Why Research Software Sustainability Won't Be Fixed by Containers

Henry Neeman, University of Oklahoma
December 21, 2018

Containers, such as Singularity and Docker, are an amazing advance in software sustainability. By allowing software developers to package not only application software but also other components of the software stack, including software dependencies, that the application needs, and with which the application is well tested, containers make the porting of applications to new platforms much more straightforward, convenient and efficient.

In the large scale research computing world, containers are a miracle in the near-term, but a looming challenge in the medium- to long-term.

A little background:

Science, Technology, Engineering and Mathematics (STEM) research software is mission-critical to virtually every STEM discipline (and many non-STEM disciplines), with thousands of software applications available, mostly as free, open source downloads, alongside a more modest number of commercial applications.

At my institution, for example, we support about 400 applications and libraries, while national supercomputing centers support about ten times as many.

Before containers, if you wanted to use an application package on a particular platform—the combination of hardware and software stack, including the operating system and one or more compilers—you had to explicitly port that application to that platform.

Such porting can be, in many cases, very labor intensive, because of quirks in every part of the software stack, from the OS to the application source code. In some cases, porting can require substantial expertise about building software in general, or even about the innards of the specific application you’re porting.

Containers are very helpful with that – so why are they a challenge?

The main issue is that containers give software developers a straightforward way to put off until tomorrow an onerous task that they have no incentive to do today.

And that means that, for each containerized STEM research software application, it’ll become harder and harder to take advantage of new hardware features, like longer vector lengths, new instruction sets, and so on.

Here’s why:

In the research software sustainability world, a key issue is that the organizations that fund research software application development—primarily national research funding agencies—are generally far less concerned with software issues and far more concerned with advancing STEM research.

As such, far more funding is available to add new science features to software applications, so that they can solve more advanced STEM research problems, than to improve the software itself, or even to port the software to new platforms.

By containerizing an application, a research software engineer can reduce the labor cost of porting to a new platform, including to a new version of a common operating system or a long-used compiler.

It’s clear why this would be attractive to a research software engineer, as it helps with prioritizing the things that their funding is intended to pay for, and reduces the cost of the things that their funding isn’t focused on.

Of course, software stacks constantly drift, with both new features and new bugs continually arising. New versions of applications typically are only tested on more recent software stacks, because the call for using those applications on obsolete software stacks is very limited.

Because of this, old versions of a software application become harder and harder to port to the latest platforms, while newer versions of an application are easier to port to new platforms (but would similarly be very difficult to port back to obsolete platforms, if there were a need for doing that).

Once an application has been containerized, then each time the research software engineer is faced with the choice between adding new science features or spending time porting to a new platform, it’s possible to defer the latter in favor of the former.

After a year of doing that, it’s still straightforward to port to a new platform – but the software is working fine, so why go to all that trouble?

After a second year, the need may be more pressing – for example, new hardware features may be available – but the labor cost of porting has gone up, so the research software engineer may choose to put off the porting again.

Each successive year, the need will be greater, but the labor cost will be higher, so the disincentive to port will be stronger.

Bear in mind that old versions of the compiler aren’t updated to use new instructions – only the few most recent versions of the compiler support that.

But the more porting is deferred to later, the harder and more labor intensive that porting will be.

After several years of this, application performance improvement will be limited to whatever can be derived naturally via improvements in memory bandwidth, interconnect speed, and disk speed.

In practice, these improve slowly compared to CPU speed (see below).

Whereas, if the applications can take advantage of CPU performance improvements, especially via new instructions (e.g., AVX, half-precision floating point), then they can also get substantial speedup from CPU improvements.

But those new instructions are available in new versions of the relevant compiler families, not in the older versions that an older container was built around.

And, as time goes on, those new versions of the compilers won’t have been tested against older platforms.

So the software drift gets worse and worse over time, while the disincentive to port to new platforms gets stronger and stronger.

Performance improvements

  • individual CPU speed improved from 53 GFLOPs per socket on Intel Nehalem W5590 in 2009 [9] to 1523 GFLOPs per socket on Intel Skylake 8180 in 2017 [10], a doubling period of 2 years;

  • memory bandwidth went from, for example, ~37 GB/sec on dual Intel Nehalem W5580 in 2009 [6,7] to ~290 GB/sec in late 2017 on dual AMD EPYC [8], a doubling period of 3 years;

  • disk drive speed improves primarily with the number of drives being used or the kind of drives (SSD vs spinning hard disk) – i.e., with dollars spent;

  • interconnect bandwidth improves slowly, and latency even more slowly, for example:

    • Mellanox QDR Infiniband at 40 Gbps and ~1 microsecond MPI point-to-point latency [1] was released in 2008 [2],

    • Mellanox FDR at 56 Gbps and ~1 microsecond latency [1] was released in late 2011 [2],

    • Mellanox EDR at 100 Gbps and ~1 microseconds latency [3] in early 2015 [2],

    • Intel Omni-Path at 100 Gbps and ~1 microseconds latency [3] in 2016 [4],

    • Mellanox HDR at 200 Gbps and ~0.7 microseconds latency [5] in 2017.


[1] J. Vienne, J. Chen, M. Wasi-ur-Rahman, N. S. Islam, H. Subramoni and D. K. Panda, 2012: “Performance Analysis and Evaluation of InfiniBand FDR and 40GigE RoCE on HPC and Cloud Computing Systems.” Proc. IEEE Hot Interconnects (HOTI-20). DOI: 10.1109/HOTI.2012.19.

[2] Infiniband Trade Association, Infiniband Roadmap. https://www.infinibandta.org/infiniband-roadmap/

[3] D. K. Panda, 2018, “Designing Scalable HPC, Deep Learning, and Cloud Middleware for Exascale Systems.” HPC Advisory Council Swiss Conference 2018, slide #15. https://www.slideshare.net/insideHPC/panda-scalable-hpcbestpracticestue100418

[4] Wikipedia Omni-Path webpage. https://en.wikipedia.org/wiki/Omni-Path

[5] Xenon High Performance Computing, 2017: “XENON will integrate Mellanox’s new 200Gb/s HDR InfiniBand interconnect infrastructure as part of their HPC offering.” https://www.xenon.com.au/xenon-will-integrate-mellanoxs-new-200gbs-hdr-infiniband-interconnect-infrastructure-part-hpc-offering/

[6] STREAM numbers on nehalem. https://www.cs.virginia.edu/stream/stream_mail/2009/0011.html

[7] Intel® Xeon® Processor W5580. https://ark.intel.com/products/37113/Intel-Xeon-Processor-W5580-8M-Cache-3-20-GHz-6-40-GT-s-Intel-QPI-

[8] AMD EPYC SoC Delivers Exceptional Results on the STREAM Benchmark on 2P Servers. https://www.amd.com/system/files/2017-06/AMD-EPYC-SoC-Delivers-Exceptional-Results.pdf

[9] Intel® Xeon® Processor W5590. https://ark.intel.com/products/41643/Intel-Xeon-Processor-W5590-8M-Cache-3-33-GHz-6-40-GT-s-Intel-QPI-

[10] Intel Xeon Platinum 8180 Processor. https://ark.intel.com/products/120496/Intel-Xeon-Platinum-8180-Processor-38-5M-Cache-2-50-GHz-