Simplifying Cluster Management…

By Nicole Hemsoth

April 22, 2013

Atipa

THE PROBLEM:
Managing clusters can be a daunting task

Higher education and research institutes around the globe are investing in HPC clusters, yet there is an all-too-common oversight during the product acquisition process… they’re not investing in the additional, dedicated man-power it takes to maintain, monitor, and  update their clusters. To the grad students and post-docs  who need the clusters for their research – and also end up being the ones in charge of maintaining and fixing them – clusters are just big, black boxes. The thought of updating the OFED drivers or troubleshooting MCE errors can too often become their impossible task.

THE SOLUTION:
Learn to leverage the deep technical insight of qualified cluster vendors willing to work with you
Damien Tourret, PhD, is a postdoctoral fellow for the Center for Interdisciplinary Research on Complex Systems at Northeastern University’s Boston campus. Recently, he was asked how their cluster has been operating and how his team, led by Distinguished Professor Alain Karma, PhD, has managed to keep the cluster running despite the lack of a cluster administrator. Following an interview with a server technology specialist here is what Damian said:

Interviewer-Tell me about yourself and how you use the cluster

Tourret: Yes, I’m a user of this cluster.  But Ari Adland, I and other grad students are basically also in charge of it. We installed it, and thanks to the interaction we’ve had with our cluster vendor we just basically plugged it in. We’re not computer scientists, we are not HPC experts, we know how to utilize HPC but we’re not that knowledgeable about managing the cluster. Those in charge of cluster maintenance are just grad students and postdocs with backgrounds in physics, material sciences, and biomedical research. We want to spend our time on the cluster doing research, not cluster management.

Our cluster vendor relationship and interaction has allowed us to do our own clustering here while focusing on our research. Basically, we just plugged our cluster in and exchanged a few emails here and there with the vendor to solve problems. Whether it’s GPUs or CPUs, what matters to us is the speedup that we can achieve to solving the problems, more than considerations about the architecture. To most users in here, clusters are big, black boxes.

Interviewer-Do you have any specific cluster problems?

Tourret: A few problems. One was related to memory slots failure, and we had to have the motherboard replaced on one of the nodes at some point.  Two DIMM slots were just not being seen by the motherboard and couldn’t run the jobs properly. That’s a problem we could not diagnose ourselves.

When we reached that level of problem our cluster provider quickly responded to our needs. When we can’t diagnose it ourselves, like a big problem with the motherboard or even a small update to the software, we’re not able to fix them like they can. We simply email Bart, one of our vendor’s HPC engineers, and our problem gets diagnosed and fixed within the day. That’s what we appreciate most.

Interviewer: Have you worked with other system integrators, and how was their support?

Tourret: I have not. That was the first time I’ve personally been in charge of a cluster. I’ve used them before, but they were managed by the IT people. Honestly, when I first arrived here, I was told “Ok you’re going to install this and that” and I asked myself, can I do that? That’s where our cluster vendor has helped a lot because I could not have done it on my own.

At one point we had a performance problem we could not understand at all. We explained the problem to our provider. They felt our code needed more memory channels for better performance and suggested a new configuration along with more memory modules which they took care of. That fixed our problem, and improved the memory access and speed of our MPI jobs.

Over the past year and a half the questions we had were like, “Hey, how do I fix this,” and the answer was “Try running this command line.” Or a response equally as simple.  And even if I don’t know what that command means, it solved the problem quickly and easily most of the time. What more do you need.

Interviewer: Who is your cluster vendor, and is there anything more you would like to say about them?

Tourret:  Atipa Technologies is our vendor. I appreciate the collaboration with them so far. Something that I really appreciated was being able to benchmark our programs with them before buying. For instance, when we wanted to try a new GPU or CPU we could just SSH in and test our real codes before making the purchase. When it’s possible, trying before you buy helps guide you to making the best purchase decisions.

A word from Atipa Technologies…

Damien Tourret is not the only one. Thousands of cluster end-users are struggling to keep clusters running on their own. Tourret is, however, one of the lucky ones. With the hindsight to purchase from a vendor who can provide priceless support and advice, as opposed to purchasing from an OEM with multiple support levels that would take days or even weeks to return a solution, his cluster has been running efficiently and reliably since the day it was delivered. In the end, what matters to researchers most is how quickly their simulations can be solved, even if the machines doing the work are mysterious, big, black boxes.

 

To find out more about Atipa Technologies solutions go to: www.atipa.com

For questions, or to request a quote contact: Dan Mantyla/ dmantyla@atipa.com

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!

