Solving Simulation Complexity

By David Lourerio

July 15, 2014

Although HPC has helped solve important problems in nuclear physics, earth sciences, meteorology, etc. since the 1960s, HPC has traditionally existed only for specialists. But, with the democratization of x86 servers, large storage systems, and high-end networking technologies, companies and research facilities can now buy clusters at a reasonable ratio (power/cost) with very powerful, complex technologies or get access to remote HPC cloud platforms.

However, even though the resources are available, widespread use has been limited due to the difficulties in accessing and using the resources and/or adapting existing HPC software and hardware that still exist. Back in the nineties, researchers could spend time getting used to those hurdles, but today business ROI drives engineers and researchers to produce results in much less time. As a result, overcoming the HPC access and usability hurdles has become crucial and this has been further exacerbated by the fact that many more users of large-scale platforms are not specialists of HPC use and programming.

This article addresses the need for HPC to become a tool that’s as simple and transparent as possible so that small and medium businesses (SMBs) can easily access the resources of mid-sized clusters and use complex applications on hybrid HPC resources. To achieve this without extensive financial outlay, end users need to execute and control the simulation of applications and data directly from their desktops.

The HPC Challenge for the Smaller Business

While R&D labs and large companies may be accustomed to accessing and exploiting large computing infrastructures, small-to-medium-businesses and smaller business units within large companies that have no dedicated computing resources or HPC experts must now deal with increasing amounts and complexity of data. These smaller groups cannot afford to abandon the advantages HPC provides, but need a way to access the processing power and capabilities that mid-sized clusters offer. This need for readily available “super applications” is first referred to by Dr. Erik Deumens, Director of Research Computing at the University of Florida in his paper “What Drives Investment in the Middle of HPC?” to describe simulations that run on mid-sized computing clusters that are fully accessible on the end-user desktop.

At an international scale, some countries have tried to address this through various resources. In France, INRIA, BPI (the French public investment bank), and GENCI launched “Initiative HPC-PME” (, an initiative aiming at providing knowledge, funds, and computing resources to enable simulation software to be powered on HPC resources for SMBs. Free Field Technologies, a French SME, participated in this program and in this testimonial, they present how improved simulation times of HPC helped them win Airbus as a customer.

In Europe, “Fortissimo” was ( launched in October 2013. In this initiative, SMBs needing HPC computation gain access to the resources of a research lab and a computing facility. SMEs like Pipistrel, for example, are using these HPC facilities to improve their simulations of lightweight aircraft designs.

In Silicon Valley, ÜberCloud (, launched by Burak Yenier and Wolfgang Gentzsch, was established to show how the SaaS (Software-as-a-Service) model can be used for HPC simulation. A number of large companies, software providers, and computing facilities have now implemented these technologies:

  • “High-resolution Computer Simulations of Blow-off in Combustion Systems” involving CSE, a US-based company
  • “Drifting Snow Around Arbitrary Structures” where end-users were SMEs like Binkz. Inc, a Canadian Based company
  • “Performance Analysis of GROMACS Molecular Dynamics for Simulating Enzyme Substrate” with the Indian SME called Polyclone Bioservices, and the second one has been released last week with use-cases about, or in the field of biology with a use case around.

Moving the Needle Forward

Although these advances have been implemented by some of these initiatives, there’s a need to take the solution further, to provide broad-scale access to many users. To understand what’s needed, let’s first take a look at what these users have in common.

All these different types of users need to upload their data, launch (large-scale) non-interactive simulations, and post-process them. This workflow might be business- or research-centered, but for both communities, there’s a very real need to get better results faster. This need far outweighs knowing if the computation involves using GPUs, fat nodes, or an ultra-fancy middleware designed specially for their purpose.

A preamble of all these tasks is access to the applications. The SaaS (Software-as-a-Service) model does fit with this goal. Through the browser we use every day to check our e-mail or visit websites, we can also work on complex and resource-demanding applications.

What barriers do SMBs need removed from HPC?

The ability to create structures that allow non-technical users to directly access hybrid resources is essential. Here we explore the characteristics of a web portal that would enable SMBs to easily gain access to them.

