Chia-Lin Yang

BioRoute: A Network-Flow-Based Routing Algorithm for the Synthesis of Digital Microfluidic Biochips

Due to recent advances in microfluidics, digital microfluidic biochips are expected to revolutionize laboratory procedures. One critical problem for biochip synthesis is the droplet routing problem. Unlike traditional very large scale integration routing problems, in addition to routing path selection, the biochip routing problem needs to address the issue of scheduling droplets under practical constraints imposed by the fluidic property and timing restriction of synthesis results. In this paper, we present the first network-flow-based routing algorithm that can concurrently route a set of noninterfering nets for the droplet routing problem on biochips. We adopt a two-stage technique of global routing followed by detailed routing. In global routing, we first identify a set of noninterfering nets and then adopt the network-flow approach to generate optimal global-routing paths for nets. In detailed routing, we present the first polynomial-time algorithm for simultaneous routing and scheduling using the global-routing paths with a negotiation-based routing scheme. Our algorithm targets at both the minimization of cells used for routing for better fault tolerance and minimization of droplet transportation time for better reliability and faster bioassay execution. Experimental results show the robustness and efficiency of our algorithm.

Push vs. pull: data movement for linked data structures

As the performance gap between the CPU and main memory continues to grow, techniques to hide memory latency are essential to deliver a high performance computer system. Prefetching can often overlap memory latency with computation for array-based numeric applications. However, prefetching for pointer-intensive applications still remains a challenging problem. Prefetching linked data structures (LDS) is difficult because the address sequence of LDS traversal does not present the same arithmetic regularity as array-based applications and the data dependence of pointer dereferences can serialize the address generation process. In this paper, we propose a cooperative hardware/software mechanism to reduce memory access latencies for linked data structures. Instead of relying on the past address history to predict future accesses, we identify the load instructions that traverse the LDS, and execute them ahead of the actual computation. To overcome the serial nature of the LDS address generation, we attach a prefetch controller to each level of the memory hierarchy and push, rather than pull, data to the CPU. Our simulations, using four pointer-intensive applications, show that the push model can achieve between 4% and 30% larger reductions in execution time compared to the pull model.

Placement of defect-tolerant digital microfluidic biochips using the T-tree formulation

Droplet-based microfluidic biochips have recently gained much attention and are expected to revolutionize the biological laboratory procedures. As biochips are adopted for the complex procedures in molecular biology, its complexity is expected to increase due to the need of multiple and concurrent assays on a chip. In this article, we formulate the placement problem of digital microfluidic biochips with a tree-based topological representation, called T-tree. To the best knowledge of the authors, this is the first work that adopts a topological representation to solve the placement problem of digital microfluidic biochips. We also consider the defect tolerant issue to avoid to use defective cells due to fabrication. Experimental results demonstrate that our approach is more efficient and effective than the previous unified synthesis and placement framework.

Multiprocessor energy-efficient scheduling with task migration considerations

This paper targets energy-efficient scheduling of tasks over multiple processors, where tasks share a common deadline. Distinct from many research results on heuristics-based energy-efficient scheduling, we propose approximation algorithms with different approximation bounds for processors with/without constraints on the maximum processor speed, where no task migration is allowed. When there is no constraint on processor speeds, we propose an approximation algorithm for two-processor scheduling to provide trade-offs among the specified error, the running time, the approximation ratio, and the memory space complexity. An approximation algorithm with a 1.13-approximation ratio for M-processor systems is also derived (M > 2). When there is an upper bound on processor speeds, an artificial-bound approach is taken to minimize the energy consumption with a 1.13-approximation ratio. An optimal scheduling algorithm is then proposed in the minimization of the energy consumption when task migration is allowed.

BioRoute: a network-flow based routing algorithm for digital microfluidic biochips

Due to the recent advances in microfluidics, digital microfluidic biochips are expected to revolutionize laboratory procedures. One critical problem for biochip synthesis is the droplet routing problem. Unlike traditional VLSI routing problems, in addition to routing path selection, the biochip routing problem needs to address the issue of scheduling droplets under the practical constraints imposed by the fluidic property and the timing restriction of the synthesis result. In this paper, we present the first network-flow based routing algorithm that can concurrently route a set of non-interfering nets for the droplet routing problem on biochips. We adopt a two-stage technique of global routing followed by detailed routing. In global routing, we first identify a set of non-interfering nets and then adopt the network-flow approach to generate optimal global-routing paths for the nets. In detailed routing, we present the first polynomial-time algorithm for simultaneous routing and scheduling using the global-routing paths with a negotiation-based routing scheme. The experimental results show the robustness and efficiency of our algorithm.

