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1. CheckFreq: Frequent, Fine-Grained DNN Checkpointing

   Mohan, Jayashree ; Phanishayee, Amar ; Chidambaram, Vijay ( February 2021 , Proceedings of the USENIX Conference on File and Storage Technologies (FAST 2021))

   Aguilera, Marcos ; Yadgar, Gala (Ed.)

   Training Deep Neural Networks (DNNs) is a resource-hungry and time-consuming task. During training, the model performs computation at the GPU to learn weights, repeatedly, over several epochs. The learned weights reside in GPU memory, and are occasionally checkpointed (written to persistent storage) for fault-tolerance. Traditionally, model parameters are checkpointed at epoch boundaries; for modern deep networks, an epoch runs for several hours. An interruption to the training job due to preemption, node failure, or process failure, therefore results in the loss of several hours worth of GPU work on recovery. We present CheckFreq, an automatic, fine-grained checkpointing framework that (1) algorithmically determines the checkpointing frequency at the granularity of iterations using systematic online profiling, (2) dynamically tunes checkpointing frequency at runtime to bound the checkpointing overhead using adaptive rate tuning, (3) maintains the training data invariant of using each item in the dataset exactly once per epoch by checkpointing data loader state using a light-weight resumable iterator, and (4) carefully pipelines checkpointing with computation to reduce the checkpoint cost by introducing two-phase checkpointing. Our experiments on a variety of models, storage backends, and GPU generations show that CheckFreq can reduce the recovery time from hours to seconds while bounding the runtime overhead within 3.5%. 

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2. Evaluating and improving the reliability of gas-phase sensor system calibrations across new locations for ambient measurements and personal exposure monitoring

   https://doi.org/10.5194/amt-12-4211-2019  

   Vikram, Sharad ; Collier-Oxandale, Ashley ; Ostertag, Michael H. ; Menarini, Massimiliano ; Chermak, Camron ; Dasgupta, Sanjoy ; Rosing, Tajana ; Hannigan, Michael ; Griswold, William G. ( January 2019 , Atmospheric Measurement Techniques)

   Abstract. Advances in ambient environmental monitoring technologies are enabling concerned communities and citizens to collect data to better understand their local environment and potential exposures. These mobile, low-cost tools make it possible to collect data with increased temporal and spatial resolution, providing data on a large scale with unprecedented levels of detail. This type of data has the potential to empower people to make personal decisions about their exposure and support the development of local strategies for reducing pollution and improving health outcomes. However, calibration of these low-cost instruments has been a challenge. Often, a sensor package is calibrated via field calibration. This involves colocating the sensor package with a high-quality reference instrument for an extended period and then applying machine learning or other model fitting technique such as multiple linear regression to develop a calibration model for converting raw sensor signals to pollutant concentrations. Although this method helps to correct for the effects of ambient conditions (e.g., temperature) and cross sensitivities with nontarget pollutants, there is a growing body of evidence that calibration models can overfit to a given location or set of environmental conditions on account of the incidental correlation between pollutant levels and environmental conditions, including diurnal cycles. As a result, a sensor package trained at a field site may provide less reliable data when moved, or transferred, to a different location. This is a potential concern for applications seeking to perform monitoring away from regulatory monitoring sites, such as personal mobile monitoring or high-resolution monitoring of a neighborhood. We performed experiments confirming that transferability is indeed a problem and show that it can be improved by collecting data from multiple regulatory sites and building a calibration model that leverages data from a more diverse data set. We deployed three sensor packages to each of three sites with reference monitors (nine packages total) and then rotated the sensor packages through the sites over time. Two sites were in San Diego, CA, with a third outside of Bakersfield, CA, offering varying environmental conditions, general air quality composition, and pollutant concentrations. When compared to prior single-site calibration, the multisite approach exhibits better model transferability for a range of modeling approaches. Our experiments also reveal that random forest is especially prone to overfitting and confirm prior results that transfer is a significant source of both bias and standard error. Linear regression, on the other hand, although it exhibits relatively high error, does not degrade much in transfer. Bias dominated in our experiments, suggesting that transferability might be easily increased by detecting and correcting for bias. Also, given that many monitoring applications involve the deployment of many sensor packages based on the same sensing technology, there is an opportunity to leverage the availability of multiple sensors at multiple sites during calibration to lower the cost of training and better tolerate transfer. We contribute a new neural network architecture model termed split-NN that splits the model into two stages, in which the first stage corrects for sensor-to-sensor variation and the second stage uses the combined data of all the sensors to build a model for a single sensor package. The split-NN modeling approach outperforms multiple linear regression, traditional two- and four-layer neural networks, and random forest models. Depending on the training configuration, compared to random forest the split-NN method reduced error 0 %–11 % for NO2 and 6 %–13 % for O3. 

