/QPACK2. Using the classical data reduction procedure, the computational time estimated per profile is between 4-5 minutes determined mainly by the computational time of the ARTM and matrix operations. We propose in this work first add a novel scheme to accelerate the processing speed of the ARTM using the powerful multi-threading setup of GPGPU based at Compute Unified Device Architecture (CUDA) and compare it with the existing schemes. Performance of the ARTM has been calculated using various settings applied on a NVIDIA graphic Card GeForce GTX 560 Compute Capability 2.1. Comparison of the execution time between sequential mode, Open-MP and CUDA has been tested in this paper.XV Workshop de Procesamiento Distribuido y Paralelo (WPDP)Red de Universidades con Carreras en Informática (RedUNCI

Performance improvements of an atmospheric radiative transfer model on GPU-based platform using CUDA

Classical applications of Atmospheric Radiative Transfer Model (ARTM) for modelization of absorption coefficient line-by-line on the atmosphere consume large computational time since seconds up to a few minutes depending on the atmospheric characterization chosen. ARTM is used together with Ground- Based or Satellite measurements to retrieve atmospheric parameters such as ozone, water vapour and temperature profiles. Nowadays in the Atmospheric Observatory of Southern Patagonia (OAPA) at the Patagonian City of Río Gallegos have been deployed a Spectral Millimeter Wave Radiometer belonging Nagoya Univ. (Japan) with the aim of retrieve stratospheric ozone profiles between 20-80 Km. Around 2 GBytes of data are recorder by the instrument per day and the ozone profiles are retrieving using one hour integration spectral data, resulting at 24 profiles per day. Actually the data reduction is performed by Laser and Application Research Center (CEILAP) group using the Matlab package ARTS/QPACK2. Using the classical data reduction procedure, the computational time estimated per profile is between 4-5 minutes determined mainly by the computational time of the ARTM and matrix operations. We propose in this work first add a novel scheme to accelerate the processing speed of the ARTM using the powerful multi-threading setup of GPGPU based at Compute Unified Device Architecture (CUDA) and compare it with the existing schemes. Performance of the ARTM has been calculated using various settings applied on a NVIDIA graphic Card GeForce GTX 560 Compute Capability 2.1. Comparison of the execution time between sequential mode, Open-MP and CUDA has been tested in this paper.XV Workshop de Procesamiento Distribuido y Paralelo (WPDP)Red de Universidades con Carreras en Informática (RedUNCI

Performance improvements of an atmospheric radiative transfer model on GPU-based platform using CUDA

Classical applications of Atmospheric Radiative Transfer Model (ARTM) for modelization of absorption coefficient line-by-line on the atmosphere consume large computational time since seconds up to a few minutes depending on the atmospheric characterization chosen. ARTM is used together with Ground- Based or Satellite measurements to retrieve atmospheric parameters such as ozone, water vapour and temperature profiles. Nowadays in the Atmospheric Observatory of Southern Patagonia (OAPA) at the Patagonian City of Río Gallegos have been deployed a Spectral Millimeter Wave Radiometer belonging Nagoya Univ. (Japan) with the aim of retrieve stratospheric ozone profiles between 20-80 Km. Around 2 GBytes of data are recorder by the instrument per day and the ozone profiles are retrieving using one hour integration spectral data, resulting at 24 profiles per day. Actually the data reduction is performed by Laser and Application Research Center (CEILAP) group using the Matlab package ARTS/QPACK2. Using the classical data reduction procedure, the computational time estimated per profile is between 4-5 minutes determined mainly by the computational time of the ARTM and matrix operations. We propose in this work first add a novel scheme to accelerate the processing speed of the ARTM using the powerful multi-threading setup of GPGPU based at Compute Unified Device Architecture (CUDA) and compare it with the existing schemes. Performance of the ARTM has been calculated using various settings applied on a NVIDIA graphic Card GeForce GTX 560 Compute Capability 2.1. Comparison of the execution time between sequential mode, Open-MP and CUDA has been tested in this paper.XV Workshop de Procesamiento Distribuido y Paralelo (WPDP)Red de Universidades con Carreras en Informática (RedUNCI

Structural and Biochemical Features of Eimeria tenella Dihydroorotate Dehydrogenase, a Potential Drug Target

