arXiv subjects

Peter Sanders

Publications and source records attributed to Peter Sanders.

At least 55 records · Page 3Linked to original sources

arXiv2023

ReStore: In-Memory REplicated STORagE for Rapid Recovery in Fault-Tolerant Algorithms

Fault-tolerant distributed applications require mechanisms to recover data lost via a process failure. On modern cluster systems it is typically impractical to request replacement resources after such a failure. Therefore, applications have to continue working with the remaining resources. This requires redistributing the workload and that the non-failed processes reload data. We present an algorithmic framework and its C++ library implementation ReStore for MPI programs that enables recovery of data after process failures. By storing all required data in memory via an appropriate data distribution and replication, recovery is substantially faster than with standard checkpointing schemes that rely on a parallel file system. As the application developer can specify which data to load, we also support shrinking recovery instead of recovery using spare compute nodes. We evaluate ReStore in both controlled, isolated environments and real applications. Our experiments show loading times of lost input data in the range of milliseconds on up to 24 576 processors and a substantial speedup of the recovery time for the fault-tolerant version of a widely used bioinformatics application.

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arXiv2022

PaCHash: Packed and Compressed Hash Tables

We introduce PaCHash, a hash table that stores its objects contiguously in an array without intervening space, even if the objects have variable size. In particular, each object can be compressed using standard compression techniques. A small search data structure allows locating the objects in constant expected time. PaCHash is most naturally described as a static external hash table where it needs a constant number of bits of internal memory per block of external memory. Here, in some sense, PaCHash beats a lower bound on the space consumption of k-perfect hashing. An implementation for fast SSDs needs about 5 bits of internal memory per block of external memory, requires only one disk access (of variable length) per search operation, and has small internal search overhead compared to the disk access cost. Our experiments show that it has lower space consumption than all previous approaches even when considering objects of identical size.

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arXiv2022

SicHash -- Small Irregular Cuckoo Tables for Perfect Hashing

A Perfect Hash Function (PHF) is a hash function that has no collisions on a given input set. PHFs can be used for space efficient storage of data in an array, or for determining a compact representative of each object in the set. In this paper, we present the PHF construction algorithm SicHash - Small Irregular Cuckoo Tables for Perfect Hashing. At its core, SicHash uses a known technique: It places objects in a cuckoo hash table and then stores the final hash function choice of each object in a retrieval data structure. We combine the idea with irregular cuckoo hashing, where each object has a different number of hash functions. Additionally, we use many small tables that we overload beyond their asymptotic maximum load factor. The most space efficient competitors often use brute force methods to determine the PHFs. SicHash provides a more direct construction algorithm that only rarely needs to recompute parts. Our implementation improves the state of the art in terms of space usage versus construction time for a wide range of configurations. At the same time, it provides very fast queries.

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arXiv2022

More Recent Advances in (Hyper)Graph Partitioning

In recent years, significant advances have been made in the design and evaluation of balanced (hyper)graph partitioning algorithms. We survey trends of the last decade in practical algorithms for balanced (hyper)graph partitioning together with future research directions. Our work serves as an update to a previous survey on the topic. In particular, the survey extends the previous survey by also covering hypergraph partitioning and streaming algorithms, and has an additional focus on parallel algorithms.

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arXiv2022

Weighted Random Sampling on GPUs

An alias table is a data structure that allows for efficiently drawing weighted random samples in constant time and can be constructed in linear time. The PSA algorithm by Hübschle-Schneider and Sanders is able to construct alias tables in parallel on the CPU. In this report, we transfer the PSA algorithm to the GPU. Our construction algorithm achieves a speedup of 17 on a consumer GPU in comparison to the PSA method on a 16-core high-end desktop CPU. For sampling, we achieve an up to 24 times higher throughput. Both operations also require several times less energy than on the CPU. Adaptations helping to achieve this include changing memory access patterns to do coalesced access. Where this is not possible, we first copy data to the faster shared memory using coalesced access. We also enhance a generalization of binary search enabling to search for a range of items in parallel. Besides naive sampling, we also give improved batched sampling algorithms.