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3. Checkpointing Workflows for Fail-Stop Errors

   https://doi.org/10.1109/CLUSTER.2017.14  

   Han, Li ; Canon, Louis-Claude ; Casanova, Henri ; Robert, Yves ; Vivien, Frederic ( September 2017 , IEEE Cluster)

   We consider the problem of orchestrating the execution of workflow applications structured as Directed Acyclic Graphs (DAGs) on parallel computing platforms that are subject to fail-stop failures. The objective is to minimize expected overall execution time, or makespan. A solution to this problem consists of a schedule of the workflow tasks on the available processors and of a decision of which application data to checkpoint to stable storage, so as to mitigate the impact of processor failures. For general DAGs this problem is hopelessly intractable. In fact, given a solution, computing its expected makespan is still a difficult problem. To address this challenge, we consider a restricted class of graphs, Minimal Series-Parallel Graphs (M-SPGS). It turns out that many real-world workflow applications are naturally structured as M-SPGS. For this class of graphs, we propose a recursive list-scheduling algorithm that exploits the M-SPG structure to assign sub-graphs to individual processors, and uses dynamic programming to decide which tasks in these sub-gaphs should be checkpointed. Furthermore, it is possible to efficiently compute the expected makespan for the solution produced by this algorithm, using a first-order approximation of task weights and existing evaluation algorithms for 2-state probabilistic DAGs. We assess the performance of our algorithm for production workflow configurations, comparing it to (i) an approach in which all application data is checkpointed, which corresponds to the standard way in which most production workflows are executed today; and (ii) an approach in which no application data is checkpointed. Our results demonstrate that our algorithm strikes a good compromise between these two approaches, leading to lower checkpointing overhead than the former and to better resilience to failure than the latter. 

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4. 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))

   null (Ed.)

   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 data 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. 

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5. CRUM: Checkpoint-Restart Support for CUDA's Unified Memory

   https://doi.org/10.1109/CLUSTER.2018.00047  

   Garg, Rohan ; Mohan, Apoorve ; Sullivan, Michael ; Cooperman, Gene ( September 2018 , Proc. of IEEE Int. Conf. on Cluster Computing (Cluster'18))

   Unified Virtual Memory (UVM) was recently introduced with CUDA version 8 and the Pascal GPU. The older CUDA programming style is akin to older large-memory UNIX applications which used to directly load and unload memory segments. Newer CUDA programs have started taking advantage of UVM for the same reasons of superior programmability that UNIX applications long ago switched to assuming the presence of virtual memory. Therefore, checkpointing of UVM has become increasing important, especially as NVIDIA CUDA continues to gain wider popularity: 87 of the top 500 supercomputers in the latest listings use NVIDIA GPUs, with a current trend of ten additional NVIDIA-based supercomputers each year. A new scalable checkpointing mechanism, CRUM (Checkpoint-Restart for Unified Memory), is demonstrated for hybrid CUDA/MPI computations across multiple computer nodes. The support for UVM is particularly attractive for programs requiring more memory than resides on the GPU, since the alternative to UVM is for the application to directly copy memory between device and host. Furthermore, CRUM supports a fast, forked checkpointing, which mostly overlaps the CUDA computation with storage of the checkpoint image in stable storage. The runtime overhead of using CRUM is 6% on average, and the time for forked checkpointing is seen to be a factor of up to 40 times less than traditional, synchronous checkpointing. 

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