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At least 1,585 records · Page 88

Automatic Generation of Algorithms for High-Speed Reliable Lossy Data Compression (Final Report)

Fast reliable data compression is urgently needed for many leading-edge scientific instruments and for exascale high-performance computing applications because they produce vast amounts of data at extremely high rates. The goal of this project has been to develop a framework named LC that is able to automatically generate high-speed lossless and reliable lossy compression and decompression algorithms that can be customized for different kinds of data. The resulting LC framework is freely available on GitHub. To achieve high-speed operation, LC outputs optimized and parallelized CPU and GPU implementations of the generated algorithms. To ensure the quality of lossily compressed data, LC guarantees the user-provided error bound. To be able to customize the compression algorithm to various use cases, LC can synthesize millions of different algorithms and automatically search for the one that works best for the given data. We have already employed LC to create state-of-the-art lossless and lossy compressors for scientific data as well as leading lossless compressors for images. We hope that LC and the customized, fast, reliable, and CPU/GPU-compatible compression algorithms that it can generate will greatly benefit the many scientific applications that need not only high trustworthiness but also high performance.

97 MATHEMATICS AND COMPUTING↗

Vegetation canopy discrimination and biomass assessment using multipolarized airborne SAR

Multipolarized airborne Synthetic Aperture Radar (SAR) data were acquired over a largely agricultural test site near Macomb, Illinois, in conjunction with the Shuttle Imaging Radar (SIR-B) experiment in October 1984. The NASA/JPL L-band SAR operating at 1.225 GHz made a series of daily overflights with azimuth view angles both parallel and orthogonal to those of SIR-B. The SAR data was digitally recorded in the quadpolarization configuration. An extensive set of ground measurements were obtained throughout the test site and include biophysical and soil measurements of approximately 400 agricultural fields. Preliminary evaluation of some of the airborne SAR imagery indicates a great potential for crop discrimination and assessment of canopy condition. False color composites constructed from the combination of three linear polarizations (HH, VV, and HV) were found to be clearly superior to any single polarization for purposes of crop classification. In addition, an image constructed using the HH return to modulate intensity and the phase difference between HH and VV returns to modulate chroma indicates a clear capability for assessment of canopy height and/or biomass. In particular, corn fields heavily damaged by infestations of corn borer are readily distinguished from noninfested fields.

Ulaby, F. T.↗

Data Reduction Pipeline for the CHARIS Integral-Field Spectrograph I: Detector Readout Calibration and Data Cube Extraction

We present the data reduction pipeline for CHARIS, a high-contrast integral-field spectrograph for the Subaru Telescope. The pipeline constructs a ramp from the raw reads using the measured nonlinear pixel response and reconstructs the data cube using one of three extraction algorithms: aperture photometry, optimal extraction, or chi-squared fitting. We measure and apply both a detector flatfield and a lenslet flatfield and reconstruct the wavelength- and position-dependent lenslet point-spread function (PSF) from images taken with a tunable laser. We use these measured PSFs to implement a chi-squared-based extraction of the data cube, with typical residuals of approximately 5 percent due to imperfect models of the under-sampled lenslet PSFs. The full two-dimensional residual of the chi-squared extraction allows us to model and remove correlated read noise, dramatically improving CHARIS's performance. The chi-squared extraction produces a data cube that has been deconvolved with the line-spread function and never performs any interpolations of either the data or the individual lenslet spectra. The extracted data cube also includes uncertainties for each spatial and spectral measurement. CHARIS's software is parallelized, written in Python and Cython, and freely available on github with a separate documentation page. Astrometric and spectrophotometric calibrations of the data cubes and PSF subtraction will be treated in a forthcoming paper.

