AWI Uses New Cray Cluster for Earth Sciences and Bioinformatics

By Linda Barney

December 22, 2016

The Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research (AWI), headquartered in Bremerhaven, Germany, is one of the country’s premier research institutes within the Helmholtz Association of German Research Centres, and is an internationally respected center of expertise for polar and marine research. In November 2015, AWI awarded Cray a contract to install a cluster supercomputer that would help the institute accelerate time to discovery. Now the effort is starting to pay off.

The new Cray CS400 system, nicknamed “Ollie” by AWI staff was installed in April 2016 and is being phased in for use by researchers across AWI. Ollie made it into the Top500 in June (365) and most recently in November (473). The system uses the Intel Xeon processor E5-2600 v4 (Broadwell) as well as Intel’s Omni-Path Architecture (OPA) fabric. The file systems chosen was BeeGFS (formerly FhGFS) parallel cluster file system to spread user data across multiple servers to improve performance and capacity scaling.

AWI now uses its new supercomputer to run advanced research applications related to climate and environmental studies, including global circulations models, regional atmospheric models, glaciology studies and other computing-intensive, numerical simulations such as bioinformatics protein simulations.

“We have just started running on the Cray HPC system and have ported the main ice flow models and are starting to do Paleo ice sheet simulations on it,” said Thomas Kleiner whose glaciology research contributes to the understanding of ice sheet dynamics in the earth system and the impact of climate change. “The new system is much larger and allows us to run more detailed simulations such as simulations of Antarctica at 5km resolutions which was not possible on our older systems. It also allows us to do many simulations at the same time which helps in our research.”

“However, we also want to run simulations further back in time which is very important for climate change modeling at AWI. Compared to other components in the earth system (e.g. atmosphere or ocean), ice sheet models are relatively inexpensive in terms of computational recourses if they run for only a few thousands years, but ice sheets have a long memory of the past climate and therefore models need to be run over very long time scales (several glacial cycles).

“Running a 1,000 year simulation of Antarctica at a 10km resolution (573 x 489 x 101 grid nodes) for climate and glacier research requires 114 CPU hours on the Cray CS400 system. However, we need a resolution of 5km to get adequate detail and also need to run multiple simulations with varying parameters for model uncertainty estimates. What we currently have to do is run simulations at a coarser resolution for many thousands of years until around 10,000 years before the present time and then run simulations at 5km resolution, where the 5km setup (1145 x 977 x 201 grid nodes) already requires 420 CPU hours per 100 years. Every model improvement in terms of considered physics requires a complete recalibration of the model to match observations (although very sparse). The parameter space is huge and needs to be investigated carefully.

“We have relevant small-scale (less than a km) processes that are controlling ice sheet internal dynamics, and on the other side global atmospheric and ocean models that deliver climatic boundary conditions to the ice sheet on course grids but require very short time steps (hours to seconds). Thus, HPC systems of the future are needed to allow us to bridge the gap between the different scales (spatially and temporally) in fully coupled Earth system models including ice sheets.”

Bioinformatics Research
In 2004, AWI established a bioinformatics group to provide services to projects requiring bioinformatics and data analysis background. This group participates in data analyses in diverse projects including phylogenetics, phylogenomics, population genetics, RNA-Seq and metatranscriptomics.

Lars Harms, a bioinformatics researcher at AWI, a new user to HPC systems, is using the Cray system to speed up metatranscriptomics research and in some cases to enable the analysis at all. “Our metatranscriptomics research, helps to analyze the functional diversity and the state of organism communities in their taxonomic composition with response patterns to environmental change, to gradients, or ecological dynamics. Processing the associated large datasets on the Cray HPC system help to speed up otherwise time-consuming tasks. Furthermore, the multi-purpose concept of the AWI Cray system including some high-memory nodes is a big advantage for our research enabling us to assemble large-scale metatranscriptomes that is not possible on the existing small-scale servers due to lack of memory.”

Harms is also performing functional annotations using BLAST and HMMER code on the Cray CS400 system. “BLAST and HMMER are typically very time consuming to run. We are using the Cray system to process these tasks in a highly parallel manner which provides a huge speed up compared to our existing platforms.” Harms found a way to speed up analyzing large datasets of protein sequences using HMMER3 even further by copying the entire hmm-database onto solid state drives (SSDs) attached directly to the system nodes. This resulted in a huge speed up due to the faster data transfer rates with the SSDs in comparison to the file system of the Cray system (Figure 1).

