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Model-based Dynamic Control of Speculative Forays in Parallel Computation
In simulations running in parallel, the processors would have to synchronize with other processors to maintain correct global order of computations. This can be done either by blocking computation until correct order is guaranteed, or by \textit{speculatively} proceeding with the best guess (based on local information) and later correcting errors if/as necessary. Since the gainful lengths of speculative forays depend on the dynamics of the application software and hardware at runtime, an online control system is necessary to dynamically choose and/or switch between the blocking and speculative strategies. In this paper, we formulate the reversible speculative computing in large-scale parallel computing as a dynamic linear feedback control (optimization) system model and evaluate its performance in terms of time and cost savings as compared to the traditional (forward) computing. We illustrate with an exact analogy in the form of vehicular travel under dynamic, delayed route information. The objective is to assist in making the optimal decision on what computational approach is to be chosen, by predicting the amount of time and cost savings (or losing) under different environments represented by different parameters and probability distribution functions. We consider the cases of Gaussian, exponential and log-normal distribution functions. The control system is intended for incorporating into speculative parallel applications such as optimistic parallel discrete event simulations to decide at runtime when and to what extent speculative execution can be performed gainfully.
Combinatorial metabolic engineering using an orthogonal tri-functional CRISPR system
Designing an optimal microbial cell factory often requires overexpression, knock-down, and knock-out of multiple gene targets. Unfortunately, such rewiring of cellular metabolism is often carried out sequentially and with low throughput. Here, we report a combinatorial metabolic engineering strategy based on an orthogonal tri-functional CRISPR system that combines transcriptional activation, transcriptional interference, and gene deletion (CRISPR-AID) in the yeast Saccharomyces cerevisiae . This strategy enables perturbation of the metabolic and regulatory networks in a modular, parallel, and high-throughput manner. We show that the application of CRISPR-AID not only to increase the production of β-carotene by 3-fold in a single step, but also to achieve 2.5-fold improvement in the display of an endoglucanase on the yeast surface by optimizing multiple metabolic engineering targets in a combinatorial manner.
NETRA: A parallel architecture for integrated vision systems 2: Algorithms and performance evaluation
In part 1 architecture of NETRA is presented. A performance evaluation of NETRA using several common vision algorithms is also presented. Performance of algorithms when they are mapped on one cluster is described. It is shown that SIMD, MIMD, and systolic algorithms can be easily mapped onto processor clusters, and almost linear speedups are possible. For some algorithms, analytical performance results are compared with implementation performance results. It is observed that the analysis is very accurate. Performance analysis of parallel algorithms when mapped across clusters is presented. Mappings across clusters illustrate the importance and use of shared as well as distributed memory in achieving high performance. The parameters for evaluation are derived from the characteristics of the parallel algorithms, and these parameters are used to evaluate the alternative communication strategies in NETRA. Furthermore, the effect of communication interference from other processors in the system on the execution of an algorithm is studied. Using the analysis, performance of many algorithms with different characteristics is presented. It is observed that if communication speeds are matched with the computation speeds, good speedups are possible when algorithms are mapped across clusters.
File concepts for parallel I/O
The subject of input/output (I/O) was often been neglected in the design of parallel computer systems, although for many problems I/O rates will limit the speedup attainable. The I/O problem is addressed by considering the role of files in parallel systems. The notion of parallel files is introduced. Parallel files provide for concurrent access by multiple processes, and utilize parallelism in the I/O system to improve performance. Parallel files can also be used conventionally by sequential programs. A set of standard parallel file organizations is proposed, based on common data partitioning techniques. Implementation strategies for the proposed organizations are suggested, using multiple storage devices. Problem areas are also identified and discussed.