Brandt, Timothy D.↗

Validation of Multi-Dimensional Stirling Engine Design Codes: Measurements in the 90-Degree Turn Test Section

The work to be presented herein was motivated largely by a desire to improve the understanding of oscillatory fluid mechanics inside a Stirling engine. To this end, a CFD project was undertaken at Cleveland State University with the goal of accurately predicting the fluid dynamics within an engine or engine component. Along with the CFD efforts, a code validation project was undertaken at the University of Minnesota. The material covered herein consists of four main parts. In section 1, an experimental investigation of a small aspect ratio impinging jet is discussed. Included in this discussion is a description of the test facilities and instrumentation. A presentation of the collected data is given and comments are made. Next, in section 2, a parallel experimental investigation is presented in which the same geometry as that of section 1 is used, but the flow conditions are changed from steady unidirectional flow to sinusoidally oscillating flow. In section Two, collected data are presented and comments are made. In section 3, a comparison is made between the results of sections 1 and 2, namely, sinusoidally oscillating flow results are compared to steady, unidirectional flow results from the same geometry. Finally, in section 4, a comparison is made between experimentally collected data (the main subject of this work) and CFD generated results. Furthermore, in appendix A, an introductory description of the primary measurement tool used in the experimental process the hot wire anemometer is given for the unfamiliar. The anemometer calibration procedure is described in appendix B. A portfolio of data reduction and data processing codes is provided in appendix C and lastly, a DVD and a roadmap of its contents is provided in an appendix D. 1.0 Unidirectional Flow Investigations 1.1 Introduction This unidirectional experimental program was undertaken to complement an oscillatory flow investigation conducted at the University of Minnesota. The oscillatory investigation is discussed thoroughly in section 2. We defer the description of the motivation behind these experiments until the introduction of section 2. The work that is discussed in this thesis began (chronologically) with oscillatory flow visualization experiments. It was decided that it would be valuable and important to investigate the flow under unidirectional conditions in the same geometry as that of the oscillatory experiments. The thought was that the unidirectional case would be less complicated to model with a CFD program (a moving boundary would be replaced with a steady state boundary condition). Thus, a series of unidirectional experiments were carried out to capture the important features of the flow within the test section. The purpose of these experiments was to provide a data set for comparison to CFD generated velocity fields. Hot-wire anemometry data were taken and flow visualization was conducted as a standard for code validation. The flow geometry was simple, such that it could be easily gridded in a CFD program. However, the geometry provided separation and transition zones, shear layers and recirculation zones. These characteristics made the flow complex and challenging for CFD computation. We comment that the order of experiments that produced this report is as follows: experimental flow visualization under oscillatory flow conditions was carried out; this was followed by unidirectional flow visualization and hot wire anemometry; finally, oscillatory hot wire anemometry was conducted. We present the results out of chronological order for the following reason: the unidirectional results are easier

Simon, Terrence W.↗

VLSI system for synthetic aperture radar /SAR/ processing

The paper discusses an SAR problem based on actual requirements set forth by NASA for a spaceborne application. The requirements for high resolution and high quality necessitate a data sampling rate of 7.5 MHz. For each data value 1,025 4-bit complex multiply + add operations are needed, which is equivalent to 7.7 GHz complex multiply + add operation rate. Since this rate is much too high for general purpose systems, a special-purpose device was sought. This paper discusses two architectures based on parallel operation of 1,025 identical cells, each of which is capable of performing arithmetic, storage, and several control operations. The operation rate in each device is only 7.5 MHz, which is quite manageable, especially with the help of a substantial degree of pipelining. A computational-mathematical analysis is used as a primary tool for evaluating the design and some of its tradeoffs. Two different approaches are discussed and compared; both are based on having 1,025 identical cells working in parallel, but differ in their dual approaches to the flow of data.

Cohen, D.↗

Multithreaded parallelization of the energy and analytic gradient in the fragment molecular orbital method

The fragment molecular orbital method in GAMESS is parallelized in a multithreaded OpenMP implementation combined with the MPI version of the two-level generalized distributed data interface. The energy and analytic gradient in gas phase and the polarizable continuum model of solvation are parallelized in this hybrid three-level scheme, achieving a large memory footprint reduction and a high parallel efficiency on Intel Xeon Phi processors. The parallel efficiency is demonstrated on the Stampede2 and Theta supercomputers using up to 2048 nodes (262 144 threads).

