Pfizer HPC Engineer Aims to Automate Software Stack Testing

By Tiffany Trader

January 17, 2019

Seeking to reign in the tediousness of manual software testing, Pfizer HPC Engineer Shahzeb Siddiqui is developing an open source software tool called buildtest, aimed at automating software stack testing by providing the community with a central repository of tests for common HPC apps and the ability to automate execution of testing. Where tools like EasyBuild (and Spack and OpenHPC) move to optimize the application build process by automating the deployment of the entire software stack to an HPC environment, buildtest takes a similar approach but focusing on application testing. In the following exchange, conducted by email, Siddiqui provides an overview of the project he founded.

HPCwire: What is buildtest and who is it for?

Shahzeb Siddiqui: Buildtest is a software stack testing framework (implemented in Python) used for automating test creation and execution. This tool is designed for HPC administrators, end-users, and software vendors.

HPCwire: Can you tell us more about the problem it is created to solve?

Siddiqui: I was tired of writing test scripts manually as all other HPC sites were doing the same, since each site has unique software and they may have hard coded paths in their test scripts. I started with this notion to automate test script creation to simplify this process and decided to expand on this framework to provide a YAML like syntax that is easily interpretable that can create a test script (shell script).

HPCwire: What is the connection to EasyBuild?

Siddiqui: The idea of buildtest was inspired by EasyBuild, where EasyBuild focuses on software installation, buildtest is focused on software testing. EasyBuild has a repository of easyconfigs (recipe) that are shared amongst the community to help build the software. Buildtest is similar in this aspect where YAML files are shared which is a recipe for building a software test.

HPCwire: How are you using buildtest at Pfizer?

Siddiqui: We use buildtest to validate two or three different software stacks for two different sites using Jenkins to automate the entire test procedure.

HPCwire: What is the status of buildtest – is it ready for adoption?

Siddiqui: Buildtest is in beta phase, it is not ready for production use. The tool is open source and easily accessible via git or installed via pip. Anyone can start using it, though features are constantly changing. I would say it would be ready for adoption by 2020. There has been need for creating a framework for software testing, but to date, there is only one other tool in this space along with buildtest called reframe that targets this need.

HPCwire: Can people try it now? Licensing info?

Siddiqui: Yes, they can try it now. License is GPLv3+

HPCwire: Would you share more about current features? Challenges and planned features?

Current features include:

  1. Module load testing
  2. Binary testing
  3. Creating job scripts
  4. Automate batch job submission
  5. Basic MPI, OpenMP testing
  6. Python,R, Perl, Ruby package testing
  7. OSU benchmark test
  8. Listing unique software, unique software version
  9. System package testing
  10. Run tests
    1. Interactive menu driven prompt
    2. Run as test suite (by app)
    3. Run individual test
    4. Run test with ctest
  1. OpenHPC integration to test OpenHPC software stack
  2. Show difference between two module trees
  3. Find test scripts and YAML configs
  4. Test threshold to indicate (WARNING, CRITICAL, SUCCESS)

Challenges

User Contribution and feedback
Lack of time

Planned Features

  1. Email integration based on test threshold
  2. Support additional benchmark
  3. Robust support for creating job script for SLURM and LSF initially, then provide support for other schedulers based on demand
  4. Automate documentation for API generation

HPCwire: What is your ultimate goal for this project?

Siddiqui: To provide a robust framework and repository where configurations or tests can be reused between HPC sites for validating software stack and improving the quality of software packages.

HPCwire: Where can our readers go for more information?

Siddiqui: They can find more information at https://buildtest.readthedocs.io/en/latest/.


Interested in a deeper dive and demo? Check out Siddiqui’s presentation from the 2018 HPC Knowledge Meeting (HPCKP’18), which took place in August.


Bio:
Shahzeb Siddiqui is an HPC engineer at Pfizer with five years of experience in the field of high-performance computing. He loves to automate everything and solve challenging problems. With an M.S in computer science from KAUST and a computer engineering bachelor’s degree from Penn State, Siddiqui is an experienced developer, DevOps practitioner, cloud engineer, and system administrator. Siddiqui is the founder of buildtest, a software stack testing framework designed to automate testing for validating software.

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!

