Performance metrics for consolidated servers

In spite of the widespread adoption of virtualization and consol- idation, there exists no consensus with respect to how to bench- mark consolidated servers that run multiple guest VMs on the same physical hardware. For example, VMware proposes VMmark which basically computes the geometric mean of normalized throughput values across the VMs; Intel uses vConsolidate which reports a weighted arithmetic average of normalized throughput values. These benchmarking methodologies focus on total system through- put (i.e., across all VMs in the system), and do not take into account per-VM performance. We argue that a benchmarking methodology for consolidated servers should quantify both total system through- put and per-VM performance in order to provide a meaningful and precise performance characterization. We therefore present two performance metrics, Total Normalized Throughput (TNT) to characterize total system performance, and Average Normalized Reduced Throughput (ANRT) to characterize per-VM performance. We compare TNT and ANRT against VMmark using published performance numbers, and report several cases for which the VM- mark score is misleading. This is, VMmark says one platform yields better performance than another, however, TNT and ANRT show that both platforms represent different trade-offs in total system throughput versus per-VM performance. Or, even worse, in a cou- ple cases we observe that VMmark yields opposite conclusions than TNT and ANRT, i.e., VMmark says one system performs better than another one which is contradicted by TNT/ANRT performance characterization

Three pitfalls in Java performance evaluation

The Java programming language has known a remarkable growth over the last decade. This is partially due to the infrastructure required to run Java ap- plications on general purpose microprocessors: a Java virtual machine (VM). The VM ensures that Java applications are portable across different hardware platforms, because it shelters the applications from the underlying system. Hence the motto write once, run (almost) anywhere. Java applications are compiled to an intermediate form, called bytecode, and consist of a number of so-called class files. The virtual machine takes care of class loading, interpreting or compiling the bytecode to the native code of the underlying hardware platform, thread scheduling, garbage collection, etc. As such, during the execution of a Java application, the VM regularly intervenes to take care of housekeeping tasks and to optimise the application as it is executing. Furthermore, the specific implementation details of most virtual machines insert non-deterministic behaviour, not into the semantic part of the execution, but rather into the lower level execution. For example, to bring a Java application up to competitive speed with classical compiled programs written in languages such as C, the virtual machine needs to optimise Java bytecode. To limit the execution overhead, most virtual machines use a time sampling mechanism to determine the hot methods in the application. This introduces non-determinism, as over several runs, the methods are not always optimised at the same moment, nor is the set of optimised methods always the same. Other factors that introduce non-determinism are the thread scheduling, garbage collection, etc. It is readily seen that performance analysis of Java applications is not as simple as it seems at first, and warrants closer inspection. In this dissertation we are mainly interested in the behaviour of Java applications and their performance. In the course of this work, we uncovered three major pitfalls that were not taken into account by researchers when analysing Java performance prior to this work. We will briefly summarise the main achievements presented in this dissertation. The first pitfall we present involves the interaction between the virtual machine, the application and the input to the application. The performance for short running applications is shown to be mainly determined by the virtual machine. For longer running applications, this influence decreases, but remains tangible. We use statistical analysis, such as principal components analysis and cluster analysis (K-means and hierarchical clustering) to demonstrate and clarify the pitfall. By means of a large number of performance char- acteristics measured using hardware performance counters, five virtual machines and fourteen benchmarks with both a small and a large input size, we demonstrate that short running workloads are primarily clustered by virtual machines. Even for long running applications from the SPECjvm98 benchmark suite, the virtual machine still exerts a large influence on the observed behaviour at the microarchitectural level. This work has shown the need for both larger and longer running benchmarks than were available prior to it – this was (partially) met by the introduction of the DaCapo benchmark suite – as well as a careful consideration when setting up an experiment to avoid measuring the virtual machine, rather than the benchmark. Prior to this work, people were quite often using simulation with short running applications (to save time) for exploring Java performance. The second pitfall we uncover involves the analysis of performance numbers. During a survey of 50 papers published at premier conferences, such as OOPSLA, PLDI, CGO, ISMM and VEE, over the past seven years, we found that a variety of approaches are used, both for experimental design – for example, the input size, virtual machines, heap sizes, etc. – and, even more importantly, for data analysis – for example, using a best out of 3 performance number. New techniques are pitted against existing work using these prevalent approaches, and conclusions regarding their successfulness in beating prior state-of-the-art are based upon them. Given the fact that the execution of Java applications usually involves non-determinism in the virtual machine – for example, when determining which methods to optimise – it should come as no surprise that the lack of statistical rigour in these prevalent approaches leads to misleading or even incorrect conclusions. By this we mean that the conclusions are either not representative of what actually happens, or even contradict reality, as modelled in a statistical manner. To circumvent this pitfall, we propose a rigorous statistical approach that uses confidence intervals to both report and compare performance numbers. We also claim that sufficient experiments should be conducted to get a reliable performance measure. The non-determinism caused by the timer-based optimisation component in a virtual machine can be eliminated using so-called replay compilation. This technique will record a compilation plan during a first execution or profiling run of the application. During a second execution, the application is iterated twice: once to compile and optimise all methods found in the compilation plan, and a second time to perform the actual measurement. It turns out however that current practice of using either a single plan – corresponding to the best performing profiling run – or a combined plan choosing the methods that were optimised in, say, more than half the profiling runs, is no match for using multiple plans. The variability observed in the plans themselves is too large to capture in one of the current practices. Consequently, using multiple plans is definitely the better option. Moreover, this allows using a matched-pair approach in the data analysis, which results in tighter confidence intervals for the mean performance number. The third pitfall we examine is the usage of global performance numbers when tuning either an application or a virtual machine. We show that Java applications exhibit phase behaviour at the method level. This means that instances of the same method show more similarity to each other, behaviourwise, than to instances of other methods. A phase can then be identified as a set of sub-trees of the dynamic call-tree, with each sub-tree headed by the same method. We present an two-step algorithm that allows correlating hardware performance counter data in step 2 with the phases determined in step 1. The information obtained can be applied to show the programmer which methods perform worse than average, for example with respect to the number of cache misses they incur. In the dissertation, we pay particular attention to statistical rigour. For each pitfall, we use statistics to demonstrate its presence. Hopefully this work will encourage other researchers to use more rigour in their work as well

