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1. Skyhook: Programmable Storage for Databases

   Jeff LeFevre, Noah Watkins ( February 2019 , Vault)

   Ceph is an open source distributed storage system that is object-based and massively scalable. Ceph provides developers with the capability to create data interfaces that can take advantage of local CPU and memory on the storage nodes (Ceph Object Storage Devices). These interfaces are powerful for application developers and can be created in C, C++, and Lua. Skyhook is an open source storage and database project in the Center for Research in Open Source Software at UC Santa Cruz. Skyhook uses these capabilities in Ceph to create specialized read/write interfaces that leverage IO and CPU within the storage layer toward database processing and management. Specifically, we develop methods to apply predicates locally as well as additional metadata and indexing capabilities using Ceph's internal indexing mechanism built on top of RocksDB. Skyhook's approach helps to enable scale-out of a single node database system by scaling out the storage layer. Our results show the performance benefits for some queries indeed scale well as the storage layer scales out.
2. Scaling databases and file apis with programmable ceph object storage

   LeFevre, Jeff Maltzahn ( February 2020 , USENIX VAULT'20)

   The Skyhook Data Management project (SkyhookDM.com) at the Center for Research in Open Source Software (cross.ucsc.edu) at UC Santa Cruz implements customized extensions through Ceph's object class interface that enables offloading database operations to the storage system. In our previous Vault '19 talk, we showed how SkyhookDM can transparently scale out databases. The SkyhookDM Ceph extensions are an example of our 'programmable storage' research efforts at UCSC, and can be accessed through commonly available external/foreign table database interfaces. Utilizing fast in-memory serialization libraries such as Google Flatbuffers and Apache Arrow, SkyhookDM currently implements common database functions such as SELECT, PROJECT, AGGREGATE, and indexing inside Ceph, along with lower-level data manipulations such as transforming data from row to column formats on RADOS servers. In this talk, we will present three of our latest developments on the SkyhookDM project since Vault '19. First, SkyhookDM can be used to also offload operations of access libraries that support plugins for backends, such as HDF5 and its Virtual Object Layer. Second, in addition to row-oriented data format using Google's Flatbuffers, we have added support for column-oriented data formats using the Apache Arrow library within our Ceph extensions. Third, we added dynamic switching between row andmore »column data formats within Ceph objects, a first step towards physical design management in storage systems, similar to physical design tuning in database systems.« less
3. Mapping Datasets to Object Storage System

   https://doi.org/202024504037  

   Xiaowei ( November 2020 , EPJ web of conferences)

   Access libraries such as ROOT[1] and HDF5[2] allow users to interact with datasets using high level abstractions, like coordinate systems and associated slicing operations. Unfortunately, the implementations of access libraries are based on outdated assumptions about storage systems interfaces and are generally unable to fully benefit from modern fast storage devices. For example, access libraries often implement buffering and data layout that assume that large, single-threaded sequential access patterns are causing less overall latency than small parallel random access: while this is true for spinning media, it is not true for flash media. The situation is getting worse with rapidly evolving storage devices such as non-volatile memory and ever larger datasets. This project explores distributed dataset mapping infrastructures that can integrate and scale out existing access libraries using Ceph’s extensible object model, avoiding re-implementation or even modifications of these access libraries as much as possible. These programmable storage extensions coupled with our distributed dataset mapping techniques enable: 1) access library operations to be offloaded to storage system servers, 2) the independent evolution of access libraries and storage systems and 3) fully leveraging of the existing load balancing, elasticity, and failure management of distributed storage systems like Ceph. They also createmore »more opportunities to conduct storage server-local optimizations specific to storage servers. For example, storage servers might include local key/value stores combined with chunk stores that require different optimizations than a local file system. As storage servers evolve to support new storage devices like non-volatile memory, these server-local optimizations can be implemented while minimizing disruptions to applications. We will report progress on the means by which distributed dataset mapping can be abstracted over particular access libraries, including access libraries for ROOT data, and how we address some of the challenges revolving around data partitioning and composability of access operations.« less
4. Algorithms and Frameworks for Accelerating Security Applications on HPC Platforms

   YU, Xiaodong ( August 2019 , Virginia Tech Theses)

