地下水流动数值模拟的并行计算方法研究

Numerical modeling of groundwater is very important for understanding groundwater flow and solving hydrogeological problem. Today, groundwater studies require massive model cells and high calculation accuracy, which are beyond single-CPU computer’s capabilities. With the development of high performance parallel computing technologies, application of parallel computing method on numerical modeling of groundwater flow becomes necessary and important. Using parallel computing can improve the ability to resolve various hydro-geological and environmental problems. In this study, parallel computing method on two main types of modern parallel computer architecture, shared memory parallel systems and distributed shared memory parallel systems, are discussed. OpenMP and MPI (PETSc) are both used to parallelize the most widely used groundwater simulator, MODFLOW. Two parallel solvers, P-PCG and P-MODFLOW, were developed for MODFLOW. The parallelized MODFLOW was used to simulate regional groundwater flow in Beishan, Gansu Province, which is a potential high-level radioactive waste geological disposal area in China. 1. The OpenMP programming paradigm was used to parallelize the PCG (preconditioned conjugate-gradient method) solver, which is one of the main solver for MODFLOW. The parallel PCG solver, P-PCG, is verified using an 8-processor computer. Both the impact of compilers and different model domain sizes were considered in the numerical experiments. The largest test model has 1000 columns, 1000 rows and 1000 layers. Based on the timing results, execution times using the P-PCG solver are typically about 1.40 to 5.31 times faster than those using the serial one. In addition, the simulation results are the exact same as the original PCG solver, because the majority of serial codes were not changed. It is worth noting that this parallelizing approach reduces cost in terms of software maintenance because only a single source PCG solver code needs to be maintained in the MODFLOW source tree. 2. P-MODFLOW, a domain decomposition–based model implemented in a parallel computing environment is developed, which allows efficient simulation of a regional-scale groundwater flow. The basic approach partitions a large model domain into any number of sub-domains. Parallel processors are used to solve the model equations within each sub-domain. The use of domain decomposition method to achieve the MODFLOW program distributed shared memory parallel computing system will process the application of MODFLOW be extended to the fleet of the most popular systems, so that a large-scale simulation could take full advantage of hundreds or even thousands parallel processors. P-MODFLOW has a good parallel performance, with the maximum speedup of 18.32 (14 processors). Super linear speedups have been achieved in the parallel tests, indicating the efficiency and scalability of the code. Parallel program design, load balancing and full use of the PETSc were considered to achieve a highly efficient parallel program. 3. The characterization of regional ground water flow system is very important for high-level radioactive waste geological disposal. The Beishan area, located in northwestern Gansu Province, China, is selected as a potential site for disposal repository. The area includes about 80000 km2 and has complicated hydrogeological conditions, which greatly increase the computational effort of regional ground water flow models. In order to reduce computing time, parallel computing scheme was applied to regional ground water flow modeling. Models with over 10 million cells were used to simulate how the faults and different recharge conditions impact regional ground water flow pattern. The results of this study provide regional ground water flow information for the site characterization of the potential high-level radioactive waste disposal.

