Abstract. SDN deployments rely on switches that come from various vendors and differ in terms of performance and available features. Understanding these differences and performance characteristics is essential for ensuring successful deployments. In this paper we measure, report, and explain the performance characteristics of flow table updates in three hardware OpenFlow switches. Our results can help controller developers to make their programs efficient. Further, we also highlight differences between the OpenFlow specification and its implementations, that if ignored, pose a serious threat to network security and correctness.

The increasing adoption of Software Defined Networking, and OpenFlow in particular, brings great hope for increasing extensibility and lowering costs of deploying new network functionality. A key component in these networks is the OpenFlow agent, a piece of software that a switch runs to enable remote programmatic access to its forwarding tables. While testing high-level network functionality, the correct behavior and interoperability of any OpenFlow agent are taken for granted. However, existing tools for testing agents are not exhaustive nor systematic, and only check that the agent's basic functionality works. In addition, the rapidly changing and sometimes vague OpenFlow specifications can result in multiple implementations that behave differently. This paper presents SOFT, an approach for testing the interoperability of OpenFlow switches. Our key insight is in automatically identifying the testing inputs that cause different OpenFlow agent implementations to behave inconsistently. To this end, we first symbolically execute each agent under test in isolation to derive which set of inputs causes which behavior. We then crosscheck all distinct behaviors across different agent implementations and evaluate whether a common input subset causes inconsistent behaviors. Our evaluation shows that our tool identified several inconsistencies between the publicly available Reference OpenFlow switch and Open vSwitch implementations.

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AbstractMotivationOxford Nanopore MinION is a portable DNA sequencer that is marketed as a device that can be deployed anywhere. Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications.ResultsWe have developed a fast base caller DeepNano-blitz that can analyze stream from up to two MinION runs in real time using a common laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow trading accuracy for speed and the results can be used for real time run monitoring (i.e. sample composition, barcode balance, species identification, etc.) or pre-filtering of results for more detailed analysis (i.e. filtering out human DNA from human–pathogen runs).Availability and ImplementationDeepNano-blitz has been developed and tested on Linux and is available under MIT license at https://github.com/fmfi-compbio/deepnano-blitzContactvladimir.boza@fmph.uniba.sk

Tolerating and recovering from link and switch failures are fundamental requirements of most networks, including Software-Defined Networks (SDNs). However, instead of traditional behaviors such as network-wide routing reconvergence, failure recovery in an SDN is determined by the specific software logic running at the controller. While this admits more freedom to respond to a failure event, it ultimately means that each controller application must include its own recovery logic, which makes the code more difficult to write and potentially more error-prone.In this paper, we propose a runtime system that automates failure recovery and enables network developers to write simpler, failure-agnostic code. To this end, upon detecting a failure, our approach first spawns a new controller instance that runs in an emulated environment consisting of the network topology excluding the failed elements. Then, it quickly replays inputs observed by the controller before the failure occurred, leading the emulated network into the forwarding state that accounts for the failed elements. Finally, it recovers the network by installing the difference ruleset between emulated and current forwarding states.

Motivation MinION is a portable nanopore sequencing device that can be easily operated in the field with features including monitoring of run progress and selective sequencing. To fully exploit these features, real-time base calling is required. Up to date, this has only been achieved at the cost of high computing requirements that pose limitations in terms of hardware availability in common laptops and energy consumption. Results We developed a new base caller DeepNano-coral for nanopore sequencing, which is optimized to run on the Coral Edge Tensor Processing Unit, a small USB-attached hardware accelerator. To achieve this goal, we have designed new versions of two key components used in convolutional neural networks for speech recognition and base calling. In our components, we propose a new way of factorization of a full convolution into smaller operations, which decreases memory access operations, memory access being a bottleneck on this device. DeepNano-coral achieves real-time base calling during sequencing with the accuracy slightly better than the fast mode of the Guppy base caller and is extremely energy efficient, using only 10 W of power. Availability https://github.com/fmfi-compbio/coral-basecaller Supplementary information Supplementary data are available at Bioinformatics online.

In this paper, we first show that transient, but grave problems such as violations of security policies can occur with real switches even when using consistent updates to Software Defined Networks. Next, we present techniques that are effective in ameliorating this problem. Our key insight is in creating a transparent layer that relies on control and data plane measurements to confirm rule updates only when the rule is visible in the data plane.

Motivation Oxford Nanopore MinION is a portable DNA sequencer that is marketed as a device that can be deployed anywhere. Current base callers, however, require a powerful GPU to analyze data produced by MinION in real time, which hampers field applications. Results We have developed a fast base caller DeepNano-blitz that can analyze stream from up to two MinION runs in real time using a common laptop CPU (i7-7700HQ), with no GPU requirements. The base caller settings allow trading accuracy for speed and the results can be used for real time run monitoring (i.e. sample composition, barcode balance, species identification, etc.) or prefiltering of results for more detailed analysis (i.e. filtering out human DNA from human–pathogen runs). Availability and implementation DeepNano-blitz has been developed and tested on Linux and Intel processors and is available under MIT license at https://github.com/fmfi-compbio/deepnano-blitz. Supplementary information Supplementary data are available at Bioinformatics online.