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” (http://www.initiative-hpc-pme.org/), 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 (http://www.fortissimo-project.eu/index.html) 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 (http://www.theubercloud.com/hpc-experiment/), 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.

david-loureiro-chapo_vignette

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!

CMU’s Latest “Card Shark” – Libratus – is Beating the Poker Pros (Again)

January 20, 2017

It’s starting to look like Carnegie Mellon University has a gambling problem – can’t stay away from the poker table. Read more…

By John Russell

IDG to Be Bought by Chinese Investors; IDC to Spin Out HPC Group

January 19, 2017

US-based publishing and investment firm International Data Group, Inc. (IDG) will be acquired by a pair of Chinese investors, China Oceanwide Holdings Group Co., Ltd. Read more…

By Tiffany Trader

Weekly Twitter Roundup (Jan. 19, 2017)

January 19, 2017

Here at HPCwire, we aim to keep the HPC community apprised of the most relevant and interesting news items that get tweeted throughout the week. Read more…

By Thomas Ayres

France’s CEA and Japan’s RIKEN to Partner on ARM and Exascale

January 19, 2017

France’s CEA and Japan’s RIKEN institute announced a multi-faceted five-year collaboration to advance HPC generally and prepare for exascale computing. Among the particulars are efforts to: build out the ARM ecosystem; work on code development and code sharing on the existing and future platforms; share expertise in specific application areas (material and seismic sciences for example); improve techniques for using numerical simulation with big data; and expand HPC workforce training. It seems to be a very full agenda. Read more…

By Nishi Katsuya and John Russell

HPE Extreme Performance Solutions

Remote Visualization: An Integral Technology for Upstream Oil & Gas

As the exploration and production (E&P) of natural resources evolves into an even more complex and vital task, visualization technology has become integral for the upstream oil and gas industry. Read more…

ARM Waving: Attention, Deployments, and Development

January 18, 2017

It’s been a heady two weeks for the ARM HPC advocacy camp. At this week’s Mont-Blanc Project meeting held at the Barcelona Supercomputer Center, Cray announced plans to build an ARM-based supercomputer in the U.K. while Mont-Blanc selected Cavium’s ThunderX2 ARM chip for its third phase of development. Last week, France’s CEA and Japan’s Riken announced a deep collaboration aimed largely at fostering the ARM ecosystem. This activity follows a busy 2016 when SoftBank acquired ARM, OpenHPC announced ARM support, ARM released its SVE spec, Fujistu chose ARM for the post K machine, and ARM acquired HPC tool provider Allinea in December. Read more…

By John Russell

Women Coders from Russia, Italy, and Poland Top Study

January 17, 2017

According to a study posted on HackerRank today the best women coders as judged by performance on HackerRank challenges come from Russia, Italy, and Poland. Read more…

By John Russell

Spurred by Global Ambitions, Inspur in Joint HPC Deal with DDN

January 17, 2017

Inspur, the fast-growth cloud computing and server vendor from China that has several systems on the current Top500 list, and DDN, a leader in high-end storage, have announced a joint sales and marketing agreement to produce solutions based on DDN storage platforms integrated with servers, networking, software and services from Inspur. Read more…

By Doug Black

Weekly Twitter Roundup (Jan. 12, 2017)

January 12, 2017

Here at HPCwire, we aim to keep the HPC community apprised of the most relevant and interesting news items that get tweeted throughout the week. Read more…

By Thomas Ayres

IDG to Be Bought by Chinese Investors; IDC to Spin Out HPC Group

January 19, 2017

US-based publishing and investment firm International Data Group, Inc. (IDG) will be acquired by a pair of Chinese investors, China Oceanwide Holdings Group Co., Ltd. Read more…

By Tiffany Trader

France’s CEA and Japan’s RIKEN to Partner on ARM and Exascale

January 19, 2017

France’s CEA and Japan’s RIKEN institute announced a multi-faceted five-year collaboration to advance HPC generally and prepare for exascale computing. Among the particulars are efforts to: build out the ARM ecosystem; work on code development and code sharing on the existing and future platforms; share expertise in specific application areas (material and seismic sciences for example); improve techniques for using numerical simulation with big data; and expand HPC workforce training. It seems to be a very full agenda. Read more…

By Nishi Katsuya and John Russell

ARM Waving: Attention, Deployments, and Development

January 18, 2017

It’s been a heady two weeks for the ARM HPC advocacy camp. At this week’s Mont-Blanc Project meeting held at the Barcelona Supercomputer Center, Cray announced plans to build an ARM-based supercomputer in the U.K. while Mont-Blanc selected Cavium’s ThunderX2 ARM chip for its third phase of development. Last week, France’s CEA and Japan’s Riken announced a deep collaboration aimed largely at fostering the ARM ecosystem. This activity follows a busy 2016 when SoftBank acquired ARM, OpenHPC announced ARM support, ARM released its SVE spec, Fujistu chose ARM for the post K machine, and ARM acquired HPC tool provider Allinea in December. Read more…

By John Russell

Spurred by Global Ambitions, Inspur in Joint HPC Deal with DDN

January 17, 2017

Inspur, the fast-growth cloud computing and server vendor from China that has several systems on the current Top500 list, and DDN, a leader in high-end storage, have announced a joint sales and marketing agreement to produce solutions based on DDN storage platforms integrated with servers, networking, software and services from Inspur. Read more…

By Doug Black

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

UberCloud Cites Progress in HPC Cloud Computing

January 10, 2017

200 HPC cloud experiments, 80 case studies, and a ton of hands-on experience gained, that’s the harvest of four years of UberCloud HPC Experiments. Read more…

By Wolfgang Gentzsch and Burak Yenier

A Conversation with Women in HPC Director Toni Collis

January 6, 2017

In this SC16 video interview, HPCwire Managing Editor Tiffany Trader sits down with Toni Collis, the director and founder of the Women in HPC (WHPC) network, to discuss the strides made since the organization’s debut in 2014. Read more…

By Tiffany Trader

BioTeam’s Berman Charts 2017 HPC Trends in Life Sciences

January 4, 2017

Twenty years ago high performance computing was nearly absent from life sciences. Today it’s used throughout life sciences and biomedical research. Genomics and the data deluge from modern lab instruments are the main drivers, but so is the longer-term desire to perform predictive simulation in support of Precision Medicine (PM). There’s even a specialized life sciences supercomputer, ‘Anton’ from D.E. Shaw Research, and the Pittsburgh Supercomputing Center is standing up its second Anton 2 and actively soliciting project proposals. There’s a lot going on. Read more…

By John Russell

AWS Beats Azure to K80 General Availability

September 30, 2016

Amazon Web Services has seeded its cloud with Nvidia Tesla K80 GPUs to meet the growing demand for accelerated computing across an increasingly-diverse range of workloads. The P2 instance family is a welcome addition for compute- and data-focused users who were growing frustrated with the performance limitations of Amazon's G2 instances, which are backed by three-year-old Nvidia GRID K520 graphics cards. Read more…

By Tiffany Trader

US, China Vie for Supercomputing Supremacy

November 14, 2016

The 48th edition of the TOP500 list is fresh off the presses and while there is no new number one system, as previously teased by China, there are a number of notable entrants from the US and around the world and significant trends to report on. Read more…

By Tiffany Trader

For IBM/OpenPOWER: Success in 2017 = (Volume) Sales

January 11, 2017

To a large degree IBM and the OpenPOWER Foundation have done what they said they would – assembling a substantial and growing ecosystem and bringing Power-based products to market, all in about three years. Read more…

By John Russell

Vectors: How the Old Became New Again in Supercomputing

September 26, 2016

Vector instructions, once a powerful performance innovation of supercomputing in the 1970s and 1980s became an obsolete technology in the 1990s. But like the mythical phoenix bird, vector instructions have arisen from the ashes. Here is the history of a technology that went from new to old then back to new. Read more…

By Lynd Stringer

Container App ‘Singularity’ Eases Scientific Computing

October 20, 2016

HPC container platform Singularity is just six months out from its 1.0 release but already is making inroads across the HPC research landscape. It's in use at Lawrence Berkeley National Laboratory (LBNL), where Singularity founder Gregory Kurtzer has worked in the High Performance Computing Services (HPCS) group for 16 years. Read more…