Application of NEM-based Pin-by-Pin HCMFD Algorithm to 3-D Core Analysis
A pin-wise reactor analysis is expected to provide a more accurate solution than the conventional nodal methods. However, a pin-wise approach is still computationally very costly though the computational performances have been enormously improved for decades. To overcome such limitation of a pin-by-pin core analysis, the HCMFD (Hybrid Course-Mesh Finite Difference) algorithm has been recently introduced. By adopting the HCMFD algorithm, a parallel computing can be applied very effectively. In the HCMFD algorithm, an iterative local-global strategy is adopted with a combination of two CMFD acceleration methods for the pin-wise core analysis. The global eigenvalue problem is solved by one-node CMFD, while the local fixed-source problems are solved by two-node CMFD based on the NEM (nodal expansion method). In the HCMFD computational scheme, a parallel computing can effectively be applied since most of the computational efforts are consumed to solve the local problems, and they can be solved in parallel. Previously, only a 2-D HCMFD algorithm was developed and its numerical efficiency was evaluated. In this paper, a 3D HCMFD scheme is introduced and some 3-D problems were analyzed to verify its applicability to 3D pin-wise core analysis. (authors)
CMS multicore scheduling strategy
In the next years, processor architectures based on much larger numbers of cores will be most likely the model to continue 'Moore's Law' style throughput gains. This not only results in many more jobs in parallel running the LHC Run 1 era monolithic applications, but also the memory requirements of these processes push the workernode architectures to the limit. One solution is parallelizing the application itself, through forking and memory sharing or through threaded frameworks. CMS is following all of these approaches and has a comprehensive strategy to schedule multicore jobs on the GRID based on the glideinWMS submission infrastructure. The main component of the scheduling strategy, a pilot-based model with dynamic partitioning of resources that allows the transition to multicore or whole-node scheduling without disallowing the use of single-core jobs, is described. This contribution also presents the experiences made with the proposed multicore scheduling schema and gives an outlook of further developments working towards the restart of the LHC in 2015.
Scalability and Portability of Two Parallel Implementations of ADI
Two domain decompositions for the implementation of the NAS Scalar Penta-diagonal Parallel Benchmark on MIMD systems are investigated, namely transposition and multi-partitioning. Hardware platforms considered are the Intel iPSC/860 and Paragon XP/S-15, and clusters of SGI workstations on ethernet, communicating through PVM. It is found that the multi-partitioning strategy offers the kind of coarse granularity that allows scaling up to hundreds of processors on a massively parallel machine. Moreover, efficiency is retained when the code is ported verbatim (save message passing syntax) to a PVM environment on a modest size cluster of workstations.
Minimizing System Noise Effects For Extreme-Scale Scientific Simulation Through Function Delegation
The primary goal of the Minimizing System Noise Effects For Extreme-Scale Scientific Simulation through Function Delegation project is to eliminate or at best strongly minimize the impact of the noise introduced by the operating system, during large scale parallel applications runs. Collective communication operations are a basic building block for parallel programing models and scientific applications. These operations often dominate execution time of applications and tend to limit their scalability. In order to address this challenge, we evaluated different strategies to adapt the collective communications underlying topologies to the hardware architecture in order to provide increased levels of performance to the parallel applications.
High-performance parallel analysis of coupled problems for aircraft propulsion
Applications are described of high-performance parallel, computation for the analysis of complete jet engines, considering its multi-discipline coupled problem. The coupled problem involves interaction of structures with gas dynamics, heat conduction and heat transfer in aircraft engines. The methodology issues addressed include: consistent discrete formulation of coupled problems with emphasis on coupling phenomena; effect of partitioning strategies, augmentation and temporal solution procedures; sensitivity of response to problem parameters; and methods for interfacing multiscale discretizations in different single fields. The computer implementation issues addressed include: parallel treatment of coupled systems; domain decomposition and mesh partitioning strategies; data representation in object-oriented form and mapping to hardware driven representation, and tradeoff studies between partitioning schemes and fully coupled treatment.
Computational Strategies for Scalable Genomics Analysis
The revolution in next-generation DNA sequencing technologies is leading to explosive data growth in genomics, posing a significant challenge to the computing infrastructure and software algorithms for genomics analysis. Various big data technologies have been explored to scale up/out current bioinformatics solutions to mine the big genomics data. In this review, we survey some of these exciting developments in the applications of parallel distributed computing and special hardware to genomics. We comment on the pros and cons of each strategy in the context of ease of development, robustness, scalability, and efficiency. Although this review is written for an audience from the genomics and bioinformatics fields, it may also be informative for the audience of computer science with interests in genomics applications.
