scholarly journals A parallelization scheme to simulate reactive transport in the subsurface environment with OGS#IPhreeqc

2015 ◽  
Vol 8 (3) ◽  
pp. 2369-2402
Author(s):  
W. He ◽  
C. Beyer ◽  
J. H. Fleckenstein ◽  
E. Jang ◽  
O. Kolditz ◽  
...  

Abstract. This technical paper presents an efficient and performance-oriented method to model reactive mass transport processes in environmental and geotechnical subsurface systems. The open source scientific software packages OpenGeoSys and IPhreeqc have been coupled, to combine their individual strengths and features to simulate thermo-hydro-mechanical-chemical coupled processes in porous and fractured media with simultaneous consideration of aqueous geochemical reactions. Furthermore, a flexible parallelization scheme using MPI (Message Passing Interface) grouping techniques has been implemented, which allows an optimized allocation of computer resources for the node-wise calculation of chemical reactions on the one hand, and the underlying processes such as for groundwater flow or solute transport on the other hand. The coupling interface and parallelization scheme have been tested and verified in terms of precision and performance.

2015 ◽  
Vol 8 (10) ◽  
pp. 3333-3348 ◽  
Author(s):  
W. He ◽  
C. Beyer ◽  
J. H. Fleckenstein ◽  
E. Jang ◽  
O. Kolditz ◽  
...  

Abstract. The open-source scientific software packages OpenGeoSys and IPhreeqc have been coupled to set up and simulate thermo-hydro-mechanical-chemical coupled processes with simultaneous consideration of aqueous geochemical reactions faster and easier on high-performance computers. In combination with the elaborated and extendable chemical database of IPhreeqc, it will be possible to set up a wide range of multiphysics problems with numerous chemical reactions that are known to influence water quality in porous and fractured media. A flexible parallelization scheme using MPI (Message Passing Interface) grouping techniques has been implemented, which allows an optimized allocation of computer resources for the node-wise calculation of chemical reactions on the one hand and the underlying processes such as for groundwater flow or solute transport on the other. This technical paper presents the implementation, verification, and parallelization scheme of the coupling interface, and discusses its performance and precision.


2020 ◽  
Author(s):  
Nicolas Seigneur ◽  
K. Ulrich Mayer

<p>In certain reactive transport applications, strong coupling between geochemical reactions and hydrodynamics exists. Dissolution and precipitation of minerals, such as the conversion between gypsum and anhydrite [1] or the precipitation of nesquehonite during CO<sub>2</sub> sequestration [2], as well as gas bubble formation [3] are geochemical processes which modify the multiphase flow dynamics, with direct feedback on reactive transport processes. In addition, heat generation induced by sulphide mineral oxidation can lead to significant increases in temperature [4], impacting flow, transport and geochemical reactions. In these instances, commonly used reactive transport modelling approaches, which rely on decoupling flow and reactive transport processes, have limitations. For density dependent or two-phase flow problems in the presence of a gas phase, the coupling between flow and reactive transport can be accounted for through a Picard iterative approach [3,5,6]. However, this approach is computationally expensive, involving the solution of nonlinear problems multiple times during each timestep, and convergence properties are often poor. More recently, a weak explicit coupling approach was developed to capture the impact of chemistry on flow by integrating water as a component and perform a volume balance calculation [7]. In the current work, a compositional approach is implemented into MIN3P-THCm, in which the flow variables (pressure, density) are expressed based on mass variables. Hence, this global implicit approach does not require solving the flow problem, but instead integrates groundwater flow processes directly into the reactive transport equations. We show that this approach yields very similar results to the commonly used approaches for single and two-phase flow. Finally, we show that, in highly coupled systems, not considering these coupled effects may lead to significant errors in simulating system evolution, highlighting the benefits of the newly developed approach.</p><p> </p><p>[1] Jowett, Cathles & Davis (1993). AAPG Bulletin, 77(3), 402-413.</p><p>[2] Harrison, Dipple, Power & Mayer (2015). Geochimica et cosmochimica Acta, 148, 477-495.</p><p>[3] Amos and Mayer (2006). Journal of contaminant hydrology, 87(1-2), 123-154.</p><p>[4] Lefebvre, Hockley, Smolensky & Gélinas (2001). Journal of contaminant hydrology, 52(1-4), 137-164.</p><p>[5] Henderson, Mayer, Parker, & Al (2009). Journal of contaminant hydrology, 106(3-4), 195-211.</p><p>[6] Sin, Lagneau and Corvisier (2017). Advances in Water Resources, 100, 62-77.</p><p>[7] Seigneur, Lagneau, Corvisier & Dauzères (2018). Advances in Water Resources 122, 355-366.</p>


2014 ◽  
Vol 571-572 ◽  
pp. 26-29
Author(s):  
Xiang Wei Duan ◽  
Wei Chang Shen ◽  
Jun Guo

The paper introduce the Mandelbrot Set and the message passing interface (MPI) and shared-memory (OpenMP), analyses the characteristic of algorithm design in the MPI and OpenMP environment, describes the implementation of parallel algorithm about Mandelbrot Set in the MPI environment and the OpenMP environment, conducted a series of evaluation and performance testing during the process of running, then the difference between the two system implementations is compared.