Graphcore Readies Launch of 16nm Colossus-IPU Chip

July 20, 2017

A second $30 million funding round for U.K. AI chip developer Graphcore sets up the company to go to market with its “intelligent processing unit” (IPU) in 2017 with scale-up production for enterprise datacenters and Read more…

By Tiffany Trader

Fine-Tuning Severe Hail Forecasting with Machine Learning

July 20, 2017

Depending on whether you’ve been caught outside during a severe hail storm, the sight of greenish tinted clouds on the horizon may cause serious knots in the pit of your stomach, or at least give you pause. There’s g Read more…

By Sean Thielen

Trinity Supercomputer’s Haswell and KNL Partitions Are Merged

July 19, 2017

Trinity supercomputer’s two partitions – one based on Intel Xeon Haswell processors and the other on Xeon Phi Knights Landing – have been fully integrated are now available for use on classified work in the Nationa Read more…

By HPCwire Staff

Fujitsu Continues HPC, AI Push

July 19, 2017

Summer is well under way, but the so-called summertime slowdown, linked with hot temperatures and longer vacations, does not seem to have impacted Fujitsu's output. The Japanese multinational has made a raft of HPC and A Read more…

By Tiffany Trader

HPE Extreme Performance Solutions

HPE Servers Deliver High Performance Remote Visualization

Whether generating seismic simulations, locating new productive oil reservoirs, or constructing complex models of the earth’s subsurface, energy, oil, and gas (EO&G) is a highly data-driven industry. Read more…

Researchers Use DNA to Store and Retrieve Digital Movie

July 18, 2017

From abacus to pencil and paper to semiconductor chips, the technology of computing has always been an ever-changing target. The human brain is probably the computer we use most (hopefully) and understand least. This mon Read more…

By John Russell

The Exascale FY18 Budget – The Next Step

July 17, 2017

On July 12, 2017, the U.S. federal budget for its Exascale Computing Initiative (ECI) took its next step forward. On that day, the full Appropriations Committee of the House of Representatives voted to accept the recomme Read more…

By Alex R. Larzelere

Summer Reading: IEEE Spectrum’s Chip Hall of Fame

July 17, 2017

Take a trip down memory lane – the Mostek MK4096 4-kilobit DRAM, for instance. Perhaps processors are more to your liking. Remember the Sh-Boom processor (1988), created by Russell Fish and Chuck Moore, and named after Read more…

By John Russell

Women in HPC Luncheon Shines Light on Female-Friendly Hiring Practices

July 13, 2017

The second annual Women in HPC luncheon was held on June 20, 2017, during the International Supercomputing Conference in Frankfurt, Germany. The luncheon provides participants the opportunity to network with industry lea Read more…

By Tiffany Trader

Graphcore Readies Launch of 16nm Colossus-IPU Chip

July 20, 2017

A second $30 million funding round for U.K. AI chip developer Graphcore sets up the company to go to market with its “intelligent processing unit” (IPU) in Read more…

By Tiffany Trader

Fine-Tuning Severe Hail Forecasting with Machine Learning

July 20, 2017

Depending on whether you’ve been caught outside during a severe hail storm, the sight of greenish tinted clouds on the horizon may cause serious knots in the Read more…

By Sean Thielen

Fujitsu Continues HPC, AI Push

July 19, 2017

Summer is well under way, but the so-called summertime slowdown, linked with hot temperatures and longer vacations, does not seem to have impacted Fujitsu's out Read more…

By Tiffany Trader

Researchers Use DNA to Store and Retrieve Digital Movie

July 18, 2017

From abacus to pencil and paper to semiconductor chips, the technology of computing has always been an ever-changing target. The human brain is probably the com Read more…

By John Russell

The Exascale FY18 Budget – The Next Step

July 17, 2017

On July 12, 2017, the U.S. federal budget for its Exascale Computing Initiative (ECI) took its next step forward. On that day, the full Appropriations Committee Read more…

By Alex R. Larzelere

Women in HPC Luncheon Shines Light on Female-Friendly Hiring Practices

July 13, 2017

The second annual Women in HPC luncheon was held on June 20, 2017, during the International Supercomputing Conference in Frankfurt, Germany. The luncheon provid Read more…

By Tiffany Trader

Satellite Advances, NSF Computation Power Rapid Mapping of Earth’s Surface

July 13, 2017

New satellite technologies have completely changed the game in mapping and geographical data gathering, reducing costs and placing a new emphasis on time series Read more…