Dihydroorotate dehydrogenase (DHODH) is a mitochondrial monotopic membrane protein that plays an essential role in the pyrimidine de novo biosynthesis and electron transport chain pathways. In Eimeria tenella, an intracellular apicomplexan parasite that causes the most severe form of chicken coccidiosis, the activity of pyrimidine salvage pathway at the intracellular stage is negligible and it relies on the pyrimidine de novo biosynthesis pathway. Therefore, the enzymes of the de novo pathway are considered potential drug target candidates for the design of compounds with activity against this parasite. Although, DHODHs from E. tenella (EtDHODH), Plasmodium falciparum (PfDHODH), and human (HsDHODH) show distinct sensitivities to classical DHODH inhibitors, in this paper,we identify ferulenol as a potent inhibitor of both EtDHODH and HsDHODH. Additionally, we report the crystal structures of EtDHODH and HsDHODH in the absence and presence of ferulenol. Comparison of these enzymes showed that despite similar overall structures, the EtDHODH has a long insertion in the N-terminal helix region that assumes a disordered configuration. In addition, the crystal structures revealed that the ferulenol binding pocket of EtDHODH is larger than that of HsDHODH. These differences can be explored to accelerate structure-based design of inhibitors specifically targeting EtDHODH

Bias correction of OMI HCHO columns based on FTIR and aircraft measurements and impact on top-down emission estimates

Spaceborne formaldehyde (HCHO) measurements constitute an excellent proxy for the sources of non-methane volatile organic compounds (NMVOCs). Past studies suggested substantial overestimations of NMVOC emissions in state-of-the-art inventories over major source regions. Here, the QA4ECV (Quality Assurance for Essential Climate Variables) retrieval of HCHO columns from OMI (Ozone Monitoring Instrument) is evaluated against (1) FTIR (Fourier-transform infrared) column observations at 26 stations worldwide and (2) aircraft in situ HCHO concentration measurements from campaigns conducted over the USA during 2012–2013. Both validation exercises show that OMI underestimates high columns and overestimates low columns. The linear regression of OMI and aircraft-based columns gives Ω$_{OMI}$=0,651 Ω$_{airc}$+2,95 x 10$^{15}$, molec. cm$^{-2}$ , with Ω$_{OMI}$ and Ω$_{airc}$ the OMI and aircraft-derived vertical columns, whereas the regression of OMI and FTIR data gives Ω$_{OMI}$= 6,59 Ω$_{FTIR}$ + 2.02 x 10$^{15}$, molec. cm$^{-2}$ . Inverse modelling of NMVOC emissions with a global model based on OMI columns corrected for biases based on those relationships leads to much-improved agreement against FTIR data and HCHO concentrations from 11 aircraft campaigns. The optimized global isoprene emissions ($\sim$ 445 Tgyr$^{-1}$) are 25 % higher than those obtained without bias correction. The optimized isoprene emissions bear both striking similarities and differences with recently published emissions based on spaceborne isoprene columns from the CrIS (Cross-track Infrared Sounder) sensor. Although the interannual variability of OMI HCHO columns is well understood over regions where biogenic emissions are dominant, and the HCHO trends over China and India clearly reflect anthropogenic emission changes, the observed HCHO decline over the southeastern USA remains imperfectly elucidated

TROPOMI–Sentinel-5 Precursor formaldehyde validation using an extensive network of ground-based Fourier-transform infrared stations

