Overlay HPC Information

•

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In this presentation from ISC'14, Christian Kniep from Bull presents: Understand Your Cluster by Overlaying Multiple Information Layers. Kniep is using Docker technology in a novel way to ease the administration of InfiniBand networks. "Today's data center managers are burdened by a lack of aligned information of multiple layers. Work-flow events like 'job XYZ starts' aligned with performance metrics and events extracted from log facilities are low-hanging fruit that is on the edge to become use-able due to open-source software like Graphite, StatsD, logstash and alike. This talk aims to show off the benefits of merging multiple layers of information within an InfiniBand cluster by using use-cases for system operation and management level personal. Mr. Kniep held two BoF sessions which described the lack of InfiniBand (ISC'12) and generic HPC monitoring (ISC'13). This years' session aims to propose a way to fix it. To drill into the issue, Mr. Kniep uses his recently started project QNIBTerminal to spin up a complete clusterstack using LXC containers."

Technology Education

©Bull 2012
Overlay HPC Information
1
Christian Kniep
R&D HPC Engineer
2014-06-25

©Bull 2014
About Me
2
‣ 10y+ SysAdmin
‣ 8y+ SysOps
‣ B.Sc. (2008-2011)
‣ 6y+ DevOps
‣ 1y+ R&D
- @CQnib
- http://blog.qnib.org
- https://github.com/ChristianKniep

©Bull 2014
My ISC History - Motivation
3

©Bull 2014
My ISC History - Description
4

©Bull 2014
HPC Software Stack (rough estimate)
5
Hardware:! ! HW-sensors/-errors
OS:! ! ! Kernel, Userland tools
MiddleWare:! MPI, ISV-libs
Software:! ! End user application
Excel:!! ! KPI, SLA
MgmtSysOps
SysOpsMgmt
User
PowerUser/ISV
ISVMgmt
Services:! ! Storage, Job Scheduler
HW

©Bull 2014
HPC Software Stack (goal)
6
Hardware:! ! HW-sensors/-errors
OS:! ! ! Kernel, Userland tools
MiddleWare:! MPI, ISV-libs
Software:! ! End user application
Excel:!! ! KPI, SLA
Services:! ! Storage, Job Scheduler
Log/Events
Perf

!
!
!
• Created my own
!
!
• No useful tools in sight
©Bull 2014
QNIB
8
‣ Cluster of n*1000+ IB nodes
• Hard to debug

!
!
!
• Created my own - Graphite-Update in late 2013
!
!
• No useful tools in sight
©Bull 2014
QNIB
9
‣ Cluster of n*1000+ IB nodes
• Hard to debug

©Bull 2014
Achieved HPC Software Stack
10
Hardware:! ! IB-sensors/-errors
OS:! ! ! Kernel, Userland tools
MiddleWare:! MPI, ISV-libs
Software:! ! End user application
Excel:!! ! KPI, SLA
Services:! ! Storage, Job Scheduler
Log/Events
Perf

©Bull 2012
QNIBTerminal - Implementation
11

©Bull 2014
QNIBTerminal -blog.qnib.org
12
haproxy haproxy
dns
helixdns
elk
kibana
logstash
etcd
carboncarbon
graphite-webgraphite-web
graphite-apigraphite-api
grafanagrafana
slurmctldslurmctld
compute0slurmd
compute<N>slurmd
Log/Events
Services Performance
Compute
elasticsearch

©Bull 2014
More Services
15
‣ Improve work-ﬂow for log-events
‣ Nagios(-like) node is missing
‣ Cluster-FileSystem
‣ LDAP
‣ Additional dashboards
‣ Inventory
‣ using InﬁniBand for communication traffic

©Bull 2014
Graph Representation
16
‣ Graph inventory needed
• Hierarchical view is not enough

©Bull 2014
Graph Representation
17
!
!
• GraphDB seems to be a good idea
comp0 comp1 comp2
ibsw0
eth1
eth10
ldap12
lustre0
ibsw2
‣ Graph inventory needed
• Hierarchical view is not enough
RETURN node=comp* WHERE
ROUTE TO lustre_service INCLUDES ibsw2

!
!
!
!
!
!
!
!
!
!
‣ Training
• New SysOps could start on virtual cluster
• ‚Strangulate’ node to replay an error.
!
!
!
!
!
!
!
‣ Showcase
• Showing a customer his (to-be) software stack
• Convince the SysOps-Team ‚they have nothing to fear‘
!
!
!
‣ complete toolchain could be automated
• Testing
• Veriﬁcation
• Q&A
!
!
‣ n*1000 containers through clustering
©Bull 2014
Conclusion
19
‣ n*100 of containers are easy (50 on my laptop)
• Running a 300 node cluster stack

©Bull 2014
Log AND Performance Management
20
‣ Metric w/o Logs are useless!