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Norepinephrine induces rapid and long-lasting phosphorylation and redistribution of connexin 43 in cortical astrocytes

Highlights: • Norepinephrine (NE) induces phosphorylation of connexin 43 (Cx43) in the brain. • This phosphorylation occurs within minutes and lasts for tens of minutes. • NE acts directly on astrocytes to induce phosphorylation of Cx43 via PKC pathway. • Phosphorylation of Cx43 induces its redistribution out from the gap junction plaque. • These data suggest biochemical gliomodulatory action of NE in the cerebral cortex. Norepinephrine (NE) modulates brain functions depending on both the internal and external environment. While the neuromodulatory actions of NE have been well characterized, the response and involvement of cortical astrocytes to physiological noradrenergic systems remain largely unknown, especially at the molecular level. In this study, we biochemically characterize the action of NE on astrocytes of the murine neocortex. NE stimulation of acute brain slices rapidly increase phosphorylation of connexin 43 (Cx43) at Serine (Ser) 368, in slices from both juvenile and adolescent animals. The phosphorylation is mediated by the protein kinase C (PKC) pathway under the α1-adrenergic receptor and remains elevated for tens of minutes following brief exposure to NE, well after the intracellular calcium level returns to normal level, suggesting the plastic nature of this phosphorylation event. Importantly, this phosphorylation event persists in the absence of neuronal transmissions, suggesting that the effect of NE on Cx43 phosphorylation is induced directly on astrocytes. Furthermore, these NE-induced phosphorylations are associated with biochemical dissociation of Cx43 from gap-junctional plaques to non-junctional compartments. Finally, we show that pharmacological manipulation of the noradrenergic system using psychoactive drugs modulates phosphorylation of Cx43 in the cerebral cortex in vivo. These data suggest that NE acts directly on astrocytes in parallel with neurons and modulates functionally critical connexin channel proteins in a plastic manner. Thus, plasticity of astrocytes induced by the “gliomodulatory” actions of NE may play important roles in their physiological as well as pharmacological actions in the brain.

60 APPLIED LIFE SCIENCES↗

Stress intensity factor models using mechanics-guided decomposition and symbolic regression

The finite element method can be used to compute accurate stress intensity factors (SIFs) for cracks with complex geometries and boundary conditions. In contrast, handbook solutions act as surrogate SIF models that provide significantly faster evaluation times. However, the development of conventional surrogate SIF models relies on manual development based on low-order parameterizations. This limits surrogate model accuracy and generalizability. Here, in this paper, we develop a framework for the automated development of mechanics-guided handbook SIF solutions by using interpretable machine learning via genetic programming for symbolic regression (GPSR). Formalizing the mechanics-based approach of Raju and Newman, SIF training data is decomposed into multiple subsets. This decomposition enables parallel GPSR model development of subfunctions, each of which accounts for specific geometrical corrections with respect to a known analytical model. Using this mechanics-based approach with GPSR allows for equations to be learned with improved accuracy and reduced complexity relative to the Raju Newman equations while maintaining the inherent interpretability of mathematical expressions. In this paper, we present equations that match the complexity of the Raju Newman equations while having reduced error, as well as equations with similar errors and reduced complexity.

42 ENGINEERING↗

Recursive Factorization of the Inverse Overlap Matrix in Linear Scaling Quantum Molecular Dynamics Simulations

We present a reduced complexity algorithm to compute the inverse overlap factors required to solve the generalized eigenvalue problem in a quantum-based molecular dynamics (MD) simulation. Our method is based on the recursive iterative re nement of an initial guess Z of the inverse overlap matrix S. The initial guess of Z is obtained beforehand either by using an approximate divide and conquer technique or dynamically, propagated within an extended Lagrangian dynamics from previous MD time steps. With this formulation, we achieve long-term stability and energy conservation even under incomplete approximate iterative re nement of Z. Linear scaling performance is obtained using numerically thresholded sparse matrix algebra based on the ELLPACK-R sparse matrix data format, which also enables e cient shared memory parallelization. As we show in this article using selfconsistent density functional based tight-binding MD, our approach is faster than conventional methods based on the direct diagonalization of the overlap matrix S for systems as small as a few hundred atoms, substantially accelerating quantum-based simulations even for molecular structures of intermediate size. For a 4,158 atom water-solvated polyalanine system we nd an average speedup factor of 122 for the computation of Z in each MD step.

