5,503 research outputs found
Harnessing the Power of Many: Extensible Toolkit for Scalable Ensemble Applications
Many scientific problems require multiple distinct computational tasks to be
executed in order to achieve a desired solution. We introduce the Ensemble
Toolkit (EnTK) to address the challenges of scale, diversity and reliability
they pose. We describe the design and implementation of EnTK, characterize its
performance and integrate it with two distinct exemplar use cases: seismic
inversion and adaptive analog ensembles. We perform nine experiments,
characterizing EnTK overheads, strong and weak scalability, and the performance
of two use case implementations, at scale and on production infrastructures. We
show how EnTK meets the following general requirements: (i) implementing
dedicated abstractions to support the description and execution of ensemble
applications; (ii) support for execution on heterogeneous computing
infrastructures; (iii) efficient scalability up to O(10^4) tasks; and (iv)
fault tolerance. We discuss novel computational capabilities that EnTK enables
and the scientific advantages arising thereof. We propose EnTK as an important
addition to the suite of tools in support of production scientific computing
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
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
Task Runtime Prediction in Scientific Workflows Using an Online Incremental Learning Approach
Many algorithms in workflow scheduling and resource provisioning rely on the
performance estimation of tasks to produce a scheduling plan. A profiler that
is capable of modeling the execution of tasks and predicting their runtime
accurately, therefore, becomes an essential part of any Workflow Management
System (WMS). With the emergence of multi-tenant Workflow as a Service (WaaS)
platforms that use clouds for deploying scientific workflows, task runtime
prediction becomes more challenging because it requires the processing of a
significant amount of data in a near real-time scenario while dealing with the
performance variability of cloud resources. Hence, relying on methods such as
profiling tasks' execution data using basic statistical description (e.g.,
mean, standard deviation) or batch offline regression techniques to estimate
the runtime may not be suitable for such environments. In this paper, we
propose an online incremental learning approach to predict the runtime of tasks
in scientific workflows in clouds. To improve the performance of the
predictions, we harness fine-grained resources monitoring data in the form of
time-series records of CPU utilization, memory usage, and I/O activities that
are reflecting the unique characteristics of a task's execution. We compare our
solution to a state-of-the-art approach that exploits the resources monitoring
data based on regression machine learning technique. From our experiments, the
proposed strategy improves the performance, in terms of the error, up to
29.89%, compared to the state-of-the-art solutions.Comment: Accepted for presentation at main conference track of 11th IEEE/ACM
International Conference on Utility and Cloud Computin
Heterogeneous hierarchical workflow composition
Workflow systems promise scientists an automated end-to-end path from hypothesis to discovery. However, expecting any single workflow system to deliver such a wide range of capabilities is impractical. A more practical solution is to compose the end-to-end workflow from more than one system. With this goal in mind, the integration of task-based and in situ workflows is explored, where the result is a hierarchical heterogeneous workflow composed of subworkflows, with different levels of the hierarchy using different programming, execution, and data models. Materials science use cases demonstrate the advantages of such heterogeneous hierarchical workflow composition.This work is a collaboration between Argonne National Laboratory and the Barcelona Supercomputing Center within the Joint Laboratory for Extreme-Scale Computing. This research is supported by the
U.S. Department of Energy, Office of Science, Office of Advanced Scientific Computing Research, under contract number DE-AC02-
06CH11357, program manager Laura Biven, and by the Spanish
Government (SEV2015-0493), by the Spanish Ministry of Science and Innovation (contract TIN2015-65316-P), by Generalitat de Catalunya (contract 2014-SGR-1051).Peer ReviewedPostprint (author's final draft
An empirical learning-based validation procedure for simulation workflow
Simulation workflow is a top-level model for the design and control of
simulation process. It connects multiple simulation components with time and
interaction restrictions to form a complete simulation system. Before the
construction and evaluation of the component models, the validation of
upper-layer simulation workflow is of the most importance in a simulation
system. However, the methods especially for validating simulation workflow is
very limit. Many of the existing validation techniques are domain-dependent
with cumbersome questionnaire design and expert scoring. Therefore, this paper
present an empirical learning-based validation procedure to implement a
semi-automated evaluation for simulation workflow. First, representative
features of general simulation workflow and their relations with validation
indices are proposed. The calculation process of workflow credibility based on
Analytic Hierarchy Process (AHP) is then introduced. In order to make full use
of the historical data and implement more efficient validation, four learning
algorithms, including back propagation neural network (BPNN), extreme learning
machine (ELM), evolving new-neuron (eNFN) and fast incremental gaussian mixture
model (FIGMN), are introduced for constructing the empirical relation between
the workflow credibility and its features. A case study on a landing-process
simulation workflow is established to test the feasibility of the proposed
procedure. The experimental results also provide some useful overview of the
state-of-the-art learning algorithms on the credibility evaluation of
simulation models
Ontology of core data mining entities
In this article, we present OntoDM-core, an ontology of core data mining
entities. OntoDM-core defines themost essential datamining entities in a three-layered
ontological structure comprising of a specification, an implementation and an application
layer. It provides a representational framework for the description of mining
structured data, and in addition provides taxonomies of datasets, data mining tasks,
generalizations, data mining algorithms and constraints, based on the type of data.
OntoDM-core is designed to support a wide range of applications/use cases, such as
semantic annotation of data mining algorithms, datasets and results; annotation of
QSAR studies in the context of drug discovery investigations; and disambiguation of
terms in text mining. The ontology has been thoroughly assessed following the practices
in ontology engineering, is fully interoperable with many domain resources and
is easy to extend
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