Combining checkpointing and data compression for large scale seismic inversion

Seismic inversion and imaging are adjoint-based optimization problems that processes up to terabytes of data, regularly exceeding the memory capacity of available computers. Data compression is an effective strategy to reduce this memory requirement by a certain factor, particularly if some loss in accuracy is acceptable. A popular alternative is checkpointing, where data is stored at selected points in time, and values at other times are recomputed as needed from the last stored state. This allows arbitrarily large adjoint computations with limited memory, at the cost of additional recomputations. In this paper we combine compression and checkpointing for the first time to compute a realistic seismic inversion. The combination of checkpointing and compression allows larger adjoint computations compared to using only compression, and reduces the recomputation overhead significantly compared to using only checkpointing

Dietary Vitamin A Impacts Refractory Telogen.

Hair follicles cycle through periods of growth (anagen), regression (catagen), rest (telogen), and release (exogen). Telogen is further divided into refractory and competent telogen based on expression of bone morphogenetic protein 4 (BMP4) and wingless-related MMTV integration site 7A (WNT7A). During refractory telogen hair follicle stem cells (HFSC) are inhibited. Retinoic acid synthesis proteins localized to the hair follicle and this localization pattern changed throughout the hair cycle. In addition, excess retinyl esters arrested hair follicles in telogen. The purpose of this study was to further define these hair cycle changes. BMP4 and WNT7A expression was also used to distinguish refractory from competent telogen in C57BL/6J mice fed different levels of retinyl esters from two previous studies. These two studies produced opposite results; and differed in the amount of retinyl esters the dams consumed and the age of the mice when the different diet began. There were a greater percentage of hair follicles in refractory telogen both when mice were bred on an unpurified diet containing copious levels of retinyl esters (study 1) and consumed excess levels of retinyl esters starting at 12 weeks of age, as well as when mice were bred on a purified diet containing adequate levels of retinyl esters (study 2) and remained on this diet at 6 weeks of age. WNT7A expression was consistent with these results. Next, the localization of vitamin A metabolism proteins in the two stages of telogen was examined. Keratin 6 (KRT6) and cellular retinoic acid binding protein 2 (CRABP2) localized almost exclusively to refractory telogen hair follicles in study 1. However, KRT6 and CRABP2 localized to both competent and refractory telogen hair follicles in mice fed adequate and high levels of retinyl esters in study 2. In mice bred and fed an unpurified diet retinol dehydrogenase SDR16C5, retinal dehydrogenase 2 (ALDH1A2), and cytochrome p450 26B1 (CYP26B1), enzymes and proteins involved in RA metabolism, localized to BMP4 positive refractory telogen hair follicles. This suggests that vitamin A may contribute to the inhibition of HFSC during refractory telogen in a dose dependent manner

Multibeam bathymetric surveys of submarine volcanoes and mega-pockmarks on the Chatham Rise, New Zealand

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Taylor & Francis for personal use, not for redistribution. The definitive version was published in New Zealand Journal of Geology and Geophysics 54 (2011): 329-339, doi:10.1080/00288306.2011.589860.Multibeam bathymetric surveys east of the South Island of New Zealand present images of submarine volcanoes and pockmarks west of Urry Knolls on the Chatham Rise, and evidence of submarine erosion on the southern margin of the Chatham Rise. Among numerous volcanic cones, diameters of the largest reach ~2000 m, and some stand as high as 400 m above the surrounding seafloor. The tops of most of the volcanic cones are flat, with hints of craters, and some with asymmetric shapes may show flank collapses. There are hints of both northeast-southwest and northwest-southeast alignments of volcanoes, but no associated faulting is apparent. Near and to the west of these volcanoes, huge pockmarks, some more than ~1 km in diameter, disrupt bottom topography. Pockmarks in this region seem to be confined to sea floor shallower than ~1200 m, but we see evidence of deeper pockmarks at water depths of up to 2100 m on profiles crossing the Bounty Trough. The pockmark field on the Chatham Rise seems to be bounded on the south by a trough near 1200 m depth; like others, we presume that contour currents have eroded the margin and created the trough.This research was supported by the National Science Foundation under grants EAR-0409564, EAR-0409609, and EAR-0409835.2012-08-3

Using automatic differentiation with the quasi-procedural method for multidisciplinary design optimaization

As computers have become increasingly powerful, the field of design optimization has moved toward higher fidelity models (involving many more variables) in the early stages of design. One way in which this movement has manifested itself is in the increasing popularity of multidisciplinary design optimization (MDO). Because the models used in MDO are large and very complicated, a modular design is desirable. Because there are many- design parameters to optimize, derivatives must be computed accurately and efficiently. This paper describes how the quasi-procedural program architecture developed by Takai and Kroo [9] and the technique of automatic differentiation [6] can be combined to effectively address these needs. The two techniques are explained, the manner in which they were integrated into a single framework is described, and the result of using this framework for an optimization problem in airplane design is presented