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arXiv2022

Scalable SAT Solving in the Cloud

Previous efforts on making Satisfiability (SAT) solving fit for high performance computing (HPC) have lead to super-linear speedups on particular formulae, but for most inputs cannot make efficient use of a large number of processors. Moreover, long latencies (minutes to days) of job scheduling make large-scale SAT solving on demand impractical for most applications. We address both issues with Mallob, a framework for job scheduling in the context of SAT solving which exploits malleability, i.e., the ability to add or remove processing power from a job during its computation. Mallob includes a massively parallel, distributed, and malleable SAT solving engine based on Hordesat with a more succinct and communication-efficient approach to clause sharing and numerous further improvements over its precursor. For example, Mallob on 640 cores outperforms an updated and improved configuration of Hordesat on 2560 cores. Moreover, Mallob can also solve many formulae in parallel while dynamically adapting the assigned resources, and jobs arriving in the system are usually initiated within a fraction of a second.

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arXiv2022

Vectorized and performance-portable Quicksort

Recent works showed that implementations of Quicksort using vector CPU instructions can outperform the non-vectorized algorithms in widespread use. However, these implementations are typically single-threaded, implemented for a particular instruction set, and restricted to a small set of key types. We lift these three restrictions: our proposed 'vqsort' algorithm integrates into the state-of-the-art parallel sorter 'ips4o', with a geometric mean speedup of 1.59. The same implementation works on seven instruction sets (including SVE and RISC-V V) across four platforms. It also supports floating-point and 16-128 bit integer keys. To the best of our knowledge, this is the fastest sort for non-tuple keys on CPUs, up to 20 times as fast as the sorting algorithms implemented in standard libraries. This paper focuses on the practical engineering aspects enabling the speed and portability, which we have not yet seen demonstrated for a Quicksort implementation. Furthermore, we introduce compact and transpose-free sorting networks for in-register sorting of small arrays, and a vector-friendly pivot sampling strategy that is robust against adversarial input.

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arXiv2022

Fast Succinct Retrieval and Approximate Membership using Ribbon

A retrieval data structure for a static function $f:S\rightarrow \{0,1\}^r$ supports queries that return $f(x)$ for any $x \in S$. Retrieval data structures can be used to implement a static approximate membership query data structure (AMQ), i.e., a Bloom filter alternative, with false positive rate $2^{-r}$. The information-theoretic lower bound for both tasks is $r|S|$ bits. While succinct theoretical constructions using $(1+o(1))r|S|$ bits were known, these could not achieve very small overheads in practice because they have an unfavorable space--time tradeoff hidden in the asymptotic costs or because small overheads would only be reached for physically impossible input sizes. With bumped ribbon retrieval (BuRR), we present the first practical succinct retrieval data structure. In an extensive experimental evaluation BuRR achieves space overheads well below 1\,\% while being faster than most previously used retrieval data structures (typically with space overheads at least an order of magnitude larger) and faster than classical Bloom filters (with space overhead $\geq 44\,\%$). This efficiency, including favorable constants, stems from a combination of simplicity, word parallelism, and high locality. We additionally describe homogeneous ribbon filter AMQs, which are even simpler and faster at the price of slightly larger space overhead.

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arXiv2022

Parallel Flow-Based Hypergraph Partitioning

We present a shared-memory parallelization of flow-based refinement, which is considered the most powerful iterative improvement technique for hypergraph partitioning at the moment. Flow-based refinement works on bipartitions, so current sequential partitioners schedule it on different block pairs to improve $k$-way partitions. We investigate two different sources of parallelism: a parallel scheduling scheme and a parallel maximum flow algorithm based on the well-known push-relabel algorithm. In addition to thoroughly engineered implementations, we propose several optimizations that substantially accelerate the algorithm in practice, enabling the use on extremely large hypergraphs (up to 1 billion pins). We integrate our approach in the state-of-the-art parallel multilevel framework Mt-KaHyPar and conduct extensive experiments on a benchmark set of more than 500 real-world hypergraphs, to show that the partition quality of our code is on par with the highest quality sequential code (KaHyPar), while being an order of magnitude faster with 10 threads.