Simplified universal access—To accommodate bandwidth, the interface must be as light as possible: no browser plugins, no java applets, no flash support, or port opening required. By stripping out all of these dependencies, the interface becomes “vanilla”—able to interface with the researcher’s smart phone, desktop, or tablet regardless of its operating system.

This simplified interface creates the necessary foundation for a SaaS model to access HPC simulation software running remotely on computing clusters. Figure 1 offers an example of interface that is able to adapt to various terminals thanks to the latest HTML/CSS/JavaScript frameworks. This framework provides access to the basic info a user needs to start working: his current projects, past jobs, etc., from anywhere.

Screen Shot 2014-07-15 at 12.10.21 PM

Fig. 1 Example of interface providing access to user’s projects and his previous works

Secured access—Small businesses also need secure access. There’s been a lot of discussion about what should be used—X.509 certificates, login and passwords, SSH public and private keys. In fact, there is no standard way of achieving security. It depends heavily on the policies you want to set-up.

Inside the clusters, you could use any of these methods. But from the user’s point of view, the processes must be unified with at least a login and password that then manages every security system underneath. By doing this, the interface reduces the barrier for the end-user.

And, transfers must be, of course, encrypted to ensure no disseminations to competitors for example.

Familiar file structure—When uploading data or dealing with the HPC computing facilities, users need something that’s familiar, that doesn’t change their habits, such as classical files managers of Windows or FTP clients. This ensures that users can process vast amounts of data without having to take an excessive amount of time to prepare the files and to post process the results afterwards.

Remote Visualization—Today, computing facilities provide both computing and graphical resources. To be able to run non-interactive computations and to then do graphical post-processing on the same site is a great improvement for end-users. If the workflow interface runs fluently from computation into post-processing, then users no longer have to go onsite and disturb administrators to transfer video streams. Instead they can use remote desktop technologies from the same interface to bridge from simulation to graphical post-processing without any additional requirements.

Link with the previous capability, e.g. simplified data transfers, the traditional workflow consisting of input simulation data staging, processind and post-processing can be run in a drastically reduced timeframe.

Screen Shot 2014-07-15 at 12.09.55 PM

Fig. 2 File management interface allowing users to transfer to and from the computing resources

Simplified graphical interface—While there are many ways to access applications—home-made scripts, proprietary code, web portals—the interface needs to offer users a way to define specific parameters or modify scripts depending on the outputs they seek. This management of applications has to be as simple as possible and take the least amount of time.

The idea of using XML files to define any kind of interfaces was vogue for a while, but such interfaces were quickly recognized as just hype since they were not productive. Instead, what’s needed is a graphical tool that provides a way to design the interface that the end-users will use to interact with the scripts that execute their applications.

In designing graphical interface access, it’s easy to go overboard and provide full access to scripts and the underlying plumbing, which adds to system complexity. Well-defined and flexible right management must be provided. Only users developing scripts should be allowed to add, update, and modify applications, and only managers should be able to access usage reporting, user management, etc.

Streamlined—As shown in Figure 3, integrating an application should be no more complex than defining a script to execute, some documentation, and the input parameters the user must provide. A specific form directing the application use can then launch for the end-user. This efficiency helps the user concentrate on the most important part of their task—running the simulation with good input data.

Screen Shot 2014-07-15 at 12.10.49 PM

Fig. 3 Web interface providing an easy way to design submission forms for non-interactive applications

Billing the user—Once a framework provides access to data and the applications and links these to a global, simple-to-use workflow, the resources need to be monitored and time spent needs to be easily allocated to cost centers. Whether computing hours are divided between certain computing facilities or allocated to business units in companies, clear and precise accounting must detail who had access to the applications and resources.

Usage reporting also needs to be available in a digital format that interfaces to accounting packages for invoice creation or be integrated into existing quota systems. Figure 4 shows an interface presenting accounting and monitoring of resources and applications usage that are the basis of billing and invoicing.

Screen Shot 2014-07-15 at 12.11.05 PM

Fig. 4 Usage statistics showing the consumption of a project on different clusters

Democratized HPC

It is through these types of improvements and simplifications that SMB employees will gain access to HPC simulation. With such a simplified interface to powerful complex resources, businesses will boost productivity and be able to efficiently do their high-end computational work in much less time.