TROPOMI (the TROPOspheric Monitoring Instrument), on board the Sentinel-5 Precursor (S5P) satellite, has been monitoring the Earth\u27s atmosphere since October 2017 with an unprecedented horizontal resolution (initially 7 km$^{2}$×3.5 km$^{2}$, upgraded to 5.5 km$^{2}$×3.5 km$^{2}$ in August 2019). Monitoring air quality is one of the main objectives of TROPOMI; it obtains measurements of important pollutants such as nitrogen dioxide, carbon monoxide, and formaldehyde (HCHO). In this paper we assess the quality of the latest HCHO TROPOMI products versions 1.1.(5-7), using ground-based solar-absorption FTIR (Fourier-transform infrared) measurements of HCHO from 25 stations around the world, including high-, mid-, and low-latitude sites. Most of these stations are part of the Network for the Detection of Atmospheric Composition Change (NDACC), and they provide a wide range of observation conditions, from very clean remote sites to those with high HCHO levels from anthropogenic or biogenic emissions. The ground-based HCHO retrieval settings have been optimized and harmonized at all the stations, ensuring a consistent validation among the sites. In this validation work, we first assess the accuracy of TROPOMI HCHO tropospheric columns using the median of the relative differences between TROPOMI and FTIR ground-based data (BIAS). The pre-launch accuracy requirements of TROPOMI HCHO are 40 %–80 %. We observe that these requirements are well reached, with the BIAS found below 80 % at all the sites and below 40 % at 20 of the 25 sites. The provided TROPOMI systematic uncertainties are well in agreement with the observed biases at most of the stations except for the highest-HCHO-level site, where it is found to be underestimated. We find that while the BIAS has no latitudinal dependence, it is dependent on the HCHO concentration levels: an overestimation (+26±5 %) of TROPOMI is observed for very low HCHO levels (8.0×10$^{15}$ molec. cm$^{-2}$). This demonstrates the great value of such a harmonized network covering a wide range of concentration levels, the sites with high HCHO concentrations being crucial for the determination of the satellite bias in the regions of emissions and the clean sites allowing a small TROPOMI offset to be determined. The wide range of sampled HCHO levels within the network allows the robust determination of the significant constant and proportional TROPOMI HCHO biases (TROPOMI =+1.10±0.05 ×10$^{15}$+0.64±0.03 × FTIR; in molecules per square centimetre). Second, the precision of TROPOMI HCHO data is estimated by the median absolute deviation (MAD) of the relative differences between TROPOMI and FTIR ground-based data. The clean sites are especially useful for minimizing a possible additional collocation error. The precision requirement of 1.2×10$^{16}$ molec. cm$^{-2}$ for a single pixel is reached at most of the clean sites, where it is found that the TROPOMI precision can even be 2 times better (0.5–0.8×10$^{15}$ molec. cm$^{-2}$ for a single pixel). However, we find that the provided TROPOMI random uncertainties may be underestimated by a factor of 1.6 (for clean sites) to 2.3 (for high HCHO levels). The correlation is very good between TROPOMI and FTIR data (R=0.88 for 3 h mean coincidences; R=0.91 for monthly means coincidences). Using about 17 months of data (from May 2018 to September 2019), we show that the TROPOMI seasonal variability is in very good agreement at all of the FTIR sites. The FTIR network demonstrates the very good quality of the TROPOMI HCHO products, which is well within the pre-launch requirements for both accuracy and precision. This paper makes suggestions for the refinement of the TROPOMI random uncertainty budget and TROPOMI quality assurance values for a better filtering of the remaining outliers

Characterization and potential for reducing optical resonances in Fourier transform infrared spectrometers of the Network for the Detection of Atmospheric Composition Change (NDACC)

Although optical components in Fourier transform infrared (FTIR) spectrometers are preferably wedged, in practice, infrared spectra typically suffer from the effects of optical resonances (“channeling”) affecting the retrieval of weakly absorbing gases. This study investigates the level of channeling of each FTIR spectrometer within the Network for the Detection of Atmospheric Composition Change (NDACC).Part of this work was supported by Ministerio de Economía y Competitividad from Spain (project INMENSE no. CGL2016-80688-P). The Altzomoni site UNAM (DGAPA (grant nos. IN111418 and IN107417)) was supported by the CONACYT (grant no. 290589) and PASPA. This work has been supported by the Federal Ministry of Education and Research (BMBF) Germany in the project TroStra (grant no. 01LG1904A)

Nitrous Oxide Profiling from Infrared Radiances (NOPIR): Algorithm Description, Application to 10 Years of IASI Observations and Quality Assessment

Nitrous oxide (N$_{2}$O) is the third most abundant anthropogenous greenhouse gas (after carbon dioxide and methane), with a long atmospheric lifetime and a continuously increasing concentration due to human activities, making it an important gas to monitor. In this work, we present a new method to retrieve N$_{2}$O concentration profiles (with up to two degrees of freedom) from each cloud-free satellite observation by the Infrared Atmospheric Sounding Interferometer (IASI), using spectral micro-windows in the N$_{2}$O ν$_{3}$ band, the Radiative Transfer for TOVS (RTTOV) tools and the Tikhonov regularization scheme. A time series of ten years (2011–2020) of IASI N$_{2}$O profiles and integrated partial columns has been produced and validated with collocated ground-based Network for the Detection of Atmospheric Composition Change (NDACC) and Total Carbon Column Observing Network (TCCON) data. The importance of consistency in the ancillary data used for the retrieval for generating consistent time series has been demonstrated. The Nitrous Oxide Profiling from Infrared Radiances (NOPIR) N$_{2}$O partial columns are of very good quality, with a positive bias of 1.8 to 4% with respect to the ground-based data, which is less than the sum of uncertainties of the compared values. At high latitudes, the comparisons are a bit worse, due to either a known bias in the ground-based data, or to a higher uncertainty in both ground-based and satellite retrievals