Dendrobium Flower Color: Histology and Genetic Manipulation

Dendrobium is the most important cut flower orchid in the world. Understanding the chemical, histological and molecular aspects of flower color is crucial for the development of breeding strategies for novel colors. The objectives of this research were to examine the histology of flower color, cloning and characterization of flavonoid biosynthetic genes, and metabolic engineering of Dendrobium flavonoid pathway to obtain new colors. In Dendrobium, anthocyanins can be confined to a single layer of cells (epidermal or suepidermal) in pale flowers. More intensely colored flowers had anthocyanin in several cell layers. Striped patterns on the perianth were due to the restriction of pigment to cells surrounding the vascular bundles. Color perception is markedly influenced by the presence or absence of carotenoids. Four types of epidermal cells were found in Dendrobium: flat, dome, elongated dome, and papillate. Epidermal cell shape and cell packing in the mesophyll affected the visual texture. Perianth parts with flat cells and a tightly packed mesophyll had a glossy texture, whereas dome cells and loosely packed mesophyll contributed a velvety texture. The labella in the majority of flowers examined had a complex epidermis with more than one epidermal cell shape, predominantly papillate epidermal cells. We were able to isolate a full clone of Dendrobium dihydroflavonol 4-reductase (dfr), and partial clones of chalcone synthase (chs), flavonoid 3'- hydroxylase (J3'h) and flavonoid 3', 5'-hydroxylase (f3'5'h), from Dendrobium Jaquelyn Thomas ‘Uniwai Prince’ (UH503). Expression data indicated that dfr and chs were expressed to the greatest degree in unopened buds. Amount of f3'h and f3’5'h mRNA was too small to detect. Southern analysis has shown that f3'h and f3'5’h is represented by 2 copies each in UH503. These clones will be extremely useful in future for flower color manipulation. Two different color genes, dfr and f3'5'h from two non-orchid plants, under the constitutive promoter ubiquitin3, were inserted into Dendrobium Icy Pink ‘Sakura’ with the intention of creating orange-red and blue shades, which are absent in commercial Dendrobium. Presence of the transgene in two sets of transformants was confirmed by PCR. Expression of the transgene from a few plants was indicated by RT-PCR and northern analyses

Scalable many-core algorithms for tridiagonal solvers

We present a novel distributed memory Tridiagonal solver library, targeting large-scale systems based on modern multi-core and many-core processor architectures. The library uses methods based on both approximate and exact algorithms. Performance comparisons with the state-of-the-art, using both a large Cray EX system and a GPU cluster show the algorithmic trade-offs required at increasing machine scale to achieve good performance, particularly considering the advent of exascale systems

OP2-Clang : a source-to-source translator using Clang/LLVM LibTooling

Domain Specific Languages or Active Library frameworks have recently emerged as an important method for gaining performance portability, where an application can be efficiently executed on a wide range of HPC architectures without significant manual modifications. Embedded DSLs such as OP2, provides an API embedded in general purpose languages such as C/C++/Fortran. They rely on source-to-source translation and code refactorization to translate the higher-level API calls to platform specific parallel implementations. OP2 targets the solution of unstructured-mesh computations, where it can generate a variety of parallel implementations for execution on architectures such as CPUs, GPUs, distributed memory clusters and heterogeneous processors making use of a wide range of platform specific optimizations. Compiler tool-chains supporting source-to-source translation of code written in mainstream languages currently lack the capabilities to carry out such wide-ranging code transformations. Clang/LLVM’s Tooling library (LibTooling) has long been touted as having such capabilities but have only demonstrated its use in simple source refactoring tasks. In this paper we introduce OP2-Clang, a source-to-source translator based on LibTooling, for OP2’s C/C++ API, capable of generating target parallel code based on SIMD, OpenMP, CUDA and their combinations with MPI. OP2-Clang is designed to significantly reduce maintenance, particularly making it easy to be extended to generate new parallelizations and optimizations for hardware platforms. In this research, we demonstrate its capabilities including (1) the use of LibTooling’s AST matchers together with a simple strategy that use parallelization templates or skeletons to significantly reduce the complexity of generating radically different and transformed target code and (2) chart the challenges and solution to generating optimized parallelizations for OpenMP, SIMD and CUDA. Results indicate that OP2-Clang produces near-identical parallel code to that of OP2’s current source-to-source translator. We believe that the lessons learnt in OP2-Clang can be readily applied to developing other similar source-to-source translators, particularly for DSLs