特大地震激发地球自由振荡的数值模拟研究

Large earthquakes, such as the Chile earthquake in 1960 and the Sumatra-Andaman earthquake on Dec 26, 2004 in Indonesia, have generated the Earth’s free oscillations. The eigenfrequencies of the Earth’s free oscillations are closely related to the Earth’s internal structures. The conventional methods, which mainly focus on calculating the eigenfrequecies by analytical ways, and the analysis on observations can not easily study the whole processes from earthquake occurrence to the Earth’s free oscillation inspired. Therefore, we try to use numerical method incorporated with large-scale parallel computing to study on the Earth’s free oscillations excited by giant earthquakes. We first give a review of researches and developments of the Earth’s free oscillation, and basical theories under spherical coordinate system. We then give a review of the numerical simulation of seismic wave propagation and basical theories of spectral element method to simulate global seismic wave propagation. As a first step to study the Earth’s free oscillations, we use a finite element method to simulate the propagation of elastic waves and the generation of oscillations of the chime bell of Marquis Yi of Zeng, by striking different parts of the bell, which possesses the oval crosssection. The bronze chime bells of Marquis Yi of Zeng are precious cultural relics of China. The bells have a two-tone acoustic characteristic, i.e., striking different parts of the bell generates different tones. By analysis of the vibration in the bell and the spectrum analysis, we further help the understanding of the mechanism of two-tone acoustic characteristics of the chime bell of Marquis Yi of Zeng. The preliminary calculations have clearly shown that two different modes of oscillation can be generated by striking different parts of the bell, and indicate that finite element numerical simulation of the processes of wave propagation and two-tone generation of the chime bell of Marquis Yi of Zeng is feasible. These analyses provide a new quantitative and visual way to explain the mystery of the two-tone acoustic characteristics. The method suggested by this study can be applied to simulate free oscillations excited by great earthquakes with complex Earth structure. Taking into account of such large-scale structure of the Earth, small-scale low-precision numerical simulation can not simply meet the requirement. The increasing capacity in high-performance parallel computing and progress on fully numerical solutions for seismic wave fields in realistic three-dimensional spherical models, Spectral element method and high-performance parallel computing were incorporated to simulate the seismic wave propagation processes in the Earth’s interior, without the effects of the Earth’s gravitational potential. The numerical simulation shows that, the results of the toroidal modes of our calculation agree well with the theoretical values, although the accuracy of our results is much limited, the calculated peaks are little distorted due to three-dimensional effects. There exist much great differences between our calculated values of spheroidal modes and theoretical values, because we don’t consider the effect the Earth’ gravitation in numerical model, which leads our values are smaller than the theoretical values. When , is much smaller, the effect of the Earth’s gravitation make the periods of spheroidal modes become shorter. However, we now can not consider effects of the Earth’s gravitational potential into the numerical model to simulate the spheroidal oscillations, but those results still demonstrate that, the numerical simulation of the Earth’s free oscillation is very feasible. We make the numerical simulation on processes of the Earth’s free oscillations under spherically symmetric Earth model using different special source mechanisms. The results quantitatively show that Earth’s free oscillations excited by different earthquakes are different, and oscillations at different locations are different for free oscillation excited by the same earthquake. We also explore how the Earth’s medium attenuation will take effects on the Earth’s free oscillations, and take comparisons with the observations. The medium attenuation can make influences on the Earth’s free oscillations, though the effects on lower-frequency fundamental oscillations are weak. At last, taking 2008 Wenchuan earthquake for example, we employ spectral element method incorporated with large-scale parallel computing technology to investigate the characteristics of seismic wave propagation excited by Wenchuan earthquake. We calculate synthetic seismograms with one-point source model and three-point source model respectively. Full 3-D visualization of the numerical results displays the profile of the seismic wave propagation with respect to time. The three-point source, which was proposed by the latest investigations through field observation and reverse estimation, can better demonstrate the spatial and temporal characteristics of the source rupture processes than one-point source. Primary results show that those synthetic signals calculated from three-point source agree well with the observations. This can further reveal that the source rupturing process of Wenchuan earthquake is a multi-rupture process, which is composed by at least three or more stages of rupture processes. In conclusion, the numerical simulation can not only solve some problems concluding the Earth’s ellipticity and anisotropy, which can be easily solved by conventional methods, but also finally solve the problems concluding topography model and lateral heterogeneity. We will try to find a way to fully implement self-gravitation in spectral element method in future, and do our best to continue researching the Earth’s free oscillations using the numerical simulations to see how the Earth’ lateral heterogeneous will affect the Earth’s free oscillations. These will make it possible to bring modal spectral data increasingly to bear on furthering our understanding of the Earth’s three-dimensional structure.

Parallel optical negabinary signed-digit computing: algorithm and optical implementation

Negabinary is a component of the positional number system. A complete set of negabinary arithmetic operations are presented, including the basic addition/subtraction logic, the two-step carry-free addition/subtraction algorithm based on negabinary signed-digit (NSD) representation, parallel multiplication, and the fast conversion from NSD to the normal negabinary in the carry-look-ahead mode. All the arithmetic operations can be performed with binary logic. By programming the binary reference bits, addition and subtraction can be realized in parallel with the same binary logic functions. This offers a technique to perform space-variant arithmetic-logic functions with space-invariant instructions. Multiplication can be performed in the tree structure and it is simpler than the modified signed-digit (MSD) counterpart. The parallelism of the algorithms is very suitable for optical implementation. Correspondingly, a general-purpose optical logic system using an electron trapping device is suggested. Various complex logic functions can be performed by programming the illumination of the data arrays without additional temporal latency of the intermediate results. The system can be compact. These properties make the proposed negabinary arithmetic-logic system a strong candidate for future applications in digital optical computing with the development of smart pixel arrays. (C) 1999 Society of Photo-Optical Instrumentation Engineers. [S0091-3286(99)00803-X].