Removing HPC complexity from the game, streamlines data analysis and simulation for the SMBs, ensuring maximum productivity and increasing competitiveness.

About the Author

David Loureiro is the CEO and co-founder of SysFera, a software innovator that simplifies management and accessibility of high performance computing (HPC) environments. David holds a Master of Science in Applied Mathematics and started his career at INRIA working on distributed grid and cloud middleware in the INRIA research team called Avalon. His research interests are focused on cloud technologies, HPC resource management, distributed computing and scientific visualization web portals.


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!

RSC Reports 500Tflops, Hot Water Cooled System Deployed at JINR

April 18, 2018

RSC, developer of supercomputers and advanced HPC systems based in Russia, today reported deployment of “the world's first 100% ‘hot water’ liquid cooled supercomputer” at Joint Institute for Nuclear Research (JI Read more…

By Staff

New Device Spots Quantum Particle ‘Fingerprint’

April 18, 2018

Majorana particles have been observed by university researchers employing a device consisting of layers of magnetic insulators on a superconducting material. The advance opens the door to controlling the elusive particle Read more…

By George Leopold

Cray Rolls Out AMD-Based CS500; More to Follow?

April 18, 2018

Cray was the latest OEM to bring AMD back into the fold with introduction today of a CS500 option based on AMD’s Epyc processor line. The move follows Cray’s introduction of an ARM-based system (XC-50) last November. Read more…

By John Russell

HPE Extreme Performance Solutions

Hybrid HPC is Speeding Time to Insight and Revolutionizing Medicine

High performance computing (HPC) is a key driver of success in many verticals today, and health and life science industries are extensively leveraging these capabilities. Read more…

Hennessy & Patterson: A New Golden Age for Computer Architecture

April 17, 2018

On Monday June 4, 2018, 2017 A.M. Turing Award Winners John L. Hennessy and David A. Patterson will deliver the Turing Lecture at the 45th International Symposium on Computer Architecture (ISCA) in Los Angeles. The Read more…

By Staff

Cray Rolls Out AMD-Based CS500; More to Follow?

April 18, 2018

Cray was the latest OEM to bring AMD back into the fold with introduction today of a CS500 option based on AMD’s Epyc processor line. The move follows Cray’ Read more…

By John Russell

IBM: Software Ecosystem for OpenPOWER is Ready for Prime Time

April 16, 2018

With key pieces of the IBM/OpenPOWER versus Intel/x86 gambit settling into place – e.g., the arrival of Power9 chips and Power9-based systems, hyperscaler sup Read more…

By John Russell

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

Cloud-Readiness and Looking Beyond Application Scaling

April 11, 2018

There are two aspects to consider when determining if an application is suitable for running in the cloud. The first, which we will discuss here under the title Read more…

By Chris Downing

Transitioning from Big Data to Discovery: Data Management as a Keystone Analytics Strategy

April 9, 2018

The past 10-15 years has seen a stark rise in the density, size, and diversity of scientific data being generated in every scientific discipline in the world. Key among the sciences has been the explosion of laboratory technologies that generate large amounts of data in life-sciences and healthcare research. Large amounts of data are now being stored in very large storage name spaces, with little to no organization and a general unease about how to approach analyzing it. Read more…

By Ari Berman, BioTeam, Inc.

IBM Expands Quantum Computing Network

April 5, 2018

IBM is positioning itself as a first mover in establishing the era of commercial quantum computing. The company believes in order for quantum to work, taming qu Read more…

By Tiffany Trader

FY18 Budget & CORAL-2 – Exascale USA Continues to Move Ahead

April 2, 2018

It was not pretty. However, despite some twists and turns, the federal government’s Fiscal Year 2018 (FY18) budget is complete and ended with some very positi Read more…

By Alex R. Larzelere

Nvidia Ups Hardware Game with 16-GPU DGX-2 Server and 18-Port NVSwitch

March 27, 2018

Nvidia unveiled a raft of new products from its annual technology conference in San Jose today, and despite not offering up a new chip architecture, there were still a few surprises in store for HPC hardware aficionados. Read more…