Ranking commercial machines through data transposition

The performance numbers reported by benchmarking consortia and corporations provide little or no insight into the performance of applications of interest that are not part of the benchmark suite. This paper describes data transposition, a novel methodology for addressing this ubiquitous benchmarking problem. Data transposition predicts the performance for an application of interest on a target machine based on its performance similarities with the industry-standard benchmarks on a limited number of predictive machines. The key idea of data transposition is to exploit machine similarity rather than workload similarity as done in prior work, i.e., data transposition identifies a predictive machine that is most similar to the target machine of interest for predicting performance for the application of interest. We demonstrate the accuracy and effectiveness of data transposition using the SPEC CPU2006 benchmarks and a set of 117 commercial machines. We report that the machine ranking obtained through data transposition correlates well with the machine ranking obtained using measured performance numbers (average correlation coefficient of 0.93). Not only does data transposition improve average correlation, we also demonstrate that data transposition is more robust towards outlier benchmarks, i.e., the worst-case correlation coefficient improves from 0.59 by prior art to 0.71. More concretely, using data transposition to predict the top-1 machine for an application of interest leads to the best performing machine for most workloads (average deficiency of 1.2% and max deficiency of 24.8% for one benchmark), whereas prior work leads to deficiencies over 100% for some workloads

Strategic programming on graph rewriting systems

We describe a strategy language to control the application of graph rewriting rules, and show how this language can be used to write high-level declarative programs in several application areas. This language is part of a graph-based programming tool built within the port-graph transformation and visualisation environment PORGY.Comment: In Proceedings IWS 2010, arXiv:1012.533

Development of a multiplex PCR assay for simultaneous detection of Theileria annulata, Babesia bovis and Anaplasma marginale in cattle

Tropical theileriosis, bovine babesiosis and anaplasmosis are tick-borne protozoan diseases that impose serious constraints on the health and productivity of domestic cattle in tropical and sub-tropical regions of the world. A common feature of these diseases is that, following recovery from primary infection, animals become persistent carriers of the pathogen and continue to play a critical role in disease epidemiology, acting as reservoirs of infection. This study describes development and evaluation of multiplex and single PCR assays for simultaneous detection of Theileria annulata, Babesia bovis and Anaplasma marginale in cattle. Following in silico screening for candidate target genes representing each of the pathogens, an optimised multiplex PCR assay was established using three primer sets, cytob1, MAR1bB2 and bovar2A, for amplification of genomic DNA of T. annulata, A. marginale and B. bovis respectively. The designed primer sets were found to be species-specific, generating amplicons of 312, 265 and 166 base pairs, respectively and were deemed suitable for the development of a multiplex assay. The sensitivity of each primer pair was evaluated using serial dilutions of parasite DNA, while specificity was confirmed by testing for amplification from DNA of different stocks of each pathogen and other Theileria, Babesia and Anaplasma species. Additionally, DNA preparations derived from field samples were used to evaluate the utility of the single and multiplex PCRs for determination of infection status. The multiplex PCR was found to detect each pathogen species with the same level of sensitivity, irrespective of whether its DNA was amplified in isolation or together with DNA representing the other pathogens. Moreover, single and multiplex PCRs were able to detect each species with equal sensitivity in serially diluted DNA representing mixtures of T. annulata, B. bovis and A. marginale, and no evidence of non-specific amplification from non-target species was observed. Validation that the multiplex PCR efficiently detects single and mixed infections from field samples was demonstrated. The developed assay represents a simple and efficient diagnostic for co-detection of tropical theileriosis, bovine babesiosis and anaplasmosis, and may be a valuable tool for epidemiological studies aimed at assessing the burden of multiple infection with tick-borne pathogens and improving control of the associated diseases in endemic regions

Detection of malaria in Malaysia by nested polymerase chain reaction amplification of dried blood spots on filter papers

Balbir Singh, Janet Cox-Singh, Andy Olivier Miller, Mohammad Shukri Abdullah, Georges Snounou, Hasan Abdul Rahman