Science On the Outskirts of In-Memory

By Nicole Hemsoth

September 4, 2013

In-memory computing has been an active topic of discussion in commercial “big data” circles, but a recent use case of its ability to address complex computational chemistry demands highlights its potential in scientific computing.

Today, GridGain Systems detailed how Portland State University made use of their In-Memory HPC offering in its attempt to build an adaptive learning system that will be able to detect diseases, offer medical diagnoses, and offer therapeutic recommendations based on biocompatible computers that can be embedded into living cells.

To highlight how the technology fits into the broader spectrum of high performance computing applications, we talked to the company’s VP of Product Management, Jon Webster. In addition to covering how this approach to in-memory computing differs from that which is being touted in the commercial sector, we hit on how it compares to other modes of handling massive datasets for scientific simulations, and how a sense of ROI comes through for users who could alternately simply throw more hardware at their problem.

GridGain’s approach to in-memory for HPC applications is somewhat different than what some of the other “in-memory” companies are producing. In fact, they term this offering as a “real-time, high performance distributed computation framework” which, for those who pay attention to another important movement from the more commercial side of the performance house, sounds a lot like Hadoop/MapReduce.

The two are different, says GridGain, noting that “if Hadoop MapReduce tasks take input from disk, produce intermediate results on disk and then output that result onto disk, GridGain does everything Hadoop does in memory—so in other words, it takes input from memory via direct API calls, produces intermediate results in memory and then creates results in-memory as well.”

In other words, it’s not just about storage, which is what so many vendors on the mainstream side are talking about when they use the term in-memory, says Webster. He says that the current approaches aren’t enough to handle complex workloads—they require what GridGain offers, at least for HPC workloads, he argues, which is actually embedding a purpose-built compute engine across a large partitioned in-memory database (which is another component to their offering) so you have all your data in memory. In essence, instead of grabbing data, processing it and putting it back, this allows users to process it with locality in mind so that data movement can be minimized.

GridGain’s framework seeks to support different execution modes, including MapReduce processing, while also offering support for other common HPC-oriented models (MPP, MPI and RPC) to help broaden their base of HPC customers.

They’ve been able to serve a number of other HPC-oriented users with this approach, including using it in financial markets for fast trade matching, risk management. Other industries that tend to fall outside the purview of what has always been considered traditional HPC like online gaming and real-time ad targeting represent a “filtering down” of technologies that have been proven at massive scale.

As you’ll hear in the interview above, this approach allowed Portland State’s researchers to do something that wouldn’t have been possible before with their current infrastructure. Webster also details what in-memory means for other HPC applications and how their approach to data-intensive workloads might evolve to meet other hardware and software architectures and frameworks.

Subscribe to HPCwire's Weekly Update!

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

A Big Memory Nvidia GH200 Next to Your Desk: Closer Than You Think

February 22, 2024

Students of the microprocessor may recall that the original 8086/8088 processors did not have floating point units. The motherboard often had an extra socket for an optional 8087 math coprocessor. The math coprocessor ma Read more…

IonQ Reports Advance on Path to Networked Quantum Computing

February 22, 2024

IonQ reported reaching a milestone in its efforts to use entangled photon-ion connectivity to scale its quantum computers. IonQ’s quantum computers are based on trapped ions which feature long coherence times and qubit Read more…

Apple Rolls out Post Quantum Security for iOS

February 21, 2024

Think implementing so-called Post Quantum Cryptography (PQC) isn't important because quantum computers able to decrypt current RSA codes don’t yet exist? Not Apple. Today the consumer electronics giant started rolling Read more…

GenAI Having Major Impact on Data Culture, Survey Says

February 21, 2024

While 2023 was the year of GenAI, the adoption rates for GenAI did not match expectations. Most organizations are continuing to invest in GenAI but are yet to derive any substantial value from it. However, the GenAI hyp Read more…

QED-C Issues New Quantum Benchmarking Paper

February 20, 2024

The Quantum Economic Development Consortium last week released a new paper on benchmarking – Quantum Algorithm Exploration using Application-Oriented Performance Benchmarks – that builds on earlier work and is an eff Read more…

AWS Solution Channel

Shutterstock 2283618597

Deep-dive into Ansys Fluent performance on Ansys Gateway powered by AWS

Today, we’re going to deep-dive into the performance and associated cost of running computational fluid dynamics (CFD) simulations on AWS using Ansys Fluent through the Ansys Gateway powered by AWS (or just “Ansys Gateway” for the rest of this post). Read more…

Atom Computing Reports Advance in Scaling Up Neutral Atom Qubit Arrays

February 15, 2024

The scale-up challenge facing quantum computing (QC) is daunting and varied. It’s commonly held that 1 million qubits (or more) will be needed to deliver practical fault tolerant QC. It’s also a varied challenge beca Read more…

A Big Memory Nvidia GH200 Next to Your Desk: Closer Than You Think

February 22, 2024

Students of the microprocessor may recall that the original 8086/8088 processors did not have floating point units. The motherboard often had an extra socket fo Read more…

Apple Rolls out Post Quantum Security for iOS

February 21, 2024

Think implementing so-called Post Quantum Cryptography (PQC) isn't important because quantum computers able to decrypt current RSA codes don’t yet exist? Not Read more…

QED-C Issues New Quantum Benchmarking Paper

February 20, 2024

The Quantum Economic Development Consortium last week released a new paper on benchmarking – Quantum Algorithm Exploration using Application-Oriented Performa Read more…

