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Register a new userImproving scalability and reliability of MPI-agnostic transparent checkpointing for production workloads at NERSC
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Added by
Prashant Singh Chouhan
Publication date
2021
fields
Informatics Engineering
and research's language is
English
Authors
Prashant Singh Chouhan
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Checkpoint/restart (C/R) provides fault-tolerant computing capability, enables long running applications, and provides scheduling flexibility for computing centers to support diverse workloads with different priority. It is therefore vital to get transparent C/R capability working at NERSC. MANA, by Garg et. al., is a transparent checkpointing tool that has been selected due to its MPI-agnostic and network-agnostic approach. However, originally written as a proof-of-concept code, MANA was not ready to use with NERSCs diverse production workloads, which are dominated by MPI and hybrid MPI+OpenMP applications. In this talk, we present ongoing work at NERSC to enable MANA for NERSCs production workloads, including fixing bugs that were exposed by the top applications at NERSC, adding new features to address system changes, evaluating C/R overhead at scale, etc. The lessons learned from making MANA production-ready for HPC applications will be useful for C/R tool developers, supercomputing centers and HPC end-users alike.
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Transparently checkpointing MPI for fault tolerance and load balancing is a long-standing problem in HPC. The problem has been complicated by the need to provide checkpoint-restart services for all combinations of an MPI implementation over all network interconnects. This work presents MANA (MPI-Agnostic Network-Agnostic transparent checkpointing), a single code base which supports all MPI implementation and interconnect combinations. The agnostic properties imply that one can checkpoint an MPI application under one MPI implementation and perhaps over TCP, and then restart under a second MPI implementation over InfiniBand on a cluster with a different number of CPU cores per node. This technique is based on a novel split-process approach, which enables two separate programs to co-exist within a single process with a single address space. This work overcomes the limitations of the two most widely adopted transparent checkpointing solutions, BLCR and DMTCP/InfiniBand, which require separate modifications to each MPI implementation and/or underlying network API. The runtime overhead is found to be insignificant both for checkpoint-restart within a single host, and when comparing a local MPI computation that was migrated to a remote cluster against an ordinary MPI computation running natively on that same remote cluster.
Mobile Edge Computing (MEC), which incorporates the Cloud, edge nodes and end devices, has shown great potential in bringing data processing closer to the data sources. Meanwhile, Federated learning (FL) has emerged as a promising privacy-preserving approach to facilitating AI applications. However, it remains a big challenge to optimize the efficiency and effectiveness of FL when it is integrated with the MEC architecture. Moreover, the unreliable nature (e.g., stragglers and intermittent drop-out) of end devices significantly slows down the FL process and affects the global models quality Xin such circumstances. In this paper, a multi-layer federated learning protocol called HybridFL is designed for the MEC architecture. HybridFL adopts two levels (the edge level and the cloud level) of model aggregation enacting different aggregation strategies. Moreover, in order to mitigate stragglers and end device drop-out, we introduce regional slack factors into the stage of client selection performed at the edge nodes using a probabilistic approach without identifying or probing the state of end devices (whose reliability is agnostic). We demonstrate the effectiveness of our method in modulating the proportion of clients selected and present the convergence analysis for our protocol. We have conducted extensive experiments with machine learning tasks in different scales of MEC system. The results show that HybridFL improves the FL training process significantly in terms of shortening the federated round length, speeding up the global models convergence (by up to 12X) and reducing end device energy consumption (by up to 58%).
We present a simple library which equips MPI implementations with truly asynchronous non-blocking point-to-point operations, and which is independent of the underlying communication infrastructure. It utilizes the MPI profiling interface (PMPI) and the MPI_THREAD_MULTIPLE thread compatibility level, and works with curre
Systematic checkpointing of the machine state makes restart of execution from a safe state possible upon detection of an error. The time and energy overhead of checkpointing, however, grows with the frequency of checkpointing. Amortizing this overhead becomes especially challenging, considering the growth of expected error rates, as checkpointing frequency tends to increase with increasing error rates. Based on the observation that due to imbalanced technology scaling, recomputing a data value can be more energy efficient than retrieving (i.e., loading) a stored copy, this paper explores how recomputation of data values (which otherwise would be read from a checkpoint from memory or secondary storage) can reduce the machine state to be checkpointed, and thereby reduce the checkpointing overhead. Specifically, the resulting amnesic checkpointing framework AmnesiCHK can reduce the storage overhead by up to 23.91%; time overhead, by 11.92%; and energy overhead, by 12.53%, respectively, even in a relatively small scale system.
X-ray scattering experiments using Free Electron Lasers (XFELs) are a powerful tool to determine the molecular structure and function of unknown samples (such as COVID-19 viral proteins). XFEL experiments are a challenge to computing in two ways: i) due to the high cost of running XFELs, a fast turnaround time from data acquisition to data analysis is essential to make informed decisions on experimental protocols; ii) data collection rates are growing exponentially, requiring new scalable algorithms. Here we report our experiences analyzing data from two experiments at the Linac Coherent Light Source (LCLS) during September 2020. Raw data were analyzed on NERSCs Cori XC40 system, using the Superfacility paradigm: our workflow automatically moves raw data between LCLS and NERSC, where it is analyzed using the software package CCTBX. We achieved real time data analysis with a turnaround time from data acquisition to full molecular reconstruction in as little as 10 min -- sufficient time for the experiments operators to make informed decisions. By hosting the data analysis on Cori, and by automating LCLS-NERSC interoperability, we achieved a data analysis rate which matches the data acquisition rate. Completing data analysis with 10 mins is a first for XFEL experiments and an important milestone if we are to keep up with data collection trends.
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