By Tiffany Trader

Dell EMC Engineers Strategy to Democratize HPC

September 29, 2016

The freshly minted Dell EMC division of Dell Technologies is on a mission to take HPC mainstream with a strategy that hinges on engineered solutions, beginning with a focus on three industry verticals: manufacturing, research and life sciences. "Unlike traditional HPC where everybody bought parts, assembled parts and ran the workloads and did iterative engineering, we want folks to focus on time to innovation and let us worry about the infrastructure," said Jim Ganthier, senior vice president, validated solutions organization at Dell EMC Converged Platforms Solution Division. Read more…

By Tiffany Trader

Lighting up Aurora: Behind the Scenes at the Creation of the DOE’s Upcoming 200 Petaflops Supercomputer

December 1, 2016

In April 2015, U.S. Department of Energy Undersecretary Franklin Orr announced that Intel would be the prime contractor for Aurora: Read more…

By Jan Rowell

Enlisting Deep Learning in the War on Cancer

December 7, 2016

Sometime in Q2 2017 the first ‘results’ of the Joint Design of Advanced Computing Solutions for Cancer (JDACS4C) will become publicly available according to Rick Stevens. He leads one of three JDACS4C pilot projects pressing deep learning (DL) into service in the War on Cancer. Read more…

By John Russell

Leading Solution Providers

D-Wave SC16 Update: What’s Bo Ewald Saying These Days

November 18, 2016

Tucked in a back section of the SC16 exhibit hall, quantum computing pioneer D-Wave has been talking up its new 2000-qubit processor announced in September. Forget for a moment the criticism sometimes aimed at D-Wave. This small Canadian company has sold several machines including, for example, ones to Lockheed and NASA, and has worked with Google on mapping machine learning problems to quantum computing. In July Los Alamos National Laboratory took possession of a 1000-quibit D-Wave 2X system that LANL ordered a year ago around the time of SC15. Read more…

By John Russell

CPU Benchmarking: Haswell Versus POWER8

June 2, 2015

With OpenPOWER activity ramping up and IBM’s prominent role in the upcoming DOE machines Summit and Sierra, it’s a good time to look at how the IBM POWER CPU stacks up against the x86 Xeon Haswell CPU from Intel. Read more…

By Tiffany Trader

Nvidia Sees Bright Future for AI Supercomputing

November 23, 2016

Graphics chipmaker Nvidia made a strong showing at SC16 in Salt Lake City last week. Read more…

By Tiffany Trader

Beyond von Neumann, Neuromorphic Computing Steadily Advances

March 21, 2016

Neuromorphic computing – brain inspired computing – has long been a tantalizing goal. The human brain does with around 20 watts what supercomputers do with megawatts. And power consumption isn’t the only difference. Fundamentally, brains ‘think differently’ than the von Neumann architecture-based computers. While neuromorphic computing progress has been intriguing, it has still not proven very practical. Read more…

By John Russell

The Exascale Computing Project Awards $39.8M to 22 Projects

September 7, 2016

The Department of Energy’s Exascale Computing Project (ECP) hit an important milestone today with the announcement of its first round of funding, moving the nation closer to its goal of reaching capable exascale computing by 2023. Read more…

By Tiffany Trader

BioTeam’s Berman Charts 2017 HPC Trends in Life Sciences

January 4, 2017

Twenty years ago high performance computing was nearly absent from life sciences. Today it’s used throughout life sciences and biomedical research. Genomics and the data deluge from modern lab instruments are the main drivers, but so is the longer-term desire to perform predictive simulation in support of Precision Medicine (PM). There’s even a specialized life sciences supercomputer, ‘Anton’ from D.E. Shaw Research, and the Pittsburgh Supercomputing Center is standing up its second Anton 2 and actively soliciting project proposals. There’s a lot going on. Read more…

By John Russell

Dell Knights Landing Machine Sets New STAC Records

November 2, 2016

The Securities Technology Analysis Center, commonly known as STAC, has released a new report characterizing the performance of the Knight Landing-based Dell PowerEdge C6320p server on the STAC-A2 benchmarking suite, widely used by the financial services industry to test and evaluate computing platforms. The Dell machine has set new records for both the baseline Greeks benchmark and the large Greeks benchmark. Read more…

By Tiffany Trader

What Knights Landing Is Not

June 18, 2016

As we get ready to launch the newest member of the Intel Xeon Phi family, code named Knights Landing, it is natural that there be some questions and potentially some confusion. Read more…

By James Reinders, Intel

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