ParaLog: enabling and accelerating online parallel monitoring of multithreaded applications

Instruction-grain lifeguards monitor the events of a running application at the level of individual instructions in order to identify and help mitigate application bugs and security exploits. Because such lifeguards impose a 10-100X slowdown on existing platforms, previous studies have proposed hardware designs to accelerate lifeguard processing. However, these accelerators are either tailored to a specific class of lifeguards or suitable only for monitoring singlethreaded programs. We present ParaLog, the first design of a system enabling fast online parallel monitoring of multithreaded parallel applications. ParaLog supports a broad class of software-defined lifeguards. We show how three existing accelerators can be enhanced to support online multithreaded monitoring, dramatically reducing lifeguard overheads. We identify and solve several challenges in monitoring parallel applications and/or parallelizing these accelerators, including (i) enforcing inter-thread data dependences, (ii) dealing with inter-thread effects that are not reflected in coherence traffic, (iii) dealing with unmonitored operating system activity, and (iv) ensuring lifeguards can access shared metadata with negligible synchronization overheads. We present our system design for both Sequentially Consistent and Total Store Ordering processors. We implement and evaluate our design on a 16 core simulated CMP, using benchmarks from SPLASH-2 and PARSEC and two lifeguards: a data-flow tracking lifeguard and a memory-access checker lifeguard. Our results show that (i) our parallel accelerators improve performance by 2-9X and 1.13-3.4X for our two lifeguards, respectively, (ii) we are 5-126X faster than the time-slicing approach required by existing techniques, and (iii) our average overheads for applications with eight threads are 51% and 28% for the two lifeguards, respectively

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead