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PyGDH: Python Grid Discretization Helper [article]

Kenneth Higa, Vincent S. Battaglia, Venkat Srinivasan
2021 Zenodo  
Mathematical models expressed in the form of discretized equations play an important role in many scientific disciplines.  ...  Typically, one starts by making a copy of body.py in our example, and naming the new file with a pyx extension ( body.pyx), the extension for a Cython source code file.  ...  Release 0.4.3 Object members and the dot operator Now that an object of the ODE class has been created, one can interact with its members by using the "dot" operator.  ... 
doi:10.5281/zenodo.4556302 fatcat:3wgd6ffsorhgliyvd7jy2mgfcu

HeapMon: A helper-thread approach to programmable, automatic, and low-overhead memory bug detection

R. Shetty, M. Kharbutli, Y. Solihin, M. Prvulovic
2006 IBM Journal of Research and Development  
First, it decouples application execution from bug monitoring, which executes as a helper thread on a separate core in a chip multiprocessor system.  ...  Its overhead is also modest: 3.1% of the cache size and a 32-KB victim cache for on-chip filter bits and 6.2% of the allocated heap memory size for state bits, which are maintained by the helper thread  ...  In the debugging mode, after completing the check for an event, the helper thread uses the ISA extensions to insert a response into the reply queue.  ... 
doi:10.1147/rd.502.0261 fatcat:5d4iluou6ncyzmbfe7blhx7loy

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

André M. Comeau, Gavin M. Douglas, Morgan G. I. Langille, Jonathan Eisen
2017 mSystems  
Our sequencing protocols, bioinformatic tutorials, and bundled software are freely available through Microbiome Helper.  ...  As the microbiome research field continues to evolve, Microbiome Helper will be updated with new protocols, scripts, and training materials.  ...  The screenshot illustrates the Ubuntu-based Microbiome Helper virtual image running within a Windows 7 operating system with both a terminal window for command-line access and the graphically based STAMP  ... 
doi:10.1128/msystems.00127-16 pmid:28066818 pmcid:PMC5209531 fatcat:j5s3wcypjrgsjhivunx4mqukdq

Good things come in threes

Pouria Derakhshanfar, Xavier Devroey, Andy Zaidman, Arie van Deursen, Annibale Panichella
2020 Proceedings of the 35th IEEE/ACM International Conference on Automated Software Engineering  
Writing a test case reproducing a reported software crash is a common practice to identify the root cause of an anomaly in the software under test.  ...  In particular, we introduce two new Helper-Objectives for crash reproduction, namely test length (to minimize) and method sequence diversity (to maximize), in addition to Crash Distance.  ...  [22] , adding helper-objectives to an existing single objective can help search algorithms escape from local optima.  ... 
doi:10.1145/3324884.3416643 fatcat:n36at4zj6ncwbja5gqvp5ttuim

Flexible Abstraction Layers for VR Application Development

Gerwin de Haan, Michal Koutek, Frits H. Post
2007 2007 IEEE Virtual Reality Conference  
The potential of our integration approach is demonstrated by rapid prototyping features, the flexible extension of core functionality and the integration of an external toolkit.  ...  The integration of the domainspecific functionality in an interactive Virtual Environment requires close collaboration between domain expert and VR developer, as well as the integration of domain-specific  ...  We thank SARA for providing PyPer, and Jorik Blaas for the interactive notebook prototype.  ... 
doi:10.1109/vr.2007.352490 dblp:conf/vr/HaanKP07 fatcat:m7azukkgkveoleyhpbk2ttmu34

Foundational MDA Patterns for Service-Oriented Computing

Colin Atkinson, Philipp Bostan, Dirk Draheim
2015 Journal of Object Technology  
Yet remote debugging solutions can prove awkward to use due to re-deployments.  ...  Given these properties we propose and validate Mercury, a remote debugging model based on reflection.  ...  The method in Script 9 is an extension of our application for the system class String, which calculates the suffix of a given filename.  ... 
doi:10.5381/jot.2015.14.1.a1 fatcat:yxlusadftfedbo3tvsjdphae6m

UCLA Parallel PIC Framework

Viktor K. Decyk, Charles D. Norton
2004 Computer Physics Communications  
It is designed with "defensive" programming in mind, meaning that it contains many error checks and debugging helps. Above all, it is designed to hide the complexity of parallel processing.  ...  Frameworks Frameworks are an emerging technology for code reuse in development of complex software systems [1, 2] .  ...  They are generally based on an object-oriented design, with interacting classes that can be specialized to produce custom applications.  ... 
doi:10.1016/j.cpc.2004.06.011 fatcat:vublqgjbcfbtnknt7vwxy3xdnm

FDR Explorer

Leo Freitas, Jim Woodcock
2007 Electronical Notes in Theoretical Computer Science  
one to interact more closely with, and have fine grained control over, FDR's behaviour and data structures.  ...  In this paper we describe the internal structures of FDR, the refinement model checker for Hoare's Communicating Sequential Processes (CSP), as well as an Application Programming Interface (API) allowing  ...  The purpose of this extension to our tool is to prove the concept that one can visualise CSP LTSs and debugging information generated by FDR, hence improving the user friendliness for CSP related tools  ... 
doi:10.1016/j.entcs.2006.08.042 fatcat:prnpthq7sfan3g5lgridpwl52a

