64,145 research outputs found
MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME
Computational experiments using spatial stochastic simulations have led to
important new biological insights, but they require specialized tools, a
complex software stack, as well as large and scalable compute and data analysis
resources due to the large computational cost associated with Monte Carlo
computational workflows. The complexity of setting up and managing a
large-scale distributed computation environment to support productive and
reproducible modeling can be prohibitive for practitioners in systems biology.
This results in a barrier to the adoption of spatial stochastic simulation
tools, effectively limiting the type of biological questions addressed by
quantitative modeling. In this paper, we present PyURDME, a new, user-friendly
spatial modeling and simulation package, and MOLNs, a cloud computing appliance
for distributed simulation of stochastic reaction-diffusion models. MOLNs is
based on IPython and provides an interactive programming platform for
development of sharable and reproducible distributed parallel computational
experiments
Report from GI-Dagstuhl Seminar 16394: Software Performance Engineering in the DevOps World
This report documents the program and the outcomes of GI-Dagstuhl Seminar
16394 "Software Performance Engineering in the DevOps World".
The seminar addressed the problem of performance-aware DevOps. Both, DevOps
and performance engineering have been growing trends over the past one to two
years, in no small part due to the rise in importance of identifying
performance anomalies in the operations (Ops) of cloud and big data systems and
feeding these back to the development (Dev). However, so far, the research
community has treated software engineering, performance engineering, and cloud
computing mostly as individual research areas. We aimed to identify
cross-community collaboration, and to set the path for long-lasting
collaborations towards performance-aware DevOps.
The main goal of the seminar was to bring together young researchers (PhD
students in a later stage of their PhD, as well as PostDocs or Junior
Professors) in the areas of (i) software engineering, (ii) performance
engineering, and (iii) cloud computing and big data to present their current
research projects, to exchange experience and expertise, to discuss research
challenges, and to develop ideas for future collaborations
Parallel and Distributed Simulation from Many Cores to the Public Cloud (Extended Version)
In this tutorial paper, we will firstly review some basic simulation concepts
and then introduce the parallel and distributed simulation techniques in view
of some new challenges of today and tomorrow. More in particular, in the last
years there has been a wide diffusion of many cores architectures and we can
expect this trend to continue. On the other hand, the success of cloud
computing is strongly promoting the everything as a service paradigm. Is
parallel and distributed simulation ready for these new challenges? The current
approaches present many limitations in terms of usability and adaptivity: there
is a strong need for new evaluation metrics and for revising the currently
implemented mechanisms. In the last part of the paper, we propose a new
approach based on multi-agent systems for the simulation of complex systems. It
is possible to implement advanced techniques such as the migration of simulated
entities in order to build mechanisms that are both adaptive and very easy to
use. Adaptive mechanisms are able to significantly reduce the communication
cost in the parallel/distributed architectures, to implement load-balance
techniques and to cope with execution environments that are both variable and
dynamic. Finally, such mechanisms will be used to build simulations on top of
unreliable cloud services.Comment: Tutorial paper published in the Proceedings of the International
Conference on High Performance Computing and Simulation (HPCS 2011). Istanbul
(Turkey), IEEE, July 2011. ISBN 978-1-61284-382-
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