DDN Strikes Balance for Parallel Storage I/O

By Alex Woodie

November 18, 2014

Today at Supercomputing 2014, DataDirect Networks lifted the veil a bit more on Infinite Memory Engine (IME), its new software that will employ Flash storage and a bunch of smart algorithms to create a buffer between HPC compute and parallel file system resources, with the goal of improving file I/O by up to 100x. The company also announced the latest release of its Exascaler, its Lustre-based storage appliance lineup.

The data patterns have been changing at HPC sites in a way that is creating bottlenecks in the I/O. While many HPC shops may think they’re primarily working with large and sequential files, the reality is that most data is relatively small and random, and that fragmented I/O creates problems when moving the data across the interconnect, says Jeff Sisilli, Sr. Director Product Marketing at DataDirect Networks.

“Parallel file systems were really built for large files,” Sisilli tells HPCwire. “What we’re finding is 90 percent of typical I/O in HPC data centers utilizes small files, those less than 32KB. What happens is, when you inject those into a parallel file system, it starts to really bring down performance.”

DDN says it overcame the restrictions in how parallel file systems were created with IME, which creates a storage tier above the file system and provides a “fast data” layer between the compute nodes in an HPC cluster and the backend file system. The software, which resides on the I/O nodes in the cluster, utilizes any available Flash solid state drives (SSDs) or other non-volatile memory (NVM) storage resources available, creating a “burst buffer” to absorb peak loads and eliminate I/O contention.

IME_diagramIME works in two ways. First, it removes any limitations of the POSIX layer, such as file locks, that can slow down communication. Secondly, algorithms bundle up the small and random I/O operations into larger files that can be more efficiently read into the file system.

In lab tests at a customer site, DDN ran IME against the S3D turbulent flow modeling software. The software was really designed for larger sequential files, but is often used in the real world with smaller and random files. In the customer’s case, these “mal-aligned and fragmented” files were causing I/O throughput across the InfiniBand interconnect to drop to 25 MBs per second.

After introducing IME, the customer was able to ingest data from the compute cluster onto IME’s SSDs at line rate. “This customer was using InfiniBand, and we were able to fill up InfiniBand all the way to line rate, and absorb at 50 GB per second,” Sisilli says.

The data wasn’t written back into the file system quite that quickly. But because the algorithms were able to align all those small files and convert fragments into full stripe writes, it did provide a speed up compared to 25MB per second. “We were able to drain out the buffer and write to the parallel file system at 4GB per second, which is two orders of magnitude faster than before,” Sisilli says.

The “net net” of IME, Sisilli says, is it frees up HPC compute cluster resources. “From the parallel file system side, we’re able to shield the parallel file system and underlying storage arrays from fragmented I/O, and have those be able to ingest optimized data and utilize much less hardware to be able to get to the performance folks need up above,” he says.

IME will work with any Lustre- or GPFS-based parallel file system. That includes DDN’s own EXAscaler line of Lustre-based storage appliances, or the storage appliances of any other vendor. There are no application modifications required to use IME, which also features data erasure encoding capabilities typicaly found in object file stores. The only requirements are that the application is POSIX compliant or uses the MPI job scheduler. DDN also provides an API that customers can use if they want to modify their apps to work with IME; the company has plans to create an ecosystem of compatible tools using this API.

There are other vendors developing similar Flash-bashed storage buffer offerings. But DDN says the fact that it’s taking an open, software-based approach gives customer an advantage over those vendors that are requiring customers to purchase specialized hardware, or those that work with only certain types of Interconnects.

IME_burst_bufferIME isn’t available yet; it’s still in technology preview mode. But when it becomes available, scalability won’t be an issue. The software will be able to corral and make available petabytes worth of Flash or NVM storage resources living across thousands of nodes, Sisilli says. “What we’re recommending is [to have in IME] anywhere between two to three amount of your compute cluster memory to have a great working space within IME to accelerate your applications and and do I/O,” he says. “That can be all the way down to terabytes, and for supercomputers, it’s multi petabytes.”

IME is still undergoing tests, and is expected to become generally available in the second quarter of 2015. DDN will offer it as an appliance or as software.

DDN also today unveiled a new release of EXAScaler. With Version 2.1, DDN has improved read and write I/O performance by 25 percent. That will give DDN a comfortable advantage over competing file systems for some time, says Roger Goff, Sr. Product Manager for DDN.

“We know what folks are about to announce because they pre-announce those things,” Goff says. “Our solution is tremendously faster than what you will see [from other vendors], particularly on a per-rack performance basis.”

Other new features in version 2.1 include support for self-encrypting drives; improved rebuild times; InfiniBand optimizations; and better integration with DDN’s Storage Fusion Xcelerator (SFX Flash Caching) software.

DDN has also standardized on the Lustre file system from Intel, called Intel Enterprise Edition for Lustre version 2.5. That brings it several new capabilities, including a new MapReduce connector for running Hadoop workloads.

“So instead of having data replicated across multiple nodes in the cluster, which is the native mode for HDFS, with this adapter, you can run those Hadoop applications and take advantages of the single-copy nature of a parallel file system, yet have the same capability of a parallel file system to scale to thousands and thousands of clients accessing that same data,” Goff says.

EXAScaler version 2.1 is available now across all three EXAScaler products, including the entry-level SFA7700, the midrange ES12k/SFA12k-20, and the high-end SFA12KX/SFA212k-40.

Related Items:

DDN Discusses Enterprise HPC Momentum

DDN’s IME Software Scales I/O Performance on the Rocky Road to Exascale

DDN Aims for Deeper, Cheaper Archives

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!

Help Wanted: QED-C Survey Spotlights Skills Sought by Quantum Industry

September 28, 2021

Developing an adequate workforce for the young but fast-growing quantum information sciences industry is seen as a critical element for success. Just what that means in terms of skillsets and positions is becoming cleare Read more…

Pittsburgh Supercomputer Powers Machine Learning Analysis of Rare East Asian Stamps

September 27, 2021

Setting aside the relatively recent rise of electronic signatures, personalized stamps have been a popular form of identification for formal documents in East Asia. These identifiers – easily forged, but culturally ubi Read more…

Purdue Researchers Peer into the ‘Fog of the Machine Learning Accelerator War’

September 27, 2021

Making sense of ML performance and benchmark data is an ongoing challenge. In light of last week’s release of the most recent MLPerf (v1.1) inference results, now is perhaps a good time to review how valuable (or not) Read more…

Quantum Monte Carlo at Exascale Could Be Key to Finding New Semiconductor Materials

September 27, 2021

Researchers are urgently trying to identify possible materials to replace silicon-based semiconductors. The processing power in modern computers continues to increase even as the size of the silicon on which components a Read more…

The Case for an Edge-Driven Future for Supercomputing

September 24, 2021

“Exascale only becomes valuable when it’s creating and using data that we care about,” said Pete Beckman, co-director of the Northwestern-Argonne Institute of Science and Engineering (NAISE), at the most recent HPC Read more…

AWS Solution Channel

Introducing AWS ParallelCluster 3

Running HPC workloads, like computational fluid dynamics (CFD), molecular dynamics, or weather forecasting typically involves a lot of moving parts. You need a hundreds or thousands of compute cores, a job scheduler for keeping them fed, a shared file system that’s tuned for throughput or IOPS (or both), loads of libraries, a fast network, and a head node to make sense of all this. Read more…

Three Universities Team for NSF-Funded ‘ACES’ Reconfigurable Supercomputer Prototype

September 23, 2021

As Moore’s law slows, HPC developers are increasingly looking for speed gains in specialized code and specialized hardware – but this specialization, in turn, can make testing and deploying code trickier than ever. Now, researchers from Texas A&M University, the University of Illinois at Urbana... Read more…

