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New developments on the cheminformatics open workflow environment CDK-Taverna

JOURNAL OF CHEMINFORMATICS 2011年第1期3卷 1-10页

作者： Truszkowski, Andreas Jayaseelan, Kalai Vanii Neumann, Stefan Willighagen, Egon L. Zielesny, Achim Steinbeck, Christoph EBI Cambridge England Univ Appl Sci Gelsenkirchen Inst Bioinformat & Cheminformat Recklinghausen Germany GNWI Gesell Nat Wissenschaftliche Informat mbH Oer Erkenschwick Germany Karolinska Inst Inst Environm Med Div Mol Toxicol S-10401 Stockholm Sweden

Background: The computational processing and analysis of small molecules is at heart of cheminformatics and structural bioinformatics and their application in e. g. metabolomics or drug discovery. Pipelining or workflow tools allow for the Lego (TM)-like, graphical assembly of I/O modules and algorithms into a complex workflow which can be easily deployed, modified and tested without the hassle of implementing it into a monolithic application. The CDK-Taverna project aims at building a free open-source cheminformatics pipelining solution through combination of different open-source projects such as Taverna, the Chemistry Development Kit (CDK) or the Waikato Environment for Knowledge Analysis (WEKA). A first integrated version 1.0 of CDK-Taverna was recently released to the public. Results: The CDK-Taverna project was migrated to the most up-to-date versions of its foundational software libraries with a complete re-engineering of its worker's architecture (version 2.0). 64-bit computing and multi-core usage by paralleled threads are now supported to allow for fast in-memory processing and analysis of large sets of molecules. Earlier deficiencies like workarounds for iterative data reading are removed. The combinatorial chemistry related reaction enumeration features are considerably enhanced. Additional functionality for calculating a natural product likeness score for small molecules is implemented to identify possible drug candidates. Finally the data analysis capabilities are extended with new workers that provide access to the open-source WEKA library for clustering and machine learning as well as training and test set partitioning. The new features are outlined with usage scenarios. Conclusions: CDK-Taverna 2.0 as an open-source cheminformatics workflow solution matured to become a freely available and increasingly powerful tool for the biosciences. The combination of the new CDK-Taverna worker family with the already available workflows developed by a lively Ta

关键词： java virtual machine Atom Signature Public Void Configuration Panel Taverna Workbench

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Providing soft real-time quality of service guarantees for java threads

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CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE 2003年第3-5期15卷 521-538页

作者： Pang, JC Shoja, GC Manning, EG Univ Victoria Dept Comp Sci Victoria BC V8W 3P6 Canada Univ Victoria Dept Elect & Comp Engn Victoria BC V8W 3P6 Canada

The java platform has many characteristics that make it very desirable for integrated continuous media processing. Unfortunately, it lacks the necessary CPU resource management facilities to support quality of service (QoS) guarantees for soft real-time multimedia tasks. In this paper, we present our new java virtual machine, Q-JVM, which brings CPU resource management to the java platform. Q-JVM is based on Sun's JVM version 1.1.5. It implements an enhanced version of the MTR-LS algorithm in its thread scheduler. Combined with admission control that could be implemented in an application-level resource manager, it is able to support QoS parameters such as fairness, bandwidth partitioning and delay bound guarantees, as well as the cumulative service guarantee. Our test results show that Q-JVM is backward compatible with the standard JVM from Sun, has low scheduling overhead, and is able to provide QoS guarantees as specified. Copyright (C) 2003 John Wiley Sons, Ltd.

关键词： java virtual machine CPU resource management QoS real-time scheduling move-to-rear list scheduling

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Techniques for obtaining high performance in java programs

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ACM COMPUTING SURVEYS 2000年第3期32卷 213-240页

作者： Kazi, IH Chen, HH Stanley, B Lilja, DJ Univ Minnesota Minnesota Supercomp Inst Dept Elect & Comp Engn Minneapolis MN 55455 USA Univ Minnesota Minnesota Supercomp Inst Dept Comp Sci & Engn Minneapolis MN 55455 USA

This survey describes research directions in techniques to improve the performance of programs written in the java programming language. The standard technique for java execution is interpretation, which provides for extensive portability of programs. A java interpreter dynamically executes java bytecodes, which comprise the instruction set of the java virtual machine (JVM). Execution time performance of java programs can be improved through compilation, possibly at the expense of portability. Various types of java compilers have been proposed, including Just-In-Time (JIT) compilers that compile bytecodes into native processor instructions on the fly;direct compilers that directly translate the java source code into the target processor's native language;and bytecode-to-source translators that generate either native code or an intermediate language, such as C, from the bytecodes. Additional techniques, including bytecode optimization, dynamic compilation, and executing java programs in parallel, attempt to improve java run-time performance while maintaining java's portability. Another alternative for executing java programs is a java processor that implements the JVM directly in hardware. In this survey, we discuss the basic features, and the advantages and disadvantages, of the various java execution techniques. We also discuss the various java benchmarks that are being used by the java community for performance evaluation of the different techniques. Finally, we conclude with a comparison of the performance of the alternative java execution techniques based on reported results.