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arXiv2021

Engineering MultiQueues: Fast Relaxed Concurrent Priority Queues

Priority queues with parallel access are an attractive data structure for applications like prioritized online scheduling, discrete event simulation, or greedy algorithms. However, a classical priority queue constitutes a severe bottleneck in this context, leading to very small throughput. Hence, there has been significant interest in concurrent priority queues with relaxed semantics. We investigate the complementary quality criteria rank error (how close are deleted elements to the global minimum) and delay (for each element x, how many elements with lower priority are deleted before x). In this paper, we introduce MultiQueues as a natural approach to relaxed priority queues based on multiple sequential priority queues. Their naturally high theoretical scalability is further enhanced by using three orthogonal ways of batching operations on the sequential queues. Experiments indicate that MultiQueues present a very good performance-quality tradeoff and considerably outperform competing approaches in at least one of these aspects. We employ a seemingly paradoxical technique of "wait-free locking" that might be of more general interest to convert sequential data structures to relaxed concurrent data structures.

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arXiv2021

Parallel Weighted Random Sampling

Data structures for efficient sampling from a set of weighted items are an important building block of many applications. However, few parallel solutions are known. We close many of these gaps both for shared-memory and distributed-memory machines. We give efficient, fast, and practicable parallel algorithms for building data structures that support sampling single items (alias tables, compressed data structures). This also yields a simplified and more space-efficient sequential algorithm for alias table construction. Our approaches to sampling $k$ out of $n$ items with/without replacement and to subset (Poisson) sampling are output-sensitive, i.e., the sampling algorithms use work linear in the number of different samples. This is also interesting in the sequential case. Weighted random permutation can be done by sorting appropriate random deviates. We show that this is possible with linear work using a nonlinear transformation of these deviates. Finally, we give a communication-efficient, highly scalable approach to (weighted and unweighted) reservoir sampling. This algorithm is based on a fully distributed model of streaming algorithms that might be of independent interest. Experiments for alias tables and sampling with replacement show near linear speedups both for construction and queries using up to 158 threads of shared-memory machines. An experimental evaluation of distributed weighted reservoir sampling on up to 256 nodes (5120 cores) also shows good speedups.

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arXiv2021

Fast, Exact and Scalable Dynamic Ridesharing

We study the problem of servicing a set of ride requests by dispatching a set of shared vehicles, which is faced by ridesharing companies such as Uber and Lyft. Solving this problem at a large scale might be crucial in the future for effectively using large fleets of autonomous vehicles. Since finding a solution for the entire set of requests that minimizes the total driving time is NP-complete, most practical approaches process the requests one by one. Each request is inserted into any vehicle's route such that the increase in driving time is minimized. Although this variant is solvable in polynomial time, it still takes considerable time in current implementations, even when inexact filtering heuristics are used. In this work, we present a novel algorithm for finding best insertions, based on (customizable) contraction hierarchies with local buckets. Our algorithm finds provably exact solutions, is still 30 times faster than a state-of-the-art algorithm currently used in industry and academia, and scales much better. When used within iterative transport simulations, our algorithm decreases the simulation time for largescale scenarios with many requests from days to hours.