OP2-Clang : a source-to-source translator using Clang/LLVM LibTooling

Domain Specific Languages or Active Library frameworks have recently emerged as an important method for gaining performance portability, where an application can be efficiently executed on a wide range of HPC architectures without significant manual modifications. Embedded DSLs such as OP2, provides an API embedded in general purpose languages such as C/C++/Fortran. They rely on source-to-source translation and code refactorization to translate the higher-level API calls to platform specific parallel implementations. OP2 targets the solution of unstructured-mesh computations, where it can generate a variety of parallel implementations for execution on architectures such as CPUs, GPUs, distributed memory clusters and heterogeneous processors making use of a wide range of platform specific optimizations. Compiler tool-chains supporting source-to-source translation of code written in mainstream languages currently lack the capabilities to carry out such wide-ranging code transformations. Clang/LLVM’s Tooling library (LibTooling) has long been touted as having such capabilities but have only demonstrated its use in simple source refactoring tasks. In this paper we introduce OP2-Clang, a source-to-source translator based on LibTooling, for OP2’s C/C++ API, capable of generating target parallel code based on SIMD, OpenMP, CUDA and their combinations with MPI. OP2-Clang is designed to significantly reduce maintenance, particularly making it easy to be extended to generate new parallelizations and optimizations for hardware platforms. In this research, we demonstrate its capabilities including (1) the use of LibTooling’s AST matchers together with a simple strategy that use parallelization templates or skeletons to significantly reduce the complexity of generating radically different and transformed target code and (2) chart the challenges and solution to generating optimized parallelizations for OpenMP, SIMD and CUDA. Results indicate that OP2-Clang produces near-identical parallel code to that of OP2’s current source-to-source translator. We believe that the lessons learnt in OP2-Clang can be readily applied to developing other similar source-to-source translators, particularly for DSLs

Locality optimized unstructured mesh algorithms on GPUs

Unstructured-mesh based numerical algorithms such as finite volume and finite element algorithms form an important class of applications for many scientific and engineering domains. The key difficulty in achieving higher performance from these applications is the indirect accesses that lead to data-races when parallelized. Current methods for handling such data-races lead to reduced parallelism and suboptimal performance. Particularly on modern many-core architectures, such as GPUs, that has increasing core/thread counts, reducing data movement and exploiting memory locality is vital for gaining good performance. In this work we present novel locality-exploiting optimizations for the efficient execution of unstructured-mesh algorithms on GPUs. Building on a two-layered coloring strategy for handling data races, we introduce novel reordering and partitioning techniques to further improve efficient execution. The new optimizations are then applied to several well established unstructured-mesh applications, investigating their performance on NVIDIA’s latest P100 and V100 GPUs. We demonstrate significant speedups (1.1–1.75×) compared to the state-of-the-art. A range of performance metrics are benchmarked including runtime, memory transactions, achieved bandwidth performance, GPU occupancy and data reuse factors and are used to understand and explain the key factors impacting performance. The optimized algorithms are implemented as an open-source software library and we illustrate its use for improving performance of existing or new unstructured-mesh applications

Improving resilience of scientific software through a domain-specific approach

In this paper we present research on improving the resilience of the execution of scientific software, an increasingly important concern in High Performance Computing (HPC). We build on an existing high-level abstraction framework, the Oxford Parallel library for Structured meshes (OPS), developed for the solution of multi-block structured mesh-based applications, and implement an algorithm in the library to carry out checkpointing automatically, without the intervention of the user. The target applications are a hydrodynamics benchmark application from the Mantevo Suite, CloverLeaf 3D, the sparse linear solver proxy application TeaLeaf, and the OpenSBLI compressible Navier–Stokes direct numerical simulation (DNS) solver. We present (1) the basic algorithm that OPS relies on to determine the optimal checkpoint in terms of size and location, (2) improvements that supply additional information to improve the decision, (3) techniques that reduce the cost of writing the checkpoints to non-volatile storage, (4) a performance analysis of the developed techniques on a single workstation and on several supercomputers, including ORNL’s Titan. Our results demonstrate the utility of the high-level abstractions approach in automating the checkpointing process and show that performance is comparable to, or better than the reference in all cases

Scalable many-core algorithms for tridiagonal solvers

We present a novel distributed memory Tridiagonal solver library, targeting large-scale systems based on modern multi-core and many-core processor architectures. The library uses methods based on both approximate and exact algorithms. Performance comparisons with the state-of-the-art, using both a large Cray EX system and a GPU cluster show the algorithmic trade-offs required at increasing machine scale to achieve good performance, particularly considering the advent of exascale systems

POTENTIAL FOR ECO- TOURISM AS A SUSTAINABLE APPROACH TO UTILIZE RESOURCES IN UP-COUNTRY TEA ESTA TES IN SRI LANKA

In the context of tea industry in Sri Lanka, ecotourism has been recognized asan economically viable, environmentally friendly, and socially acceptablenon-crop diversification mechanism to increase profits according to AsianDevelopment Bank report, 2000.The purpose of this study was to assess the potential for ecotourism inupcountry tea plantations in Sri Lanka. Six estates, namely: (1) Hellbodda;(2) Kaloogala; (3) Melfort; (4) Rothschild; (5) Sanquhar, and (6) Sogama thatare located in the Pussellawa plantation sub district have been selected as thecases.Collection of data was characterized by: (1) a field survey at each location toidentify the availability of potential resources for ecotourism (e.g. attractions,infrastructure); (2) a community survey with the estate households; (3) aseries of personnel interviews with the estate management, and (4)questionnaire-based surveys with potential local and foreign tourists to thesesites.The information collected through the field, community, and managementsurveys were used to develop an index - "Tourism Potential Index" (TPI),that explain the capacity of each estate to develop ecotourism. The resultsbased on the TPI suggest that the best location for ecotourism was theRothschild followed by Hellbodda, and Sogama. The results also show thatabout 75% of estate community was in favor of implementing an ecotourismproject, and about 84% and 78% of foreign and local tourists, respectively,are willing to visit such a project. The results highlight the necessity ofimplementing sustainable alternative projects to enhance the quality of life ofthe estate community.