关键词： languages performance java java virtual machine interpreters just-in-time compilers direct compilers bytecode-to-source translators dynamic compilation

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An analytical POC stack operations folding for continuous and discontinuous java bytecodes

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JOURNAL OF SYSTEMS ARCHITECTURE 2002年第1-3期48卷 1-16页

作者： Ton, LR Chang, LC Chung, CP Natl Chiao Tung Univ Dept Comp Sci & Informat Engn Hsinchu 300 Taiwan

The execution performance of a stack-based java virtual machine (JVM) is limited by the true data dependency. To enhance the performance of the JVM, a stack operations folding mechanism for the picojava-I/II processor was proposed by Sun Microsystems to fold 42.3% stack operations. By comparing the continuous bytecodes with predefined folding patterns in instruction decoder, the number of push/pop operations in between the operand stack and the local variable could be reduced. In this study, an enhanced POC (EPOC) folding model is proposed to further fold the discontinuous bytecodes that cannot be folded in continuous bytecodes folding mechanisms. By proposing a stack re-order buffer (SROB) to help the folding check processes, the EPOC folding model can fold the stack operations perfectly with a small size of SROB implementation. Statistical data shows that the four-foldable strategy of the EPOC folding model can eliminate 98.8% of push/pop operations with an instruction buffer size of 7 bytes and the SROB size of eight entries. (C) 2002 Elsevier Science B.V. All rights reserved.

关键词： java virtual machine stack operations folding POC folding model EPOC folding model java processor

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Have java's Security Issues Gotten out of Hand?

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COMPUTER 2012年第12期45卷 18-21页

作者： Garber, Lee

In the past year, security experts have found many vulnerabilities, some critical, in java. This represents a serious trend because java is so widely used.

关键词： Security Of Data java Security Experts java Security Issues Exploit Toolkit Security java java Runtime Environment Browsers java virtual machine

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Faster Variational Execution with Transparent Bytecode Transformation

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PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL 2018年第OOPSLA期2卷 1–30页

作者： Wong, Chu-Pan Meinicke, Jens Lazarek, Lukas Kastner, Christian Carnegie Mellon Univ Pittsburgh PA 15213 USA Univ Magdeburg Magdeburg Germany Northwestern Univ Evanston IL 60208 USA

Variational execution is a novel dynamic analysis technique for exploring highly configurable systems and accurately tracking information flow. It is able to efficiently analyze many configurations by aggressively sharing redundancies of program executions. The idea of variational execution has been demonstrated to be effective in exploring variations in the program, especially when the configuration space grows out of control. Existing implementations of variational execution often require heavy lifting of the runtime interpreter, which is painstaking and error-prone. Furthermore, the performance of this approach is suboptimal. For example, the state-of-the-art variational execution interpreter for java, VarexJ, slows down executions by 100 to 800 times over a single execution for small to medium size java programs. Instead of modifying existing JVMs, we propose to transform existing bytecode to make it variational, so it can be executed on an unmodified commodity JVM. Our evaluation shows a dramatic improvement on performance over the state-of-the-art, with a speedup of 2 to 46 times, and high efficiency in sharing computations.

关键词： java virtual machine Bytecode Transformation Variational Execution Configurable System

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A Volatile-by-Default JVM for Server Applications

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PROCEEDINGS OF THE ACM ON PROGRAMMING LANGUAGES-PACMPL 2017年第OOPSLA期1卷 1-25页

作者： Liu, Lun Millstein, Todd Musuvathi, Madanlal Univ Calif Los Angeles Los Angeles CA 90095 USA Microsoft Res Redmond WA USA

A memory consistency model (or simply memory model) defines the possible values that a shared-memory read may return in a multithreaded programming language. Choosing a memory model involves an inherent performance-programmability tradeoff. The java language has adopted a relaxed (or weak) memory model that is designed to admit most traditional compiler optimizations and obviate the need for hardware fences on most shared-memory accesses. The downside, however, is that programmers are exposed to a complex and unintuitive semantics and must carefully declare certain variables as volatile in order to enforce program orderings that are necessary for proper behavior. This paper proposes a simpler and stronger memory model for java through a conceptually small change: every variable has volatile semantics by default, but the language allows a programmer to tag certain variables, methods, or classes as relaxed and provides the current java semantics for these portions of code. This volatile-by-default semantics provides sequential consistency (SC) for all programs by default. At the same time, expert programmers retain the freedom to build performance-critical libraries that violate the SC semantics. At the outset, it is unclear if the volatile-by-default semantics is practical for java, given the cost of memory fences on today's hardware platforms. The core contribution of this paper is to demonstrate, through comprehensive empirical evaluation, that the volatile-by-default semantics is arguably acceptable for a predominant use case for java today - server-side applications running on Intel x86 architectures. We present VBD-HoTSPoT, a modification to Oracle's widely used HotSpot JVM that implements the volatile-by-default semantics for x86. To our knowledge VBD-HoTSPoT is the first implementation of SC for java in the context of a modern JVM. VBD-HoTSPoT incurs an average overhead versus the baseline HotSpot JVM of 28% for the Da Capo benchmarks, which is significant tho

