An Evaluation and Comparison of GPU Hardware and Solver Libraries for Accelerating the OPM Flow Reservoir Simulator

Realistic reservoir simulation is known to be prohibitively expensive in terms of computation time when increasing the accuracy of the simulation or by enlarging the model grid size. One method to address this issue is to parallelize the computation by dividing the model in several partitions and using multiple CPUs to compute the result using techniques such as MPI and multi-threading. Alternatively, GPUs are also a good candidate to accelerate the computation due to their massively parallel architecture that allows many floating point operations per second to be performed. The numerical iterative solver takes thus the most computational time and is challenging to solve efficiently due to the dependencies that exist in the model between cells. In this work, we evaluate the OPM Flow simulator and compare several state-of-the-art GPU solver libraries as well as custom developed solutions for a BiCGStab solver using an ILU0 preconditioner and benchmark their performance against the default DUNE library implementation running on multiple CPU processors using MPI. The evaluated GPU software libraries include a manual linear solver in OpenCL and the integration of several third party sparse linear algebra libraries, such as cuSparse, rocSparse, and amgcl. To perform our bench-marking, we use small, medium, and large use cases, starting with the public test case NORNE that includes approximately 50k active cells and ending with a large model that includes approximately 1 million active cells. We find that a GPU can accelerate a single dual-threaded MPI process up to 5.6 times, and that it can compare with around 8 dual-threaded MPI processes

Fast Simulation of Gaussian-Mode Scattering for Precision Interferometry

Understanding how laser light scatters from realistic mirror surfaces is crucial for the design, com- missioning and operation of precision interferometers, such as the current and next generation of gravitational-wave detectors. Numerical simulations are indispensable tools for this task but their utility can in practice be limited by the computational cost of describing the scattering process. In this paper we present an efficient method to significantly reduce the computational cost of optical simulations that incorporate scattering. This is accomplished by constructing a near optimal representation of the complex, multi-parameter 2D overlap integrals that describe the scattering process (referred to as a reduced order quadrature). We demonstrate our technique by simulating a near-unstable Fabry-Perot cavity and its control signals using similar optics to those installed in one of the LIGO gravitational-wave detectors. We show that using reduced order quadrature reduces the computational time of the numerical simulation from days to minutes (a speed-up of $\approx 2750 \times$) whilst incurring negligible errors. This significantly increases the feasibility of modelling interferometers with realistic imperfections to overcome current limits in state-of-the-art optical systems. Whilst we focus on the Hermite-Gaussian basis for describing the scattering of the optical fields, our method is generic and could be applied with any suitable basis. An implementation of this reduced order quadrature method is provided in the open source interferometer simulation software Finesse.Comment: 15 pages, 11 figure

Reserve options mechanism

53 pagesFinansal piyasalarda yaşanan şoklardan dolayı sermaye akımlarındaki oynaklıkların Türkiye piyasalarına etkisini minimize etmek ve Türkiye Cumhuriyet Merkez Bankası (TCMB)’nın brüt döviz rezervlerini güçlendirmek amacıyla, TCMB tarafından 2011 yılında hayata geçirilen rezerv opsiyon mekanizması (ROM), zorunlu karşılık yükümülülüğüne sahip bankalara ve finansal kurumlara bu yükümlülüklerinin belirli bir kısmını yabancı para (YP) ve altın olarak tesis etme imkanı tanımaktadır. Bu çalışmada ROM kullanım seviyelerini etkileyen faktörler incelenmekte, daha önceki çalışmalarda etkin çalıştığı konusunda şüphe duyulan ROM’un otomatik dengeleyici özelliğinin, 2018’de Türkiye piyasalarında yaşanan finansal çalkantı döneminde işlevini etkin bir şekilde yerine getirip getirmediği araştırılmaktadır. Bankacılık sektörünün ROM kullanımı davranışları incelendiğinde 2018 yılından önceki dönemde TL ve YP faiz oranlarının önemli rol oynadığı maliyet kaynaklı faktörler öne çıkarken, 2018 yılında yaşanan finansal çalkantı döneminde ise sektörün ROM kullanımı ile maliyet kaynaklı faktörler arasında önemli bir ilişki bulunamamıştır. İlgili dönemde çoklu regresyon analizi kullanılarak ROM kullanımını etkileyen faktörlerin Dolar TL kuru, Türkiye CDS oranı, banka bilançolarındaki verilen kredilerin ağırlığı, ekonomik güven endeksi ve bankacılık sektörü toplam likidite rasyosu olduğu sonucuna ulaşılmıştır. Bu çerçevede 2018 yılında Türkiye piyasalarında yaşanan finansal çalkantı dönemi gibi dönemlerde bankacılık sektörünün ROM kullanımında dikkate aldığı faktörlerin, maliyet faktörlerinden ayrıştığı, bu sebeple de böyle dönemlerde ROM’un otomatik dengeleyici özelliğinin etkin bir şekilde çalıştığı sonucuna ulaşılmıştır. Anahtar Kelimeler: Rezerv Opsiyon Mekanizması, Otomatik Dengeleyici Özelliği, Sermaye Akımları, Finansal Çalkantı, ROM Kullanımını Etkileyen FaktörlerThe reserve options mechanism (ROM) is a monetary policy tool adopted by the Central Bank of the Republic of Turkey (CBRT) to increase the efficiency of the gross reserves management and soften the possible negative effects of capital flows on the macroeconomic and financial stability. It allows banks or financial institutions, which are subject to reserve requirement, to keep certain portion of their TL reserve in foreign currency or in gold. In this study, the factors affecting ROM utilization of banking system are investigated. The automatic stabilizing feature of mechanism which is suspected in previous studies is examined throughout this paper especially focusing on 2018 financial turbulence period. Breakeven ROC, which depends on the relative cost of Turkish lira versus foreign currency funding is the main determinant of ROM utilization in Turkey for the period between 2012 and 2017. Whereas in 2018, any significant correlation between ROM utilization and the breakeven ROC cannot be found in our analysis. Using step multiple regression analysis, we have found that the factors significantly explain ROM utilization in 2018 are USDTL exchange rate, Turkey CDS rate, loan to asset ratio in banking sector, total economic confidence index and total liquidity ratio of banking sector. In this context, the result of the study indicates that during the periods like financial turbulence Turkish financial system experienced in 2018, the factors affecting ROM utilization differs from the cost related factors and this enables automatic stabilizing feature of mechanism to work efficiently. Key Words: Reserve Options Mechanism, Automatic Stabilizing Feature, Capital Flows, Financial Turbulence, Factors Affecting ROM Utilizatio

