Transparent and efficient shared-state management for optimistic simulations on multi-core machines

Traditionally, Logical Processes (LPs) forming a simulation model store their execution information into disjoint simulations states, forcing events exchange to communicate data between each other. In this work we propose the design and implementation of an extension to the traditional Time Warp (optimistic) synchronization protocol for parallel/distributed simulation, targeted at shared-memory/multicore machines, allowing LPs to share parts of their simulation states by using global variables. In order to preserve optimism's intrinsic properties, global variables are transparently mapped to multi-version ones, so to avoid any form of safety predicate verification upon updates. Execution's consistency is ensured via the introduction of a new rollback scheme which is triggered upon the detection of an incorrect global variable's read. At the same time, efficiency in the execution is guaranteed by the exploitation of non-blocking algorithms in order to manage the multi-version variables' lists. Furthermore, our proposal is integrated with the simulation model's code through software instrumentation, in order to allow the application-level programmer to avoid using any specific API to mark or to inform the simulation kernel of updates to global variables. Thus we support full transparency. An assessment of our proposal, comparing it with a traditional message-passing implementation of variables' multi-version is provided as well. © 2012 IEEE

A Wait-free Multi-word Atomic (1,N) Register for Large-scale Data Sharing on Multi-core Machines

We present a multi-word atomic (1,N) register for multi-core machines exploiting Read-Modify-Write (RMW) instructions to coordinate the writer and the readers in a wait-free manner. Our proposal, called Anonymous Readers Counting (ARC), enables large-scale data sharing by admitting up to $2^{32}-2$ concurrent readers on off-the-shelf 64-bits machines, as opposed to the most advanced RMW-based approach which is limited to 58 readers. Further, ARC avoids multiple copies of the register content when accessing it---this affects classical register's algorithms based on atomic read/write operations on single words. Thus it allows for higher scalability with respect to the register size. Moreover, ARC explicitly reduces improves performance via a proper limitation of RMW instructions in case of read operations, and by supporting constant time for read operations and amortized constant time for write operations. A proof of correctness of our register algorithm is also provided, together with experimental data for a comparison with literature proposals. Beyond assessing ARC on physical platforms, we carry out as well an experimentation on virtualized infrastructures, which shows the resilience of wait-free synchronization as provided by ARC with respect to CPU-steal times, proper of more modern paradigms such as cloud computing.Comment: non

Best practices for HPM-assisted performance engineering on modern multicore processors

Many tools and libraries employ hardware performance monitoring (HPM) on modern processors, and using this data for performance assessment and as a starting point for code optimizations is very popular. However, such data is only useful if it is interpreted with care, and if the right metrics are chosen for the right purpose. We demonstrate the sensible use of hardware performance counters in the context of a structured performance engineering approach for applications in computational science. Typical performance patterns and their respective metric signatures are defined, and some of them are illustrated using case studies. Although these generic concepts do not depend on specific tools or environments, we restrict ourselves to modern x86-based multicore processors and use the likwid-perfctr tool under the Linux OS.Comment: 10 pages, 2 figure

Easier Debugging of Multithreaded Software

Software activation is a technique designed to avoid illegal use of a licensed software. This is achieved by having a legitimate user enter a software activation key to validate the purchase of the software. Generally, a software is a single-threaded program. From an attacker’s perspective, who does not wish to pay for this software, it is not hard to reverse engineer such a single threaded program and trace its path of execution. With tools such as OllyDbg, the attacker can look into the disassembled code of this software and find out where the verification logic is being performed and then patch it to skip the verification altogether. In order to make the attacker’s task difficult, a multi-threaded approach towards software development was proposed [1]. According to this approach, you should break the verification logic into several pieces, each of which should run in a separate thread. Any debugger, such as OllyDbg, is capable of single-stepping through only one thread at a time, although it is aware of the existence of other threads. This makes it difficult for an attacker to trace the verification logic. Not just for an attacker, it is also difficult for any ethical developer to debug a multithreaded program. The motivation behind this project is to develop the prototype of a debugger that will make it easer to trace the execution path of a multi-threaded program. The intended debugger has to be able to single-step through all of the threads in lockstep

Transparent support for partial rollback in software transactional memories

The Software Transactional Memory (STM) paradigm has gained momentum thanks to its ability to provide synchronization transparency in concurrent applications. With this paradigm, accesses to data structures that are shared among multiple threads are carried out within transactions, which are properly handled by the STM layer with no intervention by the application code. In this article we propose an enhancement of typical STM architectures which allows supporting partial rollback of active transactions, as opposed to the typical case where a rollback of a transaction entails squashing all the already-performed work. Our partial rollback scheme is still transparent to the application programmer and has been implemented for x86-64 architectures and for the ELF format, thus being largely usable on POSIX-compliant systems hosted on top of off-the-shelf architectures. We integrated it within the TinySTM open-source library and we present experimental results for the STAMP STM benchmark run on top of a 32-core HP ProLiant server. © 2013 Springer-Verlag

Reference Based Genome Compression

DNA sequencing technology has advanced to a point where storage is becoming the central bottleneck in the acquisition and mining of more data. Large amounts of data are vital for genomics research, and generic compression tools, while viable, cannot offer the same savings as approaches tuned to inherent biological properties. We propose an algorithm to compress a target genome given a known reference genome. The proposed algorithm first generates a mapping from the reference to the target genome, and then compresses this mapping with an entropy coder. As an illustration of the performance: applying our algorithm to James Watson's genome with hg18 as a reference, we are able to reduce the 2991 megabyte (MB) genome down to 6.99 MB, while Gzip compresses it to 834.8 MB.Comment: 5 pages; Submitted to the IEEE Information Theory Workshop (ITW) 201

Design and Validation of a Software Defined Radio Testbed for DVB-T Transmission

This paper describes the design and validation of a Software Defined Radio (SDR) testbed, which can be used for Digital Television transmission using the Digital Video Broadcasting - Terrestrial (DVB-T) standard. In order to generate a DVB-T-compliant signal with low computational complexity, we design an SDR architecture that uses the C/C++ language and exploits multithreading and vectorized instructions. Then, we transmit the generated DVB-T signal in real time, using a common PC equipped with multicore central processing units (CPUs) and a commercially available SDR modem board. The proposed SDR architecture has been validated using fixed TV sets, and portable receivers. Our results show that the proposed SDR architecture for DVB-T transmission is a low-cost low-complexity solution that, in the worst case, only requires less than 22% of CPU load and less than 170 MB of memory usage, on a 3.0 GHz Core i7 processor. In addition, using the same SDR modem board, we design an off-line software receiver that also performs time synchronization and carrier frequency offset estimation and compensation

Validation of hardware events for successful performance pattern identification in High Performance Computing

Hardware performance monitoring (HPM) is a crucial ingredient of performance analysis tools. While there are interfaces like LIKWID, PAPI or the kernel interface perf\_event which provide HPM access with some additional features, many higher level tools combine event counts with results retrieved from other sources like function call traces to derive (semi-)automatic performance advice. However, although HPM is available for x86 systems since the early 90s, only a small subset of the HPM features is used in practice. Performance patterns provide a more comprehensive approach, enabling the identification of various performance-limiting effects. Patterns address issues like bandwidth saturation, load imbalance, non-local data access in ccNUMA systems, or false sharing of cache lines. This work defines HPM event sets that are best suited to identify a selection of performance patterns on the Intel Haswell processor. We validate the chosen event sets for accuracy in order to arrive at a reliable pattern detection mechanism and point out shortcomings that cannot be easily circumvented due to bugs or limitations in the hardware