How Meltdown and Spectre Patches Will Affect HPC Workloads

By Rosemary Francis

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 application performance by 10-30 percent. The patch makes any call from user space into the operating system much more expensive, so I/O intensive applications are likely to be the worst hit. What does this really mean for HPC workloads?

Optimisation has always been important to HPC, but the new patches have moved the goal posts. Profiling applications and how they access data on disk and over the network is going to be key to getting a handle on what the worst problems are going to be. Losing a third of your compute overhead is an understandably scary prospect, but this doesn’t have to be a thoroughly lose-lose situation.

Consider the following aspects of your workloads now to mitigate potential performance damage as much as possible.

1.     Our workflows use third-party tools – there’s nothing I can do, right?

It’s common to use a mix of third-party and in-house tools. Optimising in-house applications is a resourcing issue, but possible. When third-party tools have performance problems, you are often on your own, even if they are open source.

It is, however, still worth investigating performance drops of third-party workflows. As well as being able to feed data back to your vendor or to the user community, there are always changes you can make to the way a program runs that affects the I/O. For example, do you use environment variables to configure that application? Long PATH variables and similar settings can cause applications to trawl the file system with sequences of failed open() or stat() calls many times in a single execution.

These failed I/O calls or distributed accesses cause problems for shared file systems even before you have installed the KPTI patch. Once the patch has been applied it’s likely that the affect of those unnecessary meta data operations will increase for the program performing them as well as for the shared file system struggling under the load.

So even if you have a workflow with just a wrapper script to launch it and a single third-party binary that won’t ever be updated, it is still a very good idea to work out where you are spending your time. Even something as simple as moving temporary files from shared to local storage is likely to give you a win.

2.     Genome pipelines and other fans of small files

Genome pipelines are well known for using a lot of small files to map DNA segments against a reference genome. Other HPC applications in oil and gas, EDA and finance sometimes do the same. Part of the reason for this is a need to honour legacy working practices because in science it can be hard to prove the validity of your work if it is using entirely new software, but it’s also a limitation of the algorithms used in these applications.

Small files necessarily mean small I/O and lots of meta data, but worse than that, often small files are accessed in smaller chunks, further exacerbating the problem. Why is this a problem? Let’s assume that small I/O is anything under 32KB, depending on the architecture of your system. Files under 4KB can be easily written off as an unsolvable problem, but if you access the data in less than 4KB blocks then there is definitely scope for the problem to be a lot worse than it needs to be. Closing a file after every small write or checking the existence of every file before opening it will also magnify the performance impact of the security patches.

Small I/O isn’t limited to applications that use small files. Older libraries and code that hasn’t been profiled will often use system calls that perform small reads and writes. Sometimes gigabytes of data are read or written one byte at a time. This behaviour is very common in almost all compute environments and will be catastrophic for local performance as well as any shared file system or database.

3.     Will the performance drop caused by the patches impact local or shared storage the most?

Reports so far of the impact of the patches on shared file systems have not been good. In time, those who maintain the file system will be able to make some performance improvements based on the new compute landscape, but no one is going to be able to escape the performance drop entirely. Shared storage is an important part of most HPC clusters and cloud infrastructure. When accessing anything remotely there will be a performance hit over local storage, but the KPTI patch will be hitting performance at both ends.

Some workloads will be slowed down mainly by their own behaviour and I/O patterns. This is good news for the shared file system because anything that throttles accesses gives the file system a bit more time to keep up.

Unfortunately, I/O intensive workloads that have bad local performance are also likely to be those hitting the file system the hardest and will be the worst affected by any slow down of the file system. The only way to know the impact of the patch on your cluster and workloads is to try it and measure it; the complexity of modern HPC systems means that an effect on one resource cannot predict the performance of another.

4.     My application doesn’t do that much I/O so do I still have to worry?

Much has been made of the effect the KPTI patches will have on I/O performance, but the impact will be seen on all system calls. This means calls such as gettimeofday() will get more expensive. Applications with strict timing constraints will make lots of such calls and may well have poorly constructed timing constraints broken by the new delays in accessing even small amounts of data.

Ask yourself, does you program really need that fancy progress bar? You could be paying a lot more for features like this in the future.

5.    Is MPI I/O better or worse?

HPC applications don’t just do POSIX I/O: MPI libraries are a popular way of sharing data and coordinating applications across many thousands of compute ranks. All MPI libraries use POSIX I/O underneath the hood, perhaps not a surprise to many, but what will surprise some is the way they do it.

MPI libraries have evolved over time and seemingly similar calls can have very different implementations with varying reliance on small system calls. We are back to discussing small I/O because high-level constructs such as tables and matrices of data are often accessed with very small reads and writes.

The good news is that many MPI libraries are binary compatible for the most part, so changing the library once a performance problem has been identified is not as difficult as optimising other types of I/O, but it is something that you may not have control over. Artificial benchmarks such as IOR that let you compare MPI libraries are unlikely to give you much insight into the real impact of the KPTI patch because real workloads are so different from the orderly I/O that those benchmarks stress. Again, the only way to find out where time is being spent is to profile a real application.

