29243423
Design Alternatives and Performance Trade-Offs for Implementing MPI-2 over InfiniBand
MPICH2 provides a layered architecture to achieve both portability and performance. For implementations of MPI-2 over InfiniBand, it provides the flexibility for researchers at the RDMA channel, CH3 or ADI3 layer. In this paper we analyze the performance and complexity trade-offs associated with implementations at these layers. We describe our designs and implementations, as well as optimizations at each layer. To show the performance impacts of these design schemes and optimizations, we evaluate our implementations with different micro-benchmarks, HPCC and NAS test suite. Our experiments show that although the ADI3 layers adds complexity in implementation, the benefits achieved through optimizations justify moving to the ADI layer to extract the best performance.
1603873
Application-Transparent Checkpoint/Restart for MPI Programs over InfiniBand
Ultra-scale computer clusters with high speed interconnects, such as InfiniBand, are being widely deployed for their excellent performance and cost effectiveness. However, the failure rate on these clusters also increases along with their augmented number of components. Thus, it becomes critical for such systems to be equipped with fault tolerance support. In this paper, we present our design and implementation of checkpoint/restart framework for MPI programs running over InfiniBand clusters. Our design enables low-overhead, application-transparent checkpointing. It uses coordinated protocol to save the current state of the whole MPI job to reliable storage, which allows users to perform rollback recovery if the system runs into faulty states later. Our solution has been incorporated into MVAPICH2, an open-source high performance MPI-2 implementation over InfiniBand. Performance evaluation of this implementation has been carried out using NAS benchmarks, HPL benchmark, and a real-world application called GROMACS. Experimental results indicate that in our design, the overhead to take checkpoints is low, and the performance impact for checkpointing applications periodically is insignificant. For example, time for checkpointing GROMACS is less than 0.3% of the execution time, and its performance only decreases by 4% with checkpoints taken every minute. To the best of our knowledge, this work is the first report of checkpoint/restart support for MPI over InfiniBand clusters in the literature
7610617
High Performance VMM-Bypass I/O in Virtual Machines
Currently, I/O device virtualization models in virtual machine (VM) environments require involvement of a virtual machine monitor (VMM) and/or a privileged VM for each I/O operation, which may turn out to be a performance bottleneck for systems with high I/O demands, especially those equipped with modern high speed interconnects such as InfiniBand. 
 
In this paper, we propose a new device virtualization model called VMM-bypass I/O, which extends the idea of OS-bypass originated from user-level communication. Essentially, VMM-bypass allows time-critical I/O operations to be carried out directly in guest VMs without involvement of the VMM and/or a privileged VM. By exploiting the intelligence found in modern high speed network interfaces, VMM-bypass can significantly improve I/O and communication performance for VMs without sacrificing safety or isolation. 
 
To demonstrate the idea of VMM-bypass, we have developed a prototype called Xen-IB, which offers InfiniBand virtualization support in the Xen 3.0 VM environment. Xen-IB runs with current InfiniBand hardware and does not require modifications to existing user-level applications or kernel-level drivers that use InfiniBand. Our performance measurements show that Xen-IB is able to achieve nearly the same raw performance as the original InfiniBand driver running in a non-virtualized environment.
2376785
Designing Efficient Asynchronous Memory Operations Using Hardware Copy Engine: A Case Study with I/OAT
Memory copies for bulk data transport incur large overheads due to CPU stalling, small register-size data movement, etc. Intel's I/O Acceleration Technology offers an asynchronous memory copy engine in kernel space which alleviates such overheads. In this paper, we propose a set of designs for asynchronous memory operations in user space for both single process (as an offloaded memcpy()) and lPC using the copy engine. We analyze our design based on overlap efficiency, performance and cache utilization. Our microbenchmark results show that using the copy engine for performing memory copies can achieve close to 87% overlap with computation. Further, the copy engine improves the copy latency of bulk memory data transfers by 50% and avoids cache pollution effects. With the emergence of multi-core architectures, the support for asynchronous memory operations holds a lot of promise in reducing the gap between the memory and processor performance.
12648516
Experiments in impulsive manipulation
In this paper, we present the results of our experimental effort in one form of impulsive manipulation: tapping. Our previous work studied the mechanics of tapping a planar object which then slides on a support surface, coming to rest due to friction. This work addresses the practical issues in creating a system which uses this mode of manipulation. We begin with the design of tapping devices-end effecters designed to deliver an impulse to an object, and report some of the issues we have found to be important in their design. Our next step was to perform single-tap experiments in order to fit and evaluate the models of impact and sliding. These experiments have shown that objects rotate less than predicted; we have found that the addition of a scaling factor for the torque due to friction enables the models to predict object motion reasonably well. In order to do positioning experiments, we developed a number of planning methods (or feedback control strategies) to compensate for errors in modeling, parameters, and actuation. These planning methods were successfully used to demonstrate a positioning task. We also have experimentally demonstrated that tapping can be used to position an object more precisely than the manipulator can position the tapping device. We offer some sensitivity analysis in support of this result.
33589927
Towards Context-Aware Knowledge Management in e-Enterprises
10270257
Layout Effects on Sociogram Perception
This paper describes a within-subjects experiment in which we compare the relative effectiveness of five sociogram drawing conventions in communicating underlying network substance, based on user task performance and usability preference, in order to examine effects of different spatial layout formats on human sociogram perception. We also explore the impact of edge crossings, a widely accepted readability aesthetic. Subjective data were gathered based on the methodology of Purchase et al.[14] Objective data were collected through an online system. 
 
We found that both edge crossings and conventions pose significant affects on user preference and task performance of finding groups, but either has little impact on the perception of actor status. On the other hand, the node positioning and angular resolution might be more important in perceiving actor status. In visualizing social networks, it is important to note that the techniques that are highly preferred by users do not necessarily lead to best task performance.
1537043
Topological Map Merging
When multiple robots cooperatively explore an environment, maps from individual robots must be merged to produce a single globally consistent map. This is a challenging problem when the robots do not have a common reference frame or global positioning. In this paper, we describe an algorithm for merging embedded topological maps. Topological maps provide a concise description of the navigability of an environment, and, with measurements easily collected during exploration, the vertices of the map can be embedded in a metric space. Our algorithm uses both the structure and the geometry of topological maps to determine the best correspondence between maps with single or multiple overlapping regions. Experiments with simulated and real-world data demonstrate the efficacy of our algorithm.
17604511
POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome
One possible path towards understanding the biological function of a target protein is through the discovery of how it interfaces within protein-protein interaction networks. The goal of this study was to create a virtual protein-protein interaction model using the concepts of orthologous conservation (or interologs) to elucidate the interacting networks of a particular target protein. POINT (the prediction of interactome database) is a functional database for the prediction of the human protein-protein interactome based on available orthologous interactome datasets. POINT integrates several publicly accessible databases, with emphasis placed on the extraction of a large quantity of mouse, fruit fly, worm and yeast protein-protein interactions datasets from the Database of Interacting Proteins (DIP), followed by conversion of them into a predicted human interactome. In addition, protein-protein interactions require both temporal synchronicity and precise spatial proximity. POINT therefore also incorporates correlated mRNA expression clusters obtained from cell cycle microarray databases and subcellular localization from Gene Ontology to further pinpoint the likelihood of biological relevance of each predicted interacting sets of protein partners.