36 MATERIALS SCIENCE↗

The Thermal Plumbing System of Stromboli Volcano, Aeolian Islands (Italy) Inferred From Electrical Conductivity and Induced Polarization Tomography

Abstract We performed the first 3D island‐scale tomography of the electrical conductivity of Stromboli volcano (Aeolian Islands, Italy) using 2D acquisition lines (37.2 km) and a total of 18,880 measurements and 2,402 unique electrode locations. This 3D data set was inverted using a Gauss‐Newton algorithm, parallel‐processing on an unstructured tetrahedral mesh containing 678,420 finite‐element nodes and 3,580,145 elements to account for the topography of the volcanic island. The tomogram exhibits a conductive body (10 −2 –1.0 S m −1 ) consistent with the location of CO 2 and temperature anomalies observed at the ground surface. It corresponds to the hydrothermal system with high electrical conductivity associated with alteration. In order to confirm this interpretation, a 2.5D large‐scale induced polarization tomography was performed crossing the volcano. The joint interpretation of the conductivity and normalized chargeability is done with a petrophysical model previously tested and verified at both shield‐ and strato‐volcanoes. This model implies that alteration (through the effect of the cation exchange capacity associated with clay minerals and zeolites) plays a strong role in both controlling the electrical conductivity and normalized chargeability at Stromboli volcano. A temperature tomogram, derived from the geoelectrical measurements, is consistent with surface temperature anomalies and the Very Long Period (VLP) seismicity related to the mild‐explosive activity. This survey displays at 600 m a.s.l. a lateral shift in the highest temperature location, also corresponding to the source of VLP seismicity. Structural boundaries have a major role in the hottest hydrothermal fluids rising below the active crater terrace of Stromboli volcano.

58 GEOSCIENCES↗

An expanded registry of candidate cis -regulatory elements

Mammalian genomes contain millions of regulatory elements that control the complex patterns of gene expression. Previously, the ENCODE consortium mapped biochemical signals across hundreds of cell types and tissues and integrated these data to develop a registry containing 0.9 million human and 300,000 mouse candidate cis-regulatory elements (cCREs) annotated with potential functions. Here we have expanded the registry to include 2.37 million human and 967,000 mouse cCREs, leveraging new ENCODE datasets and enhanced computational methods. This expanded registry covers hundreds of unique cell and tissue types, providing a comprehensive understanding of gene regulation. Functional characterization data from assays such as STARR-seq, massively parallel reporter assay, CRISPR perturbation and transgenic mouse assays have profiled more than 90% of human cCREs, revealing complex regulatory functions. We identified thousands of novel silencer cCREs and demonstrated their dual enhancer and silencer roles in different cellular contexts. Integrating the registry with other ENCODE annotations facilitates genetic variation interpretation and trait-associated gene identification, exemplified by the identification of KLF1 as a novel causal gene for red blood cell traits. This expanded registry is a valuable resource for studying the regulatory genome and its impact on health and disease.

Moore, Jill E. [Univ. of Massachusetts, Worchester↗

Evolution of the ROOT Tree I/O

The ROOT TTree data format encodes hundreds of petabytes of High Energy and Nuclear Physics events. Its columnar layout drives rapid analyses, as only those parts (“branches”) that are really used in a given analysis need to be read from storage. Its unique feature is the seamless C++ integration, which allows users to directly store their event classes without explicitly defining data schemas. In this contribution, we present the status and plans of the future ROOT 7 event I/O. Along with the ROOT 7 interface modernization, we aim for robust, where possible compile-time safe C++ interfaces to read and write event data. On the performance side, we show first benchmarks using ROOT’s new experimental I/O subsystem that combines the best of TTrees with recent advances in columnar data formats. A core ingredient is a strong separation of the high-level logical data layout (C++ classes) from the low-level physical data layout (storage backed nested vectors of simple types). We show how the new, optimized physical data layout speeds up serialization and deserialization and facilitates parallel, vectorized and bulk operations. This lets ROOT I/O run optimally on the upcoming ultra-fast NVRAM storage devices, as well as file-less storage systems such as object stores.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Wide-angle effects for peculiar velocities