6.     Can I escape the problem by moving my workloads to the cloud?

Unfortunately, virtualised workloads are still affected by the vulnerability and need to be patched. That goes for containerised workloads as well.

Moving applications to the cloud usually involves some kind of re-architecture to reduce the reliance on shared storage and to take advantage of the high-performance and low-cost storage options available. Getting a handle on how your applications use storage and where their dependencies are is part of this process, so optimising for the KPTI patch is work that can almost come for free as part of the efforts to embrace the future. Some I/O patterns will be worse in the cloud and some will be better, but that was true before anyone knew about Meltdown and Spectre.

So all in all, HPC applications are going to be affected by the patches in varying degrees. The cheerful news is that a lot of the impact on performance can be mitigated by optimisation efforts where the resources are available. Using third-party tools and libraries doesn’t render you helpless – there still might be room for easy wins in performance.

Let’s hope that the situation doesn’t become even more complicated as the HPC industry works to come with more solutions. Given the complexity of most HPC workloads and systems already, anything that can be done to simplify and optimise systems rather than add layers of fixes will surely be good for future growth.

About the Author

Dr. Rosemary Francis is CEO and founder of Ellexus, the I/O profiling company (www.ellexus.com). Ellexus makes application profiling and monitoring tools that can be run on a live compute cluster to protect from rogue jobs and noisy neighbours, make cloud migration easy and allow a cluster to be scaled rapidly. The system- and storage-agnostic tools provide end-to-end visibility into exactly what applications and users are up to. We don’t just give you data about what your programs are doing; our tools include expertise on what is going wrong and how you can fix it.

Subscribe to HPCwire's Weekly Update!

Be the most informed person in the room! Stay ahead of the tech trends with industry updates delivered to you every week!

Under The Wire: Nearly HPC News (June 13, 2024)

June 13, 2024

As managing editor of the major global HPC news source, the term "news fire hose" is often mentioned. The analogy is quite correct. In any given week, there are many interesting stories, and only a few ever become headli Read more…

Quantum Tech Sector Hiring Stays Soft

June 13, 2024

New job announcements in the quantum tech sector declined again last month, according to an Quantum Economic Development Consortium (QED-C) report issued last week. “Globally, the number of new, public postings for Qu Read more…

Labs Keep Supercomputers Alive for Ten Years as Vendors Pull Support Early

June 12, 2024

Laboratories are running supercomputers for much longer, beyond the typical lifespan, as vendors prematurely deprecate the hardware and stop providing support. A typical supercomputer lifecycle is about five to six years Read more…

MLPerf Training 4.0 – Nvidia Still King; Power and LLM Fine Tuning Added

June 12, 2024

There are really two stories packaged in the most recent MLPerf  Training 4.0 results, released today. The first, of course, is the results. Nvidia (currently king of accelerated computing) wins again, sweeping all nine Read more…

Highlights from GlobusWorld 2024: The Conference for Reimagining Research IT

June 11, 2024

The Globus user conference, now in its 22nd year, brought together over 180 researchers, system administrators, developers, and IT leaders from 55 top research computing centers, national labs, federal agencies, and univ Read more…

Nvidia Shipped 3.76 Million Data-center GPUs in 2023, According to Study

June 10, 2024

Nvidia had an explosive 2023 in data-center GPU shipments, which totaled roughly 3.76 million units, according to a study conducted by semiconductor analyst firm TechInsights. Nvidia's GPU shipments in 2023 grew by more Read more…

Under The Wire: Nearly HPC News (June 13, 2024)

June 13, 2024

As managing editor of the major global HPC news source, the term "news fire hose" is often mentioned. The analogy is quite correct. In any given week, there are Read more…

Labs Keep Supercomputers Alive for Ten Years as Vendors Pull Support Early

June 12, 2024

Laboratories are running supercomputers for much longer, beyond the typical lifespan, as vendors prematurely deprecate the hardware and stop providing support. Read more…

MLPerf Training 4.0 – Nvidia Still King; Power and LLM Fine Tuning Added

June 12, 2024

There are really two stories packaged in the most recent MLPerf  Training 4.0 results, released today. The first, of course, is the results. Nvidia (currently Read more…

Highlights from GlobusWorld 2024: The Conference for Reimagining Research IT

June 11, 2024

The Globus user conference, now in its 22nd year, brought together over 180 researchers, system administrators, developers, and IT leaders from 55 top research Read more…

Nvidia Shipped 3.76 Million Data-center GPUs in 2023, According to Study

June 10, 2024

Nvidia had an explosive 2023 in data-center GPU shipments, which totaled roughly 3.76 million units, according to a study conducted by semiconductor analyst fir Read more…

ASC24 Expert Perspective: Dongarra, Hoefler, Yong Lin

June 7, 2024

One of the great things about being at an ASC (Asia Supercomputer Community) cluster competition is getting the chance to interview various industry experts and Read more…

