Multi-simulation coordinator

Last updated

MUSIC (Multi-Simulation Coordinator) is software developed and released by the INCF and Royal Institute of Technology (KTH) School of Computer Science and Communication in Stockholm, Sweden. [1] MUSIC is designed for interconnecting large scale neuronal network simulators, either with each other or with other tools. [2] It allows spike events and continuous time series to be communicated between such applications in a cluster computer. The typical usage cases are connecting models developed for different simulators and connecting a parallel simulator to a post-processing tool.

MUSIC provides a standardized software interface (API) on top of the message-passing interface (MPI) for communication among parallel applications for large-scale computational neuroscience simulations. It enables the transfer of massive amounts of event information and continuous values from one parallel application to another, including those using different data allocation strategies. [3] In the design of the standard interface, care was taken to allow easy adaptation of existing simulators and to permit third-party development and community-sharing of reusable and interoperable software tools for parallel processing. Three simulators currently have MUSIC interfaces: Moose, NEURON and NEST. [4]

The MUSIC software library and its documentation are publicly available through the INCF Software Center. [5]

Related Research Articles

A simulation is an approximate imitation of the operation of a process or system; that represents its operation over time.

System on a chip type of integrated circuit

A system on chip is an integrated circuit that integrates all or most components of a computer or other electronic system. These components almost always include a central processing unit (CPU), memory, input/output ports and secondary storage – all on a single substrate or microchip, the size of a coin. It must contain digital, analog, mixed-signal, and often radio frequency signal processing functions, otherwise it will only be considered as an "Application Processor". As they are integrated on a single substrate, SoCs consume much less power and take up much less area than multi-chip designs with equivalent functionality. Because of this, SoCs are very common in the mobile computing and edge computing markets. Systems-on-chip are typically fabricated using metal–oxide–semiconductor (MOS) technology, and are commonly used in embedded systems and the Internet of Things. Higher-performance SoCs are often paired with dedicated and physically separate memory and secondary storage chips, that may be layered on top of the SoC in what's known as a Package on package (PoP) configuration.

Application software computer software designed to perform a group of coordinated functions, tasks, or activities for the benefit of the user

Application software is a program or group of programs designed for end users. Examples of an application include a word processor, a spreadsheet, an accounting application, a web browser, an email client, a media player, a file viewer, an aeronautical flight simulator, a console game or a photo editor. The collective noun application software refers to all applications collectively. This contrasts with system software, which is mainly involved with running the computer.

Neuroinformatics is a research field concerned with the organization of neuroscience data by the application of computational models and analytical tools. These areas of research are important for the integration and analysis of increasingly large-volume, high-dimensional, and fine-grain experimental data. Neuroinformaticians provide computational tools, mathematical models, and create interoperable databases for clinicians and research scientists. Neuroscience is a heterogeneous field, consisting of many and various sub-disciplines. In order for our understanding of the brain to continue to deepen, it is necessary that these sub-disciplines are able to share data and findings in a meaningful way; Neuroinformaticians facilitate this.

International Neuroinformatics Coordinating Facility

The International Neuroinformatics Coordinating Facility is an international non-profit organization with the mission to develop, evaluate, and endorse standards and best practices that embrace the principles of Open, FAIR, and Citable neuroscience. INCF also provides training on how standards and best practices facilitate reproducibility and enables the publishing of the entirety of research output, including data and code. INCF was established in 2005 by recommendations of the Global Science Forum working group of the OECD. The INCF is hosted by the Karolinska Institutet in Stockholm, Sweden.. As on October 2019, the INCF has active nodes in 18 countries. The Executive Director is Linda Lanyon, and the Governing Board Chair is Maryann Martone

System integration is defined in engineering as the process of bringing together the component sub-systems into one system and ensuring that the subsystems function together as a system, and in information technology as the process of linking together different computing systems and software applications physically or functionally, to act as a coordinated whole.

Simulation software is based on the process of modeling a real phenomenon with a set of mathematical formulas. It is, essentially, a program that allows the user to observe an operation through simulation without actually performing that operation. Simulation software is used widely to design equipment so that the final product will be as close to design specs as possible without expensive in process modification. Simulation software with real-time response is often used in gaming, but it also has important industrial applications. When the penalty for improper operation is costly, such as airplane pilots, nuclear power plant operators, or chemical plant operators, a mock up of the actual control panel is connected to a real-time simulation of the physical response, giving valuable training experience without fear of a disastrous outcome.

GENESIS is a simulation environment for constructing realistic models of neurobiological systems at many levels of scale including: sub-cellular processes, individual neurons, networks of neurons, and neuronal systems. These simulations are “computer-based implementations of models whose primary objective is to capture what is known of the anatomical structure and physiological characteristics of the neural system of interest”. GENESIS is intended to quantify the physical framework of the nervous system in a way that allows for easy understanding of the physical structure of the nerves in question. “At present only GENESIS allows parallelized modeling of single neurons and networks on multiple-instruction-multiple-data parallel computers.” Development of GENESIS software spread from its home at Caltech to labs at the University of Texas at San Antonio, the University of Antwerp, the National Centre for Biological Sciences in Bangalore, the University of Colorado, the Pittsburgh Supercomputing Center, the San Diego Supercomputer Center, and Emory University.

