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As we approach the era of exa-scale computing, fault tolerance is of growing importance. The increasing number of cores as well as the increased complexity of modern heterogenous systems result in substantial decrease of the expected mean time between failures. Among the different fault tolerance techniques, checkpoint/restart is vastly adopted in supercomputing systems. Although many supercomputers in the TOP 500 list use GPUs, only a few checkpoint restart mechanism support GPUs.In this paper, we extend an application level checkpoint library, called fault tolerance interface (FTI), to support multi-node/multi-GPU checkpoints. In contrast to previous work, our library includes a memory manager, which upon a checkpoint invocation tracks the actual location of the data to be stored and handles the data accordingly. We analyze the overhead of the checkpoint/restart procedure and we present a series of optimization steps to massively decrease the checkpoint and recovery time of our implementation. To further reduce the checkpoint time we present a differential checkpoint approach which writes only the updated data to the checkpoint file. Our approach is evaluated and, in the best case scenario, the execution time of a normal checkpoint is reduced by 15x in contrast with a non-optimized version, in the case of differential checkpoint the overhead can drop to 2.6% when checkpointing every 30s. The research leading to these results has received funding from the European Union’s Horizon 2020 Programme under the LEGaTO Project (www.legato-project.eu), grant agreement #780681.

One of the major challenges in using extreme scale systems efficiently is to mitigate the impact of faults. Application-level checkpoint/restart (CR) methods provide the best trade-off between productivity, robustness, and performance. There are many solutions implementing CR at the application level. They all provide advanced I/O capabilities to minimize the overhead introduced by CR. Nevertheless, there is still room for improvement in terms of programmability and flexibility, because end-users must manually serialize and deserialize application state using low-level APIs, modify the flow of the application to consider restarts, or rewrite CR code whenever the backend library changes. In this work, we propose a set of compiler directives and clauses that allow users to specify CR operations in a simple way. Our approach supports the common CR features provided by all the CR libraries. However, it can also be extended to support advanced features that are only available in some CR libraries, such as differential checkpointing, the use of HDF5 format, and the possibility of using fault-tolerance-dedicated threads. The result of our evaluation revealed a high increase in programmability. On average, we reduced the number of lines of code by 71%, 94%, and 64% for FTI, SCR, and VeloC, respectively, and no additional overhead was perceived using our solution compared to using the backend libraries directly. Finally, portability is enhanced because our programming model allows the use of any backend library without changing any code. This work is supported by the Spanish Ministerio de Ciencia, Innovación y Universidades (TIN2015-65316-P) and by the Generalitat de Catalunya (2014-SGR-1051). This project received funding from the European Union’s Seventh Framework Programme (FP7/2007-2013) and the Horizon 2020 (H2020) funding framework under grant agreement no. H2020-FETHPC-754304 (DEEPEST).

The first exa-scale supercomputers are expected to be operational in China, USA, Japan and Europe within the early 2020’s. This allows scientists to execute applications at extreme scale with more than 1018 floating point operations per second (exa-FLOPS). However, the number of FLOPS is not the only parameter that determines the final performance. In order to store intermediate results or to provide fault tolerance, most applications need to perform a considerable amount of I/O operations during runtime. The performance of those operations is determined by the throughput from volatile (e.g. DRAM) to non-volatile stable storage. Regarding the slow growth in network bandwidth compared to the computing capacity on the nodes, it is highly beneficial to deploy local stable storage such as the new non-volatile memories (NVMe), in order to avoid the transfer through the network to the parallel file system. In this work, we analyse the performance of three different storage levels of the CTE-POWER9 cluster, located at the Barcelona Supercomputing Center (BSC). We compare the throughputs of SSD, NVMe on the nodes to the GPFS under various scenarios and settings. We measured a maximum performance on 16 nodes of 83 GB/s using NVMe devices, 5.6 GB/s for SSD devices and 4.4 GB/s for writes to the GPFS. This project has received funding from the European Union’sHorizon 2020 research and innovation programme under the Marie Sklodowska-Curiegrant agreement No 708566 (DURO). Part of the research presented here has receivedfunding from the European Union’s Seventh Framework Programme (FP7/2007-2013)and the Horizon 2020 (H2020) funding framework under grant agreement no. H2020-FETHPC-754304 (DEEP-EST). The present publication reflects only the authors’views. The European Commission is not liable for any use that might be made ofthe information contained therein.

The coming exascale era is a great opportunity for high performance computing (HPC) applications. However, high failure rates on these systems will hazard the successful completion of their execution. Bit-flip errors in dynamic random access memory (DRAM) account for a noticeable share of the failures in supercomputers. Hardware mechanisms, such as error correcting code (ECC), can detect and correct single-bit errors and can detect some multi-bit errors while others can go undiscovered. Unfortunately, detected multi-bit errors will most of the time force the termination of the application and lead to a global restart. Thus, other strategies at the software level are needed to tolerate these type of faults more efficiently and to avoid a global restart. In this work, we extend the FTI checkpointing library to facilitate the implementation of custom recovery strategies for MPI applications, minimizing the overhead introduced when coping with soft errors. The new functionalities are evaluated by implementing local forward recovery on three HPC benchmarks with different reliability requirements. Our results demonstrate a reduction on the recovery times by up to 14%. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 708566 (DURO). This research is also supported by the Ministry of Economy and Competitiveness of Spain and FEDER funds of the EU (Projects TIN2016-75845-P and the predoctoral grant of Nuria Losada ref. BES-2014-068066), and by the Galician Government (Xunta de Galicia) under the Consolidation Program of Competitive Research (ref. ED431C 2017/04).

Pleural thickenings can be found in asbestos exposed patient’s lung. Non-invasive diagnosis including CT imaging can detect aggressive malignant pleural mesothelioma in its early stage. In order to create a quantitative documentation of automatic detected pleural thickenings over time, the differences in volume and thickness of the detected thickenings have to be calculated. Physicians usually estimate the change of each thickening via visual comparison which provides neither quantitative nor qualitative measures. In this work, automatic spatiotemporal matching techniques of the detected pleural thickenings at two points of time based on the semi-automatic registration have been developed, implemented, and tested so that the same thickening can be compared fully automatically. As result, the application of the mapping technique using the principal components analysis turns out to be advantageous than the feature-based mapping using centroid and mean Hounsfield Units of each thickening, since the resulting sensitivity was improved to 98.46% from 42.19%, while the accuracy of feature-based mapping is only slightly higher (84.38% to 76.19%).

The efficient utilization of current supercomputing systems with deep storage hierarchies demands scientific applications that are capable of leveraging such heterogeneous hardware. Fault tolerance, and checkpointing in particular, is one of the most time-consuming aspects if not handled correctly. High checkpoint performance can be achieved using optimized multilevel checkpoint and restart libraries. Unfortunately, those libraries do not allow for restarts with a modified number of processes or scientific post-processing of the checkpointed data. This is because they typically use an N-N checkpointing scheme and opaque file-formats. In this article, we present a novel mechanism to asynchronously store checkpoints into a self-descriptive file format and load the data upon recovery with a different number of processes. We provide an API that defines the process-local data as part of a globally shared dataset. Our measurements demonstrate a low overhead between 0.6% and 2.5% for a 2.25 TB checkpoint with 6K processes. Part of the research presented here has received funding from the Horizon 2020 (H2020) funding framework under grant/award number: 824158; Energy oriented Centre of Excellence II (EoCoE-II). The present publication reflects only the authors’ views. The European Commission is not liable for any use that might be made of the information contained therein. This work was partially performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under contract DEAC52-07NA2734 (LLNLCONF-811845).