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arXiv2021

High-Quality Hypergraph Partitioning

This paper considers the balanced hypergraph partitioning problem, which asks for partitioning the vertices into $k$ disjoint blocks of bounded size while minimizing an objective function over the hyperedges. Here, we consider the most commonly used connectivity metric. We describe our open source hypergraph partitioner KaHyPar which is based on the successful multi-level approach -- driving it to the extreme of one level for (almost) every vertex. Using carefully designed data structures and dynamic update techniques, this approach offers a very good time-quality tradeoff. We present two preprocessing techniques -- pin sparsification using locality sensitive hashing and community detection based on the Louvain algorithm. The community structure is used to guide the coarsening process that incrementally contracts vertices. Portfolio-based partitioning of the contracted hypergraph already achieves good initial solutions. While reversing the contractions, a combination of highly-localized direct $k$-way local search and flow-based techniques that take a more global view, refine the partition to achieve high quality. Optionally, a memetic algorithm evolves a pool of solution candidates to obtain even higher quality. We evaluate KaHyPar on a large set of instances from a wide range of application domains. With respect to quality, KaHyPar outperforms all previously considered systems that can handle large hypergraphs such as hMETIS, PaToH, Mondriaan, or Zoltan. KaHyPar is also faster than most of these systems except for PaToH which represents a different speed-quality tradeoff. The results even extend to the special case of graph partitioning, where specialized systems such as KaHIP should have an advantage.

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arXiv2021

Deep Multilevel Graph Partitioning

Partitioning a graph into blocks of "roughly equal" weight while cutting only few edges is a fundamental problem in computer science with a wide range of applications. In particular, the problem is a building block in applications that require parallel processing. While the amount of available cores in parallel architectures has significantly increased in recent years, state-of-the-art graph partitioning algorithms do not work well if the input needs to be partitioned into a large number of blocks. Often currently available algorithms compute highly imbalanced solutions, solutions of low quality, or have excessive running time for this case. This is because most high-quality general-purpose graph partitioners are multilevel algorithms which perform graph coarsening to build a hierarchy of graphs, initial partitioning to compute an initial solution, and local improvement to improve the solution throughout the hierarchy. However, for large number of blocks, the smallest graph in the hierarchy that is used for initial partitioning still has to be large. In this work, we substantially mitigate these problems by introducing deep multilevel graph partitioning and a shared-memory implementation thereof. Our scheme continues the multilevel approach deep into initial partitioning -- integrating it into a framework where recursive bipartitioning and direct k-way partitioning are combined such that they can operate with high performance and quality. Our approach is stronger, more flexible, arguably more elegant, and reduces bottlenecks for parallelization compared to other multilevel approaches. For example, for large number of blocks our algorithm is on average an order of magnitude faster than competing algorithms while computing balanced partitions with comparable solution quality. For small number of blocks, our algorithms are the fastest among competing systems with comparable quality.

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arXiv2021

Shared-Memory n-level Hypergraph Partitioning

We present a shared-memory algorithm to compute high-quality solutions to the balanced $k$-way hypergraph partitioning problem. This problem asks for a partition of the vertex set into $k$ disjoint blocks of bounded size that minimizes the connectivity metric (i.e., the sum of the number of different blocks connected by each hyperedge). High solution quality is achieved by parallelizing the core technique of the currently best sequential partitioner KaHyPar: the most extreme $n$-level version of the widely used multilevel paradigm, where only a single vertex is contracted on each level. This approach is made fast and scalable through intrusive algorithms and data structures that allow precise control of parallelism through atomic operations and fine-grained locking. We perform extensive experiments on more than 500 real-world hypergraphs with up to $140$ million vertices and two billion pins (sum of hyperedge sizes). We find that our algorithm computes solutions that are on par with a comparable configuration of KaHyPar while being an order of magnitude faster on average. Moreover, we show that recent non-multilevel algorithms specifically designed to partition large instances have considerable quality penalties and no clear advantage in running time.