San Diego Supercomputer Center to Welcome ‘Expanse’ Supercomputer in 2020

July 18, 2019

With a $10 million dollar award from the National Science Foundation, San Diego Supercomputer Center (SDSC) at the University of California San Diego is procuring a new supercomputer, called Expanse, to be deployed next Read more…

By Staff report

Informing Designs of Safer, More Efficient Aircraft with Exascale Computing

July 18, 2019

During the process of designing an aircraft, aeronautical engineers must perform predictive simulations to understand how airflow around the plane impacts flight characteristics. However, modeling the complexities and su Read more…

By Rob Johnson

How Fast is Your Rubik Solver; This One’s Probably Faster

July 18, 2019

In the race to solve Rubik’s Cube, the time-to-finish keeps shrinking. This year Philipp Weyer from Germany won the 10th World Cube Association (WCA) Championship held in Melbourne, Australia, with a 6.74-second perfo Read more…

By John Russell

HPE Extreme Performance Solutions

Bring the Combined Power of HPC and AI to Your Business Transformation

A growing number of commercial businesses are implementing HPC solutions to derive actionable business insights, to run higher performance applications and to gain a competitive advantage. Read more…

IBM Accelerated Insights

Smarter Technology Revs Up Red Bull Racing

In 21st century business, companies that effectively leverage their information resources – thrive. As it turns out, the same is true in Formula One racing. Read more…

Intel Debuts Pohoiki Beach, Its 8M Neuron Neuromorphic Development System

July 17, 2019

Neuromorphic computing has received less fanfare of late than quantum computing whose mystery has captured public attention and which seems to have generated more efforts (academic, government, and commercial) but whose Read more…

By John Russell

Informing Designs of Safer, More Efficient Aircraft with Exascale Computing

July 18, 2019

During the process of designing an aircraft, aeronautical engineers must perform predictive simulations to understand how airflow around the plane impacts fligh Read more…

By Rob Johnson

Intel Debuts Pohoiki Beach, Its 8M Neuron Neuromorphic Development System

July 17, 2019

Neuromorphic computing has received less fanfare of late than quantum computing whose mystery has captured public attention and which seems to have generated mo Read more…

By John Russell

Goonhilly Unveils New Immersion-Cooled Platform, Doubles Down on Sustainability Mission

July 16, 2019

Goonhilly Earth Station has opened its new datacenter – an enhancement to its existing tier 3 facility – in Cornwall, England, touting an ambitious commitme Read more…

By Oliver Peckham

ISC19 Cluster Competition: Application Results, Finally!

July 15, 2019

Our exhaustive coverage of the ISC19 Student Cluster Competition continues as we discuss the application scores below. While the scores were typically high, som Read more…

By Dan Olds

Nvidia Expands DGX-Ready AI Program to 19 Countries

July 11, 2019

Nvidia’s DGX-Ready Data Center Program, announced in January and designed to provide colo and public cloud-like options to access the company’s GPU-powered Read more…

By Doug Black

Argonne Team Makes Record Globus File Transfer

July 10, 2019

A team of scientists at Argonne National Laboratory has broken a data transfer record by moving a staggering 2.9 petabytes of data for a research project.  The data – from three large cosmological simulations – was generated and stored on the Summit supercomputer at the Oak Ridge Leadership Computing Facility (OLCF)... Read more…

By Oliver Peckham

Nvidia, Google Tie in Second MLPerf Training ‘At-Scale’ Round

July 10, 2019

Results for the second round of the AI benchmarking suite known as MLPerf were published today with Google Cloud and Nvidia each picking up three wins in the at Read more…

By Tiffany Trader

Applied Materials Embedding New Memory Technologies in Chips

July 9, 2019

Applied Materials, the $17 billion Santa Clara-based materials engineering company for the semiconductor industry, today announced manufacturing systems enablin Read more…

By Doug Black

High Performance (Potato) Chips

May 5, 2006

In this article, we focus on how Procter & Gamble is using high performance computing to create some common, everyday supermarket products. Tom Lange, a 27-year veteran of the company, tells us how P&G models products, processes and production systems for the betterment of consumer package goods. Read more…

By Michael Feldman

Cray, AMD to Extend DOE’s Exascale Frontier

May 7, 2019

Cray and AMD are coming back to Oak Ridge National Laboratory to partner on the world’s largest and most expensive supercomputer. The Department of Energy’s Read more…

By Tiffany Trader

Graphene Surprises Again, This Time for Quantum Computing

May 8, 2019

Graphene is fascinating stuff with promise for use in a seeming endless number of applications. This month researchers from the University of Vienna and Institu Read more…

By John Russell

AMD Verifies Its Largest 7nm Chip Design in Ten Hours

June 5, 2019

AMD announced last week that its engineers had successfully executed the first physical verification of its largest 7nm chip design – in just ten hours. The AMD Radeon Instinct Vega20 – which boasts 13.2 billion transistors – was tested using a TSMC-certified Calibre nmDRC software platform from Mentor. Read more…

By Oliver Peckham

TSMC and Samsung Moving to 5nm; Whither Moore’s Law?

