Disengaged Scheduling for Fair, Protected Access to Fast Computational Accelerators

Today’s operating systems treat GPUs and other computational accelerators as if they were simple devices, with bounded and predictable response times. With accelerators assuming an increasing share of the workload on modern machines, this strategy is already problematic, and likely to become untenable soon. If the operating system is to enforce fair sharing of the machine, it must assume responsibility for accelerator scheduling and resource management. Fair, safe scheduling is a particular challenge on fast accelerators, which allow applications to avoid kernel-crossing overhead by interacting directly with the device. We propose a disengaged scheduling strategy in which the kernel intercedes between applications and the accelerator on an infrequent basis, to monitor their use of accelerator cycles and to determine which applications should be granted access over the next time interval. Our strategy assumes a well defined, narrow interface exported by the accelerator. We build upon such an interface, systematically inferred for the latest Nvidia GPUs. We construct several example schedulers, including Disengaged Timeslice with overuse control that guarantees fairness and Disengaged Fair Queueing that is effective in limiting resource idleness, but probabilistic. Both schedulers ensure fair sharing of the GPU, even among uncooperative or adversarial applications; Disengaged Fair Queueing incurs a 4 % overhead on average (max 18%) compared to direct devic

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

<p>Abstract</p> <p>Background</p> <p>The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation.</p> <p>Results</p> <p>A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from <url>http://dna.uio.no/swipe/</url> under the GNU Affero General Public License.</p> <p>Conclusions</p> <p>Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.</p

Virtual Machine Support for Many-Core Architectures: Decoupling Abstract from Concrete Concurrency Models

The upcoming many-core architectures require software developers to exploit concurrency to utilize available computational power. Today's high-level language virtual machines (VMs), which are a cornerstone of software development, do not provide sufficient abstraction for concurrency concepts. We analyze concrete and abstract concurrency models and identify the challenges they impose for VMs. To provide sufficient concurrency support in VMs, we propose to integrate concurrency operations into VM instruction sets. Since there will always be VMs optimized for special purposes, our goal is to develop a methodology to design instruction sets with concurrency support. Therefore, we also propose a list of trade-offs that have to be investigated to advise the design of such instruction sets. As a first experiment, we implemented one instruction set extension for shared memory and one for non-shared memory concurrency. From our experimental results, we derived a list of requirements for a full-grown experimental environment for further research

Message length effects for solving polynomial systems on a hypercube

Polynomial systems of equations frequently arise in solid modelling, robotics, computer vision, chemistry, chemical engineering, and mechanical engineering. Locally convergent iterative methods such as quasi-Newton methods may diverge or fail to find all meaningful solutions of a polynomial system. Recently a homotopy algorithm has been proposed for polynomial systems that is guaranteed globally convergent (always converges from an arbitrary starting point) with probability one, finds all solutions to the polynomial system, and has a large amount of inherent parallelism. For this homotopy algorithm and a given decomposition strategy, the communication overhead for several possible communication stritegies is explored empirically in this paper. The experiments were conducted on an iPSC-32 hypercube.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/27982/1/0000415.pd