516 research outputs found
Exascale Deep Learning for Climate Analytics
We extract pixel-level masks of extreme weather patterns using variants of
Tiramisu and DeepLabv3+ neural networks. We describe improvements to the
software frameworks, input pipeline, and the network training algorithms
necessary to efficiently scale deep learning on the Piz Daint and Summit
systems. The Tiramisu network scales to 5300 P100 GPUs with a sustained
throughput of 21.0 PF/s and parallel efficiency of 79.0%. DeepLabv3+ scales up
to 27360 V100 GPUs with a sustained throughput of 325.8 PF/s and a parallel
efficiency of 90.7% in single precision. By taking advantage of the FP16 Tensor
Cores, a half-precision version of the DeepLabv3+ network achieves a peak and
sustained throughput of 1.13 EF/s and 999.0 PF/s respectively.Comment: 12 pages, 5 tables, 4, figures, Super Computing Conference November
11-16, 2018, Dallas, TX, US
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
A Tale of Two Data-Intensive Paradigms: Applications, Abstractions, and Architectures
Scientific problems that depend on processing large amounts of data require
overcoming challenges in multiple areas: managing large-scale data
distribution, co-placement and scheduling of data with compute resources, and
storing and transferring large volumes of data. We analyze the ecosystems of
the two prominent paradigms for data-intensive applications, hereafter referred
to as the high-performance computing and the Apache-Hadoop paradigm. We propose
a basis, common terminology and functional factors upon which to analyze the
two approaches of both paradigms. We discuss the concept of "Big Data Ogres"
and their facets as means of understanding and characterizing the most common
application workloads found across the two paradigms. We then discuss the
salient features of the two paradigms, and compare and contrast the two
approaches. Specifically, we examine common implementation/approaches of these
paradigms, shed light upon the reasons for their current "architecture" and
discuss some typical workloads that utilize them. In spite of the significant
software distinctions, we believe there is architectural similarity. We discuss
the potential integration of different implementations, across the different
levels and components. Our comparison progresses from a fully qualitative
examination of the two paradigms, to a semi-quantitative methodology. We use a
simple and broadly used Ogre (K-means clustering), characterize its performance
on a range of representative platforms, covering several implementations from
both paradigms. Our experiments provide an insight into the relative strengths
of the two paradigms. We propose that the set of Ogres will serve as a
benchmark to evaluate the two paradigms along different dimensions.Comment: 8 pages, 2 figure
Grid infrastructures for secure access to and use of bioinformatics data: experiences from the BRIDGES project
The BRIDGES project was funded by the UK Department of Trade and Industry (DTI) to address the needs of cardiovascular research scientists investigating the genetic causes of hypertension as part of the Wellcome Trust funded (£4.34M) cardiovascular functional genomics (CFG) project. Security was at the heart of the BRIDGES project and an advanced data and compute grid infrastructure incorporating latest grid authorisation technologies was developed and delivered to the scientists. We outline these grid infrastructures and describe the perceived security requirements at the project start including data classifications and how these evolved throughout the lifetime of the project. The uptake and adoption of the project results are also presented along with the challenges that must be overcome to support the secure exchange of life science data sets. We also present how we will use the BRIDGES experiences in future projects at the National e-Science Centre
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
XSEDE Scientific Workflow Use Case L3 Architectural Response
This document is the Level 3 Architectural Response for the XSEDE Scientific Workflow Use Case.National Science Foundation OCI-1053575Ope
ASCR/HEP Exascale Requirements Review Report
This draft report summarizes and details the findings, results, and
recommendations derived from the ASCR/HEP Exascale Requirements Review meeting
held in June, 2015. The main conclusions are as follows. 1) Larger, more
capable computing and data facilities are needed to support HEP science goals
in all three frontiers: Energy, Intensity, and Cosmic. The expected scale of
the demand at the 2025 timescale is at least two orders of magnitude -- and in
some cases greater -- than that available currently. 2) The growth rate of data
produced by simulations is overwhelming the current ability, of both facilities
and researchers, to store and analyze it. Additional resources and new
techniques for data analysis are urgently needed. 3) Data rates and volumes
from HEP experimental facilities are also straining the ability to store and
analyze large and complex data volumes. Appropriately configured
leadership-class facilities can play a transformational role in enabling
scientific discovery from these datasets. 4) A close integration of HPC
simulation and data analysis will aid greatly in interpreting results from HEP
experiments. Such an integration will minimize data movement and facilitate
interdependent workflows. 5) Long-range planning between HEP and ASCR will be
required to meet HEP's research needs. To best use ASCR HPC resources the
experimental HEP program needs a) an established long-term plan for access to
ASCR computational and data resources, b) an ability to map workflows onto HPC
resources, c) the ability for ASCR facilities to accommodate workflows run by
collaborations that can have thousands of individual members, d) to transition
codes to the next-generation HPC platforms that will be available at ASCR
facilities, e) to build up and train a workforce capable of developing and
using simulations and analysis to support HEP scientific research on
next-generation systems.Comment: 77 pages, 13 Figures; draft report, subject to further revisio
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