IDD – A Platform Enabling Differential Debugging

Martin Vassilev, Vassil Vassilev, Alexander Penev
2020 Cybernetics and Information Technologies  
The interactive debugging session runs side by side both executables and allows to examine and to compare various internal states.  ...  The differential debugging technique performs analysis of the regressed system and identifying the cause of the unexpected behavior by comparing to a previous version of the same system.  ...  The interactive debuggers are most useful when the software systems are compiled with debug symbols.  ... 
doi:10.2478/cait-2020-0004 fatcat:amew4pvaajc4be256mbmesb3r4

FDR Explorer

Leo Freitas, Jim Woodcock
2008 Formal Aspects of Computing  
one to interact more closely with, and have fine grained control over, FDR's behaviour and data structures.  ...  In this paper we describe the internal structures of FDR, the refinement model checker for Hoare's Communicating Sequential Processes (CSP), as well as an Application Programming Interface (API) allowing  ...  The purpose of this extension to our tool is to prove the concept that one can visualise CSP LTSs and debugging information generated by FDR, hence improving the user friendliness for CSP related tools  ... 
doi:10.1007/s00165-008-0074-7 fatcat:5y7zqdpmevg5rnsaxnh2eu52yq

A Framework for Visual Dynamic Analysis of Ray Tracing Algorithms

Hristo Lesev, Alexander Penev
2014 Cybernetics and Information Technologies  
A novel approach is presented for recording high volume data about ray tracing rendering systems' runtime state and its subsequent dynamic analysis and interactive visualization in the algorithm computational  ...  Our framework extracts light paths traced by the system and leverages on a powerful filtering subsystem, helping interactive visualization and exploration of the desired subset of recorded data.  ...  This involves an enormous amount of data flowing through the system and makes conventional debugging not a preferred option.  ... 
doi:10.2478/cait-2014-0018 fatcat:xymzqqlchnc37apv3zsidstg44

Experience Integrating a New Compiler and a New Garbage Collector Into Rotor

Todd Anderson, Marsha Eng, Neal Glew, Brian Lewis, Vijay Menon, James Stichnoth
2004 Journal of Object Technology  
We had to change our JIT compiler to support Rotor's calling conventions, helper functions, and exception model.  ...  It is particularly attractive for research because of its complete implementation and extensive libraries, and because its modular design allows different implementations of certain components such as  ...  Other helpers assist in debugging, while still more support additional functionality such as remoting.  ... 
doi:10.5381/jot.2004.3.9.a3 fatcat:bxu63zxh5bgnjdcdijug6kq5fy

Debugging programs that use atomic blocks and transactional memory

Ferad Zyulkyarov, Tim Harris, Osman S. Unsal, Adrían Cristal, Mateo Valero
2010 SIGPLAN notices  
We describe the design and implementation of an extension to the WinDbg debugger, enabling support for C# programs using atomic blocks and TM.  ...  programmer manipulate synchronization from within the debuggere.g., enlarging the scope of an atomic block to try to identify a bug.  ...  Our design consists of two components: a debugger extension library (TmDbgExt) and an STM-library debug helper (TmTargetDbg). Figure 1 shows the structure of the system.  ... 
doi:10.1145/1837853.1693463 fatcat:h7d5ecftxrhbbehbfygtcdshwy

Debugging programs that use atomic blocks and transactional memory

Ferad Zyulkyarov, Tim Harris, Osman S. Unsal, Adrían Cristal, Mateo Valero
2010 Proceedings of the 15th ACM SIGPLAN symposium on Principles and practice of parallel programming - PPoPP '10  
We describe the design and implementation of an extension to the WinDbg debugger, enabling support for C# programs using atomic blocks and TM.  ...  programmer manipulate synchronization from within the debuggere.g., enlarging the scope of an atomic block to try to identify a bug.  ...  Our design consists of two components: a debugger extension library (TmDbgExt) and an STM-library debug helper (TmTargetDbg). Figure 1 shows the structure of the system.  ... 
doi:10.1145/1693453.1693463 dblp:conf/ppopp/ZyulkyarovHUCV10 fatcat:cen4utcuk5bj5liapheukui6em

Towards Providing On-Demand Expert Support for Software Developers

Yan Chen, Steve Oney, Walter S. Lasecki
2016 Proceedings of the 2016 CHI Conference on Human Factors in Computing Systems - CHI '16  
The second study explores the interactions between developers and remote "experts" in supporting roles.  ...  Software development is an expert task that requires complex reasoning and the ability to recall language or API-specific details.  ...  P3: "How to make an AJAX get call from JavaScript" Debugging Requests Two participants also requested help debugging their code.  ... 
doi:10.1145/2858036.2858512 dblp:conf/chi/ChenOL16 fatcat:wqtbqs7645h2jbhsispq6fulw4
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