Algorithm-Based Fault Tolerance for Two-Sided Dense Matrix Factorizations

The mean time between failure (MTBF) of large supercomputers is decreasing, and future exascale computers are expected to have a MTBF of around 30 minutes. Therefore, it is urgent to prepare important algorithms for future machines with such a short MTBF. Eigenvalue problems (EVP) and singular value problems (SVP) are common in engineering and scientific research. Solving EVP and SVP numerically involves two-sided matrix factorizations: the Hessenberg reduction, the tridiagonal reduction, and the bidiagonal reduction. These three factorizations are computation intensive, and have long running times. They are prone to suffer from computer failures. We designed algorithm-based fault tolerant (ABFT) algorithms for the parallel Hessenberg reduction and the parallel tridiagonal reduction. The ABFT algorithms target fail-stop errors. These two fault tolerant algorithms use a combination of ABFT and diskless checkpointing. ABFT is used to protect frequently modified data . We carefully design the ABFT algorithm so the checksums are valid at the end of each iterative cycle. Diskless checkpointing is used for rarely modified data. These checkpoints are in the form of checksums, which are small in size, so the time and storage cost to store them in main memory is small. Also, there are intermediate results which need to be protected for a short time window. We store a copy of this data on the neighboring process in the process grid. We also designed algorithm-based fault tolerant algorithms for the CPU-GPU hybrid Hessenberg reduction algorithm and the CPU-GPU hybrid bidiagonal reduction algorithm. These two fault tolerant algorithms target silent errors. Our design employs both ABFT and diskless checkpointing to provide data redundancy. The low cost error detection uses two dot products and an equality test. The recovery protocol uses reverse computation to roll back the state of the matrix to a point where it is easy to locate and correct errors. We provided theoretical analysis and experimental verification on the correctness and efficiency of our fault tolerant algorithm design. We also provided mathematical proof on the numerical stability of the factorization results after fault recovery. Experimental results corroborate with the mathematical proof that the impact is mild

Algorithm-based Fault Tolerance for Dense Matrix Factorizations, Multiple Failures and Accuracy

Dense matrix factorizations, such as LU, Cholesky and QR, are widely used for scientific applications that require solving systems of linear equations, eigenvalues and linear least squares problems. Such computations are normally carried out on supercomputers, whose ever-growing scale induces a fast decline of the Mean Time To Failure (MTTF). This article proposes a new hybrid approach, based on Algorithm-Based Fault Tolerance (ABFT), to help matrix factorizations algorithms survive fail-stop failures. We consider extreme conditions, such as the absence of any reliable node and the possibility of losing both data and checksum from a single failure. We will present a generic solution for protecting the right factor, where the updates are applied, of all above mentioned factorizations. For the left factor, where the panel has been applied, we propose a scalable checkpointing algorithm. This algorithm features high degree of checkpointing parallelism and cooperatively utilizes the checksum storage leftover from the right factor protection. The fault-tolerant algorithms derived from this hybrid solution is applicable to a wide range of dense matrix factorizations, with minor modifications. Theoretical analysis shows that the fault tolerance overhead decreases inversely to the scaling in the number of computing units and the problem size. Experimental results of LU and QR factorization on the Kraken (Cray XT5) supercomputer validate the theoretical evaluation and confirm negligible overhead, with- and without-errors. Applicability to tolerate multiple failures and accuracy after multiple recovery is also considered.</jats:p

Hard and Soft Error Resilience for One-sided Dense Linear Algebra Algorithms

Dense matrix factorizations, such as LU, Cholesky and QR, are widely used by scientific applications that require solving systems of linear equations, eigenvalues and linear least squares problems. Such computations are normally carried out on supercomputers, whose ever-growing scale induces a fast decline of the Mean Time To Failure (MTTF). This dissertation develops fault tolerance algorithms for one-sided dense matrix factorizations, which handles Both hard and soft errors. For hard errors, we propose methods based on diskless checkpointing and Algorithm Based Fault Tolerance (ABFT) to provide full matrix protection, including the left and right factor that are normally seen in dense matrix factorizations. A horizontal parallel diskless checkpointing scheme is devised to maintain the checkpoint data with scalable performance and low space overhead, while the ABFT checksum that is generated before the factorization constantly updates itself by the factorization operations to protect the right factor. In addition, without an available fault tolerant MPI supporting environment, we have also integrated the Checkpoint-on-Failure(CoF) mechanism into one-sided dense linear operations such as QR factorization to recover the running stack of the failed MPI process. Soft error is more challenging because of the silent data corruption, which leads to a large area of erroneous data due to error propagation. Full matrix protection is developed where the left factor is protected by column-wise local diskless checkpointing, and the right factor is protected by a combination of a floating point weighted checksum scheme and soft error modeling technique. To allow practical use on large scale system, we have also developed a complexity reduction scheme such that correct computing results can be recovered with low performance overhead. Experiment results on large scale cluster system and multicore+GPGPU hybrid system have confirmed that our hard and soft error fault tolerance algorithms exhibit the expected error correcting capability, low space and performance overhead and compatibility with double precision floating point operation