Purdue Researchers Peer into the ‘Fog of the Machine Learning Accelerator War’

September 27, 2021

Making sense of ML performance and benchmark data is an ongoing challenge. In light of last week’s release of the most recent MLPerf (v1.1) inference results, Read more…

Quantum Monte Carlo at Exascale Could Be Key to Finding New Semiconductor Materials

September 27, 2021

Researchers are urgently trying to identify possible materials to replace silicon-based semiconductors. The processing power in modern computers continues to in Read more…

The Case for an Edge-Driven Future for Supercomputing

September 24, 2021

“Exascale only becomes valuable when it’s creating and using data that we care about,” said Pete Beckman, co-director of the Northwestern-Argonne Institut Read more…

Three Universities Team for NSF-Funded ‘ACES’ Reconfigurable Supercomputer Prototype

September 23, 2021

As Moore’s law slows, HPC developers are increasingly looking for speed gains in specialized code and specialized hardware – but this specialization, in turn, can make testing and deploying code trickier than ever. Now, researchers from Texas A&M University, the University of Illinois at Urbana... Read more…

Qubit Stream: Monte Carlo Advance, Infosys Joins the Fray, D-Wave Meeting Plans, and More

September 23, 2021

It seems the stream of quantum computing reports never ceases. This week – IonQ and Goldman Sachs tackle Monte Carlo on quantum hardware, Cambridge Quantum pu Read more…

Asetek Announces It Is Exiting HPC to Protect Future Profitability

September 22, 2021

Liquid cooling specialist Asetek, well-known in HPC circles for its direct-to-chip cooling technology that is inside some of the fastest supercomputers in the world, announced today that it is exiting the HPC space amid multiple supply chain issues related to the pandemic. Although pandemic supply chain... Read more…

TACC Supercomputer Delves Into Protein Interactions

September 22, 2021

Adenosine triphosphate (ATP) is a compound used to funnel energy from mitochondria to other parts of the cell, enabling energy-driven functions like muscle contractions. For ATP to flow, though, the interaction between the hexokinase-II (HKII) enzyme and the proteins found in a specific channel on the mitochondria’s outer membrane. Now, simulations conducted on supercomputers at the Texas Advanced Computing Center (TACC) have simulated... Read more…

The Latest MLPerf Inference Results: Nvidia GPUs Hold Sway but Here Come CPUs and Intel

September 22, 2021

The latest round of MLPerf inference benchmark (v 1.1) results was released today and Nvidia again dominated, sweeping the top spots in the closed (apples-to-ap Read more…

Ahead of ‘Dojo,’ Tesla Reveals Its Massive Precursor Supercomputer

June 22, 2021

In spring 2019, Tesla made cryptic reference to a project called Dojo, a “super-powerful training computer” for video data processing. Then, in summer 2020, Tesla CEO Elon Musk tweeted: “Tesla is developing a [neural network] training computer called Dojo to process truly vast amounts of video data. It’s a beast! … A truly useful exaflop at de facto FP32.” Read more…

Enter Dojo: Tesla Reveals Design for Modular Supercomputer & D1 Chip

August 20, 2021

Two months ago, Tesla revealed a massive GPU cluster that it said was “roughly the number five supercomputer in the world,” and which was just a precursor to Tesla’s real supercomputing moonshot: the long-rumored, little-detailed Dojo system. “We’ve been scaling our neural network training compute dramatically over the last few years,” said Milan Kovac, Tesla’s director of autopilot engineering. Read more…

Esperanto, Silicon in Hand, Champions the Efficiency of Its 1,092-Core RISC-V Chip

August 27, 2021

Esperanto Technologies made waves last December when it announced ET-SoC-1, a new RISC-V-based chip aimed at machine learning that packed nearly 1,100 cores onto a package small enough to fit six times over on a single PCIe card. Now, Esperanto is back, silicon in-hand and taking aim... Read more…