One challenge that Harms still faces is the need to optimize software. He said, “Much of the existing software code and tools were developed to work on a single server and need to be optimized to take advantage of parallel processing capabilities of modern processors and HPC systems.”

Given the high cost of energy in Europe, maximizing energy efficiency is a top AWS priority. Malte Thoma, AWI system administrator, emphasized that energy efficiency was a major consideration when selecting a new HPC system. The Cray CS400 is an air cooled system that can control energy consumption on a per job level by allowing users and administrators to set the maximum frequency of the processor. This is done by using a cpu frequency setting in the slurm.epilog and slurm.prolog files as well as an AWI written bash-script tool which reduces maximum performance if the temperature in the room exceeds specific limits. The CS400 system provides the ability to set a general power limit for all or a fraction of nodes to conserve energy using features of the Intel Node Manager (server firmware that provides fine-grained power control).

When the Cray CS400 system is running each node and CPU, it consumes approximately 150KW of power. If the system is idle and CPUs are in HPC performance mode, it consumes 100KW. If all nodes are switched into the power save mode and the computer is idle, energy usage goes down to 55 KW—which is a reduction of almost a third in energy usage. The system can also switch between a performance mode and a power save mode. When a user starts a job, the nodes are put into performance mode but automatically switch back to power save mode when the job finishes.

Unique Modeling and System Profiling Tools
AWI scientists develop software systems, tools or libraries to support AWI staff on their individual research. The researchers, system administrator and IT team use Cray and Intel compilers as well as other tools in optimizing code. There are a number of existing AWI projects such as FESOM, MITgcm and MPI-ESM running on other platforms which are not yet run on the Cray system. The team is also performing benchmarking or profiling work on MPI or OpenMP modifying code to improve parallelization and vectorization.

According to Dr. Natalja Rakowsky, “A major optimization was performed when the sea-ice-ocean-model FESOM was redesigned switching from finite elements to finite volumes. The data structure was improved considerably. Both codes operate on a grid that is unstructured-triangular in the horizontal, and consists of layers in 3D (Z coordinates). FESOM collects the variables along the horizontal first, layer by layer. This results in indirect addressing in all loops, and in a lot of cache misses, because many computations are performed along the vertical. FESOM2 has the vertical as the first dimension, allowing direct addressing along the inner loop and often vectorization becomes possible. Cache misses remain an issue in all 2D (horizontal) computations. Here, we found a way to renumber the grid nodes to reduce the number of cache misses, see http://epic.awi.de/30632/1/IMUM2011_SFC_Rakowskyetal.pdf (the code presented here, TsunAWI, can be regarded as a simplified, 2D-only branch of FESOM).”

Other optimizations in preparation are:

  • reduce load inbalancing by a better domain decomposition (getting a high quality equal distribution of 2D and 3D nodes is not easy, and sea ice is not even taken into account yet)
  • asynchronous MPI
  • check major loops for vectorization, avoid some divisions (replace by precomputed inverse)
  • from serial to parallel I/O

The glaciology, bioinformatics and other research at AWI continue to generate huge amounts of data that will take advantage of the HPC resources. “For our research, we must find ways to process all of this data. Supercomputers can help us solve the issue of processing more data quickly, allowing us to do research that was not possible before,” states Harms.

Author Bio:
Linda Barney is the founder and owner of Barney and Associates, a technical/marketing writing, training and web design firm in Beaverton, OR.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industy updates delivered to you every week!

Simulating Car Crashes with Supercomputers – and Lego

October 18, 2019

It’s an experiment many of us have carried out at home: crashing two Lego creations into each other, bricks flying everywhere. But for the researchers at the General German Automobile Club (ADAC) – which is comparabl Read more…

By Oliver Peckham

NASA Uses Deep Learning to Monitor Solar Weather

October 17, 2019

Solar flares may be best-known as sci-fi MacGuffins, but those flares – and other space weather – can have serious impacts on not only spacecraft and satellites, but also on Earth-based systems such as radio communic Read more…

By Oliver Peckham

Federated Learning Applied to Cancer Research

October 17, 2019

The ability to share and analyze data while protecting patient privacy is giving medical researchers a new tool in their efforts to use what one vendor calls “federated learning” to train models based on diverse data Read more…