Aid administration of bilateral, multilateral and non-government organisations in the primary education sector: A comparative case study analysis of Zambia

This is a study of the administration of aid by bilateral, multilateral and non-government organisations in Zambia during the period 1990 to 2000. The particular purpose of this study is to compare the aid programs administered by the above organisations to the primary education sector using a case study approach. The study critically analyses how the performance of these organisation is or is not influenced by setting clear objectives, by elaborating planning processes and implementation arrangements. The study uses a matrix table developed through a NUD*IST retrieval reports generated from the data collected from each organisation’s documentation and in-depth interviews with key personnel. The study responds to five key research questions. These are: (a) what are the dominant objectives for each program: (b) how these objectives are structured: (c) what is the nature of the planning process: (d) what are the main channels for executing the programs: and what are the outcomes of the programs. The findings show that the aid organisations in the study have played a major role administering primary education sector programs through the provision of finance and technical assistance, however, most of these organisations, especially the bilateral and multilateral organisations, have not been very effective in delivering value to Zambia’s primary educations sector. Even though bilateral and multilateral aid organisations may have clearly defined objectives and elaborate planning processes, they normally use other agencies to implement their programs. The research shows that this causes loss of focus and control which consequently affects the performance of the programs. Non-government organisations, the third category of aid organisations, on the other hand, are directly involved in the implementation of the programs even though they may have no set objectives or elaborate planning processes. Their approach is to involve the members of the local communities in the selection and planning of specific projects based on local need. These organisations, therefore, register better performance as they maintain more control and are unable to ensure more successful outcomes

Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery

Molecular similarity is a key concept in drug discovery. It is based on the assumption that structurally similar molecules frequently have similar properties. Assessment of similarity between small molecules has been highly effective in the discovery and development of various drugs. Especially, two-dimensional (2D) similarity approaches have been quite popular due to their simplicity, accuracy and efficiency. Recently, the focus has been shifted toward the development of methods involving the representation and comparison of three-dimensional (3D) conformation of small molecules. Among the 3D similarity methods, evaluation of shape similarity is now gaining attention for its application not only in virtual screening but also in molecular target prediction, drug repurposing and scaffold hopping. A wide range of methods have been developed to describe molecular shape and to determine the shape similarity between small molecules. The most widely used methods include atom distance-based methods, surface-based approaches such as spherical harmonics and 3D Zernike descriptors, atom-centered Gaussian overlay based representations. Several of these methods demonstrated excellent virtual screening performance not only retrospectively but also prospectively. In addition to methods assessing the similarity between small molecules, shape similarity approaches have been developed to compare shapes of protein structures and binding pockets. Additionally, shape comparisons between atomic models and 3D density maps allowed the fitting of atomic models into cryo-electron microscopy maps. This review aims to summarize the methodological advances in shape similarity assessment highlighting advantages, disadvantages and their application in drug discovery

PubChem3D: Similar conformers

<p>Abstract</p> <p>Background</p> <p>PubChem is a free and open public resource for the biological activities of small molecules. With many tens of millions of both chemical structures and biological test results, PubChem is a sizeable system with an uneven degree of available information. Some chemical structures in PubChem include a great deal of biological annotation, while others have little to none. To help users, PubChem pre-computes "neighboring" relationships to relate similar chemical structures, which may have similar biological function. In this work, we introduce a "Similar Conformers" neighboring relationship to identify compounds with similar 3-D shape and similar 3-D orientation of functional groups typically used to define pharmacophore features.</p> <p>Results</p> <p>The first two diverse 3-D conformers of 26.1 million PubChem Compound records were compared to each other, using a shape Tanimoto (ST) of 0.8 or greater and a color Tanimoto (CT) of 0.5 or greater, yielding 8.16 billion conformer neighbor pairs and 6.62 billion compound neighbor pairs, with an average of 253 "Similar Conformers" compound neighbors per compound. Comparing the 3-D neighboring relationship to the corresponding 2-D neighboring relationship ("Similar Compounds") for molecules such as caffeine, aspirin, and morphine, one finds unique sets of related chemical structures, providing additional significant biological annotation. The PubChem 3-D neighboring relationship is also shown to be able to group a set of non-steroidal anti-inflammatory drugs (NSAIDs), despite limited PubChem 2-D similarity.</p> <p>In a study of 4,218 chemical structures of biomedical interest, consisting of many known drugs, using more diverse conformers per compound results in more 3-D compound neighbors per compound; however, the overlap of the compound neighbor lists per conformer also increasingly resemble each other, being 38% identical at three conformers and 68% at ten conformers. Perhaps surprising is that the average count of conformer neighbors per conformer increases rather slowly as a function of diverse conformers considered, with only a 70% increase for a ten times growth in conformers per compound (a 68-fold increase in the conformer pairs considered).</p> <p>Neighboring 3-D conformers on the scale performed, if implemented naively, is an intractable problem using a modest sized compute cluster. Methodology developed in this work relies on a series of filters to prevent performing 3-D superposition optimization, when it can be determined that two conformers cannot possibly be a neighbor. Most filters are based on Tanimoto equation volume constraints, avoiding incompatible conformers; however, others consider preliminary superposition between conformers using reference shapes.</p> <p>Conclusion</p> <p>The "Similar Conformers" 3-D neighboring relationship locates similar small molecules of biological interest that may go unnoticed when using traditional 2-D chemical structure graph-based methods, making it complementary to such methodologies. The computational cost of 3-D similarity methodology on a wide scale, such as PubChem contents, is a considerable issue to overcome. Using a series of efficient filters, an effective throughput rate of more than 150,000 conformers per second per processor core was achieved, more than two orders of magnitude faster than without filtering.</p

The liberalisation of European railway markets - laissez faire versus interventionism: a comparative analysis of the approaches to railway privatisation in the United Kingdom and Germany.

This thesis comprises railway innovation in the 19th century, railway regulation, recent railway reforms across Europe and a theoretical analysis. The historical study is complemented by an investigation of the rationale for extensive regulations and eventual nationalisation of railway systems. The nationalisation schemes granted exclusive rights to public undertakings to provide a public railway and sometimes more extensive transport services. Notwithstanding subsidies and a protectionist railway policy, the railways could not compete successfully with other modes of transport; the railway industry's market share steadily declined across the European Community. As a result the European Community passed legislation to reverse the deteriorating trend. This legislation and its national interpretations are evaluated before proceeding to brief case studies of the railway liberalisation undertaken in France, the Netherlands and Sweden; the German and British approaches to railway reform are then analysed in greater detail. Arguing that liberalisation was often a watered down version of privatisation schemes that had been compromised in the political process, the thesis develops an alternative model of privatisation, centred on a concept of market-based integration and a competitive railway market. It is proposed that the current crisis on the British railways and the slow progress of railways in other countries could be resolved by means of this concept

Report on carbon reductions in new non-domestic buildings

This report investigates the opportunities for achieving zero carbon new non-domestic buildings. Although this is an important element in reducing the carbon emissions associated with non-domestic buildings, it does not present the whole picture. Given the rate of replacement of the non-domestic building stock attention must be given to the refurbishment of existing stock in order to achieve the carbon emissions savings required to meet national carbon reduction targets going forward. In addition, this report concentrates only on the energy consumed directly by new nondomestic buildings and does not consider the overall building carbon footprint. This carbon footprint, which could include the links between the building and transport networks, logistics, water use, embodied energy and construction energy use for example, would present a more holistic picture of the carbon emissions associated with non-domestic buildings