By Ken Chiacchia and Tiffany Jolley

Intel Skylake: Xeon Goes from Chip to Platform

July 13, 2017

With yesterday’s New York unveiling of the new “Skylake” Xeon Scalable processors, Intel made multiple runs at multiple competitive threats and strategic Read more…

By Doug Black

Google Pulls Back the Covers on Its First Machine Learning Chip

April 6, 2017

This week Google released a report detailing the design and performance characteristics of the Tensor Processing Unit (TPU), its custom ASIC for the inference Read more…

By Tiffany Trader

Quantum Bits: D-Wave and VW; Google Quantum Lab; IBM Expands Access

March 21, 2017

For a technology that’s usually characterized as far off and in a distant galaxy, quantum computing has been steadily picking up steam. Just how close real-wo Read more…

By John Russell

HPC Compiler Company PathScale Seeks Life Raft

March 23, 2017

HPCwire has learned that HPC compiler company PathScale has fallen on difficult times and is asking the community for help or actively seeking a buyer for its a Read more…

By Tiffany Trader

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

Trump Budget Targets NIH, DOE, and EPA; No Mention of NSF

March 16, 2017

President Trump’s proposed U.S. fiscal 2018 budget issued today sharply cuts science spending while bolstering military spending as he promised during the cam Read more…

By John Russell

CPU-based Visualization Positions for Exascale Supercomputing

March 16, 2017

In this contributed perspective piece, Intel’s Jim Jeffers makes the case that CPU-based visualization is now widely adopted and as such is no longer a contrarian view, but is rather an exascale requirement. Read more…

By Jim Jeffers, Principal Engineer and Engineering Leader, Intel

Nvidia’s Mammoth Volta GPU Aims High for AI, HPC

May 10, 2017

At Nvidia's GPU Technology Conference (GTC17) in San Jose, Calif., this morning, CEO Jensen Huang announced the company's much-anticipated Volta architecture a Read more…

By Tiffany Trader

Facebook Open Sources Caffe2; Nvidia, Intel Rush to Optimize

April 18, 2017

From its F8 developer conference in San Jose, Calif., today, Facebook announced Caffe2, a new open-source, cross-platform framework for deep learning. Caffe2 is the successor to Caffe, the deep learning framework developed by Berkeley AI Research and community contributors. Read more…

By Tiffany Trader

Leading Solution Providers

How ‘Knights Mill’ Gets Its Deep Learning Flops

June 22, 2017

Intel, the subject of much speculation regarding the delayed, rewritten or potentially canceled “Aurora” contract (the Argonne Lab part of the CORAL “ Read more…

By Tiffany Trader

Reinders: “AVX-512 May Be a Hidden Gem” in Intel Xeon Scalable Processors

June 29, 2017

Imagine if we could use vector processing on something other than just floating point problems.  Today, GPUs and CPUs work tirelessly to accelerate algorithms Read more…

By James Reinders

MIT Mathematician Spins Up 220,000-Core Google Compute Cluster

April 21, 2017

On Thursday, Google announced that MIT math professor and computational number theorist Andrew V. Sutherland had set a record for the largest Google Compute Engine (GCE) job. Sutherland ran the massive mathematics workload on 220,000 GCE cores using preemptible virtual machine instances. Read more…

By Tiffany Trader

Google Debuts TPU v2 and will Add to Google Cloud

May 25, 2017

Not long after stirring attention in the deep learning/AI community by revealing the details of its Tensor Processing Unit (TPU), Google last week announced the Read more…

By John Russell

Russian Researchers Claim First Quantum-Safe Blockchain

May 25, 2017

The Russian Quantum Center today announced it has overcome the threat of quantum cryptography by creating the first quantum-safe blockchain, securing cryptocurrencies like Bitcoin, along with classified government communications and other sensitive digital transfers. Read more…

By Doug Black

Groq This: New AI Chips to Give GPUs a Run for Deep Learning Money

April 24, 2017

CPUs and GPUs, move over. Thanks to recent revelations surrounding Google’s new Tensor Processing Unit (TPU), the computing world appears to be on the cusp of Read more…

By Alex Woodie

Six Exascale PathForward Vendors Selected; DoE Providing $258M

June 15, 2017

The much-anticipated PathForward awards for hardware R&D in support of the Exascale Computing Project were announced today with six vendors selected – AMD Read more…

By John Russell

Top500 Results: Latest List Trends and What’s in Store

June 19, 2017

Greetings from Frankfurt and the 2017 International Supercomputing Conference where the latest Top500 list has just been revealed. Although there were no major Read more…

By Tiffany Trader

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