Avoiding Application Porting Pitfalls

By Tim Leite

September 28, 2007

Historically, compute clusters have emerged as a less expensive, more practical option for harnessing high performance computing power using systems that were already available in-house. In highly technical settings, such as academia and national laboratories, many researchers and IT managers could not afford to purchase supercomputers so they networked systems together to creatively solve complex computational problems.

The original Beowulf cluster built at NASA in the late 1990s is the epitome of this paradigm shift. Over the last decade, with the evolution of programming standards, refinements in packaging, and improvements in interconnect technology, compute clusters are becoming increasingly attractive to commercial companies. Commercial organizations are choosing cluster environments, not just for financial reasons, but also for their computational scalability. When companies need more power and reach, they simply add another server to their cluster. As a result, clusters have become more appealing to certain high-growth commercial sectors, such as financial services, as a viable alternative for high performance computing.

While there are many companies interested in taking advantage of clusters, many have not yet made the leap. One of the primary reasons for not moving to a cluster environment is that many of these organizations have legacy applications that run well on a traditional server. The cost to migrate the application to a cluster is too high. To further complicate the situation, the application may be a mission-critical asset and to attempt to migrate it to a new system is considered too risky.

Many programs that continue to run on VMS-based platforms fall into this category. The system is reliable and the application executes properly. So despite being considered by many as outdated technology, the organization relying on the VMS-based program would have no short-term migration plan.

However, there are factors driving change. From a performance perspective, compute clusters are becoming more powerful, so organizations are sacrificing performance by staying with outdated platforms. From a personnel perspective, keeping applications on older platforms is becoming riskier, as there are fewer and fewer trained experts in these older technology areas.

When applications are initially developed, there are steps that can be taken to make a future migration less painful and risky. For existing applications that require migration or porting, such as ones being moved to a cluster environment, there are a number of potential porting issues to address along the way. The following provides a brief overview of those issues and how companies can avoid them before they get started.

Preserving Computational Accuracy While Porting Proprietary Applications

While using standard software solutions in a compute cluster helps companies ensure application compatibility with minimum conversion issues, the truth is that many companies have a number of custom, proprietary applications that need to be ported. When porting proprietary applications, the real challenge is to ensure that computational accuracy stays intact when the process is complete.

One of the most reliable sources of computational integrity is commercial numerical libraries. Commercial libraries utilize the numerical representation of the architecture for computational consistency. For example, the convergence criteria for a nonlinear least squares optimization algorithm may be based on a system-specific parameter, such as the largest relative floating point spacing versus a hard-coded value. The hard-coded value may work fine on the original development system, but when porting that algorithm to a system with a different floating point representation, there is a high likelihood that the algorithm will not perform as expected. Relying on the commercial version of the algorithm will avoid these potential problems and significantly reduce the amount of debugging time needed when porting applications to a new environment. 

If proprietary applications are already developed, companies can retrofit them with commercial libraries before porting to a new platform. If the proprietary application is “home-grown,” an organization may consider substituting algorithms from a commercial library for algorithms that were developed in-house or obtained as open source. There are a variety of reasons why the home-grown application may not perform reliably on a new platform. The algorithm from a commercial library is designed to execute consistently across all supported platforms.

Optimizing Performance and Scalability without Sacrificing Portability

Hardware vendors offer companies more alternatives than ever before for setting up cluster environments. Besides the hardware, they also recommend applicable software as well as services. The hardware vendors have spent considerable effort to help customers optimize applications on their particular platform. These efforts by vendors to optimize the performance on the supported platform are truly a result of the evolution of high performance computing itself.

In its early days, the mechanisms to make high performance computing work were in the public domain. A good example is the Message Passing Interface (MPI), the defacto standard for many years for communication between processes in a compute cluster environment. As MPI has evolved, the major hardware vendors with compute cluster offerings have developed optimized message passing interfaces for their own platforms.

While it’s recommended to use these vendor optimized mechanisms for high performance applications, it will add complexity. When porting applications between hardware platforms, if the algorithms used in application development are home grown, they need to be thoroughly tested to ensure they perform reliably. Again, using algorithms from a commercial library designed to execute consistently across multiple supported platforms can reduce porting risks.

Porting Proprietary Applications in Different Languages

Porting can be problematic if an organization has developed applications in a variety of different languages such as Fortran, C or Java. Porting programs of this nature to a new environment introduces more obstacles than porting a single language program. Generally, an organization that has multiple language programs is intent on standardizing on one particular language and converting as many of the programs as possible to that language.

However, dealing with multiple porting components, a platform migration, a performance impact, and a language migration can quickly become very complex. As stated above, utilizing commercial libraries can ease this transition significantly. Some commercial libraries offer the same computational algorithms in multiple languages.

Therefore if a company has a program that utilizes an interpolation function from a library in a Fortran application and they choose to migrate to C, then they may reference the C version of that function without compromising the accuracy of the calculation. When factoring in a cluster environment in this scenario, the application performance also comes into question. Will the language-converted application perform well on the new system?

Again, third party technology should help in this area. If the application was written in-house or uses embedded public domain software, all of that code would need to be rewritten in the new language and optimized for performance. By relying on optimized versions of software from a vendor, the amount of recoding will be reduced and leveraging the performance of the new system may be automatic.

Libraries Are Gaining More Power in Parallel Processing

As compute clusters become more prevalent and powerful, computational libraries continue to evolve to assist the developer in leveraging the cluster technology. Building parallel processing-enabled applications can be difficult, and commercial libraries can help programmers avoid some of the issues associated with optimizing code for a cluster. In fact, some libraries have introduced techniques that assist not only the sophisticated programmer but also the novice distributed computing developer. Examples of such features include:

  • Functions to initialize the MPI environment and perform computations with minimal exposure to intricacies of MPI. (In general, the maturing of the MPI component of cluster-based solutions has resulted in fewer porting issues for developers.)
  • Functions to simplify the movement and formatting of data for use in an MPI environment.
  • Error checking techniques that not only provide descriptive error messages but also track the location of the error in a parallel environment.

In addition to the capabilities and techniques described above, another benefit of commercial libraries is simply risk reduction. The commercial library vendor will grow the capabilities of their library while continuing to address the computational accuracy, portability and language issues discussed earlier in this article.

Considerations for Clustering

To recap, before organizations take advantage of a compute cluster, they need to consider what kind of proprietary applications they already have, and what level of developer expertise exists to properly recompile, test, debug, and possibly convert to a new language before porting them to cluster systems.

Companies should also choose native libraries that can operate with a range of computing environments to avoid the pitfalls of porting, while still taking advantage of all the benefits of cluster systems. Knowing some of these pitfalls and complexities of porting to cluster systems will, in the long run, help companies save time and money.

—–

About the Author

Tim Leite is the Director of Corporate Development and Educational Programs for Visual Numerics, Inc. Tim is responsible for many of the product related corporate partnerships. In his education role, he is responsible for establishing partnerships with academic institutions and facilitating the computational requirements of researchers and instructors within the academic community.

Tim has been with Visual Numerics for 21 years in various roles. He started as a mathematical programmer working with algorithms in the areas of linear algebra, transforms, nonlinear systems of equations, and numerical optimization. He was also responsible for optimizing algorithm performance for high performance computing systems. Other roles at Visual Numerics included Technical Support Manager, Product Manager, and Software Development Director.

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!

Top500: US Maintains Performance Lead; Arm Tops Green500

November 18, 2019

The 54th Top500, revealed today at SC19, is a familiar list: the U.S. Summit (ORNL) and Sierra (LLNL) machines, offering 148.6 and 94.6 petaflops respectively, remain in first and second place. The only new entrants in t Read more…

By Tiffany Trader

ScaleMatrix and Nvidia Launch ‘Deploy Anywhere’ DGX HPC and AI in a Controlled Enclosure

November 18, 2019

HPC and AI in a phone booth: ScaleMatrix and Nvidia announced today at the SC19 conference in Denver a joint offering that puts up to 13 petaflops of Nvidia DGX-1 compute power in an air conditioned, water-cooled ScaleMa Read more…

By Doug Black

HPE and NREL Collaborate on AI Ops to Accelerate Exascale Efficiency and Resilience

November 18, 2019

The ever-expanding complexity of high-performance computing continues to elevate the concerns posed by massive energy consumption and increasing points of failure. Now, the AI Ops collaboration between Hewlett Packard En Read more…

By Oliver Peckham

Intel Debuts New GPU – Ponte Vecchio – and Outlines Aspirations for oneAPI

November 17, 2019

Intel today revealed a few more details about its forthcoming Xe line of GPUs – the top SKU is named Ponte Vecchio and will be used in Aurora, the first planned U.S. exascale computer. Intel also provided a glimpse of Read more…

By John Russell

SC19: Welcome to Denver

November 17, 2019

A significant swath of the HPC community has come to Denver for SC19, which began today (Sunday) with a rich technical program. As is customary, the ribbon cutting for the Expo Hall opening is Monday at 6:45pm, with the Read more…

By Tiffany Trader

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…

IBM Accelerated Insights

Data Management – The Key to a Successful AI Project

 

Five characteristics of an awesome AI data infrastructure

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

AI is powered by data

While neural networks seem to get all the glory, data is the unsung hero of AI projects – data lies at the heart of everything from model training to tuning to selection to validation. Read more…

SC19’s HPC Impact Showcase Chair: AI + HPC a ‘Speed Train’

November 16, 2019

This year’s chair of the HPC Impact Showcase at the SC19 conference in Denver is Lori Diachin, who has spent her career at the spearhead of HPC. Currently deputy director for the U.S. Department of Energy’s (DOE) Exascale Computing Project (ECP), Diachin is also... Read more…

By Doug Black

Top500: US Maintains Performance Lead; Arm Tops Green500

November 18, 2019

The 54th Top500, revealed today at SC19, is a familiar list: the U.S. Summit (ORNL) and Sierra (LLNL) machines, offering 148.6 and 94.6 petaflops respectively, Read more…

By Tiffany Trader

ScaleMatrix and Nvidia Launch ‘Deploy Anywhere’ DGX HPC and AI in a Controlled Enclosure

November 18, 2019

HPC and AI in a phone booth: ScaleMatrix and Nvidia announced today at the SC19 conference in Denver a joint offering that puts up to 13 petaflops of Nvidia DGX Read more…

By Doug Black

Intel Debuts New GPU – Ponte Vecchio – and Outlines Aspirations for oneAPI

November 17, 2019

Intel today revealed a few more details about its forthcoming Xe line of GPUs – the top SKU is named Ponte Vecchio and will be used in Aurora, the first plann Read more…

By John Russell

SC19: Welcome to Denver

November 17, 2019

A significant swath of the HPC community has come to Denver for SC19, which began today (Sunday) with a rich technical program. As is customary, the ribbon cutt Read more…

By Tiffany Trader

SC19’s HPC Impact Showcase Chair: AI + HPC a ‘Speed Train’

November 16, 2019

This year’s chair of the HPC Impact Showcase at the SC19 conference in Denver is Lori Diachin, who has spent her career at the spearhead of HPC. Currently deputy director for the U.S. Department of Energy’s (DOE) Exascale Computing Project (ECP), Diachin is also... Read more…

By Doug Black

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

Intel AI Summit: New ‘Keem Bay’ Edge VPU, AI Product Roadmap

November 12, 2019

At its AI Summit today in San Francisco, Intel touted a raft of AI training and inference hardware for deployments ranging from cloud to edge and designed to support organizations at various points of their AI journeys. The company revealed its Movidius Myriad Vision Processing Unit (VPU)... Read more…

By Doug Black

IBM Adds Support for Ion Trap Quantum Technology to Qiskit

November 11, 2019

After years of percolating in the shadow of quantum computing research based on superconducting semiconductors – think IBM, Rigetti, Google, and D-Wave (quant Read more…

By John Russell

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

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

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

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

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

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

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

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

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

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

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

Dell Ramps Up HPC Testing of AMD Rome Processors

October 21, 2019

Dell Technologies is wading deeper into the AMD-based systems market with a growing evaluation program for the latest Epyc (Rome) microprocessors from AMD. In a 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

Cray, Fujitsu Both Bringing Fujitsu A64FX-based Supercomputers to Market in 2020

November 12, 2019

The number of top-tier HPC systems makers has shrunk due to a steady march of M&A activity, but there is increased diversity and choice of processing compon Read more…

By Tiffany Trader

Xilinx vs. Intel: FPGA Market Leaders Launch Server Accelerator Cards

August 6, 2019

The two FPGA market leaders, Intel and Xilinx, both announced new accelerator cards this week designed to handle specialized, compute-intensive workloads and un Read more…

By Doug Black

When Dense Matrix Representations Beat Sparse

September 9, 2019

In our world filled with unintended consequences, it turns out that saving memory space to help deal with GPU limitations, knowing it introduces performance pen Read more…

By James Reinders

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