Robotics simulator simulator used to create application for a physical robot without depending on the actual machine, thus saving cost and time. In some case, these applications can be transferred onto the physical robot without modifications

A robotics simulator is a simulator used to create application for a physical robot without depending on the actual machine, thus saving cost and time. In some case, these applications can be transferred onto the physical robot without modifications.

The Multicore Association was founded in 2005. Multicore Association is a member-funded, non-profit, industry consortium focused on the creation of open standard APIs, specifications, and guidelines that allow system developers and programmers to more readily adopt multicore technology into their applications.

Live, Virtual, & Constructive (LVC) Simulation is a broadly used taxonomy for classifying Models and Simulation (M&S). However, categorizing a simulation as a live, virtual, or constructive environment is problematic since there is no clear division between these categories. The degree of human participation in a simulation is infinitely variable, as is the degree of equipment realism. The categorization of simulations also lacks a category for simulated people working real equipment.

NeuroML is an XML based model description language that aims to provide a common data format for defining and exchanging models in computational neuroscience. The focus of NeuroML is on models which are based on the biophysical and anatomical properties of real neurons.

The Functional Mock-up Interface defines a standardized interface to be used in computer simulations to develop complex cyber-physical systems.

Message passing in computer clusters

Message passing is an inherent element of all computer clusters. All computer clusters, ranging from homemade Beowulfs to some of the fastest supercomputers in the world, rely on message passing to coordinate the activities of the many nodes they encompass. Message passing in computer clusters built with commodity servers and switches is used by virtually every internet service.

NEST (software) simulation software for spiking neural network models

NEST is a simulation software for spiking neural network models, including large-scale neuronal networks. NEST was initially developed by Markus Diesmann and Marc-Oliver Gewaltig and is now developed and maintained by the NEST Initiative.

In co-simulation the different subsystems which form a coupled problem are modeled and simulated in a distributed manner. Hence, the modeling is done on the subsystem level without having the coupled problem in mind. Furthermore, the coupled simulation is carried out by running the subsystems in a black-box manner. During the simulation the subsystems will exchange data. Co-simulation can be considered as the joint simulation of the already well-established tools and semantics; when they are simulated with their suitable solvers. Co-simulation proves its advantage in validation of multi-domain and cyber physical system by offering a flexible solution which allows consideration of multiple domains with different time steps, at the same time. As the calculation load is shared among simulators, co-simulation also enables the possibility of large scale system assessment.

The Bernstein Network Computational Neuroscience is a research network in the field of computational neuroscience; this field brings together experimental approaches in neurobiology with theoretical models and computer simulations. It unites different scientific disciplines, such as physics, biology, mathematics, medical science, psychology, computer science, engineering and philosophy in the endeavor to understand how the brain functions. The close combination of neurobiological experiments with theoretical models and computer simulations allows scientists of the Bernstein Network to pursue innovative approaches with regard to one of the most complex structures nature has created in the course of evolution: the natural brain.

The CAPE-OPEN Interface Standard consists of a series of specifications to expand the range of application of process simulation technologies. The CAPE-OPEN specifications comprise a set of software interfaces that allow plug and play inter-operability between a given Process Modelling Environment and a third-party Process Modelling Component.

Viktor K. Jirsa is a German physicist and neuroscientist, director of research at the Centre national de la recherche scientifique (CNRS), director of the Institut de Neuroscience des Systèmes and co-director of the Fédération Hospitalo-Universitaire (FHU) EPINEXT "Epilepsy and Disorders of Neuronal Excitability" in Marseille, France. He is workpackage leader in the Epinov project funded in the context of the RHU3 call and coordinated by Prof. Fabrice Bartolomei.

References

  1. msandstr. "The MUlti-SImulator Coordinator (MUSIC) — INCF Neuroinformatics Portal". www.incf.org. Archived from the original on 2015-11-21. Retrieved 2015-11-20.
  2. "MUSIC - Multi-Simulation Coordinator Request for Comments" (PDF).
  3. Djurfeldt, Mikael (2010-03-02). "Run-Time Interoperability Between Neuronal Network Simulators Based on the MUSIC Framework". Neuroinformatics. 8 (1): 43–60. doi:10.1007/s12021-010-9064-z. PMC   2846392 . PMID   20195795.
  4. ylva. "MUSIC — INCF Neuroinformatics Portal". www.incf.org. Archived from the original on 2015-11-21. Retrieved 2015-11-20.
  5. "MUSIC — INCF Software Center". software.incf.org. Retrieved 2015-11-20.