By Tiffany Trader

Inventor Claims to Have Solved Floating Point Error Problem

January 17, 2018

"The decades-old floating point error problem has been solved," proclaims a press release from inventor Alan Jorgensen. The computer scientist has filed for and Read more…

By Tiffany Trader

Researchers Measure Impact of ‘Meltdown’ and ‘Spectre’ Patches on HPC Workloads

January 17, 2018

Computer scientists from the Center for Computational Research, State University of New York (SUNY), University at Buffalo have examined the effect of Meltdown Read more…

By Tiffany Trader

Russian Nuclear Engineers Caught Cryptomining on Lab Supercomputer

February 12, 2018

Nuclear scientists working at the All-Russian Research Institute of Experimental Physics (RFNC-VNIIEF) have been arrested for using lab supercomputing resources to mine crypto-currency, according to a report in Russia’s Interfax News Agency. Read more…

By Tiffany Trader

How the Cloud Is Falling Short for HPC

March 15, 2018

The last couple of years have seen cloud computing gradually build some legitimacy within the HPC world, but still the HPC industry lies far behind enterprise I Read more…

By Chris Downing

Chip Flaws ‘Meltdown’ and ‘Spectre’ Loom Large

January 4, 2018

The HPC and wider tech community have been abuzz this week over the discovery of critical design flaws that impact virtually all contemporary microprocessors. T Read more…

By Tiffany Trader

Fast Forward: Five HPC Predictions for 2018

December 21, 2017

What’s on your list of high (and low) lights for 2017? Volta 100’s arrival on the heels of the P100? Appearance, albeit late in the year, of IBM’s Power9? Read more…

By John Russell

How Meltdown and Spectre Patches Will Affect HPC Workloads

January 10, 2018

There have been claims that the fixes for the Meltdown and Spectre security vulnerabilities, named the KPTI (aka KAISER) patches, are going to affect applicatio Read more…

By Rosemary Francis

Nvidia Responds to Google TPU Benchmarking

April 10, 2017

Nvidia highlights strengths of its newest GPU silicon in response to Google's report on the performance and energy advantages of its custom tensor processor. Read more…

By Tiffany Trader

Leading Solution Providers

Deep Learning at 15 PFlops Enables Training for Extreme Weather Identification at Scale

March 19, 2018

Petaflop per second deep learning training performance on the NERSC (National Energy Research Scientific Computing Center) Cori supercomputer has given climate Read more…

By Rob Farber

Lenovo Unveils Warm Water Cooled ThinkSystem SD650 in Rampup to LRZ Install

February 22, 2018

This week Lenovo took the wraps off the ThinkSystem SD650 high-density server with third-generation direct water cooling technology developed in tandem with par Read more…

By Tiffany Trader

AI Cloud Competition Heats Up: Google’s TPUs, Amazon Building AI Chip

February 12, 2018

Competition in the white hot AI (and public cloud) market pits Google against Amazon this week, with Google offering AI hardware on its cloud platform intended Read more…

By Doug Black

HPC and AI – Two Communities Same Future

January 25, 2018

According to Al Gara (Intel Fellow, Data Center Group), high performance computing and artificial intelligence will increasingly intertwine as we transition to Read more…

By Rob Farber

New Blueprint for Converging HPC, Big Data

January 18, 2018

After five annual workshops on Big Data and Extreme-Scale Computing (BDEC), a group of international HPC heavyweights including Jack Dongarra (University of Te Read more…

By John Russell

US Plans $1.8 Billion Spend on DOE Exascale Supercomputing

April 11, 2018

On Monday, the United States Department of Energy announced its intention to procure up to three exascale supercomputers at a cost of up to $1.8 billion with th Read more…

By Tiffany Trader

Momentum Builds for US Exascale

January 9, 2018

2018 looks to be a great year for the U.S. exascale program. The last several months of 2017 revealed a number of important developments that help put the U.S. Read more…

By Alex R. Larzelere

Google Chases Quantum Supremacy with 72-Qubit Processor

March 7, 2018

Google pulled ahead of the pack this week in the race toward "quantum supremacy," with the introduction of a new 72-qubit quantum processor called Bristlecone. Read more…

By Tiffany Trader

  • arrow
  • Click Here for More Headlines
  • arrow
Share This