©Bull 2014
Log AND Performance Management
21
‣ Metric w/o Logs are useless!!
• and the other way around…

©Bull 2014
Log AND Performance Management
22
!
!
• overlapping is king
‣ Metric w/o Logs are useless!!
• and the other way around…

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In this deck from the Stanford HPC Conference, Nicole Xu from Stanford University describes how she transformed a common jellyfish into a bionic creature that is part animal and part machine. "Animal locomotion and bioinspiration have the potential to expand the performance capabilities of robots, but current implementations are limited. Mechanical soft robots leverage engineered materials and are highly controllable, but these biomimetic robots consume more power than corresponding animal counterparts. Biological soft robots from a bottom-up approach offer advantages such as speed and controllability but are limited to survival in cell media. Instead, biohybrid robots that comprise live animals and self- contained microelectronic systems leverage the animals’ own metabolism to reduce power constraints and body as an natural scaffold with damage tolerance. We demonstrate that by integrating onboard microelectronics into live jellyfish, we can enhance propulsion up to threefold, using only 10 mW of external power input to the microelectronics and at only a twofold increase in cost of transport to the animal. This robotic system uses 10 to 1000 times less external power per mass than existing swimming robots in literature and can be used in future applications for ocean monitoring to track environmental changes." Watch the video: https://youtu.be/HrmJFyvInj8 Learn more: https://sanfrancisco.cbslocal.com/2020/02/05/stanford-research-project-common-jellyfish-bionic-sea-creatures/ and http://www.hpcadvisorycouncil.com/events/2020/stanford-workshop/ Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

Machine Learning for Weather Forecasts

inside-BigData.com

In this deck from the Stanford HPC Conference, Peter Dueben from the European Centre for Medium-Range Weather Forecasts (ECMWF) presents: Machine Learning for Weather Forecasts. "I will present recent studies that use deep learning to learn the equations of motion of the atmosphere, to emulate model components of weather forecast models and to enhance usability of weather forecasts. I will than talk about the main challenges for the application of deep learning in cutting-edge weather forecasts and suggest approaches to improve usability in the future." Peter is contributing to the development and optimization of weather and climate models for modern supercomputers. He is focusing on a better understanding of model error and model uncertainty, on the use of reduced numerical precision that is optimised for a given level of model error, on global cloud- resolving simulations with ECMWF's forecast model, and the use of machine learning, and in particular deep learning, to improve the workflow and predictions. Peter has graduated in Physics and wrote his PhD thesis at the Max Planck Institute for Meteorology in Germany. He worked as Postdoc with Tim Palmer at the University of Oxford and has taken up a position as University Research Fellow of the Royal Society at the European Centre for Medium-Range Weather Forecasts (ECMWF) in 2017. Watch the video: https://youtu.be/ks3fkRj8Iqc Learn more: https://www.ecmwf.int/ and http://www.hpcadvisorycouncil.com/events/2020/stanford-workshop/ Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

HPC AI Advisory Council Update

inside-BigData.com

In this deck, Gilad Shainer from the HPC AI Advisory Council describes how this organization fosters innovation in the high performance computing community. "The HPC-AI Advisory Council’s mission is to bridge the gap between high-performance computing (HPC) and Artificial Intelligence (AI) use and its potential, bring the beneficial capabilities of HPC and AI to new users for better research, education, innovation and product manufacturing, bring users the expertise needed to operate HPC and AI systems, provide application designers with the tools needed to enable parallel computing, and to strengthen the qualification and integration of HPC and AI system products." Watch the video: https://wp.me/p3RLHQ-lNz Learn more: http://hpcadvisorycouncil.com Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

Fugaku Supercomputer joins fight against COVID-19

inside-BigData.com

Today RIKEN in Japan announced that the Fugaku supercomputer will be made available for research projects aimed to combat COVID-19. "Fugaku is currently being installed and is scheduled to be available to the public in 2021. However, faced with the devastating disaster unfolding before our eyes, RIKEN and MEXT decided to make a portion of the computational resources of Fugaku available for COVID-19-related projects ahead of schedule while continuing the installation process. Fugaku is being developed not only for the progress in science, but also to help build the society dubbed as the “Society 5.0” by the Japanese government, where all people will live safe and comfortable lives. The current initiative to fight against the novel coronavirus is driven by the philosophy behind the development of Fugaku." Initial Projects Exploring new drug candidates for COVID-19 by "Fugaku" Yasushi Okuno, RIKEN / Kyoto University Prediction of conformational dynamics of proteins on the surface of SARS-Cov-2 using Fugaku Yuji Sugita, RIKEN Simulation analysis of pandemic phenomena Nobuyasu Ito, RIKEN Fragment molecular orbital calculations for COVID-19 proteins Yuji Mochizuki, Rikkyo University

Energy Efficient Computing using Dynamic Tuning

inside-BigData.com

In this deck from the Performance Optimisation and Productivity group, Lubomir Riha from IT4Innovations presents: Energy Efficient Computing using Dynamic Tuning. "We now live in a world of power-constrained architectures and systems and power consumption represents a significant cost factor in the overall HPC system economy. For these reasons, in recent years researchers, supercomputing centers and major vendors have developed new tools and methodologies to measure and optimize the energy consumption of large-scale high performance system installations. Due to the link between energy consumption, power consumption and execution time of an application executed by the final user, it is important for these tools and the methodology used to consider all these aspects, empowering the final user and the system administrator with the capability of finding the best configuration given different high level objectives. This webinar focused on tools designed to improve the energy-efficiency of HPC applications using a methodology of dynamic tuning of HPC applications, developed under the H2020 READEX project. The READEX methodology has been designed for exploiting the dynamic behaviour of software. At design time, different runtime situations (RTS) are detected and optimized system configurations are determined. RTSs with the same configuration are grouped into scenarios, forming the tuning model. At runtime, the tuning model is used to switch system configurations dynamically. The MERIC tool, that implements the READEX methodology, is presented. It supports manual or binary instrumentation of the analysed applications to simplify the analysis. This instrumentation is used to identify and annotate the significant regions in the HPC application. Automatic binary instrumentation annotates regions with significant runtime. Manual instrumentation, which can be combined with automatic, allows code developer to annotate regions of particular interest." Watch the video: https://wp.me/p3RLHQ-lJP Learn more: https://pop-coe.eu/blog/14th-pop-webinar-energy-efficient-computing-using-dynamic-tuning and https://code.it4i.cz/vys0053/meric Sign up for our insideHPC Newsletter: http://insidehpc.com/newslett

HPC at Scale Enabled by DDN A3i and NVIDIA SuperPOD

inside-BigData.com

In this deck from GTC Digital, William Beaudin from DDN presents: HPC at Scale Enabled by DDN A3i and NVIDIA SuperPOD. Enabling high performance computing through the use of GPUs requires an incredible amount of IO to sustain application performance. We'll cover architectures that enable extremely scalable applications through the use of NVIDIA’s SuperPOD and DDN’s A3I systems. The NVIDIA DGX SuperPOD is a first-of-its-kind artificial intelligence (AI) supercomputing infrastructure. DDN A³I with the EXA5 parallel file system is a turnkey, AI data storage infrastructure for rapid deployment, featuring faster performance, effortless scale, and simplified operations through deeper integration. The combined solution delivers groundbreaking performance, deploys in weeks as a fully integrated system, and is designed to solve the world's most challenging AI problems. Watch the video: https://wp.me/p3RLHQ-lIV Learn more: https://www.ddn.com/download/nvidia-superpod-ddn-a3i-ai400-appliance-with-the-exa5-filesystem/ and https://www.nvidia.com/en-us/gtc/ Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

State of ARM-based HPC

inside-BigData.com

In this deck, Paul Isaacs from Linaro presents: State of ARM-based HPC. This talk provides an overview of applications and infrastructure services successfully ported to Aarch64 and benefiting from scale. "With its debut on the TOP500, the 125,000-core Astra supercomputer at New Mexico’s Sandia Labs uses Cavium ThunderX2 chips to mark Arm’s entry into the petascale world. In Japan, the Fujitsu A64FX Arm-based CPU in the pending Fugaku supercomputer has been optimized to achieve high-level, real-world application performance, anticipating up to one hundred times the application execution performance of the K computer. K was the first computer to top 10 petaflops in 2011." Watch the video: https://wp.me/p3RLHQ-lIT Learn more: https://www.linaro.org/ Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

Versal Premium ACAP for Network and Cloud Acceleration

inside-BigData.com

Today Xilinx announced Versal Premium, the third series in the Versal ACAP portfolio. The Versal Premium series features highly integrated, networked and power-optimized cores and the industry’s highest bandwidth and compute density on an adaptable platform. Versal Premium is designed for the highest bandwidth networks operating in thermally and spatially constrained environments, as well as for cloud providers who need scalable, adaptable application acceleration. Versal is the industry’s first adaptive compute acceleration platform (ACAP), a revolutionary new category of heterogeneous compute devices with capabilities that far exceed those of conventional silicon architectures. Developed on TSMC’s 7-nanometer process technology, Versal Premium combines software programmability with dynamically configurable hardware acceleration and pre-engineered connectivity and security features to enable a faster time-to- market. The Versal Premium series delivers up to 3X higher throughput compared to current generation FPGAs, with built-in Ethernet, Interlaken, and cryptographic engines that enable fast and secure networks. The series doubles the compute density of currently deployed mainstream FPGAs and provides the adaptability to keep pace with increasingly diverse and evolving cloud and networking workloads. Learn more: https://insidehpc.com/2020/03/xilinx-announces-versal-premium-acap-for-network-and-cloud-acceleration/ Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