Towards self-verification in finite difference code generation

Code generation from domain-specific languages is becoming increasingly popular as a method to obtain optimised low-level code that performs well on a given platform and for a given problem instance. Ensuring the correctness of generated codes is crucial. At the same time, testing or manual inspection of the code is problematic, as the generated code can be complex and hard to read. Moreover, the generated code may change depending on the problem type, domain size, or target platform, making conventional code review or testing methods impractical. As a solution, we propose the integration of formal verification tools into the code generation process. We present a case study in which the CIVL verification tool is combined with the Devito finite difference framework that generates optimised stencil code for PDE solvers from symbolic equations. We show a selection of properties of the generated code that can be automatically specified and verified during the code generation process. Our approach allowed us to detect a previously unknown bug in the Devito code generation tool

Formation of linear planform chimneys controlled by preferential hydrocarbon leakage and anisotropic stresses in faulted fine-grained sediments, offshore Angola

A new type of gas chimney exhibiting an unconventional linear planform is found. These chimneys are termed Linear Chimneys, which have been observed in 3-D seismic data offshore of Angola. Linear Chimneys occur parallel to adjacent faults, often within preferentially oriented tier-bound fault networks of diagenetic origin (also known as anisotropic polygonal faults, PFs), in salt-deformational domains. These anisotropic PFs are parallel to salt-tectonic-related structures, indicating their submission to horizontal stress perturbations generated by the latter. Only in areas with these anisotropic PF arrangements do chimneys and their associated gas-related structures, such as methane-derived authigenic carbonates and pockmarks, have linear planforms. In areas with the classic isotropic polygonal fault arrangements, the stress state is isotropic, and gas expulsion structures of the same range of sizes exhibit circular geometry. These events indicate that chimney's linear planform is heavily influenced by stress anisotropy around faults. The initiation of polygonal faulting occurred 40 to 80&thinsp;m below the present day seafloor and predates Linear Chimney formation. The majority of Linear Chimneys nucleated in the lower part of the PF tier below the impermeable portion of fault planes and a regional impermeable barrier within the PF tier. The existence of polygonal fault-bound traps in the lower part of the PF tier is evidenced by PF cells filled with gas. These PF gas traps restricted the leakage points of overpressured gas-charged fluids along the lower portion of PFs, hence controlling the nucleation sites of chimneys. Gas expulsion along the lower portion of PFs preconfigured the spatial organisation of chimneys. Anisotropic stress conditions surrounding tectonic and anisotropic polygonal faults coupled with the impermeability of PFs determined the directions of long-term gas migration and linear geometries of chimneys. Methane-related carbonates that precipitated above Linear Chimneys inherited the same linear planform geometry, and both structures record the timing of gas leakage and palaeo-stress state; thus, they can be used as a tool to reconstruct orientations of stress in sedimentary successions. This study demonstrates that overpressure hydrocarbon migration via hydrofracturing may be energetically more favourable than migration along pre-existing faults.</p

Increased fluid flow activity in shallow sediments at the 3 km Long Hugin Fracture in the central North Sea

The North Sea hosts a wide variety of seafloor seeps that may be important for transfer of chemical species, such as methane, from the Earth's interior to its exterior. Here we provide geochemical and geophysical evidence for fluid flow within shallow sediments at the recently discovered, 3-km long Hugin Fracture in the Central North Sea. Although venting of gas bubbles was not observed, concentrations of dissolved methane were significantly elevated (up to six-times background values) in the water column at various locations above the fracture, and microbial mats that form in the presence of methane were observed at the seafloor. Seismic amplitude anomalies revealed a bright spot at a fault bend that may be the source of the water column methane. Sediment porewaters recovered in close proximity to the Hugin Fracture indicate the presence of fluids from two different shallow (<500m) sources: (i) a reduced fluid characterized by elevated methane concentrations and/or high levels of dissolved sulfide (up to 6 mmol L−1), and (ii) a low-chlorinity fluid (Cl ∼305 mmol L−1) that has low levels of dissolved methane and/or sulfide. The area of the seafloor affected by the presence of methane-enriched fluids is similar to the footprint of seepage from other morphological features in the North Sea

Automated derivation of the adjoint of high-level transient finite element programs

In this paper we demonstrate a new technique for deriving discrete adjoint and tangent linear models of finite element models. The technique is significantly more efficient and automatic than standard algorithmic differentiation techniques. The approach relies on a high-level symbolic representation of the forward problem. In contrast to developing a model directly in Fortran or C++, high-level systems allow the developer to express the variational problems to be solved in near-mathematical notation. As such, these systems have a key advantage: since the mathematical structure of the problem is preserved, they are more amenable to automated analysis and manipulation. The framework introduced here is implemented in a freely available software package named dolfin-adjoint, based on the FEniCS Project. Our approach to automated adjoint derivation relies on run-time annotation of the temporal structure of the model, and employs the FEniCS finite element form compiler to automatically generate the low-level code for the derived models. The approach requires only trivial changes to a large class of forward models, including complicated time-dependent nonlinear models. The adjoint model automatically employs optimal checkpointing schemes to mitigate storage requirements for nonlinear models, without any user management or intervention. Furthermore, both the tangent linear and adjoint models naturally work in parallel, without any need to differentiate through calls to MPI or to parse OpenMP directives. The generality, applicability and efficiency of the approach are demonstrated with examples from a wide range of scientific applications