45,294 research outputs found
High-throughput Binding Affinity Calculations at Extreme Scales
Resistance to chemotherapy and molecularly targeted therapies is a major
factor in limiting the effectiveness of cancer treatment. In many cases,
resistance can be linked to genetic changes in target proteins, either
pre-existing or evolutionarily selected during treatment. Key to overcoming
this challenge is an understanding of the molecular determinants of drug
binding. Using multi-stage pipelines of molecular simulations we can gain
insights into the binding free energy and the residence time of a ligand, which
can inform both stratified and personal treatment regimes and drug development.
To support the scalable, adaptive and automated calculation of the binding free
energy on high-performance computing resources, we introduce the High-
throughput Binding Affinity Calculator (HTBAC). HTBAC uses a building block
approach in order to attain both workflow flexibility and performance. We
demonstrate close to perfect weak scaling to hundreds of concurrent multi-stage
binding affinity calculation pipelines. This permits a rapid time-to-solution
that is essentially invariant of the calculation protocol, size of candidate
ligands and number of ensemble simulations. As such, HTBAC advances the state
of the art of binding affinity calculations and protocols
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
Synapse: Synthetic Application Profiler and Emulator
We introduce Synapse motivated by the needs to estimate and emulate workload
execution characteristics on high-performance and distributed heterogeneous
resources. Synapse has a platform independent application profiler, and the
ability to emulate profiled workloads on a variety of heterogeneous resources.
Synapse is used as a proxy application (or "representative application") for
real workloads, with the added advantage that it can be tuned at arbitrary
levels of granularity in ways that are simply not possible using real
applications. Experiments show that automated profiling using Synapse
represents application characteristics with high fidelity. Emulation using
Synapse can reproduce the application behavior in the original runtime
environment, as well as reproducing properties when used in a different
run-time environments
A General Spatio-Temporal Clustering-Based Non-local Formulation for Multiscale Modeling of Compartmentalized Reservoirs
Representing the reservoir as a network of discrete compartments with
neighbor and non-neighbor connections is a fast, yet accurate method for
analyzing oil and gas reservoirs. Automatic and rapid detection of coarse-scale
compartments with distinct static and dynamic properties is an integral part of
such high-level reservoir analysis. In this work, we present a hybrid framework
specific to reservoir analysis for an automatic detection of clusters in space
using spatial and temporal field data, coupled with a physics-based multiscale
modeling approach. In this work a novel hybrid approach is presented in which
we couple a physics-based non-local modeling framework with data-driven
clustering techniques to provide a fast and accurate multiscale modeling of
compartmentalized reservoirs. This research also adds to the literature by
presenting a comprehensive work on spatio-temporal clustering for reservoir
studies applications that well considers the clustering complexities, the
intrinsic sparse and noisy nature of the data, and the interpretability of the
outcome.
Keywords: Artificial Intelligence; Machine Learning; Spatio-Temporal
Clustering; Physics-Based Data-Driven Formulation; Multiscale Modelin
A Bayesian Consistent Dual Ensemble Kalman Filter for State-Parameter Estimation in Subsurface Hydrology
Ensemble Kalman filtering (EnKF) is an efficient approach to addressing
uncertainties in subsurface groundwater models. The EnKF sequentially
integrates field data into simulation models to obtain a better
characterization of the model's state and parameters. These are generally
estimated following joint and dual filtering strategies, in which, at each
assimilation cycle, a forecast step by the model is followed by an update step
with incoming observations. The Joint-EnKF directly updates the augmented
state-parameter vector while the Dual-EnKF employs two separate filters, first
estimating the parameters and then estimating the state based on the updated
parameters. In this paper, we reverse the order of the forecast-update steps
following the one-step-ahead (OSA) smoothing formulation of the Bayesian
filtering problem, based on which we propose a new dual EnKF scheme, the
Dual-EnKF. Compared to the Dual-EnKF, this introduces a new update
step to the state in a fully consistent Bayesian framework, which is shown to
enhance the performance of the dual filtering approach without any significant
increase in the computational cost. Numerical experiments are conducted with a
two-dimensional synthetic groundwater aquifer model to assess the performance
and robustness of the proposed Dual-EnKF, and to evaluate its
results against those of the Joint- and Dual-EnKFs. The proposed scheme is able
to successfully recover both the hydraulic head and the aquifer conductivity,
further providing reliable estimates of their uncertainties. Compared with the
standard Joint- and Dual-EnKFs, the proposed scheme is found more robust to
different assimilation settings, such as the spatial and temporal distribution
of the observations, and the level of noise in the data. Based on our
experimental setups, it yields up to 25% more accurate state and parameters
estimates
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