The Pulse of HPC: Tracking 4.5 Million Heartbeats of 3D Coronary Flow

February 15, 2024

Working in Duke University's Randles Lab, Cyrus Tanade, a National Science Foundation graduate student fellow and Ph.D. candidate in biomedical engineering, is Read more…

It Doesn’t Get Much SWEETER: The Winter HPC Computing Festival in Corpus Christi

February 14, 2024

(Main Photo by Visit Corpus Christi CrowdRiff) Texas A&M University's High-Performance Research Computing (HPRC) team hosted the "SWEETER Winter Comput Read more…

Q-Roundup: Diraq’s War Chest, DARPA’s Bet on Topological Qubits, Citi/Classiq Explore Optimization, WEF’s Quantum Blueprint

February 13, 2024

Yesterday, Australian start-up Diraq added $15 million to its war chest (now $120 million) to build a fault tolerant computer based on quantum dots. Last week D Read more…

2024 Winter Classic: Razor Thin Margins in HPL/HPCG

February 12, 2024

The first task for the 11 teams in the 2024 Winter Classic student cluster competition was to run and optimize the LINPACK and HPCG benchmarks. As usual, the Read more…

2024 Winter Classic: We’re Back!

February 9, 2024

The fourth edition of the Winter Classic Invitational Student Cluster Competition is up and running. This year, we have 11 teams of eager students representin Read more…

CORNELL I-WAY DEMONSTRATION PITS PARASITE AGAINST VICTIM

October 6, 1995

Ithaca, NY --Visitors to this year's Supercomputing '95 (SC'95) conference will witness a life-and-death struggle between parasite and victim, using virtual Read more…

SGI POWERS VIRTUAL OPERATING ROOM USED IN SURGEON TRAINING

October 6, 1995

Surgery simulations to date have largely been created through the development of dedicated applications requiring considerable programming and computer graphi Read more…

U.S. Will Relax Export Restrictions on Supercomputers

October 6, 1995

New York, NY -- U.S. President Bill Clinton has announced that he will definitely relax restrictions on exports of high-performance computers, giving a boost Read more…

Dutch HPC Center Will Have 20 GFlop, 76-Node SP2 Online by 1996

October 6, 1995

Amsterdam, the Netherlands -- SARA, (Stichting Academisch Rekencentrum Amsterdam), Academic Computing Services of Amsterdam recently announced that it has pur Read more…

Cray Delivers J916 Compact Supercomputer to Solvay Chemical

October 6, 1995

Eagan, Minn. -- Cray Research Inc. has delivered a Cray J916 low-cost compact supercomputer and Cray's UniChem client/server computational chemistry software Read more…

NEC Laboratory Reviews First Year of Cooperative Projects

October 6, 1995

Sankt Augustin, Germany -- NEC C&C (Computers and Communication) Research Laboratory at the GMD Technopark has wrapped up its first year of operation. Read more…

Sun and Sybase Say SQL Server 11 Benchmarks at 4544.60 tpmC

October 6, 1995

Mountain View, Calif. -- Sun Microsystems, Inc. and Sybase, Inc. recently announced the first benchmark results for SQL Server 11. The result represents a n Read more…

New Study Says Parallel Processing Market Will Reach $14B in 1999

October 6, 1995

Mountain View, Calif. -- A study by the Palo Alto Management Group (PAMG) indicates the market for parallel processing systems will increase at more than 4 Read more…

Leading Solution Providers

Contributors

CORNELL I-WAY DEMONSTRATION PITS PARASITE AGAINST VICTIM

October 6, 1995

Ithaca, NY --Visitors to this year's Supercomputing '95 (SC'95) conference will witness a life-and-death struggle between parasite and victim, using virtual Read more…

SGI POWERS VIRTUAL OPERATING ROOM USED IN SURGEON TRAINING

October 6, 1995

Surgery simulations to date have largely been created through the development of dedicated applications requiring considerable programming and computer graphi Read more…

U.S. Will Relax Export Restrictions on Supercomputers

October 6, 1995

New York, NY -- U.S. President Bill Clinton has announced that he will definitely relax restrictions on exports of high-performance computers, giving a boost Read more…

Dutch HPC Center Will Have 20 GFlop, 76-Node SP2 Online by 1996

October 6, 1995

Amsterdam, the Netherlands -- SARA, (Stichting Academisch Rekencentrum Amsterdam), Academic Computing Services of Amsterdam recently announced that it has pur Read more…

Cray Delivers J916 Compact Supercomputer to Solvay Chemical

October 6, 1995

Eagan, Minn. -- Cray Research Inc. has delivered a Cray J916 low-cost compact supercomputer and Cray's UniChem client/server computational chemistry software Read more…

NEC Laboratory Reviews First Year of Cooperative Projects

October 6, 1995

Sankt Augustin, Germany -- NEC C&C (Computers and Communication) Research Laboratory at the GMD Technopark has wrapped up its first year of operation. Read more…

Sun and Sybase Say SQL Server 11 Benchmarks at 4544.60 tpmC

October 6, 1995

Mountain View, Calif. -- Sun Microsystems, Inc. and Sybase, Inc. recently announced the first benchmark results for SQL Server 11. The result represents a n Read more…

New Study Says Parallel Processing Market Will Reach $14B in 1999

October 6, 1995

Mountain View, Calif. -- A study by the Palo Alto Management Group (PAMG) indicates the market for parallel processing systems will increase at more than 4 Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire