NL4Py: Agent-Based Modeling in Python with Parallelizable NetLogo Workspaces

NL4Py is a NetLogo controller software for Python, for the rapid, parallel execution of NetLogo models. NL4Py provides both headless (no graphical user interface) and GUI NetLogo workspace control through Python. Spurred on by the increasing availability of open-source computation and machine learning libraries on the Python package index, there is an increasing demand for such rapid, parallel execution of agent-based models through Python. NetLogo, being the language of choice for a majority of agent-based modeling driven research projects, requires an integration to Python for researchers looking to perform statistical analyses of agent-based model output using these libraries. Unfortunately, until the recent introduction of PyNetLogo, and now NL4Py, such a controller was unavailable. This article provides a detailed introduction into the usage of NL4Py and explains its client-server software architecture, highlighting architectural differences to PyNetLogo. A step-by-step demonstration of global sensitivity analysis and parameter calibration of the Wolf Sheep Predation model is then performed through NL4Py. Finally, NL4Py's performance is benchmarked against PyNetLogo and its combination with IPyParallel, and shown to provide significant savings in execution time over both configurations

Many-Task Computing and Blue Waters

This report discusses many-task computing (MTC) generically and in the context of the proposed Blue Waters systems, which is planned to be the largest NSF-funded supercomputer when it begins production use in 2012. The aim of this report is to inform the BW project about MTC, including understanding aspects of MTC applications that can be used to characterize the domain and understanding the implications of these aspects to middleware and policies. Many MTC applications do not neatly fit the stereotypes of high-performance computing (HPC) or high-throughput computing (HTC) applications. Like HTC applications, by definition MTC applications are structured as graphs of discrete tasks, with explicit input and output dependencies forming the graph edges. However, MTC applications have significant features that distinguish them from typical HTC applications. In particular, different engineering constraints for hardware and software must be met in order to support these applications. HTC applications have traditionally run on platforms such as grids and clusters, through either workflow systems or parallel programming systems. MTC applications, in contrast, will often demand a short time to solution, may be communication intensive or data intensive, and may comprise very short tasks. Therefore, hardware and software for MTC must be engineered to support the additional communication and I/O and must minimize task dispatch overheads. The hardware of large-scale HPC systems, with its high degree of parallelism and support for intensive communication, is well suited for MTC applications. However, HPC systems often lack a dynamic resource-provisioning feature, are not ideal for task communication via the file system, and have an I/O system that is not optimized for MTC-style applications. Hence, additional software support is likely to be required to gain full benefit from the HPC hardware

Analysis, Tracing, Characterization and Performance Modeling of Select ASCI Applications for BlueGene/L Using Parallel Discrete Event Simulation

Caltech's Jet Propulsion Laboratory (JPL) and Center for Advanced Computer Architecture (CACR) are conducting application and simulation analyses of Blue Gene/L[1] in order to establish a range of effectiveness of the architecture in performing important classes of computations and to determine the design sensitivity of the global interconnect network in support of real world ASCI application execution

IMP Science Gateway: from the Portal to the Hub of Virtual Experimental Labs in Materials Science

"Science gateway" (SG) ideology means a user-friendly intuitive interface between scientists (or scientific communities) and different software components + various distributed computing infrastructures (DCIs) (like grids, clouds, clusters), where researchers can focus on their scientific goals and less on peculiarities of software/DCI. "IMP Science Gateway Portal" (http://scigate.imp.kiev.ua) for complex workflow management and integration of distributed computing resources (like clusters, service grids, desktop grids, clouds) is presented. It is created on the basis of WS-PGRADE and gUSE technologies, where WS-PGRADE is designed for science workflow operation and gUSE - for smooth integration of available resources for parallel and distributed computing in various heterogeneous distributed computing infrastructures (DCI). The typical scientific workflows with possible scenarios of its preparation and usage are presented. Several typical use cases for these science applications (scientific workflows) are considered for molecular dynamics (MD) simulations of complex behavior of various nanostructures (nanoindentation of graphene layers, defect system relaxation in metal nanocrystals, thermal stability of boron nitride nanotubes, etc.). The user experience is analyzed in the context of its practical applications for MD simulations in materials science, physics and nanotechnologies with available heterogeneous DCIs. In conclusion, the "science gateway" approach - workflow manager (like WS-PGRADE) + DCI resources manager (like gUSE)- gives opportunity to use the SG portal (like "IMP Science Gateway Portal") in a very promising way, namely, as a hub of various virtual experimental labs (different software components + various requirements to resources) in the context of its practical MD applications in materials science, physics, chemistry, biology, and nanotechnologies.Comment: 6 pages, 5 figures, 3 tables; 6th International Workshop on Science Gateways, IWSG-2014 (Dublin, Ireland, 3-5 June, 2014). arXiv admin note: substantial text overlap with arXiv:1404.545