24,459 research outputs found
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
GROMACS is a widely used package for biomolecular simulation, and over the
last two decades it has evolved from small-scale efficiency to advanced
heterogeneous acceleration and multi-level parallelism targeting some of the
largest supercomputers in the world. Here, we describe some of the ways we have
been able to realize this through the use of parallelization on all levels,
combined with a constant focus on absolute performance. Release 4.6 of GROMACS
uses SIMD acceleration on a wide range of architectures, GPU offloading
acceleration, and both OpenMP and MPI parallelism within and between nodes,
respectively. The recent work on acceleration made it necessary to revisit the
fundamental algorithms of molecular simulation, including the concept of
neighborsearching, and we discuss the present and future challenges we see for
exascale simulation - in particular a very fine-grained task parallelism. We
also discuss the software management, code peer review and continuous
integration testing required for a project of this complexity.Comment: EASC 2014 conference proceedin
Monitoring Partially Synchronous Distributed Systems using SMT Solvers
In this paper, we discuss the feasibility of monitoring partially synchronous
distributed systems to detect latent bugs, i.e., errors caused by concurrency
and race conditions among concurrent processes. We present a monitoring
framework where we model both system constraints and latent bugs as
Satisfiability Modulo Theories (SMT) formulas, and we detect the presence of
latent bugs using an SMT solver. We demonstrate the feasibility of our
framework using both synthetic applications where latent bugs occur at any time
with random probability and an application involving exclusive access to a
shared resource with a subtle timing bug. We illustrate how the time required
for verification is affected by parameters such as communication frequency,
latency, and clock skew. Our results show that our framework can be used for
real-life applications, and because our framework uses SMT solvers, the range
of appropriate applications will increase as these solvers become more
efficient over time.Comment: Technical Report corresponding to the paper accepted at Runtime
Verification (RV) 201
Run Time Approximation of Non-blocking Service Rates for Streaming Systems
Stream processing is a compute paradigm that promises safe and efficient
parallelism. Modern big-data problems are often well suited for stream
processing's throughput-oriented nature. Realization of efficient stream
processing requires monitoring and optimization of multiple communications
links. Most techniques to optimize these links use queueing network models or
network flow models, which require some idea of the actual execution rate of
each independent compute kernel within the system. What we want to know is how
fast can each kernel process data independent of other communicating kernels.
This is known as the "service rate" of the kernel within the queueing
literature. Current approaches to divining service rates are static. Modern
workloads, however, are often dynamic. Shared cloud systems also present
applications with highly dynamic execution environments (multiple users,
hardware migration, etc.). It is therefore desirable to continuously re-tune an
application during run time (online) in response to changing conditions. Our
approach enables online service rate monitoring under most conditions,
obviating the need for reliance on steady state predictions for what are
probably non-steady state phenomena. First, some of the difficulties associated
with online service rate determination are examined. Second, the algorithm to
approximate the online non-blocking service rate is described. Lastly, the
algorithm is implemented within the open source RaftLib framework for
validation using a simple microbenchmark as well as two full streaming
applications.Comment: technical repor
Characterisation of an automated Dual Piston Pressure Swing Adsorption (DP-PSA) system
AbstractThe drive to fast Pressure Swing Adsorption (PSA) processes leads to the challenge of designing and analysing experiments that allow the testing of adsorbents under fast cycle conditions. Here we present the Dual Piston-Pressure Swing Adsorption (DP-PSA) system and the accompanying mathematical model designed for this purpose. The comparisons of experimental and simulation results show that for slow cycles often an isothermal model is sufficient. However, for fast cycles the temperature profile over the cycle has to be taken into account to describe accurately the experimental curves; this is essential for the estimation of the parameters of the adsorbent material under fast cycle conditions
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