NVM duet: unified working memory and persistent store architecture

Emerging non-volatile memory (NVM) technologies have gained a lot of attention recently. The byte-addressability and high density of NVM enable computer architects to build large-scale main memory systems. NVM has also been shown to be a promising alternative to conventional persistent store. With NVM, programmers can persistently retain in-memory data structures without writing them to disk. Therefore, one can envision that in the future, NVM will play the role of both working memory and persistent store at the same time. Persistent store demands consistency and durability guarantees, thereby imposing new design constraints on the memory system. Consistency is achieved at the expense of serializing multiple write operations. Durability requires memory cells to guarantee non-volatility and thus reduces the write speed. Therefore, a unified architecture oblivious to these two use cases would lead to suboptimal design. In this paper, we propose a novel unified working memory and persistent store architecture, NVM Duet, which provides the required consistency and durability guarantees for persistent store while relaxing these constraints if accesses to NVM are for working memory. A cross-layer design approach is adopted to achieve the design goal. Overall, simulation results demonstrate that NVM Duet achieves up to 1.68x (1.32x on average) speedup compared with the baseline design.

Temporal floorplanning using the T-tree formulation

Improving logic capacity by time-sharing, dynamically reconfigurable FPGAs are employed to handle designs of high complexity and functionality. We model each task as a 3D-box and deal with the temporal floorplanning/placement problem for dynamically reconfigurable FPGA architectures. We present a tree-based data structure, called T-trees, to represent the spatial and temporal relations among tasks. Each node in a T-tree has at most three children which represent the dimensional relationship among tasks. For the T-tree, we develop an efficient packing method and derive the condition to ensure the satisfaction of precedence constraints which model the temporal ordering among tasks induced by the execution of dynamically reconfigurable FPGAs. Experimental results show that our tree-based formulation can achieve significantly better solution quality with less execution time than the most recent state-of-the-art work.

A progressive-ILP based routing algorithm for cross-referencing biochips

Due to recent advances in microfluidics technology, digital microfluidic biochips and their associated CAD problems have gained much attention, most of which has been devoted to direct-addressing biochips. In this paper, we solve the droplet routing problem under the more scalable cross-referencing biochip paradigm, which uses row/column addressing scheme to activate electrodes. We propose the first droplet routing algorithm that directly solves the problem of routing in cross-referencing biochips. The main challenge of this type of biochips is the electrode interference which prevents simultaneous movement of multiple droplets. We first present a basic integer linear programming (ILP) formulation to optimally solve the droplet routing problem. Due to its complexity, we also propose a progressive ILP scheme to determine the locations of droplets at each time step. Experimental results demonstrate the efficiency and effectiveness of our progressive ILP scheme on a set of practical bio assays.

Age-based PCM wear leveling with nearly zero search cost

Improving the endurance of PCM is a fundamental issue when the technology is considered as an alternative to main memory usage. In the design of memory-based wear leveling approaches, a major challenge is how to efficiently determine the appropriate memory pages for allocation or swapping. In this paper, we present an efficient wear-leveling design that is compatible with existing virtual memory management. Two implementations, namely, bucket-based and array-based wear leveling, with nearly zero search cost are proposed to tradeoff time and space complexity. The results of experiments conducted based on popular benchmarks to evaluate the efficacy of the proposed design are very encouraging.

Thermal modeling for 3D-ICs with integrated microchannel cooling

Integrated microchannel liquid-cooling technology is envisioned as a viable solution to alleviate an increasing thermal stress imposed by 3D stacked ICs. Thermal modeling for microchannel cooling is challenging due to its complicated thermal-wake effect, a localized temperature wake phenomenon downstream of a heated source in the flow. This paper presents a fast and accurate thermal-wake aware thermal model for integrated microchannel 3D ICs. Validation results show the proposed thermal model achieves more than 400× speed up and only 2.0% error in comparison with a commercial numerical simulation tool. We also demonstrate the use of the proposed thermal model for thermal optimization during the IC placement stage. We find that due to the thermal-wake effect, tiles are placed in the descending order of power magnitude along the flow direction. We also find that modeling thermal-wakes is critical for generating a thermal-aware placement for integrated microchannel-cooled 3D IC. It could result in up to 25°C peak temperature difference according to our experiments.