   Typical cybersecurity solutions emphasize on achieving defense functionalities. However, execution efficiency and scalability are equally important, especially for real-world deployment. Straightforward mappings of cybersecurity applications onto HPC platforms may significantly underutilize the HPC devices’ capacities. On the other hand, the sophisticated implementations are quite difficult: they require both in-depth understandings of cybersecurity domain-specific characteristics and HPC architecture and system model. In our work, we investigate three sub-areas in cybersecurity, including mobile software security, network security, and system security. They have the following performance issues, respectively: 1) The flow- and context-sensitive static analysis for the large and complex Android APKs are incredibly time-consuming. Existing CPU-only frameworks/tools have to set a timeout threshold to cease the program analysis to trade the precision for performance. 2) Network intrusion detection systems (NIDS) use automata processing as its searching core and requires line-speed processing. However, achieving high-speed automata processing is exceptionally difficult in both algorithm and implementation aspects. 3) It is unclear how the cache configurations impact time-driven cache side-channel attacks’ performance. This question remains open because it is difficult to conduct comparative measurement to study the impacts. In this dissertation, we demonstrate how application-specific characteristics can be leveraged to optimize implementations on various typesmore »of HPC for faster and more scalable cybersecurity executions. For example, we present a new GPU-assisted framework and a collection of optimization strategies for fast Android static data-flow analysis that achieve up to 128X speedups against the plain GPU implementation. For network intrusion detection systems (IDS), we design and implement an algorithm capable of eliminating the state explosion in out-of-order packet situations, which reduces up to 400X of the memory overhead. We also present tools for improving the usability of Micron’s Automata Processor. To study the cache configurations’ impact on time-driven cache side-channel attacks’ performance, we design an approach to conducting comparative measurement. We propose a quantifiable success rate metric to measure the performance of time-driven cache attacks and utilize the GEM5 platform to emulate the configurable cache.« less
5. The Deep Learning Epilepsy Detection Challenge: Design, Implementation, and Test of a New Crowd-Sourced AI Challenge Ecosystem

   Kiral, Isabell ; Roy, Subhrajit ; Mummert, Todd ; Braz, Alan ; Tsay, Jason ; Tang, Jianbin ; Asif, Umar ; Schaffter, Thomas ; Mehmet, Eren ; Picone, Joseph ; et al ( April 2019 , Challenges in Machine Learning Competitions for All (CiML))