Multiphysics Simulation of DPC Criticality: Scoping Calculations and Coupling Strategy.
Objectives for Multi-Physics Simulations include: Provide a systematic framework for multi-process modeling — Conduct parallel model development efforts that cover the technical areas needed to support criticality consequence screening in performance assessment (PA) and that will be more closely integrated as development proceeds; Investigate separate effects — Allow partitioning of the overall waste package (WP) internal criticality multi-physics modeling effort during development activities, for study of specific processes that can later be coupled if warranted from interpretation of results; Study scaling and bounding approaches — Where possible, represent criticality consequences in PA using simplification of uncertain criticality event frequency and magnitude, bounding of consequences for screening purposes, and scaling of consequences to multiple WPs; and, Integration among participants — Multiple modeling teams (mainly SNL and ORNL, and their collaborators) will work on different parts of the in-package criticality phenomenology. Insights generated this way will be combined for more realistic coupled modeling, and for validation.
Analysis and Simulation of the Simplified Aircraft-Based Paired Approach Concept With the ALAS Alerting Algorithm in Conjunction With Echelon and Offset Strategies
This report presents analytical and simulation results of an investigation into proposed operational concepts for closely spaced parallel runways, including the Simplified Aircraft-based Paired Approach (SAPA) with alerting and an escape maneuver, MITRE?s echelon spacing and no escape maneuver, and a hybrid concept aimed at lowering the visibility minima. We found that the SAPA procedure can be used at 950 ft separations or higher with next-generation avionics and that 1150 ft separations or higher is feasible with current-rule compliant ADS-B OUT. An additional 50 ft reduction in runway separation for the SAPA procedure is possible if different glideslopes are used. For the echelon concept we determined that current generation aircraft cannot conduct paired approaches on parallel paths using echelon spacing on runways less than 1400 ft apart and next-generation aircraft will not be able to conduct paired approach on runways less than 1050 ft apart. The hybrid concept added alerting and an escape maneuver starting 1 NM from the threshold when flying the echelon concept. This combination was found to be effective, but the probability of a collision can be seriously impacted if the turn component of the escape maneuver has to be disengaged near the ground (e.g. 300 ft or below) due to airport buildings and surrounding terrain. We also found that stabilizing the approach path in the straight-in segment was only possible if the merge point was at least 1.5 to 2 NM from the threshold unless the total system error can be sufficiently constrained on the offset path and final turn.
Solidification texture, variant selection, and phase fraction in a spot-melt electron-beam powder bed fusion processed Ti-6Al-4V
The effect of a spot melt strategy on the solidification texture, variant selection, phase fraction, and their variations along the build height was investigated in comparison to a conventional linear melt strategy. Ti-6Al-4V alloy samples were manufactured by an electron-beam powder bed fusion process using two different melt strategies and characterized using high-energy synchrotron x-ray diffraction. The linear and spot melt cases resulted in β<100> cube and fiber textures, respectively, with the cube/fiber axis nearly parallel to the build direction. The α phase exhibited Burgers orientation relationship (BOR) with the parent β phase for both melt strategies. Although all of the key texture components and the BOR between the α and β phases were consistently observed in both cases along the build height, there were several measurable differences between the two. At the top of the build height, the β<100> build texture intensity was stronger in the linear case. However, the texture intensity in the linear case decreased gradually from the top to near the substrate, whereas the spot melt case did not show this trend. Moreover, the BOR was examined along the build height and the results showed that there is a distinct variant selection in the spot melt case, unlike the linear case. Specifically, the planar variants sharing ($\bar101$) β || (0002) α with [$\bar2\bar2\bar2$]β and [$2\bar22$]β were the most prominent in the spot melt, but no preference was identified in the directional variants. The β phase fraction was slightly lower in the spot melt case compared to the linear case. In both the cases, the β phase fraction decreased moving towards the substrate but remained significantly higher than that of the powder feedstock. Overall, the novel spot melt strategy produced a more homogeneous microstructure in terms of both the phase fraction and texture across the build height.
