New hardware support transactional memory and parallel debugging in multicore processors

This thesis contributes to the area of hardware support for parallel programming by introducing new hardware elements in multicore processors, with the aim of improving the performance and optimize new tools, abstractions and applications related with parallel programming, such as transactional memory and data race detectors. Specifically, we configure a hardware transactional memory system with signatures as part of the hardware support, and we develop a new hardware filter for reducing the signature size. We also develop the first hardware asymmetric data race detector (which is also able to tolerate them), based also in hardware signatures. Finally, we propose a new module of hardware signatures that solves some of the problems that we found in the previous tools related with the lack of flexibility in hardware signatures

Dynamically detecting and tolerating IF-Condition Data Races

An IF-Condition Invariance Violation (ICIV) occurs when, after a thread has computed the control expression of an IF statement and while it is executing the THEN or ELSE clauses, another thread updates variables in the IF’s control expression. An ICIV can be easily detected, and is likely to be a sign of a concurrency bug in the code. Typically, the ICIV is caused by a data race, which we call IF-Condition Data Race (ICR). In this paper, we analyze the data races reported in the bug databases of popular software systems and show that ICRs occur relatively often. Then, we present two techniques to handle ICRs dynamically. They rely on simple code transformations and, in one case, additional hardware help. One of them (SW-IF) detects the races, while the other (HW-IF) detects and prevents them. We evaluate SW-IF and HW-IF using a variety of applica-tions. We show that these new techniques are effective at finding new data race bugs and run with low overhead. Specifically, HW-IF finds 5 new (unreported) race bugs and SW-IF finds 3 of them. In addition, 8-threaded executions of SPLASH-2 codes show that, on average, SW-IF adds 2 % execution overhead, while HW-IF adds less than 1%. 1

PARSNIP: Performant Architecture for Race Safety with No Impact on Precision

Data race detection is a useful dynamic analysis for multithreaded programs that is a key building block in record-and-replay, enforcing strong consistency models, and detecting concurrency bugs. Existing software race detectors are precise but slow, and hardware support for precise data race detection relies on assumptions like type safety that many programs violate in practice. We propose PARSNIP, a fully precise hardware-supported data race detector. PARSNIP exploits new insights into the redundancy of race detection metadata to reduce storage overheads. PARSNIP also adopts new race detection metadata encodings that accelerate the common case while preserving soundness and completeness. When bounded hardware resources are exhausted, PARSNIP falls back to a software race detector to preserve correctness. PARSNIP does not assume that target programs are type safe, and is thus suitable for race detection on arbitrary code. Our evaluation of PARSNIP on several PARSEC benchmarks shows that performance overheads range from negligible to 2.6x, with an average overhead of just 1.5x. Moreover, Parsnip outperforms the state-of-the-art Radish hardware race detector by 4.6x

Finding and Tolerating Concurrency Bugs.

Shared-memory multi-threaded programming is inherently more difficult than single-threaded programming. The main source of complexity is that, the threads of an application can interleave in so many different ways. To ensure correctness, a programmer has to test all possible thread interleavings, which, however, is impractical. Many rare thread interleavings remain untested in production systems, and they are the major cause for a majority of concurrency bugs. Given that untested interleavings are the major cause of a majority of the concurrency bugs, this dissertation explores two possible ways to tackle concurrency bugs in this dissertation. One is to expose untested interleavings during testing to find concurrency bugs. The other is to avoid untested interleavings during production runs to tolerate concurrency bugs. The key is an efficient and effective way to encode and remember tested interleavings. This dissertation first discusses two hypotheses about concurrency bugs: the small scope hypothesis and the value independent hypothesis. Based on these two hypotheses, this dissertation defines a set of interleaving patterns, called interleaving idioms, which are used to encode tested interleavings. The empirical analysis shows that the idiom based interleaving encoding scheme is able to represent most of the concurrency bugs that are used in the study. Then, this dissertation discusses an open source testing tool called Maple. It memoizes tested interleavings and actively seeks to expose untested interleavings. The results show that Maple is able to expose concurrency bugs and expose interleavings faster than other conventional testing techniques. Finally, this dissertation discusses two parallel runtime system designs which seek to avoid untested interleavings during production runs to tolerate concurrency bugs. Avoiding untested interleavings significantly improve correctness because most of the concurrency bugs are caused by untested interleavings. Also, the performance overhead for disallowing untested interleavings is low as commonly occuring interleavings should have been tested in a well-tested program.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/99765/1/jieyu_1.pd