ABSTRACT The line-of-sight peculiar velocities of galaxies contribute to their observed redshifts, breaking the translational invariance of galaxy clustering down to a rotational invariance around the observer. This becomes important when the line-of-sight direction varies significantly across a survey, leading to what are known as ‘wide-angle’ effects in redshift-space distortions. Wide-angle effects will also be present in measurements of the momentum field, i.e. the galaxy density-weighted velocity field, in upcoming peculiar velocity surveys. In this work, we study how wide-angle effects modify the predicted correlation function and power spectrum for momentum statistics, both in autocorrelation and in cross-correlation with the density field. Using both linear theory and the Zel'dovich approximation, we find that deviations from the plane-parallel limit are large and could become important in data analysis for low-redshift surveys. We point out that even multipoles in the cross-correlation between density and momentum are non-zero regardless of the choice of line of sight, and therefore contain new cosmological information that could be exploited. We discuss configuration space, Fourier space, and spherical analyses; providing exact expressions in each case rather than relying on an expansion in small angles. We hope these expressions will be of use in the analysis of upcoming surveys for redshift-space distortions and peculiar velocities.

79 ASTRONOMY AND ASTROPHYSICS↗

Life cycle of streaks in the buffer layer of wall-bounded turbulence

In this work, streaks in the buffer layer of wall-bounded turbulence are tracked in time to study their life cycle. Spatially and temporally resolved direct numerical simulation data are used to analyze the strong wall-parallel movements conditioned to low-speed streamwise flow. The analysis of the streaks shows that there is a clear distinction between wall-attached and detached streaks, and that the wall-attached streaks can be further categorized into streaks that are contained in the buffer layer and the ones that reach the outer region. The results reveal that streaks are born in the buffer layer, coalescing with each other to create larger streaks that are still attached to the wall. Once the streak becomes large enough, it starts to meander due to the large streamwise-to-wall-normal aspect ratio, and consequently the elongation in the streamwise direction, which makes it more difficult for the streak to be oriented strictly in the streamwise direction. While the continuous interaction of the streaks allows the superstructure to span extremely long temporal and length scales, individual streak components are relatively small and short-lived. Tall-attached streaks eventually split into wall-attached and wall-detached components. These wall-detached streaks have a strong wall-normal velocity away from the wall, similar to ejections or bursts observed in the literature. Conditionally averaging the flow fields to these split events show that the detached streak has not only a larger wall-normal velocity compared to the wall-attached counterpart, it also has a larger (less negative) streamwise velocity, similar to the velocity field at the tip of a vortex cluster.

42 ENGINEERING↗

Thin Film Morphological Characteristics of a Perfluorinated Anion Exchange Membrane

Anion exchange membranes (AEMs) are a promising technology for fuel cell applications. Most of the research done to date was focused on membrane development, electrode fabrication, or cell performance. Studies of the polymer catalyst interface are needed in order to advance the science of these devices and achieve further improvements. In this work we have studied these interfacial properties using grazing-incidence small-angle x-ray scattering (GISAXS). Thin films of a perfluorinated anion exchange polymer were spin cast onto bare, or silver or platinum coated flat silicon substrates. From the GISAXS data, we can conclude that the polymer chains align parallel to the plain silicon or silver coated substrate at higher thicknesses, >17 nm and, >13 nm respectively. However, on the coated platinum substrate the alignment is somewhere between parallel and perpendicular. The in-plane alignment of ionomer on the surface constrains the swelling of water channels which affects the transport of reactants and products.

30 DIRECT ENERGY CONVERSION↗

Pairwise Sequence Alignment Library

Vector extensions, such as SSE, have been part of the x86 CPU since the 1990s, with applications in graphics, signal processing, and scientific applications. Although many algorithms and applications can naturally benefit from automatic vectorization techniques, there are still many that are difficult to vectorize due to their dependence on irregular data structures, dense branch operations, or data dependencies. Sequence alignment, one of the most widely used operations in bioinformatics workflows, has a computational footprint that features complex data dependencies. The trend of widening vector registers adversely affects the state-of-the-art sequence alignment algorithm based on striped data layouts. Therefore, a novel SIMD implementation of a parallel scan-based sequence alignment algorithm that can better exploit wider SIMD units was implemented as part of the Parallel Sequence Alignment Library (parasail). Parasail features: Reference implementations of all known vectorized sequence alignment approaches. Implementations of Smith Waterman (SW), semi-global (SG), and Needleman Wunsch (NW) sequence alignment algorithms. Implementations across all modern CPU instruction sets including AVX2 and KNC. Language interfaces for C/C++ and Python.