HPC and Climate: Coastal Hurricanes Around the World Are Intensifying Faster

June 6, 2024

Hurricanes are among the world's most destructive natural hazards. Their environment shapes their ability to deliver damage; conditions like warm ocean waters, Read more…

ASC24: The Battle, The Apps, and The Competitors

June 5, 2024

The ASC24 (Asia Supercomputer Community) Student Cluster Competition was one for the ages. More than 350 university teams worked for months in the preliminary competition to earn one of the 25 final competition slots. The winning teams... Read more…

Atos Outlines Plans to Get Acquired, and a Path Forward

May 21, 2024

Atos – via its subsidiary Eviden – is the second major supercomputer maker outside of HPE, while others have largely dropped out. The lack of integrators and Atos' financial turmoil have the HPC market worried. If Atos goes under, HPE will be the only major option for building large-scale systems. Read more…

Comparing NVIDIA A100 and NVIDIA L40S: Which GPU is Ideal for AI and Graphics-Intensive Workloads?

October 30, 2023

With long lead times for the NVIDIA H100 and A100 GPUs, many organizations are looking at the new NVIDIA L40S GPU, which it’s a new GPU optimized for AI and g Read more…

Nvidia H100: Are 550,000 GPUs Enough for This Year?

August 17, 2023

The GPU Squeeze continues to place a premium on Nvidia H100 GPUs. In a recent Financial Times article, Nvidia reports that it expects to ship 550,000 of its lat Read more…

Everyone Except Nvidia Forms Ultra Accelerator Link (UALink) Consortium

May 30, 2024

Consider the GPU. An island of SIMD greatness that makes light work of matrix math. Originally designed to rapidly paint dots on a computer monitor, it was then Read more…

Choosing the Right GPU for LLM Inference and Training

December 11, 2023

Accelerating the training and inference processes of deep learning models is crucial for unleashing their true potential and NVIDIA GPUs have emerged as a game- Read more…

Nvidia’s New Blackwell GPU Can Train AI Models with Trillions of Parameters

March 18, 2024

Nvidia's latest and fastest GPU, codenamed Blackwell, is here and will underpin the company's AI plans this year. The chip offers performance improvements from Read more…

Synopsys Eats Ansys: Does HPC Get Indigestion?

February 8, 2024

Recently, it was announced that Synopsys is buying HPC tool developer Ansys. Started in Pittsburgh, Pa., in 1970 as Swanson Analysis Systems, Inc. (SASI) by John Swanson (and eventually renamed), Ansys serves the CAE (Computer Aided Engineering)/multiphysics engineering simulation market. Read more…

Some Reasons Why Aurora Didn’t Take First Place in the Top500 List

May 15, 2024

The makers of the Aurora supercomputer, which is housed at the Argonne National Laboratory, gave some reasons why the system didn't make the top spot on the Top Read more…

Leading Solution Providers

Contributors

AMD MI3000A

How AMD May Get Across the CUDA Moat

October 5, 2023

When discussing GenAI, the term "GPU" almost always enters the conversation and the topic often moves toward performance and access. Interestingly, the word "GPU" is assumed to mean "Nvidia" products. (As an aside, the popular Nvidia hardware used in GenAI are not technically... Read more…

The NASA Black Hole Plunge

May 7, 2024

We have all thought about it. No one has done it, but now, thanks to HPC, we see what it looks like. Hold on to your feet because NASA has released videos of wh Read more…

Google Announces Sixth-generation AI Chip, a TPU Called Trillium

May 17, 2024

On Tuesday May 14th, Google announced its sixth-generation TPU (tensor processing unit) called Trillium.  The chip, essentially a TPU v6, is the company's l Read more…

Intel’s Next-gen Falcon Shores Coming Out in Late 2025 

April 30, 2024

It's a long wait for customers hanging on for Intel's next-generation GPU, Falcon Shores, which will be released in late 2025.  "Then we have a rich, a very Read more…

GenAI Having Major Impact on Data Culture, Survey Says

February 21, 2024

While 2023 was the year of GenAI, the adoption rates for GenAI did not match expectations. Most organizations are continuing to invest in GenAI but are yet to Read more…

Q&A with Nvidia’s Chief of DGX Systems on the DGX-GB200 Rack-scale System

March 27, 2024

Pictures of Nvidia's new flagship mega-server, the DGX GB200, on the GTC show floor got favorable reactions on social media for the sheer amount of computing po Read more…

Intel Plans Falcon Shores 2 GPU Supercomputing Chip for 2026  

August 8, 2023

Intel is planning to onboard a new version of the Falcon Shores chip in 2026, which is code-named Falcon Shores 2. The new product was announced by CEO Pat Gel Read more…

How the Chip Industry is Helping a Battery Company

May 8, 2024

Chip companies, once seen as engineering pure plays, are now at the center of geopolitical intrigue. Chip manufacturing firms, especially TSMC and Intel, have b Read more…

  • arrow
  • Click Here for More Headlines
  • arrow
HPCwire