June 12, 2019

With reports that Taiwan Semiconductor Manufacturing Co. (TMSC) and Samsung are moving quickly to 5nm manufacturing, it’s a good time to again ponder whither goes the venerable Moore’s law. Shrinking feature size has of course been the primary hallmark of achieving Moore’s law... Read more…

By John Russell

Deep Learning Competitors Stalk Nvidia

May 14, 2019

There is no shortage of processing architectures emerging to accelerate deep learning workloads, with two more options emerging this week to challenge GPU leader Nvidia. First, Intel researchers claimed a new deep learning record for image classification on the ResNet-50 convolutional neural network. Separately, Israeli AI chip startup Hailo.ai... Read more…

By George Leopold

Nvidia Embraces Arm, Declares Intent to Accelerate All CPU Architectures

June 17, 2019

As the Top500 list was being announced at ISC in Frankfurt today with an upgraded petascale Arm supercomputer in the top third of the list, Nvidia announced its Read more…

By Tiffany Trader

Top500 Purely Petaflops; US Maintains Performance Lead

June 17, 2019

With the kick-off of the International Supercomputing Conference (ISC) in Frankfurt this morning, the 53rd Top500 list made its debut, and this one's for petafl Read more…

By Tiffany Trader

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 Launches Cascade Lake Xeons with Up to 56 Cores

April 2, 2019

At Intel's Data-Centric Innovation Day in San Francisco (April 2), the company unveiled its second-generation Xeon Scalable (Cascade Lake) family and debuted it Read more…

By Tiffany Trader

Cray – and the Cray Brand – to Be Positioned at Tip of HPE’s HPC Spear

May 22, 2019

More so than with most acquisitions of this kind, HPE’s purchase of Cray for $1.3 billion, announced last week, seems to have elements of that overused, often Read more…

By Doug Black and Tiffany Trader

A Behind-the-Scenes Look at the Hardware That Powered the Black Hole Image

June 24, 2019

Two months ago, the first-ever image of a black hole took the internet by storm. A team of scientists took years to produce and verify the striking image – an Read more…

By Oliver Peckham

Announcing four new HPC capabilities in Google Cloud Platform

April 15, 2019

When you’re running compute-bound or memory-bound applications for high performance computing or large, data-dependent machine learning training workloads on Read more…

By Wyatt Gorman, HPC Specialist, Google Cloud; Brad Calder, VP of Engineering, Google Cloud; Bart Sano, VP of Platforms, Google Cloud

Chinese Company Sugon Placed on US ‘Entity List’ After Strong Showing at International Supercomputing Conference

June 26, 2019

After more than a decade of advancing its supercomputing prowess, operating the world’s most powerful supercomputer from June 2013 to June 2018, China is keep Read more…

By Tiffany Trader

Why Nvidia Bought Mellanox: ‘Future Datacenters Will Be…Like High Performance Computers’

March 14, 2019

“Future datacenters of all kinds will be built like high performance computers,” said Nvidia CEO Jensen Huang during a phone briefing on Monday after Nvidia revealed scooping up the high performance networking company Mellanox for $6.9 billion. Read more…

By Tiffany Trader

It’s Official: Aurora on Track to Be First US Exascale Computer in 2021

March 18, 2019

The U.S. Department of Energy along with Intel and Cray confirmed today that an Intel/Cray supercomputer, "Aurora," capable of sustained performance of one exaf Read more…

By Tiffany Trader

In Wake of Nvidia-Mellanox: Xilinx to Acquire Solarflare

April 25, 2019

With echoes of Nvidia’s recent acquisition of Mellanox, FPGA maker Xilinx has announced a definitive agreement to acquire Solarflare Communications, provider Read more…

By Doug Black

  • arrow
  • Click Here for More Headlines
  • arrow
Do NOT follow this link or you will be banned from the site!
Share This