Dynamic Analysis of Embedded Software

abstract: Most embedded applications are constructed with multiple threads to handle concurrent events. For optimization and debugging of the programs, dynamic program analysis is widely used to collect execution information while the program is running. Unfortunately, the non-deterministic behavior of multithreaded embedded software makes the dynamic analysis difficult. In addition, instrumentation overhead for gathering execution information may change the execution of a program, and lead to distorted analysis results, i.e., probe effect. This thesis presents a framework that tackles the non-determinism and probe effect incurred in dynamic analysis of embedded software. The thesis largely consists of three parts. First of all, we discusses a deterministic replay framework to provide reproducible execution. Once a program execution is recorded, software instrumentation can be safely applied during replay without probe effect. Second, a discussion of probe effect is presented and a simulation-based analysis is proposed to detect execution changes of a program caused by instrumentation overhead. The simulation-based analysis examines if the recording instrumentation changes the original program execution. Lastly, the thesis discusses data race detection algorithms that help to remove data races for correctness of the replay and the simulation-based analysis. The focus is to make the detection efficient for C/C++ programs, and to increase scalability of the detection on multi-core machines.Dissertation/ThesisDoctoral Dissertation Computer Science 201

Software lock elision for x86 machine code

More than a decade after becoming a topic of intense research there is no transactional memory hardware nor any examples of software transactional memory use outside the research community. Using software transactional memory in large pieces of software needs copious source code annotations and often means that standard compilers and debuggers can no longer be used. At the same time, overheads associated with software transactional memory fail to motivate programmers to expend the needed effort to use software transactional memory. The only way around the overheads in the case of general unmanaged code is the anticipated availability of hardware support. On the other hand, architects are unwilling to devote power and area budgets in mainstream microprocessors to hardware transactional memory, pointing to transactional memory being a "niche" programming construct. A deadlock has thus ensued that is blocking transactional memory use and experimentation in the mainstream. This dissertation covers the design and construction of a software transactional memory runtime system called SLE_x86 that can potentially break this deadlock by decoupling transactional memory from programs using it. Unlike most other STM designs, the core design principle is transparency rather than performance. SLE_x86 operates at the level of x86 machine code, thereby becoming immediately applicable to binaries for the popular x86 architecture. The only requirement is that the binary synchronise using known locking constructs or calls such as those in Pthreads or OpenMP libraries. SLE_x86 provides speculative lock elision (SLE) entirely in software, executing critical sections in the binary using transactional memory. Optionally, the critical sections can also be executed without using transactions by acquiring the protecting lock. The dissertation makes a careful analysis of the impact on performance due to the demands of the x86 memory consistency model and the need to transparently instrument x86 machine code. It shows that both of these problems can be overcome to reach a reasonable level of performance, where transparent software transactional memory can perform better than a lock. SLE_x86 can ensure that programs are ready for transactional memory in any form, without being explicitly written for it

Sympatric serpentine endemic Monardella (Lamiaceae) Species Maintain Habitat Differences Despite Hybridization

Ecological differentiation and genetic isolation are thought to be critical in facilitating coexistence between related species, but the relative importance of these phenomena and the interactions between them are not well understood. Here, we examine divergence in abiotic habitat affinity and the extent of hybridization and introgression between two rare species of Monardella (Lamiaceae) that are both restricted to the same serpentine soil exposure in California. Although broadly sympatric, they are found in microhabitats that differ consistently in soil chemistry, slope, rockiness and vegetation. We identify one active hybrid zone at a site with intermediate soil and above-ground characteristics, and we document admixture patterns indicative of extensive and asymmetric introgression from one species into the other. We find that genetic distance among heterospecific populations is related to geographic distance, such that the extent of apparent introgression is partly explained by the spatial proximity to the hybrid zone. Our work shows that plant species can maintain morphological and ecological integrity in the face of weak genetic isolation, intermediate habitats can facilitate the establishment of hybrids, and that the degree of apparent introgression a population experiences is related to its geographic location rather than its local habitat characteristics

The genomic basis of the plant island syndrome in Darwin’s giant daisies

The repeated, rapid and often pronounced patterns of evolutionary divergence observed in insular plants, or the ‘plant island syndrome’, include changes in leaf phenotypes, growth, as well as the acquisition of a perennial lifestyle. Here, we sequence and describe the genome of the critically endangered, Galápagos-endemic species Scalesia atractyloides Arnot., obtaining a chromosome-resolved, 3.2-Gbp assembly containing 43,093 candidate gene models. Using a combination of fossil transposable elements, k-mer spectra analyses and orthologue assignment, we identify the two ancestral genomes, and date their divergence and the polyploidization event, concluding that the ancestor of all extant Scalesia species was an allotetraploid. There are a comparable number of genes and transposable elements across the two subgenomes, and while their synteny has been mostly conserved, we find multiple inversions that may have facilitated adaptation. We identify clear signatures of selection across genes associated with vascular development, growth, adaptation to salinity and flowering time, thus finding compelling evidence for a genomic basis of the island syndrome in one of Darwin’s giant daisies