Physics-Based Analysis of Cell Imbalances and Aging in Lithium-Ion Battery Modules and Packs
Lithium-ion battery (LIB) packs are a key solution for grid-scale energy storage, enabling grid resilience and supporting critical infrastructure. LIB modules and packs experience current imbalances and uneven cell aging due to various design and operational factors, and require a battery management system (BMS) to continuously monitor and control. In this context, a physics-based modeling framework for LIB modules and packs (liionpack) was enhanced to identify design and control strategies that minimize current imbalance and improve module/pack operation. Simulations of an 8-cell parallel-connected module demonstrate that reducing current imbalance leads to more uniform cell aging and improved module/pack-level degradation predictions. The analysis shows that current imbalance are affected by the electrical resistances. Terminal location significantly affects imbalance, with opposite-end terminal connections at intermediate branches minimizing the imbalance, and the pack circuit construction influences the accuracy of physics-based analysis at the pack scale. This framework enables design optimization of modules and packs through a fast and easy evaluation of pack performance and aging, and supports the development of aging-informed balancing strategies compatible with BMS implementation. Thereby, offering practical pathways to improve reliability and cycle life predictions in large-scale battery energy storage systems.
Parallel image compression
A parallel compression algorithm for the 16,384 processor MPP machine was developed. The serial version of the algorithm can be viewed as a combination of on-line dynamic lossless test compression techniques (which employ simple learning strategies) and vector quantization. These concepts are described. How these concepts are combined to form a new strategy for performing dynamic on-line lossy compression is discussed. Finally, the implementation of this algorithm in a massively parallel fashion on the MPP is discussed.
Impact of media and antifoam selection on monoclonal antibody production and quality using a high throughput micro-bioreactor system
Monoclonal antibody production in commercial scale cell culture bioprocessing requires a thorough understanding of the engineering process and components used throughout manufacturing. It is important to identify high impact components early on during the lifecycle of a biotechnology-derived product. While cell culture media selection is of obvious importance to the health and productivity of mammalian bioreactor operations, other components such as antifoam selection can also play an important role in bioreactor cell culture. Silicone polymer-based antifoams were known to have negative impacts on cell health, production, and downstream filtration and purification operations. High throughput screening in micro-scale bioreactors provides an efficient strategy to identify initial operating parameters. Here, we utilized a micro-scale parallel bioreactor system to study an IgG1 producing CHO cell line, to screen Dynamis, ProCHO5, PowerCHO2, EX-Cell Advanced, and OptiCHO media, and 204, C, EX-Cell, SE-15, and Y-30 antifoams and their impacts on IgG1 production, cell growth, aggregation, and process control. This study found ProCHO5, EX-Cell Advanced, and PowerCHO2 media supported strong cellular growth profiles, with an IVCD of 25-35 3 106 cells-d/ mL, while maintaining specific antibody production (Qp> 2 pg/cell-d) for our model cell line and a monomer percentage above 94%. Antifoams C, EX-Cell, and SE-15 were capable of providing adequate control of foaming while antifoam 204 and Y-30 noticeably stunted cellular growth. This work highlights the utility of high throughput micro bioreactors and the importance of identifying both positive and negative impacts of media and antifoam selection on a model IgG1 producing CHO cell line.
Long-time dynamics through parallel trajectory splicing
Simulating the atomistic evolution of materials over long time scales is a longstanding challenge, especially for complex systems where the distribution of barrier heights is very heterogeneous. Such systems are difficult to investigate using conventional long-time scale techniques, and the fact that they tend to remain trapped in small regions of configuration space for extended periods of time strongly limits the physical insights gained from short simulations. We introduce a novel simulation technique, Parallel Trajectory Splicing (ParSplice), that aims at addressing this problem through the timewise parallelization of long trajectories. The computational efficiency of ParSplice stems from a speculation strategy whereby predictions of the future evolution of the system are leveraged to increase the amount of work that can be concurrently performed at any one time, hence improving the scalability of the method. ParSplice is also able to accurately account for, and potentially reuse, a substantial fraction of the computational work invested in the simulation. We validate the method on a simple Ag surface system and demonstrate substantial increases in efficiency compared to previous methods. As a result, we then demonstrate the power of ParSplice through the study of topology changes in Ag 42 Cu 13 core–shell nanoparticles.