System Description for a Scalable, Fault-Tolerant, Distributed Garbage Collector

We describe an efficient and fault-tolerant algorithm for distributed cyclic garbage collection. The algorithm imposes few requirements on the local machines and allows for flexibility in the choice of local collector and distributed acyclic garbage collector to use with it. We have emphasized reducing the number and size of network messages without sacrificing the promptness of collection throughout the algorithm. Our proposed collector is a variant of back tracing to avoid extensive synchronization between machines. We have added an explicit forward tracing stage to the standard back tracing stage and designed a tuned heuristic to reduce the total amount of work done by the collector. Of particular note is the development of fault-tolerant cooperation between traces and a heuristic that aggressively reduces the set of suspect objects.Comment: 47 pages, LaTe

Autonomic log/restore for advanced optimistic simulation systems

In this paper we address state recoverability in optimistic simulation systems by presenting an autonomic log/restore architecture. Our proposal is unique in that it jointly provides the following features: (i) log/restore operations are carried out in a completely transparent manner to the application programmer, (ii) the simulation-object state can be scattered across dynamically allocated non-contiguous memory chunks, (iii) two differentiated operating modes, incremental vs non-incremental, coexist via transparent, optimized run-time management of dual versions of the same application layer, with dynamic selection of the best suited operating mode in different phases of the optimistic simulation run, and (iv) determinationof the best suited mode for any time frame is carried out on the basis of an innovative modeling/optimization approach that takes into account stability of each operating mode vs variations of the model execution parameters. © 2010 IEEE

Transparently Mixing Undo Logs and Software Reversibility for State Recovery in Optimistic PDES

The rollback operation is a fundamental building block to support the correct execution of a speculative Time Warp-based Parallel Discrete Event Simulation. In the literature, several solutions to reduce the execution cost of this operation have been proposed, either based on the creation of a checkpoint of previous simulation state images, or on the execution of negative copies of simulation events which are able to undo the updates on the state. In this paper, we explore the practical design and implementation of a state recoverability technique which allows to restore a previous simulation state either relying on checkpointing or on the reverse execution of the state updates occurred while processing events in forward mode. Differently from other proposals, we address the issue of executing backward updates in a fully-transparent and event granularity-independent way, by relying on static software instrumentation (targeting the x86 architecture and Linux systems) to generate at runtime reverse update code blocks (not to be confused with reverse events, proper of the reverse computing approach). These are able to undo the effects of a forward execution while minimizing the cost of the undo operation. We also present experimental results related to our implementation, which is released as free software and fully integrated into the open source ROOT-Sim (ROme OpTimistic Simulator) package. The experimental data support the viability and effectiveness of our proposal

Fast Recompilation of Object Oriented Modules

Once a program file is modified, the recompilation time should be minimized, without sacrificing execution speed or high level object oriented features. The recompilation time is often a problem for the large graphical interactive distributed applications tackled by modern OO languages. A compilation server and fast code generator were developed and integrated with the SRC Modula-3 compiler and Linux ELF dynamic linker. The resulting compilation and recompilation speedups are impressive. The impact of different language features, processor speed, and application size are discussed

A single-system model predicts recognition memory and repetition priming in amnesia

We challenge the claim that there are distinct neural systems for explicit and implicit memory by demonstrating that a formal single-system model predicts the pattern of recognition memory (explicit) and repetition priming (implicit) in amnesia. In the current investigation, human participants with amnesia categorized pictures of objects at study and then, at test, identified fragmented versions of studied (old) and nonstudied (new) objects (providing a measure of priming), and made a recognition memory judgment (old vs new) for each object. Numerous results in the amnesic patients were predicted in advance by the single-system model, as follows: (1) deficits in recognition memory and priming were evident relative to a control group; (2) items judged as old were identified at greater levels of fragmentation than items judged new, regardless of whether the items were actually old or new; and (3) the magnitude of the priming effect (the identification advantage for old vs new items) overall was greater than that of items judged new. Model evidence measures also favored the single-system model over two formal multiple-systems models. The findings support the single-system model, which explains the pattern of recognition and priming in amnesia primarily as a reduction in the strength of a single dimension of memory strength, rather than a selective explicit memory system deficit

A single-system account of the relationship between priming, recognition, and fluency.

A single-system computational model of priming and recognition was applied to studies that have looked at the relationship between priming, recognition, and fluency in continuous identification paradigms. The model was applied to 3 findings that have been interpreted as evidence for a multiple-systems account: (a) priming can occur for items not recognized; (b) the pattern of identification reaction times (RTs) to hits, misses, correct rejections, and false alarms can change as a function of recognition performance; and (c) fluency effects (shorter RTs to words judged old vs. judged new) and priming effects (shorter RTs to old vs. new words) can be observed in amnesic patients at levels comparable with healthy adults despite impaired or near-chance recognition. The authors' simulations suggest, contrary to previous interpretations, that these results are consistent with a single-system account

Autonomic State Management for Optimistic Simulation Platforms

We present the design and implementation of an autonomic state manager (ASM) tailored for integration within optimistic parallel discrete event simulation (PDES) environments based on the C programming language and the executable and linkable format (ELF), and developed for execution on x8664 architectures. With ASM, the state of any logical process (LP), namely the individual (concurrent) simulation unit being part of the simulation model, is allowed to be scattered on dynamically allocated memory chunks managed via standard API (e.g., malloc/free). Also, the application programmer is not required to provide any serialization/deserialization module in order to take a checkpoint of the LP state, or to restore it in case a causality error occurs during the optimistic run, or to provide indications on which portions of the state are updated by event processing, so to allow incremental checkpointing. All these tasks are handled by ASM in a fully transparent manner via (A) runtime identification (with chunk-level granularity) of the memory map associated with the LP state, and (B) runtime tracking of the memory updates occurring within chunks belonging to the dynamic memory map. The co-existence of the incremental and non-incremental log/restore modes is achieved via dual versions of the same application code, transparently generated by ASM via compile/link time facilities. Also, the dynamic selection of the best suited log/restore mode is actuated by ASM on the basis of an innovative modeling/optimization approach which takes into account stability of each operating mode with respect to variations of the model/environmental execution parameters

Sciunits: Reusable Research Objects

Science is conducted collaboratively, often requiring knowledge sharing about computational experiments. When experiments include only datasets, they can be shared using Uniform Resource Identifiers (URIs) or Digital Object Identifiers (DOIs). An experiment, however, seldom includes only datasets, but more often includes software, its past execution, provenance, and associated documentation. The Research Object has recently emerged as a comprehensive and systematic method for aggregation and identification of diverse elements of computational experiments. While a necessary method, mere aggregation is not sufficient for the sharing of computational experiments. Other users must be able to easily recompute on these shared research objects. In this paper, we present the sciunit, a reusable research object in which aggregated content is recomputable. We describe a Git-like client that efficiently creates, stores, and repeats sciunits. We show through analysis that sciunits repeat computational experiments with minimal storage and processing overhead. Finally, we provide an overview of sharing and reproducible cyberinfrastructure based on sciunits gaining adoption in the domain of geosciences