17069073
On the effectiveness of buffered and multiple arm disks
Access patterns to input/output files are usually sequential and local; a small number of files are open for each job and the file is generally read or written sequentially. This implies that if files are allocated in contiguous disk storage, the disk arms will rarely be required to move. Disk seeks can be almost entirely eliminated by using multiple arms, whereby if there are several open files on a given spindle, there will be an arm for each. Even better results can be obtained by using electronic storage such as magnetic bubbles, CCD's or electron beam memories to buffer portions of the disk. Such buffers not only eliminate seek time but reduce rotational latency to negligible amounts and decrease transfer time. We study, using trace driven simulation, the effectiveness of both buffers and multiple arms. For the data used, our experiments show that a minimum total buffer capacity of 20 tracks is required in a buffered disk. Best hit ratio results are obtained with individual buffer sizes upwards of one quarter cylinder. Three cylinder size buffers give very high hit ratios, on the order of 96%, and this appears to be a good choice for buffer size and number. LRU buffer scheduling is found to work well; comparisons with optimal, look-ahead buffer scheduling are made. Some possible models for the frequency of seeks are briefly considered.
36713689
Performance Characterization of Optimizing Compilers
Optimizing compilers have become an essential component in achieving high levels of performance. Various simple and sophisticated optimizations are implemented at different stages of compilation to yield significant improvements, but little work has been done in characterizing the effectiveness of optimizers, or in understanding where most of this improvement comes from. We study the performance impact of optimization in the context of our methodology for CPU performance characterization based on the abstract machine model. The model considers all machines to be different implementations of the same high level language abstract machine; in previous research, the model has been used as a basis to analyze machine and benchmark performance. We show that our model can be extended to characterize the performance improvement provided by optimizers and to predict the run time of optimized programs, and measure the effectiveness of several compilers in implementing different optimization techniques. >
14423694
Characteristics of I/O traffic in personal computer and server workloads
Understanding the characteristics of I/O traffic is increasingly important as the performance gap between the processor and disk-based storage continues to widen. Moreover, recent advances in technology, coupled with market demands, have led to new and exciting developments in storage systems, particularly network storage, storage utilities, and intelligent self-optimizing storage. In this paper, we empirically examine the physical I/O traffic of a wide range of server and personal computer (PC) workloads, focusing on how these workloads will be affected by the recent developments in storage systems. As part of our analysis, we compare our results with historical data and re-examine some rules of thumb (e.g., one bit of I/O per second for each instruction per second of processing power) that have been widely used for designing computer systems. We find that the I/O traffic is bursty and appears to exhibit self-similar characteristics. Our analysis also indicates that there is little cross-correlation between traffic volumes of server workloads, which suggests that aggregating these workloads will likely help to smooth out the traffic and enable more efficient utilization of resources. We discover that there is significant potential for harnessing "free" system resources to perform background tasks such as optimization of disk block layout. In general, we observe that the characteristics of the I/O traffic are relatively insensitive to the extent of upstream caching, and thus our results still apply, on a qualitative level, when the upstream cache is increased in size.
12460438
Evaluation of cache consistency algorithm performance
As more computer systems turn to multiprocessing for improved performance, additional research is needed to evaluate and improve the performance of cache consistency protocols. In this study, we use trace-driven simulation to examine the performance of several consistency protocols, including some new adaptive protocols which have not been examined in prior research. This study uses a wider variety of traces than have been previously analyzed, including some production applications from a vector mini-supercomputer system, and presents a wider variety of analyses than have been previously presented for a given workload. We find that the sharing characteristics of application programs have a large bearing on the relative performance of the different protocols. Update-based protocols outperform invalidate-based protocols when accesses so shared data are highly interleaved among different processors (fine-grain sharing), while invalidate-based protocols are superior if one processor performs all accesses to shared data over long periods of time (coarse-grain sharing). Adaptive protocols provide the best overall performance across all applications; we present a new protocol called Update-Once, which yields the highest average performance. In even the best cases, however, estimated processor utilizations are unacceptably low due to the overhead to maintain consistent caches. To extract good performance from multiprocessor systems, existing application programs must be recoded to reduce sharing between processors.
3191261
Multiprocessor memory organization and memory interference
ture of shared memory in a multiprocessor computer system is examined with particular attention to noninterleaved memory. Alternative memory organizations are compared and it is shown that a home memory organization, in which each processor is associated with one or more memories in which its address space is concentrated, is quite effective in reducing memory interference. Home memory organization is shown to be particularly suited to certain specialized computational problems as well as to possess advantages in terms of interference and reliability for general purpose computation. Results for interleaved memory are drawn from previous work and are used for comparison. Trace-driven simulations are used to verify the conclusions of the analysis.
11584462
The automatic improvement of locality in storage systems
Disk I/O is increasingly the performance bottleneck in computer systems despite rapidly increasing disk data transfer rates. In this article, we propose Automatic Locality-Improving Storage (ALIS), an introspective storage system that automatically reorganizes selected disk blocks based on the dynamic reference stream to increase effective storage performance. ALIS is based on the observations that sequential data fetch is far more efficient than random access, that improving seek distances produces only marginal performance improvements, and that the increasingly powerful processors and large memories in storage systems have ample capacity to reorganize the data layout and redirect the accesses so as to take advantage of rapid sequential data transfer. Using trace-driven simulation with a large set of real workloads, we demonstrate that ALIS considerably outperforms prior techniques, improving the average read performance by up to 50% for server workloads and by about 15% for personal computer workloads. We also show that the performance improvement persists as disk technology evolves. Since disk performance in practice is increasing by only about 8% per year, the benefit of ALIS may correspond to as much as several years of technological progress.
2203322
Debugging sequential circuits using Boolean satisfiability
Logic debugging of today's complex sequential circuits is an important problem. In this paper, a logic debugging methodology for multiple errors in sequential circuits with no state equivalence is developed. The proposed approach reduces the problem of debugging to an instance of Boolean satisfiability. This formulation takes advantage of modern Boolean satisfiability solvers that handle large circuits in a computationally efficient manner. An extensive suite of experiments with large sequential circuits confirm the robustness and efficiency of the proposed approach. The results further suggest that Boolean satisfiability provides an effective platform for sequential logic debugging.
37361807
Robust Fuzzy Extractors and Authenticated Key Agreement from Close Secrets
Consider two parties holding correlated random variables W and W′, respectively, that are within distance t of each other in some metric space. These parties wish to agree on a uniformly distributed secret key R by sending a single message over an insecure channel controlled by an all-powerful adversary. We consider both the keyless case, where the parties share no additional secret information, and the keyed case, where the parties share a long-term secret SK that they can use to generate a sequence of session keys {Rj} using multiple pairs {(Wj, W′j)}. The former has applications to, e.g., biometric authentication, while the latter arises in, e.g., the bounded storage model with errors. 
 
