Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userParallel Tensor Compression for Large-Scale Scientific Data
131
0
0.0
(
0
)
Added by
Grey Ballard
Publication date
2015
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
As parallel computing trends towards the exascale, scientific data produced by high-fidelity simulations are growing increasingly massive. For instance, a simulation on a three-dimensional spatial grid with 512 points per dimension that tracks 64 variables per grid point for 128 time steps yields 8~TB of data, assuming double precision. By viewing the data as a dense five-way tensor, we can compute a Tucker decomposition to find inherent low-dimensional multilinear structure, achieving compression ratios of up to 5000 on real-world data sets with negligible loss in accuracy. So that we can operate on such massive data, we present the first-ever distributed-memory parallel implementation for the Tucker decomposition, whose key computations correspond to parallel linear algebra operations, albeit with nonstandard data layouts. Our approach specifies a data distribution for tensors that avoids any tensor data redistribution, either locally or in parallel. We provide accompanying analysis of the computation and communication costs of the algorithms. To demonstrate the compression and accuracy of the method, we apply our approach to real-world data sets from combustion science simulations. We also provide detailed performance results, including parallel performance in both weak and strong scaling experiments.
rate research
Read More
Our goal is compression of massive-scale grid-structured data, such as the multi-terabyte output of a high-fidelity computational simulation. For such data sets, we have developed a new software package called TuckerMPI, a parallel C++/MPI software package for compressing distributed data. The approach is based on treating the data as a tensor, i.e., a multidimensional array, and computing its truncated Tucker decomposition, a higher-order analogue to the truncated singular value decomposition of a matrix. The result is a low-rank approximation of the original tensor-structured data. Compression efficiency is achieved by detecting latent global structure within the data, which we contrast to most compression methods that are focused on local structure. In this work, we describe TuckerMPI, our implementation of the truncated Tucker decomposition, including details of the data distribution and in-memory layouts, the parallel and serial implementations of the key kernels, and analysis of the storage, communication, and computational costs. We test the software on 4.5 terabyte and 6.7 terabyte data sets distributed across 100s of nodes (1000s of MPI processes), achieving compression rates between 100-200,000$times$ which equates to 99-99.999% compression (depending on the desired accuracy) in substantially less time than it would take to even read the same dataset from a parallel filesystem. Moreover, we show that our method also allows for reconstruction of partial or down-sampled data on a single node, without a parallel computer so long as the reconstructed portion is small enough to fit on a single machine, e.g., in the instance of reconstructing/visualizing a single down-sampled time step or computing summary statistics.
The paper presents a combination of the time-parallel parallel full approximation scheme in space and time (PFASST) with a parallel multigrid method (PMG) in space, resulting in a mesh-based solver for the three-dimensional heat equation with a uniquely high degree of efficient concurrency. Parallel scaling tests are reported on the Cray XE6 machine Monte Rosa on up to 16,384 cores and on the IBM Blue Gene/Q system JUQUEEN on up to 65,536 cores. The efficacy of the combined spatial- and temporal parallelization is shown by demonstrating that using PFASST in addition to PMG significantly extends the strong-scaling limit. Implications of using spatial coarsening strategies in PFASSTs multi-level hierarchy in large-scale parallel simulations are discussed.
For over a decade now we have been witnessing the success of {em massive parallel computation} (MPC) frameworks, such as MapReduce, Hadoop, Dryad, or Spark. One of the reasons for their success is the fact that these frameworks are able to accurately capture the nature of large-scale computation. In particular, compared to the classic distributed algorithms or PRAM models, these frameworks allow for much more local computation. The fundamental question that arises in this context is though: can we leverage this additional power to obtain even faster parallel algorithms? A prominent example here is the {em maximum matching} problem---one of the most classic graph problems. It is well known that in the PRAM model one can compute a 2-approximate maximum matching in $O(log{n})$ rounds. However, the exact complexity of this problem in the MPC framework is still far from understood. Lattanzi et al. showed that if each machine has $n^{1+Omega(1)}$ memory, this problem can also be solved $2$-approximately in a constant number of rounds. These techniques, as well as the approaches developed in the follow up work, seem though to get stuck in a fundamental way at roughly $O(log{n})$ rounds once we enter the near-linear memory regime. It is thus entirely possible that in this regime, which captures in particular the case of sparse graph computations, the best MPC round complexity matches what one can already get in the PRAM model, without the need to take advantage of the extra local computation power. In this paper, we finally refute that perplexing possibility. That is, we break the above $O(log n)$ round complexity bound even in the case of {em slightly sublinear} memory per machine. In fact, our improvement here is {em almost exponential}: we are able to deliver a $(2+epsilon)$-approximation to maximum matching, for any fixed constant $epsilon>0$, in $O((log log n)^2)$ rounds.
Matrix computations, especially iterative PDE solving (and the sparse matrix vector multiplication subproblem within) using conjugate gradient algorithm, and LU/Cholesky decomposition for solving system of linear equations, form the kernel of many applications, such as circuit simulators, computational fluid dynamics or structural analysis etc. The problem of designing approaches for parallelizing these computations, to get good speedups as much as possible as per Amdahls law, has been continuously researched upon. In this paper, we discuss approaches based on the use of finite projective geometry graphs for these two problems. For the problem of conjugate gradient algorithm, the approach looks at an alternative data distribution based on projective-geometry concepts. It is proved that this data distribution is an optimal data distribution for scheduling the main problem of dense matrix-vector multiplication. For the problem of parallel LU/Cholesky decomposition of general matrices, the approach is motivated by the recently published scheme for interconnects of distributed systems, perfect difference networks. We find that projective-geometry based graphs indeed offer an exciting way of parallelizing these computations, and in fact many others. Moreover, their applications ranges from architectural ones (interconnect choice) to algorithmic ones (data distributions).
Seismic inversion and imaging are adjoint-based optimization problems that processes up to terabytes of data, regularly exceeding the memory capacity of available computers. Data compression is an effective strategy to reduce this memory requirement by a certain factor, particularly if some loss in accuracy is acceptable. A popular alternative is checkpointing, where data is stored at selected points in time, and values at other times are recomputed as needed from the last stored state. This allows arbitrarily large adjoint computations with limited memory, at the cost of additional recomputations. In this paper we combine compression and checkpointing for the first time to compute a realistic seismic inversion. The combination of checkpointing and compression allows larger adjoint computations compared to using only compression, and reduces the recomputation overhead significantly compared to using only checkpointing.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