By George Leopold

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

NSB 2020 S&E Indicators Dig into Workforce and Education

October 16, 2019

Every two years the National Science Board is required by Congress to issue a report on the state of science and engineering in the U.S. This year, in a departure from past practice, the NSB has divided the 2020 S&E Read more…

By John Russell

AWS Solution Channel

Making High Performance Computing Affordable and Accessible for Small and Medium Businesses with HPC on AWS

High performance computing (HPC) brings a powerful set of tools to a broad range of industries, helping to drive innovation and boost revenue in finance, genomics, oil and gas extraction, and other fields. Read more…

HPE Extreme Performance Solutions

Intel FPGAs: More Than Just an Accelerator Card

FPGA (Field Programmable Gate Array) acceleration cards are not new, as they’ve been commercially available since 1984. Typically, the emphasis around FPGAs has centered on the fact that they’re programmable accelerators, and that they can truly offer workload specific hardware acceleration solutions without requiring custom silicon. Read more…

IBM Accelerated Insights

How Do We Power the New Industrial Revolution?

[Attend the IBM LSF, HPC & AI User Group Meeting at SC19 in Denver on November 19!]

Almost everyone is talking about artificial intelligence (AI). Read more…

What’s New in HPC Research: Rabies, Smog, Robots & More

October 14, 2019

In this bimonthly feature, HPCwire highlights newly published research in the high-performance computing community and related domains. From parallel programming to exascale to quantum computing, the details are here. Read more…

By Oliver Peckham

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

NSB 2020 S&E Indicators Dig into Workforce and Education

October 16, 2019

Every two years the National Science Board is required by Congress to issue a report on the state of science and engineering in the U.S. This year, in a departu Read more…

By John Russell

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Summit Simulates Braking – on Mars

October 14, 2019

NASA is planning to send humans to Mars by the 2030s – and landing on the surface will be considerably trickier than landing a rover like Curiosity. To solve Read more…

By Staff report

Trovares Drives Memory-Driven, Property Graph Analytics Strategy with HPE

October 10, 2019

Trovares, a high performance property graph analytics company, has partnered with HPE and its Superdome Flex memory-driven servers on a cybersecurity capability the companies say “routinely” runs near-time workloads on 24TB-capacity systems... Read more…

By Doug Black

Intel, Lenovo Join Forces on HPC Cluster for Flatiron

October 9, 2019

An HPC cluster with deep learning techniques will be used to process petabytes of scientific data as part of workload-intensive projects spanning astrophysics to genomics. AI partners Intel and Lenovo said they are providing... Read more…

By George Leopold

Optimizing Offshore Wind Farms with Supercomputer Simulations

October 9, 2019

Offshore wind farms offer a number of benefits; many of the areas with the strongest winds are located offshore, and siting wind farms offshore ameliorates many of the land use concerns associated with onshore wind farms. Some estimates say that, if leveraged, offshore wind power... Read more…

By Oliver Peckham

Harvard Deploys Cannon, New Lenovo Water-Cooled HPC Cluster

October 9, 2019

Harvard's Faculty of Arts & Sciences Research Computing (FASRC) center announced a refresh of their primary HPC resource. The new cluster, called Cannon after the pioneering American astronomer Annie Jump Cannon, is supplied by Lenovo... Read more…

By Tiffany Trader

Supercomputer-Powered AI Tackles a Key Fusion Energy Challenge

August 7, 2019

Fusion energy is the Holy Grail of the energy world: low-radioactivity, low-waste, zero-carbon, high-output nuclear power that can run on hydrogen or lithium. T Read more…

By Oliver Peckham

DARPA Looks to Propel Parallelism

September 4, 2019

As Moore’s law runs out of steam, new programming approaches are being pursued with the goal of greater hardware performance with less coding. The Defense Advanced Projects Research Agency is launching a new programming effort aimed at leveraging the benefits of massive distributed parallelism with less sweat. Read more…

By George Leopold

Cray Wins NNSA-Livermore ‘El Capitan’ Exascale Contract

August 13, 2019

Cray has won the bid to build the first exascale supercomputer for the National Nuclear Security Administration (NNSA) and Lawrence Livermore National Laborator Read more…