Extensions of Task-based Runtime for High Performance Dense Linear Algebra Applications

On the road to exascale computing, the gap between hardware peak performance and application performance is increasing as system scale, chip density and inherent complexity of modern supercomputers are expanding. Even if we put aside the difficulty to express algorithmic parallelism and to efficiently execute applications at large scale, other open questions remain. The ever-growing scale of modern supercomputers induces a fast decline of the Mean Time To Failure. A generic, low-overhead, resilient extension becomes a desired aptitude for any programming paradigm. This dissertation addresses these two critical issues, designing an efficient unified linear algebra development environment using a task-based runtime, and extending a task-based runtime with fault tolerant capabilities to build a generic framework providing both soft and hard error resilience to task-based programming paradigm. To bridge the gap between hardware peak performance and application perfor- mance, a unified programming model is designed to take advantage of a lightweight task-based runtime to manage the resource-specific workload, and to control the data ow and parallel execution of tasks. Under this unified development, linear algebra tasks are abstracted across different underlying heterogeneous resources, including multicore CPUs, GPUs and Intel Xeon Phi coprocessors. Performance portability is guaranteed and this programming model is adapted to a wide range of accelerators, supporting both shared and distributed-memory environments. To solve the resilient challenges on large scale systems, fault tolerant mechanisms are designed for a task-based runtime to protect applications against both soft and hard errors. For soft errors, three additions to a task-based runtime are explored. The first recovers the application by re-executing minimum number of tasks, the second logs intermediary data between tasks to minimize the necessary re-execution, while the last one takes advantage of algorithmic properties to recover the data without re- execution. For hard errors, we propose two generic approaches, which augment the data logging mechanism for soft errors. The first utilizes non-volatile storage device to save logged data, while the second saves local logged data on a remote node to protect against node failure. Experimental results have confirmed that our soft and hard error fault tolerant mechanisms exhibit the expected correctness and efficiency

Resilience in Numerical Methods: A Position on Fault Models and Methodologies

Future extreme-scale computer systems may expose silent data corruption (SDC) to applications, in order to save energy or increase performance. However, resilience research struggles to come up with useful abstract programming models for reasoning about SDC. Existing work randomly flips bits in running applications, but this only shows average-case behavior for a low-level, artificial hardware model. Algorithm developers need to understand worst-case behavior with the higher-level data types they actually use, in order to make their algorithms more resilient. Also, we know so little about how SDC may manifest in future hardware, that it seems premature to draw conclusions about the average case. We argue instead that numerical algorithms can benefit from a numerical unreliability fault model, where faults manifest as unbounded perturbations to floating-point data. Algorithms can use inexpensive "sanity" checks that bound or exclude error in the results of computations. Given a selective reliability programming model that requires reliability only when and where needed, such checks can make algorithms reliable despite unbounded faults. Sanity checks, and in general a healthy skepticism about the correctness of subroutines, are wise even if hardware is perfectly reliable.Comment: Position Pape

Algorithm-Directed Crash Consistence in Non-Volatile Memory for HPC

Fault tolerance is one of the major design goals for HPC. The emergence of non-volatile memories (NVM) provides a solution to build fault tolerant HPC. Data in NVM-based main memory are not lost when the system crashes because of the non-volatility nature of NVM. However, because of volatile caches, data must be logged and explicitly flushed from caches into NVM to ensure consistence and correctness before crashes, which can cause large runtime overhead. In this paper, we introduce an algorithm-based method to establish crash consistence in NVM for HPC applications. We slightly extend application data structures or sparsely flush cache blocks, which introduce ignorable runtime overhead. Such extension or cache flushing allows us to use algorithm knowledge to \textit{reason} data consistence or correct inconsistent data when the application crashes. We demonstrate the effectiveness of our method for three algorithms, including an iterative solver, dense matrix multiplication, and Monte-Carlo simulation. Based on comprehensive performance evaluation on a variety of test environments, we demonstrate that our approach has very small runtime overhead (at most 8.2\% and less than 3\% in most cases), much smaller than that of traditional checkpoint, while having the same or less recomputation cost.Comment: 12 page

Matrix Factorization at Scale: a Comparison of Scientific Data Analytics in Spark and C+MPI Using Three Case Studies

We explore the trade-offs of performing linear algebra using Apache Spark, compared to traditional C and MPI implementations on HPC platforms. Spark is designed for data analytics on cluster computing platforms with access to local disks and is optimized for data-parallel tasks. We examine three widely-used and important matrix factorizations: NMF (for physical plausability), PCA (for its ubiquity) and CX (for data interpretability). We apply these methods to TB-sized problems in particle physics, climate modeling and bioimaging. The data matrices are tall-and-skinny which enable the algorithms to map conveniently into Spark's data-parallel model. We perform scaling experiments on up to 1600 Cray XC40 nodes, describe the sources of slowdowns, and provide tuning guidance to obtain high performance