Jeff Daily, PNNL↗

Kokkos Version 2.0

The Kokkos library implements thread-parallel execution policies and shared-memory multidimensional array data structures that enable applications and domain libraries to develop computational kernels that are performance portable across multicore-CPU and manycore-accelerator (e.g. GPU) computing architectures.

SciDAC↗

Benefits of Integration of Aerojet Rocketdyne and RTI Advanced Gasification Technologies for Hydrogen-Rich Syngas Production

The key objective for this project was to evaluate the potential to achieve substantial reductions in the production cost of H 2 -rich syngas via coal gasification with near-zero emissions due to the cumulative and synergistic benefits realized when multiple advanced technologies are integrated into the overall conversion process. In this project, Aerojet Rocketdyne’s (AR’s) advanced gasification technology (currently being offered as R-GAS™) and RTI International’s (RTI’s) advanced warm syngas cleanup technologies were evaluated via a number of comparative techno-economic case studies. AR’s advanced gasification technology consists of a dry solids pump and a compact gasifier system. Based on the unique design of this gasifier, it has been shown to reduce the capital cost of the gasification block by between 40 and 50%. At the start of this project, actual experimental work had been demonstrated through pilot plant systems for both the gasifier and dry solids pump. RTI’s advanced warm syngas cleanup technologies consist primarily of RTI’s Warm Gas Desulfurization Process (WDP) technology, which effectively allows decoupling of the sulfur and CO 2 removal allowing for more flexibility in the selection of the CO 2 removal technology, plus associated advanced technologies for direct sulfur recovery and water gas shift (WGS). WDP has been demonstrated at pre-commercial scale using an activated amine carbon dioxide recovery process which would not have been possible if a majority of the sulfur had not been removed from the syngas by WDP. This pre-commercial demonstration of RTI’s advanced warm syngas cleanup system was conducted in parallel to the activities on this project. The technical data and cost information from this pre-commercial demonstration were extensively used in this project during the techno-economic analysis. With this project, both of RTI’s advanced WGS technologies were investigated. Because RT’s advanced fixed-bed WGS (AFWGS) process was successfully implemented in the WDP pre-commercial demonstration test mentioned above, this technology was used as part of RTI’s advanced warm syngas technology package for the techno-economic analyses for this project. RTI’s advanced transport-reactor-based WGS (ATWGS) process was still conceptual at the start of this project, but one of the tasks for this project was to evaluate the technical feasibility of this technology. In each of the three application-based comparison studies conducted as part of this project, the reference case was based on an existing Department of Energy National Energy Technology Laboratory (DOE/NETL) system study. Each of these references cases used existing commercial technology and the system resulted in > 90% carbon capture. In the comparison studies for the use of the hydrogen-rich syngas generated in either an Integrated Gasification Combined Cycle (IGCC) or a Coal-to-Methanol (CTM) plant, the comparison cases consisted of the reference case, a case with the integration of each individual advanced technology (either AR or RTI), and finally a case with the integration of all the advanced technologies (AR and RTI combined). In the Coal-to-Liquids (CTL) comparison study, the comparison study consisted of only three cases, which included a reference case, a case with just RTI’s advanced syngas cleaning technology, and a case with AR’s and RTI’s advanced technologies. The results from these comparison studies showed that the integration of the advanced technologies did result in substantial benefits, and by far the greatest benefits were achieved for cases integrating all the advanced technologies. For the IGCC study, the fully integrated case resulted in a 1.4% net efficiency improvement, an 18% reduction in capital cost per kW of capacity, a 12% reduction in the operating cost per kWh, and a 75–79% reduction in sulfur emissions. For the CTM case, the fully integrated plant resulted in a 22% reduction in capital cost, a 13% reduction in operating costs, a > 99% net reduction in sulfur emissions, and a reduction of 13–15% in CO 2 emissions. Because the capital cost represents over 60% of the methanol Required Selling Price (RSP), the significant reduction in the capital cost for the advanced technology case resulted in an 18% reduction in methanol RSP. For the CTL case, the fully integrated plant resulted in a 16% reduction in capital cost, which represented a 13% reduction in diesel RSP. Finally, the technical feasibility analysis of RTI’s ATWGS process demonstrated that a fluid-bed catalyst with sufficient attrition resistance and WGS activity could be made and that the process achieved about a 24% reduction in capital cost compared to a conventional fixed-bed commercial process.

08 HYDROGEN↗