Our results improve upon previous work in several respects: 
 
– The best previous solution for the keyless case with no errors (i.e., t=0) requires the min-entropy of W to exceed 2|W|/3. We show a solution when the min-entropy of W exceeds the minimal threshold |W|/2. 
 
– Previous solutions for the keyless case in the presence of errors (i.e., t>0) required random oracles. We give the first constructions (for certain metrics) in the standard model. 
 
– Previous solutions for the keyed case were stateful. We give the first stateless solution.
15197279
On the complexity of finding common approximate substrings
Problems associated with finding strings that are within a specified Hamming distance of a given set of strings occur in several disciplines. In this paper, we use techniques from parameterized complexity to assess non-polynomial time algorithmic options and complexity for the COMMON APPROXIMATE SUBSTRING (CAS) problem. Our analyses indicate under which parameter restrictions useful algorithms are possible, and include both class membership and parameterized reductions to prove class hardness. In order to achieve fixed-parameter tractability, either a fixed string length or both a fixed size alphabet and fixed substring length are sufficient. Fixing either the string length or the alphabet size and Hamming distance is shown to be necessary, unless W[1] = FPT. An assortment of parameterized class membership and hardness results cover all other parameterized variants, showing in particular the effect of fixing the number of strings.
18711767
Semantic Generalisation and the Inference of Meaning
In this paper, a computational model of a successful negotiated communication system is presented, in which language agents develop their own meanings in response to their environment and attempt to infer the meanings of others’ utterances. The inherent uncertainty in the process of meaning inference in the system leads to variation in the agents’ internal semantic representations, which then itself drives language change in the form of semantic generalisation.
4331453
Computational prediction of novel components of lung transcriptional networks
MOTIVATION
Little is known regarding the transcriptional mechanisms involved in forming and maintaining epithelial cell lineages of the mammalian respiratory tract.


RESULTS
Herein, a motif discovery approach was used to identify novel transcriptional regulators in the lung using genes previously found to be regulated by Foxa2 or Wnt signaling pathways. A human-mouse comparison of both novel and known motifs was also performed. Some of the factors and families identified here were previously shown to be involved epithelial cell differentiation (ETS family, HES-1 and MEIS-1), and ciliogenesis (RFX family), but have never been characterized in lung epithelia. Other unidentified over-represented motifs suggest the existence of novel mammalian lung transcription factors. Of the fraction of motifs examined we describe 25 transcription factor family predictions for lung. Fifteen novel factors were shown here to be expressed in mouse lung, and/or human bronchial or distal lung epithelial tissues or lung epithelial cell lineages.


AVAILABILITY
DME: http://rulai.cshl.edu/dme. MATCOMPARE: http://rulai.cshl.edu/MatCompare. MOTIFCLASS is available from the authors.