2017 ◽  
Vol 2017 ◽  
pp. 1-12 ◽  
Author(s):  
Anuj Sharma ◽  
Irene Moulitsas

High-resolution numerical methods and unstructured meshes are required in many applications of Computational Fluid Dynamics (CFD). These methods are quite computationally expensive and hence benefit from being parallelized. Message Passing Interface (MPI) has been utilized traditionally as a parallelization strategy. However, the inherent complexity of MPI contributes further to the existing complexity of the CFD scientific codes. The Partitioned Global Address Space (PGAS) parallelization paradigm was introduced in an attempt to improve the clarity of the parallel implementation. We present our experiences of converting an unstructured high-resolution compressible Navier-Stokes CFD solver from MPI to PGAS Coarray Fortran. We present the challenges, methodology, and performance measurements of our approach using Coarray Fortran. With the Cray compiler, we observe Coarray Fortran as a viable alternative to MPI. We are hopeful that Intel and open-source implementations could be utilized in the future.


Author(s):  
NENAD STANKOVIC ◽  
KANG ZHANG

The attractiveness of visual programming stems in large part from the direct interaction with program elements as if they were real objects, since people deal better with concrete objects than with the abstract. This paper describes a new graph based software visualization tool for parallel message-passing programming named Visper that combines the levels of abstraction at which message-passing parallel programs are expressed and makes use of compositional programming. Central to the tool is the Process Communication Graph that correlates both the control and data flow graphs into a single graph formalism, without a need for complex textual annotation. The graph can express static and runtime communication and replication structures, as found in Message Passing Interface (MPI) and Parallel Virtual Machine (PVM). It also forms the basis for visualizing parallel debugging and performance.


Geofluids ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-14
Author(s):  
Zhaoyun Hou ◽  
Tianfu Xu ◽  
Guanhong Feng ◽  
Bo Feng ◽  
Yilong Yuan ◽  
...  

Strong chemical reactions in the geothermal systems may cause sealing of fractures, which reduces the permeability in the reservoir and subsequently affects the heat production. However, it is difficult to reveal the sealing range in a deeply buried reservoir based on a limited number of downhole logs. This study recreated the sealing processes of the fault-controlled geothermal system in the Guide Basin, China, by reactive transport modeling. The modeling domain was discretized based on multiple interacting continua (MINC) approach, to address the nonequilibrium heat transport processes between the matrix and conduit in the fractured fault damage zone. Once the model was validated by observations of major ions in spring water and downhole temperature logs in the discharge area, it was used to determine the coupled processes of fluid, heat, and chemical transport in the reservoir and the resultant sealing ranges. It was found that the dissolution of albite and K-feldspar leads to the precipitation of smectite-Ca and illite in the middle and bottom of the fault under the condition of high concentration of Ca2+ and Mg2+ in the recharge water. Calcite veins were formed in discharge zone, because the horizontal fast flow in shallow subsurface zone supplied abundant Ca2+ and HCO3-. As a consequence, the permeability in the discharge zone reduced by 15% when compared to the original permeability of 100 mD. Moreover, another three self-sealing areas were formed near the recharge zone, the deep upgradient zone, and the downgradient area where the fast upward fluid flow occurred. Self-sealing subsequently prevented the deep circulation of the flow and heat absorption, which tends to make the fault-controlled geothermal system inactive.


Author(s):  
George W. Leaver ◽  
Martin J. Turner ◽  
James S. Perrin ◽  
Paul M. Mummery ◽  
Philip J. Withers

Remote scientific visualization, where rendering services are provided by larger scale systems than are available on the desktop, is becoming increasingly important as dataset sizes increase beyond the capabilities of desktop workstations. Uptake of such services relies on access to suitable visualization applications and the ability to view the resulting visualization in a convenient form. We consider five rules from the e-Science community to meet these goals with the porting of a commercial visualization package to a large-scale system. The application uses message-passing interface (MPI) to distribute data among data processing and rendering processes. The use of MPI in such an interactive application is not compatible with restrictions imposed by the Cray system being considered. We present details, and performance analysis, of a new MPI proxy method that allows the application to run within the Cray environment yet still support MPI communication required by the application. Example use cases from materials science are considered.


2000 ◽  
Vol 10 (04) ◽  
pp. 371-382 ◽  
Author(s):  
SOULLA LOUCA ◽  
NEOPHYTOS NEOPHYTOU ◽  
ADRIANOS LACHANAS ◽  
PARASKEVAS EVRIPIDOU

In this paper, we propose the design and development of a fault tolerant and recovery scheme for the Message Passing Interface (MPI). The proposed scheme consists of a detection mechanism for detecting process failures, and a recovery mechanism. Two different cases are considered, both assuming the existence of a monitoring process, the Observer which triggers the recovery procedure in case of failure. In the first case, each process keeps a buffer with its own message traffic to be used in case of failure, while the implementor uses periodical tests for notification of failure by the Observer. The recovery function simulates all the communication of the processes with the dead one by re-sending to the replacement process all the messages destined for the dead one. In the second case, the Observer receives and stores all message traffic, and sends to the replacement all the buffered messages destined for the dead process. Solutions are provided to the dead communicator problem caused by the death of a process. A description of the prototype developed is provided along with the results of the experiments performed for efficiency and performance.


Author(s):  
Joanna Krupska ◽  
Adam Mytlewski

Durability and efficiency are important conditions for long-term operation ofroad transport companies. In the operating aspect, the first parameter determines the quality of the manufacturing capacity and the ability to provide repetitive transport processes. The second parameter affects the long-term ability to use resources and the subsequent results of operations. The conducted study on stability and efficiency of the operating systems of road companies indicates the existence of, on the one hand, a large variation of approaches, and on the other, a clear dominance of intense and efficient behaviour in combination with ensuring the repetitiveness of processes.


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