关键词： memory consistency models volatile by default sequential consistency java virtual machine

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Optimizing type-specific instrumentation on the JVM with reflective supertype information

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JOURNAL OF VISUAL LANGUAGES AND COMPUTING 2018年第Dec.期49卷 29-45页

作者： Rosa, Andrea Binder, Walter Univ Svizzera Italiana Fac Informat Via Giuseppe Buffi 13 Lugano Switzerland

Reflective supertype information (RSI) is useful for many instrumentation-based type-specific analyses on the java virtual machine (JVM). On the one hand, while such information can be obtained when performing the instrumentation within the same JVM process executing the instrumented program, in-process instrumentation severely limits the bytecode coverage of the analysis. On the other hand, performing the instrumentation in a separate process can achieve full bytecode coverage, but complete RSI is generally not available, often requiring the insertion of expensive runtime type checks in the instrumented program. In this article, we present a novel technique to accurately reify complete RSI in a separate instrumentation process. This is challenging, because the observed application may make use of custom classloaders and the loaded classes in one application execution are generally only known upon termination of the application. We implement our technique in an extension of the dynamic analysis framework DiSL. The resulting framework guarantees full bytecode coverage, while providing RSI. Evaluation results on a task profiler demonstrate that our technique can achieve speedups up to a factor of 6.24 x wrt. resorting to runtime type checks in the instrumentation code for an analysis with full bytecode coverage.

关键词： Dynamic analysis Reflective information Bytecode instrumentation java virtual machine

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Toward an SGX-Friendly java Runtime

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IEEE TRANSACTIONS ON COMPUTERS 2024年第1期73卷 44-57页

作者： Wu, Mingyu Li, Zhe Chen, Haibo Zang, Binyu Wang, Shaojun Yu, Lei Li, Sanhong Song, Haitao Shanghai Jiao Tong Univ Inst Parallel & Distributed Syst Shanghai 200240 Peoples R China Shanghai AI Lab Shanghai 200232 Peoples R China Minist Educ Engn Res Ctr Domain Specif Operating Syst Shanghai 200240 Peoples R China Alibaba Cloud Hangzhou 311121 Zhejiang Peoples R China Shanghai Jiao Tong Univ Shanghai Artificial Intelligence Res Shanghai 200240 Peoples R China

Hardware enclaves assist in constructing a trusted execution environment (TEE) to store private code and data and thus become an appealing solution to enhance applications' security. Nevertheless, state-of-the-art enclave implementations like Intel Software Guard Extensions (SGX) have severe performance issues and hinder the deployment of more complicated applications, especially those written in high-level languages like java. To reduce the performance overhead, prior work has partitioned applications or rebuilt lightweight language runtimes, but they either require manual labor from developers or fail to provide full-fledged support for existing applications. This work instead provides SAJ, a runtime built upon a full-fledged java virtual machine (JVM) and thus requires no modifications to applications. SAJ first analyzes the performance of vanilla JVMs running in enclaves and finds that the memory management overhead and boot phase are culprits for performance slowdown. For memory management, SAJ introduces SGX-aware heap layout and garbage collector, which reduces both GC and application execution time. As for the boot phase, SAJ introduces an address-conscious launching mechanism to improve the boot performance. The evaluation under representative java applications shows that SAJ can reduce the overall GC pause time, application time, and boot time by 2.93x, 2.58x, and 2.73x on average, respectively.

关键词： Trusted execution environment SGX java virtual machine memory management

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Optimizing Aspectual Execution Mechanisms for Embedded Applications

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ELECTRONIC NOTES IN THEORETICAL COMPUTER SCIENCE 2009年第2期238卷 35-45页

作者： Hundt, Christine Glesner, Sabine Tech Univ Berlin Inst Software Technol & Theoret Comp Sci D-10587 Berlin Germany

Applications for small embedded mobile devices are becoming larger and more complex resulting in the need for advanced modularization mechanisms. Aspect-oriented modularization is a promising approach to solve this problem, but the overhead of the existing programming languages restricts their practicability for small devices with limited resources. In this paper, we identify opportunities to optimize the aspectual execution mechanism at different levels within the virtual machine. First experiments show that these optimizations improve the execution time considerably, thus proving that with adequate optimizations, we enable the use of advanced aspect-oriented modularization techniques for small device java applications.

关键词： aspect-orientation embedded systems mobile devices java virtual machine optimization

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