DIB on the Xerox workstation

DIB - A Distributed Implementation of Backtracking is a general-purpose package which allows applications that use tree-traversal algorithms such as backtrack and branch-and-bound to be easily implemented on a multicomputer. The application program needs to specify only the root of the recursion tree, the computation to be performed at each node, and how to generate children at each node. In addition, the application program may optionally specify how to synthesize values of tree nodes from their children\u27s values and how to disseminate information in the tree. DIB uses a distributed algorithm, transparent to the application programmer, that can divide the problem into subproblems and dynamically allocate them to any number of machines. It can also recover from failures of machines. DIB can now run on the Xerox workstation network at Rochester Institute of Technology. Speedup is achievable for exhaustive traversal and branch-and-bound, with only a small fraction of the time is spent in communication

High performance subgraph mining in molecular compounds

Structured data represented in the form of graphs arises in several fields of the science and the growing amount of available data makes distributed graph mining techniques particularly relevant. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. The problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiver-initiated, load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening dataset, where the approach attains close-to linear speedup in a network of workstations

Dynamic load balancing for the distributed mining of molecular structures

In molecular biology, it is often desirable to find common properties in large numbers of drug candidates. One family of methods stems from the data mining community, where algorithms to find frequent graphs have received increasing attention over the past years. However, the computational complexity of the underlying problem and the large amount of data to be explored essentially render sequential algorithms useless. In this paper, we present a distributed approach to the frequent subgraph mining problem to discover interesting patterns in molecular compounds. This problem is characterized by a highly irregular search tree, whereby no reliable workload prediction is available. We describe the three main aspects of the proposed distributed algorithm, namely, a dynamic partitioning of the search space, a distribution process based on a peer-to-peer communication framework, and a novel receiverinitiated load balancing algorithm. The effectiveness of the distributed method has been evaluated on the well-known National Cancer Institute’s HIV-screening data set, where we were able to show close-to linear speedup in a network of workstations. The proposed approach also allows for dynamic resource aggregation in a non dedicated computational environment. These features make it suitable for large-scale, multi-domain, heterogeneous environments, such as computational grids

Parallelized reliability estimation of reconfigurable computer networks

A parallelized system, ASSURE, for computing the reliability of embedded avionics flight control systems which are able to reconfigure themselves in the event of failure is described. ASSURE accepts a grammar that describes a reliability semi-Markov state-space. From this it creates a parallel program that simultaneously generates and analyzes the state-space, placing upper and lower bounds on the probability of system failure. ASSURE is implemented on a 32-node Intel iPSC/860, and has achieved high processor efficiencies on real problems. Through a combination of improved algorithms, exploitation of parallelism, and use of an advanced microprocessor architecture, ASSURE has reduced the execution time on substantial problems by a factor of one thousand over previous workstation implementations. Furthermore, ASSURE's parallel execution rate on the iPSC/860 is an order of magnitude faster than its serial execution rate on a Cray-2 supercomputer. While dynamic load balancing is necessary for ASSURE's good performance, it is needed only infrequently; the particular method of load balancing used does not substantially affect performance

Towards better algorithms for parallel backtracking

Many algorithms in operations research and artificial intelligence are based on depth first search in implicitly defined trees. For parallelizing these algorithms, a load balancing scheme is needed which is able to evenly distribute parts of an irregularly shaped tree over the processors. It should work with minimal interprocessor communication and without prior knowledge of the tree\u27s shape. Previously known load balancing algorithms either require sending a message for each tree node or they only work efficiently for large search trees. This paper introduces new randomized dynamic load balancing algorithms for {\em tree structured computations}, a generalization of backtrack search.These algorithms only need to communicate when necessary and have an asymptotically optimal scalability for many important cases. They work work on hypercubes, butterflies, meshes and many other architectures

Efficient Parallel Random Sampling : Vectorized, Cache-Efficient, and Online

We consider the problem of sampling $n$ numbers from the range $\{1,\ldots,N\}$ without replacement on modern architectures. The main result is a simple divide-and-conquer scheme that makes sequential algorithms more cache efficient and leads to a parallel algorithm running in expected time $\mathcal{O}(n/p+\log p)$ on $p$ processors, i.e., scales to massively parallel machines even for moderate values of $n$. The amount of communication between the processors is very small (at most $\mathcal{O}(\log p)$) and independent of the sample size. We also discuss modifications needed for load balancing, online sampling, sampling with replacement, Bernoulli sampling, and vectorization on SIMD units or GPUs

Towards an abstract parallel branch and bound machine

Many (parallel) branch and bound algorithms look very different from each other at first glance. They exploit, however, the same underlying computational model. This phenomenon can be used to define branch and bound algorithms in terms of a set of basic rules that are applied in a specific (predefined) order. In the sequential case, the specification of Mitten's rules turns out to be sufficient for the development of branch and bound algorithms. In the parallel case, the situation is a bit more complicated. We have to consider extra parameters such as work distribution and knowledge sharing. Here, the implementation of parallel branch and bound algorithms can be seen as a tuning of the parameters combined with the specification of Mitten's rules. These observations lead to generic systems, where the user provides the specifications of the problem to be solved, and the system generates a branch and bound algorithm running on a specific architecture. We will discuss some proposals that appeared in the literature. Next, we raise the question whether the proposed models are flexible enough. We analyze the design decisions to be taken when implementing a parallel branch and bound algorithm. It results in a classification model, which is validated by checking whether it captures existing branch and bound implementations. Finally, we return to the issue of flexibility of existing systems, and propose to add an abstract machine model to the generic framework. The model defines a virtual parallel branch and bound machine, within which the design decisions can be expressed in terms of the abstract machine. We will outline some ideas on which the machine may be based, and present directions of future work