CentOS Replacement Rocky Linux Is Now in GA and Under Independent Control

June 21, 2021

The Rocky Enterprise Software Foundation (RESF) is announcing the general availability of Rocky Linux, release 8.4, designed as a drop-in replacement for the soon-to-be discontinued CentOS. The GA release is launching six-and-a-half months after Red Hat deprecated its support for the widely popular, free CentOS server operating system. The Rocky Linux development effort... Read more…

Intel Completes LLVM Adoption; Will End Updates to Classic C/C++ Compilers in Future

August 10, 2021

Intel reported in a blog this week that its adoption of the open source LLVM architecture for Intel’s C/C++ compiler is complete. The transition is part of In Read more…

Hot Chips: Here Come the DPUs and IPUs from Arm, Nvidia and Intel

August 25, 2021

The emergence of data processing units (DPU) and infrastructure processing units (IPU) as potentially important pieces in cloud and datacenter architectures was Read more…

AMD-Xilinx Deal Gains UK, EU Approvals — China’s Decision Still Pending

July 1, 2021

AMD’s planned acquisition of FPGA maker Xilinx is now in the hands of Chinese regulators after needed antitrust approvals for the $35 billion deal were receiv Read more…

Google Launches TPU v4 AI Chips

May 20, 2021

Google CEO Sundar Pichai spoke for only one minute and 42 seconds about the company’s latest TPU v4 Tensor Processing Units during his keynote at the Google I Read more…

Leading Solution Providers

Contributors

HPE Wins $2B GreenLake HPC-as-a-Service Deal with NSA

September 1, 2021

In the heated, oft-contentious, government IT space, HPE has won a massive $2 billion contract to provide HPC and AI services to the United States’ National Security Agency (NSA). Following on the heels of the now-canceled $10 billion JEDI contract (reissued as JWCC) and a $10 billion... Read more…

10nm, 7nm, 5nm…. Should the Chip Nanometer Metric Be Replaced?

June 1, 2020

The biggest cool factor in server chips is the nanometer. AMD beating Intel to a CPU built on a 7nm process node* – with 5nm and 3nm on the way – has been i Read more…

Julia Update: Adoption Keeps Climbing; Is It a Python Challenger?

January 13, 2021

The rapid adoption of Julia, the open source, high level programing language with roots at MIT, shows no sign of slowing according to data from Julialang.org. I Read more…

Quantum Roundup: IBM, Rigetti, Phasecraft, Oxford QC, China, and More

July 13, 2021

IBM yesterday announced a proof for a quantum ML algorithm. A week ago, it unveiled a new topology for its quantum processors. Last Friday, the Technical Univer Read more…

Frontier to Meet 20MW Exascale Power Target Set by DARPA in 2008

July 14, 2021

After more than a decade of planning, the United States’ first exascale computer, Frontier, is set to arrive at Oak Ridge National Laboratory (ORNL) later this year. Crossing this “1,000x” horizon required overcoming four major challenges: power demand, reliability, extreme parallelism and data movement. Read more…

Intel Launches 10nm ‘Ice Lake’ Datacenter CPU with Up to 40 Cores

April 6, 2021

The wait is over. Today Intel officially launched its 10nm datacenter CPU, the third-generation Intel Xeon Scalable processor, codenamed Ice Lake. With up to 40 Read more…

Intel Unveils New Node Names; Sapphire Rapids Is Now an ‘Intel 7’ CPU

July 27, 2021

What's a preeminent chip company to do when its process node technology lags the competition by (roughly) one generation, but outmoded naming conventions make it seem like it's two nodes behind? For Intel, the response was to change how it refers to its nodes with the aim of better reflecting its positioning within the leadership semiconductor manufacturing space. Intel revealed its new node nomenclature, and... Read more…

The Latest MLPerf Inference Results: Nvidia GPUs Hold Sway but Here Come CPUs and Intel

September 22, 2021

The latest round of MLPerf inference benchmark (v 1.1) results was released today and Nvidia again dominated, sweeping the top spots in the closed (apples-to-ap Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire