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Toward Efficient Interactions between Python and Native Libraries [article]

Jialiang Tan, Yu Chen, Zhenming Liu, Bin Ren, Shuaiwen Leon Song, Xipeng Shen, Xu Liu
2021 pre-print
Interaction between Python code and native libraries introduces performance losses because of the abstraction lying on the boundary of Python and native libraries.  ...  Many modern software packages utilize Python for high-level algorithm design and depend on native libraries written in C/C++/Fortran for efficient computation kernels.  ...  This work is supported in part by NSF grants CNS-2050007, CRII-1755769, OAC-1835821, IIS-2008557, CCF-1703487, CCF-2028850 and CCF-2047516, a Department of Energy (DOE) grant DE-SC0013700.  ... 
doi:10.1145/3468264.3468541 arXiv:2107.00064v1 fatcat:wasn3qtbrvdtnmf77dng3utfgm

PTools: an opensource molecular docking library

Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, Martin Zacharias
2009 BMC Structural Biology  
Results: We present an object-oriented Python/C++ library to help the development of new docking methods.  ...  The library is already in use for protein-protein and protein-DNA docking with the ATTRACT program and for simulation analysis.  ...  Finally, we acknowledge Marc Guéroult for testing the library and Charles Robert for his useful comments on the manuscript.  ... 
doi:10.1186/1472-6807-9-27 pmid:19409097 pmcid:PMC2685806 fatcat:u4y3mba56vhwjfphag53ovig5u

Multilingual Interfaces for Parallel Coupling in Multiphysics and Multiscale Systems [chapter]

Everest T. Ong, J. Walter Larson, Boyana Norris, Robert L. Jacob, Michael Tobis, Michael Steder
2007 Lecture Notes in Computer Science  
We describe the method used for automatically generating the bindings using the Babel language interoperability tool, and illustrate with short examples how MCT can be used from the C++ and Python languages  ...  Another potential problem in these coupled systems is language interoperability between their various constituent codes.  ...  The Python MCT programming model differs from MCT's native Fortran as follows: module use is replaced with Python package import; declaration is replaced with invocation of a constructor; and library routines  ... 
doi:10.1007/978-3-540-72584-8_122 fatcat:tli4cmeu6vhhjn3eiolpqwwo7u

Native structure-based modeling and simulation of biomolecular systems per mouse click

Benjamin Lutz, Claude Sinner, Stefan Bozic, Ivan Kondov, Alexander Schug
2014 BMC Bioinformatics  
Results: Here, we establish an efficient infrastructure for native structure-based models to support the community and enable high-throughput simulations on remote computing resources via GridBeans and  ...  Native structure-based models, also called Gō-type models, are based on energy landscape theory and the principle of minimal frustration.  ...  These studies have found dominance of native interactions to non-native ones and good agreement between results from CG SBM simulations and more fine-grained models [31] .  ... 
doi:10.1186/1471-2105-15-292 pmid:25176255 pmcid:PMC4162935 fatcat:diorayfnhfcg3eennkdd62w5ny

Interlanguage parallel scripting for distributed-memory scientific computing

Justin M. Wozniak, Timothy G. Armstrong, Ketan Maheshwari, Daniel S. Katz, Michael Wilde, Ian T. Foster
2015 Proceedings of the 10th Workshop on Workflows in Support of Large-Scale Science - WORKS '15  
We present a new approach to these problems in which the Swift scripting system is used to integrate high-level scripts written in Python, R, and Tcl with native code developed in C, C++, and Fortran,  ...  Scripting languages such as Python and R have been widely adopted as tools for the development of scientific software because of the expressiveness of the languages and their available libraries.  ...  Any opinion, finding, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.  ... 
doi:10.1145/2822332.2822338 dblp:conf/sc/WozniakAMKWF15 fatcat:q4dpgsmusra4bibelpkhijrbd4

Toward Interlanguage Parallel Scripting for Distributed-Memory Scientific Computing

Justin M. Wozniak, Timothy G. Armstrong, Ketan C. Maheshwari, Daniel S. Katz, Michael Wilde, Ian T. Foster
2015 2015 IEEE International Conference on Cluster Computing  
We present here a new approach to these problems in which the Swift scripting system is used to integrate high-level scripts written in Python, R, and Tcl, with native code developed in C, C++, and Fortran  ...  Scripting languages such as Python and R have been widely adopted as tools for the productive development of scientific software because of the power and expressiveness of the languages and available libraries  ...  Any opinion, finding, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.  ... 
doi:10.1109/cluster.2015.74 dblp:conf/cluster/WozniakAMKWF15 fatcat:kg2qojdvubbqhf75lhfzs6m2ae

A Performance Evaluation of Erasure Coding Libraries for Cloud-Based Data Stores [chapter]

Dorian Burihabwa, Pascal Felber, Hugues Mercier, Valerio Schiavoni
2016 Lecture Notes in Computer Science  
Second, the usage of high-level languages such as Python, which allow for portable and dependable client-side front-ends, to interact with efficient C-based libraries does not cause noticeable overhead  ...  We call the libraries via a common access layer and software wrappers implemented in Python. Python provides an easy mean to bind to such libraries via its built-in support for native code.  ... 
doi:10.1007/978-3-319-39577-7_13 fatcat:djtshetkb5bl3g2l4c4vxqzkb4

The best of most worlds

Adam T. Sampson, Paul S. Andrews
2010 Proceedings of the 9th Workshop on Parallel/High-Performance Object-Oriented Scientific Computing - POOSC '10  
These simulations are often sophisticated pieces of software with numerous design trade-offs between performance and ease of development and use.  ...  The framework uses the concept of shared objects to communicate data between simulation components.  ...  Acknowledgments This work is part of the CoSMoS project, funded by EPSRC grants EP/E053505/1 and EP/E049419/1.  ... 
doi:10.1145/2039312.2039319 fatcat:qfx22wzgjfhgfe4bddh4rxg2k4

Interfacing the internet of a trillion things

Bradford Campbell, Pat Pannuto, Prabal Dutta
2015 Proceedings of the Second International Workshop on the Swarm at the Edge of the Cloud - SWEC '15  
We realize our system with three environments that can execute accessors, Python, Java, and Node.js, a range of accessors for both IoT and legacy devices, and a browser-based application for interacting  ...  support is limited and inconsistent.  ...  The current performance of the Python implementation is largely an implementation detail, and already new libraries such as PyV8 [12] are emerging to run JavaScript from Python with much higher efficiency  ... 
doi:10.1145/2756755.2756762 dblp:conf/cpsweek/CampbellPD15 fatcat:ktf5udka3jhcxpxhr2u73hpy3q

PyXNAT: XNAT in Python

Yannick Schwartz, Alexis Barbot, Benjamin Thyreau, Vincent Frouin, Gaël Varoquaux, Aditya Siram, Daniel S. Marcus, Jean-Baptiste Poline
2012 Frontiers in Neuroinformatics  
We introduce here PyXNAT, a Python module that interacts with The Extensible Neuroimaging Archive Toolkit (XNAT) through native Python calls across multiple operating systems.  ...  Finally PyXNAT aims to be efficient and easy to use, both as a backend library to build XNAT clients and as an alternative frontend from the command line.  ...  We also thank the NIPY community for their tools and advice in general, and all the PyXNAT users for their feedback and patience.  ... 
doi:10.3389/fninf.2012.00012 pmid:22654752 pmcid:PMC3354345 fatcat:fuljhisqqraevf4x6lmda7i7au

mzResults: An Interactive Viewer for Interrogation and Distribution of Proteomics Results

James T. Webber, Manor Askenazi, Jarrod A. Marto
2011 Molecular & Cellular Proteomics  
Based upon our recently described API 1 -based framework for mass spectrometry data analysis (3, 4), we created an interactive viewer (mzResults) that is built on established database standards and enables  ...  The growing use of mass spectrometry in the context of biomedical research has been accompanied by an increased demand for distribution of results in a format that facilitates rapid and efficient validation  ...  Acknowledgments-We thank Eric Smith for preparation of figures, and members of the Marto lab for helpful discussions.  ... 
doi:10.1074/mcp.m110.003970 pmid:21266631 pmcid:PMC3098584 fatcat:7g422ax5orejzhx6lcmnryf6j4

Virtual Interactive Hand Gestures Recognition System in Real Time Environment

T. B. Patil, Aakash Jain, Supriya C. Sawant, Debnath Bhattacharyya, Hye-Jin Kim
2016 International Journal of Database Theory and Application  
Gestures are used for directing to an individual, to get his devotion and convey statistics about temporal and spatial physiognomies.  ...  The system takes inputs several hand gestures then processes its meaning and verifies it with the stored gestures in database and results the corresponding output on the screen.  ...  Computational Efficiency Generally, Vision based interaction often needs real-time systems.  ... 
doi:10.14257/ijdta.2016.9.7.05 fatcat:xjavn4j7yfhbdan2ypjwtpzuvu

A Survey on Spatio-temporal Data Analytics Systems [article]

Md Mahbub Alam and Luis Torgo and Albert Bifet
2021 arXiv   pre-print
, and (3) programming languages and software tools for processing spatio-temporal data.  ...  This survey also portrays the importance and future of spatial and spatio-temporal data analytics.  ...  On the contrary, DASK [53] is a Python library for parallel and distributed computing that scales Python natively.  ... 
arXiv:2103.09883v1 fatcat:ndpqz67bvnghpng36o3liqlr2q

Cloud-Native Repositories for Big Scientific Data

Ryan Abernathey, Tom Augspurger, Anderson Banihirwe, Charles Blackmon-Luca, Tim Crone, Chelle Gentemann, Joe Hamman, Naomi Henderson, Chiara Lepore, Theo Mccaie, Niall Robinson, Rich Signell
2021 Computing in science & engineering (Print)  
This way of working suffers from limitations as scientific datasets grow toward the petabyte scale.  ...  These objectives motivate a set of best practices for cloud-native data repositories: analysis-ready data, cloudoptimized (ARCO) formats, and loose coupling with data-proximate computing.  ...  Users interact with the Data Catalog using the Intake library.  ... 
doi:10.1109/mcse.2021.3059437 fatcat:gbyixgevmzbgfathdbcx4vsvvq

somoclu: An Efficient Parallel Library for Self-Organizing Maps

Peter Wittek, Shi Chao Gao, Ik Soo Lim, Li Zhao
2017 Journal of Statistical Software  
Python, R and MATLAB interfaces facilitate interactive use. Apart from fast execution, memory use is highly optimized, enabling training large emergent maps even on a single computer.  ...  It builds on OpenMP for multicore execution, and on MPI for distributing the workload across the nodes in a cluster.  ...  Acknowledgement The first author was supported by the European Commission Seventh Framework Programme under Grant Agreement Number FP7-601138 PERICLES and by the AWS in Education Machine Learning Grant  ... 
doi:10.18637/jss.v078.i09 fatcat:tawf5tfgzffl5ezvbd4yeyy5si
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