Fast Computing For Lurr Of Earthquake Prediction

The LURR theory is a new approach for earthquake prediction, which achieves good results in earthquake prediction within the China mainland and regions in America, Japan and Australia. However, the expansion of the prediction region leads to the refinement of its longitude and latitude, and the increase of the time period. This requires increasingly more computations, and the volume of data reaches the order of GB, which will be very difficult for a single CPU. In this paper, a new method was introduced to solve this problem. Adopting the technology of domain decomposition and parallelizing using MPI, we developed a new parallel tempo-spatial scanning program.

A New Designed Two-Dimensional Bifurcation Parallel-Plate Flow Chamber

解决平行平板流槽每次实验只能观测壁面培养细胞受一种剪应力作用的问题。作者在平行平板流槽的基础上,首次提出了一种改进后的流槽--二维平板分叉流槽。通过数值模拟,给出了流体作定常流动时,流速和壁面剪应力的分布。结果发现,利用这种二维平板分叉流槽可以研究壁面培养的细胞在不同大小剪应力作用下的力学行为。该研究结果为流槽的合理设计和使用,并分析剪应力空间分布对内皮细胞的影响有重要实际意义。

A Label-Free Protein Microfluidic Array for Parallel Immunoassays

A label-free protein microfluidic array for immunoassays based on the combination of imaging ellipsometry and an integrated microfluidic system is presented. Proteins can be patterned homogeneously on substrate in array format by the microfluidic system simultaneously. After preparation, the protein array can be packed in the microfluidic system which is full of buffer so that proteins are not exposed to denaturing conditions. With simple microfluidic channel junction, the protein microfluidic array can be used in serial or parallel format to analyze single or multiple samples simultaneously. Imaging ellipsometry is used for the protein array reading with a label-free format. The biological and medical applications of the label-free protein microfluidic array are demonstrated by screening for antibody–antigen interactions, measuring the concentration of the protein solution and detecting five markers of hepatitis B.

Experimental Investigation On The Holdup Distribution Of Oil-Water Two-Phase Flow In Horizontal Parallel Tubes

An experimental investigation was conducted to study the holdup distribution of oil and water two-phase flow in two parallel tubes with unequal tube diameter. Tests were performed using white oil (of viscosity 52 mPa s and density 860 kg/m(3)) and tap water as liquid phases at room temperature and atmospheric outlet pressure. Measurements were taken of water flow rates from 0.5 to 12.5 m(3)/h and input oil volume fractions from 3 to 94 %. Results showed that there were different flow pattern maps between the run and bypass tubes when oil-water two-phase flow is found in the parallel tubes. At low input fluid flow rates, a large deviation could be found on the average oil holdup between the bypass and the run tubes. However, with increased input oil fraction at constant water flow rate, the holdup at the bypass tube became close to that at the run tube. Furthermore, experimental data showed that there was no significant variation in flow pattern and holdup between the run and main tubes. In order to calculate the holdup in the form of segregated flow, the drift flux model has been used here.

Large Scale Numerical Simulations For Multi-Phase Fluid Dynamics With Moving Interfaces

This short communication presents our recent studies to implement numerical simulations for multi-phase flows on top-ranked supercomputer systems with distributed memory architecture. The numerical model is designed so as to make full use of the capacity of the hardware. Satisfactory scalability in terms of both the parallel speed-up rate and the size of the problem has been obtained on two high rank systems with massively parallel processors, the Earth Simulator (Earth simulator research center, Yokohama Kanagawa, Japan) and the TSUBAME (Tokyo Institute of Technology, Tokyo, Japan) supercomputers.