   The DeepLearningEpilepsyDetectionChallenge: design, implementation, andtestofanewcrowd-sourced AIchallengeecosystem Isabell Kiral*, Subhrajit Roy*, Todd Mummert*, Alan Braz*, Jason Tsay, Jianbin Tang, Umar Asif, Thomas Schaffter, Eren Mehmet, The IBM Epilepsy Consortium◊ , Joseph Picone, Iyad Obeid, Bruno De Assis Marques, Stefan Maetschke, Rania Khalaf†, Michal Rosen-Zvi† , Gustavo Stolovitzky† , Mahtab Mirmomeni† , Stefan Harrer† * These authors contributed equally to this work † Corresponding authors: rkhalaf@us.ibm.com, rosen@il.ibm.com, gustavo@us.ibm.com, mahtabm@au1.ibm.com, sharrer@au.ibm.com ◊ Members of the IBM Epilepsy Consortium are listed in the Acknowledgements section J. Picone and I. Obeid are with Temple University, USA. T. Schaffter is with Sage Bionetworks, USA. E. Mehmet is with the University of Illinois at Urbana-Champaign, USA. All other authors are with IBM Research in USA, Israel and Australia. Introduction This decade has seen an ever-growing number of scientific fields benefitting from the advances in machine learning technology and tooling. More recently, this trend reached the medical domain, with applications reaching from cancer diagnosis [1] to the development of brain-machine-interfaces [2]. While Kaggle has pioneered the crowd-sourcing of machine learning challenges to incentivise data scientists from around the world to advance algorithm and model design, the increasing complexity of problem statements demands of participants to be expert datamore »scientists, deeply knowledgeable in at least one other scientific domain, and competent software engineers with access to large compute resources. People who match this description are few and far between, unfortunately leading to a shrinking pool of possible participants and a loss of experts dedicating their time to solving important problems. Participation is even further restricted in the context of any challenge run on confidential use cases or with sensitive data. Recently, we designed and ran a deep learning challenge to crowd-source the development of an automated labelling system for brain recordings, aiming to advance epilepsy research. A focus of this challenge, run internally in IBM, was the development of a platform that lowers the barrier of entry and therefore mitigates the risk of excluding interested parties from participating. The challenge: enabling wide participation With the goal to run a challenge that mobilises the largest possible pool of participants from IBM (global), we designed a use case around previous work in epileptic seizure prediction [3]. In this “Deep Learning Epilepsy Detection Challenge”, participants were asked to develop an automatic labelling system to reduce the time a clinician would need to diagnose patients with epilepsy. Labelled training and blind validation data for the challenge were generously provided by Temple University Hospital (TUH) [4]. TUH also devised a novel scoring metric for the detection of seizures that was used as basis for algorithm evaluation [5]. In order to provide an experience with a low barrier of entry, we designed a generalisable challenge platform under the following principles: 1. No participant should need to have in-depth knowledge of the specific domain. (i.e. no participant should need to be a neuroscientist or epileptologist.) 2. No participant should need to be an expert data scientist. 3. No participant should need more than basic programming knowledge. (i.e. no participant should need to learn how to process fringe data formats and stream data efficiently.) 4. No participant should need to provide their own computing resources. In addition to the above, our platform should further • guide participants through the entire process from sign-up to model submission, • facilitate collaboration, and • provide instant feedback to the participants through data visualisation and intermediate online leaderboards. The platform The architecture of the platform that was designed and developed is shown in Figure 1. The entire system consists of a number of interacting components. (1) A web portal serves as the entry point to challenge participation, providing challenge information, such as timelines and challenge rules, and scientific background. The portal also facilitated the formation of teams and provided participants with an intermediate leaderboard of submitted results and a final leaderboard at the end of the challenge. (2) IBM Watson Studio [6] is the umbrella term for a number of services offered by IBM. Upon creation of a user account through the web portal, an IBM Watson Studio account was automatically created for each participant that allowed users access to IBM's Data Science Experience (DSX), the analytics engine Watson Machine Learning (WML), and IBM's Cloud Object Storage (COS) [7], all of which will be described in more detail in further sections. (3) The user interface and starter kit were hosted on IBM's Data Science Experience platform (DSX) and formed the main component for designing and testing models during the challenge. DSX allows for real-time collaboration on shared notebooks between team members. A starter kit in the form of a Python notebook, supporting the popular deep learning libraries TensorFLow [8] and PyTorch [9], was provided to all teams to guide them through the challenge process. Upon instantiation, the starter kit loaded necessary python libraries and custom functions for the invisible integration with COS and WML. In dedicated spots in the notebook, participants could write custom pre-processing code, machine learning models, and post-processing algorithms. The starter kit provided instant feedback about participants' custom routines through data visualisations. Using the notebook only, teams were able to run the code on WML, making use of a compute cluster of IBM's resources. The starter kit also enabled submission of the final code to a data storage to which only the challenge team had access. (4) Watson Machine Learning provided access to shared compute resources (GPUs). Code was bundled up automatically in the starter kit and deployed to and run on WML. WML in turn had access to shared storage from which it requested recorded data and to which it stored the participant's code and trained models. (5) IBM's Cloud Object Storage held the data for this challenge. Using the starter kit, participants could investigate their results as well as data samples in order to better design custom algorithms. (6) Utility Functions were loaded into the starter kit at instantiation. This set of functions included code to pre-process data into a more common format, to optimise streaming through the use of the NutsFlow and NutsML libraries [10], and to provide seamless access to the all IBM services used. Not captured in the diagram is the final code evaluation, which was conducted in an automated way as soon as code was submitted though the starter kit, minimising the burden on the challenge organising team. Figure 1: High-level architecture of the challenge platform Measuring success The competitive phase of the "Deep Learning Epilepsy Detection Challenge" ran for 6 months. Twenty-five teams, with a total number of 87 scientists and software engineers from 14 global locations participated. All participants made use of the starter kit we provided and ran algorithms on IBM's infrastructure WML. Seven teams persisted until the end of the challenge and submitted final solutions. The best performing solutions reached seizure detection performances which allow to reduce hundred-fold the time eliptologists need to annotate continuous EEG recordings. Thus, we expect the developed algorithms to aid in the diagnosis of epilepsy by significantly shortening manual labelling time. Detailed results are currently in preparation for publication. Equally important to solving the scientific challenge, however, was to understand whether we managed to encourage participation from non-expert data scientists. Figure 2: Primary occupation as reported by challenge participants Out of the 40 participants for whom we have occupational information, 23 reported Data Science or AI as their main job description, 11 reported being a Software Engineer, and 2 people had expertise in Neuroscience. Figure 2 shows that participants had a variety of specialisations, including some that are in no way related to data science, software engineering, or neuroscience. No participant had deep knowledge and experience in data science, software engineering and neuroscience. Conclusion Given the growing complexity of data science problems and increasing dataset sizes, in order to solve these problems, it is imperative to enable collaboration between people with differences in expertise with a focus on inclusiveness and having a low barrier of entry. We designed, implemented, and tested a challenge platform to address exactly this. Using our platform, we ran a deep-learning challenge for epileptic seizure detection. 87 IBM employees from several business units including but not limited to IBM Research with a variety of skills, including sales and design, participated in this highly technical challenge.« less