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arXiv2021

Engineering In-place (Shared-memory) Sorting Algorithms

We present sorting algorithms that represent the fastest known techniques for a wide range of input sizes, input distributions, data types, and machines. A part of the speed advantage is due to the feature to work in-place. Previously, the in-place feature often implied performance penalties. Our main algorithmic contribution is a blockwise approach to in-place data distribution that is provably cache-efficient. We also parallelize this approach taking dynamic load balancing and memory locality into account. Our comparison-based algorithm, In-place Superscalar Samplesort (IPS$^4$o), combines this technique with branchless decision trees. By taking cases with many equal elements into account and by adapting the distribution degree dynamically, we obtain a highly robust algorithm that outperforms the best in-place parallel comparison-based competitor by almost a factor of three. IPS$^4$o also outperforms the best comparison-based competitors in the in-place or not in-place, parallel or sequential settings. IPS$^4$o even outperforms the best integer sorting algorithms in a wide range of situations. In many of the remaining cases (often involving near-uniform input distributions, small keys, or a sequential setting), our new in-place radix sorter turns out to be the best algorithm. Claims to have the, in some sense, "best" sorting algorithm can be found in many papers which cannot all be true. Therefore, we base our conclusions on extensive experiments involving a large part of the cross product of 21 state-of-the-art sorting codes, 6 data types, 10 input distributions, 4 machines, 4 memory allocation strategies, and input sizes varying over 7 orders of magnitude. This confirms the robust performance of our algorithms while revealing major performance problems in many competitors outside the concrete set of measurements reported in the associated publications.

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arXiv2020

Scalable Shared-Memory Hypergraph Partitioning

Hypergraph partitioning is an important preprocessing step for optimizing data placement and minimizing communication volumes in high-performance computing applications. To cope with ever growing problem sizes, it has become increasingly important to develop fast parallel partitioning algorithms whose solution quality is competitive with existing sequential algorithms. To this end, we present Mt-KaHyPar, the first shared-memory multilevel hypergraph partitioner with parallel implementations of many techniques used by the sequential, high-quality partitioning systems: a parallel coarsening algorithm that uses parallel community detection as guidance, initial partitioning via parallel recursive bipartitioning with work-stealing, a scalable label propagation refinement algorithm, and the first fully-parallel direct $k$-way formulation of the classical FM algorithm. Experiments performed on a large benchmark set of instances from various application domains demonstrate the scalability and effectiveness of our approach. With 64 cores, we observe self-relative speedups of up to 51 and a harmonic mean speedup of 23.5. In terms of solution quality, we outperform the distributed hypergraph partitioner Zoltan on 95% of the instances while also being a factor of 2.1 faster. With just four cores,Mt-KaHyPar is also slightly faster than the fastest sequential multilevel partitioner PaToH while producing better solutions on 83% of all instances. The sequential high-quality partitioner KaHyPar still finds better solutions than our parallel approach, especially when using max-flow-based refinement. This, however, comes at the cost of considerably longer running times.

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arXiv2020

Engineering Faster Sorters for Small Sets of Items

Sorting a set of items is a task that can be useful by itself or as a building block for more complex operations. That is why a lot of effort has been put into finding sorting algorithms that sort large sets as fast as possible. But the more sophisticated and complex the algorithms become, the less efficient they are for small sets of items due to large constant factors. We aim to determine if there is a faster way than insertion sort to sort small sets of items to provide a more efficient base case sorter. We looked at sorting networks, at how they can improve the speed of sorting few elements, and how to implement them in an efficient manner by using conditional moves. Since sorting networks need to be implemented explicitly for each set size, providing networks for larger sizes becomes less efficient due to increased code sizes. To also enable the sorting of slightly larger base cases, we adapted sample sort to Register Sample Sort, to break down those larger sets into sizes that can in turn be sorted by sorting networks. From our experiments we found that when sorting only small sets, the sorting networks outperform insertion sort by a factor of at least 1.76 for any array size between six and sixteen, and by a factor of 2.72 on average across all machines and array sizes. When integrating sorting networks as a base case sorter into Quicksort, we achieved far less performance improvements, which is probably due to the networks having a larger code size and cluttering the L1 instruction cache. But for x86 machines with a larger L1 instruction cache of 64 KiB or more, we obtained speedups of 12.7% when using sorting networks as a base case sorter in std::sort. In conclusion, the desired improvement in speed could only be achieved under special circumstances, but the results clearly show the potential of using conditional moves in the field of sorting algorithms.

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