By Tiffany Trader

AMD Launches Epyc Rome, First 7nm CPU

August 8, 2019

From a gala event at the Palace of Fine Arts in San Francisco yesterday (Aug. 7), AMD launched its second-generation Epyc Rome x86 chips, based on its 7nm proce Read more…

By Tiffany Trader

Ayar Labs to Demo Photonics Chiplet in FPGA Package at Hot Chips

August 19, 2019

Silicon startup Ayar Labs continues to gain momentum with its DARPA-backed optical chiplet technology that puts advanced electronics and optics on the same chip Read more…

By Tiffany Trader

Using AI to Solve One of the Most Prevailing Problems in CFD

October 17, 2019

How can artificial intelligence (AI) and high-performance computing (HPC) solve mesh generation, one of the most commonly referenced problems in computational engineering? A new study has set out to answer this question and create an industry-first AI-mesh application... Read more…

By James Sharpe

D-Wave’s Path to 5000 Qubits; Google’s Quantum Supremacy Claim

September 24, 2019

On the heels of IBM’s quantum news last week come two more quantum items. D-Wave Systems today announced the name of its forthcoming 5000-qubit system, Advantage (yes the name choice isn’t serendipity), at its user conference being held this week in Newport, RI. Read more…

By John Russell

Chinese Company Sugon Placed on US ‘Entity List’ After Strong Showing at International Supercomputing Conference

June 26, 2019

After more than a decade of advancing its supercomputing prowess, operating the world’s most powerful supercomputer from June 2013 to June 2018, China is keep Read more…

By Tiffany Trader

Leading Solution Providers

ISC 2019 Virtual Booth Video Tour

CRAY
CRAY
DDN
DDN
DELL EMC
DELL EMC
GOOGLE
GOOGLE
ONE STOP SYSTEMS
ONE STOP SYSTEMS
PANASAS
PANASAS
VERNE GLOBAL
VERNE GLOBAL

A Behind-the-Scenes Look at the Hardware That Powered the Black Hole Image

June 24, 2019

Two months ago, the first-ever image of a black hole took the internet by storm. A team of scientists took years to produce and verify the striking image – an Read more…

By Oliver Peckham

Intel Confirms Retreat on Omni-Path

August 1, 2019

Intel Corp.’s plans to make a big splash in the network fabric market for linking HPC and other workloads has apparently belly-flopped. The chipmaker confirmed to us the outlines of an earlier report by the website CRN that it has jettisoned plans for a second-generation version of its Omni-Path interconnect... Read more…

By Staff report

Crystal Ball Gazing: IBM’s Vision for the Future of Computing

October 14, 2019

Dario Gil, IBM’s relatively new director of research, painted a intriguing portrait of the future of computing along with a rough idea of how IBM thinks we’ Read more…

By John Russell

Kubernetes, Containers and HPC

September 19, 2019

Software containers and Kubernetes are important tools for building, deploying, running and managing modern enterprise applications at scale and delivering enterprise software faster and more reliably to the end user — while using resources more efficiently and reducing costs. Read more…

By Daniel Gruber, Burak Yenier and Wolfgang Gentzsch, UberCloud

Intel Debuts Pohoiki Beach, Its 8M Neuron Neuromorphic Development System

July 17, 2019

Neuromorphic computing has received less fanfare of late than quantum computing whose mystery has captured public attention and which seems to have generated mo Read more…

By John Russell

Rise of NIH’s Biowulf Mirrors the Rise of Computational Biology

July 29, 2019

The story of NIH’s supercomputer Biowulf is fascinating, important, and in many ways representative of the transformation of life sciences and biomedical res Read more…

By John Russell

Quantum Bits: Neven’s Law (Who Asked for That), D-Wave’s Steady Push, IBM’s Li-O2- Simulation

July 3, 2019

Quantum computing’s (QC) many-faceted R&D train keeps slogging ahead and recently Japan is taking a leading role. Yesterday D-Wave Systems announced it ha Read more…

By John Russell

With the Help of HPC, Astronomers Prepare to Deflect a Real Asteroid

September 26, 2019

For years, NASA has been running simulations of asteroid impacts to understand the risks (and likelihoods) of asteroids colliding with Earth. Now, NASA and the European Space Agency (ESA) are preparing for the next, crucial step in planetary defense against asteroid impacts: physically deflecting a real asteroid. Read more…

By Oliver Peckham

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This