Zettar: Moving Massive Amounts of Data across Any Distance Efficiently

inside-BigData.com

In this video from the Rice Oil & Gas Conference, Chin Fang from Zettar presents: Moving Massive Amounts of Data across Any Distance Efficiently. The objective of this talk is to present two on-going projects aiming at improving and ensuring highly efficient bulk transferring or streaming of massive amounts of data over digital connections across any distance. It examines the current state of the art, a few very common misconceptions, the differences among the three major type of data movement solutions, a current initiative attempting to improve the data movement efficiency from the ground up, and another multi-stage project that shows how to conduct long distance large scale data movement at speed and scale internationally. Both projects have real world motivations, e.g. the ambitious data transfer requirements of Linac Coherent Light Source II (LCLS-II) [1], a premier preparation project of the U.S. DOE Exascale Computing Initiative (ECI) [2]. Their immediate goals are described and explained, together with the solution used for each. Findings and early results are reported. Possible future works are outlined. Watch the video: https://wp.me/p3RLHQ-lBX Learn more: https://www.zettar.com/ and https://rice2020oghpc.rice.edu/program-2/ Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

Scaling TCO in a Post Moore's Era

inside-BigData.com

In this deck from the Rice Oil & Gas Conference, Bradley McCredie from AMD presents: Scaling TCO in a Post Moore's Law Era. "While foundries bravely drive forward to overcome the technical and economic challenges posed by scaling to 5nm and beyond, Moore’s law alone can provide only a fraction of the performance / watt and performance / dollar gains needed to satisfy the demands of today’s high performance computing and artificial intelligence applications. To close the gap, multiple strategies are required. First, new levels of innovation and design efficiency will supplement technology gains to continue to deliver meaningful improvements in SoC performance. Second, heterogenous compute architectures will create x-factor increases of performance efficiency for the most critical applications. Finally, open software frameworks, APIs, and toolsets will enable broad ecosystems of application level innovation." Watch the video: Learn more: http://amd.com and https://rice2020oghpc.rice.edu/program-2/ Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

CUDA-Python and RAPIDS for blazing fast scientific computing

inside-BigData.com

In this deck from the ECSS Symposium, Abe Stern from NVIDIA presents: CUDA-Python and RAPIDS for blazing fast scientific computing. "We will introduce Numba and RAPIDS for GPU programming in Python. Numba allows us to write just-in-time compiled CUDA code in Python, giving us easy access to the power of GPUs from a powerful high-level language. RAPIDS is a suite of tools with a Python interface for machine learning and dataframe operations. Together, Numba and RAPIDS represent a potent set of tools for rapid prototyping, development, and analysis for scientific computing. We will cover the basics of each library and go over simple examples to get users started. Finally, we will briefly highlight several other relevant libraries for GPU programming." Watch the video: https://wp.me/p3RLHQ-lvu Learn more: https://developer.nvidia.com/rapids and https://www.xsede.org/for-users/ecss/ecss-symposium Sign up for our insideHPC Newsletter: http://insidehp.com/newsletter

Introducing HPC with a Raspberry Pi Cluster

inside-BigData.com

In this deck from FOSDEM 2020, Colin Sauze from Aberystwyth University describes the development of a RaspberryPi cluster for teaching an introduction to HPC. "The motivation for this was to overcome four key problems faced by new HPC users: * The availability of a real HPC system and the effect running training courses can have on the real system, conversely the availability of spare resources on the real system can cause problems for the training course. * A fear of using a large and expensive HPC system for the first time and worries that doing something wrong might damage the system. * That HPC systems are very abstract systems sitting in data centres that users never see, it is difficult for them to understand exactly what it is they are using. * That new users fail to understand resource limitations, in part because of the vast resources in modern HPC systems a lot of mistakes can be made before running out of resources. A more resource constrained system makes it easier to understand this. The talk will also discuss some of the technical challenges in deploying an HPC environment to a Raspberry Pi and attempts to keep that environment as close to a "real" HPC as possible. The issue to trying to automate the installation process will also be covered." Learn more: https://github.com/colinsauze/pi_cluster and https://fosdem.org/2020/schedule/events/ Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

Overview of HPC Interconnects

inside-BigData.com

In this deck from ATPESC 2019, Ken Raffenetti from Argonne presents an overview of HPC interconnects. "The Argonne Training Program on Extreme-Scale Computing (ATPESC) provides intensive, two-week training on the key skills, approaches, and tools to design, implement, and execute computational science and engineering applications on current high-end computing systems and the leadership-class computing systems of the future." Watch the video: https://wp.me/p3RLHQ-luc Learn more: https://extremecomputingtraining.anl.gov/ Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

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HPC at Scale Enabled by DDN A3i and NVIDIA SuperPOD

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