The GLEON Research And PRAGMA Lake Expedition -- GRAPLE -- is a collaborative effort between computer science and lake ecology researchers. It aims to improve our understanding and predictive capacity of the threats to the water quality of our freshwater resources, including climate change. This paper presents GRAPLEr, a distributed computing system used to address the modeling needs of GRAPLE researchers. GRAPLEr integrates and applies overlay virtual network, high-throughput computing, and Web service technologies in a novel way. First, its user-level IP-over-P2P (IPOP) overlay network allows compute and storage resources distributed across independently-administered institutions (including private and public clouds) to be aggregated into a common virtual network, despite the presence of firewalls and network address translators. Second, resources aggregated by the IPOP virtual network run unmodified high-throughput computing middleware (HTCondor) to enable large numbers of model simulations to be executed concurrently across the distributed computing resources. Third, a Web service interface allows end users to submit job requests to the system using client libraries that integrate with the R statistical computing environment. The paper presents the GRAPLEr architecture, describes its implementation and reports on its performance for batches of General Lake Model (GLM) simulations across three cloud infrastructures (University of Florida, CloudLab, and Microsoft Azure).
Several HTCondor-based high-throughput computing systems have been deployed in support of scientific applications. One representative example is the Open Science Grid (OSG @cite_4 ), which features a distributed set of HTCondor clusters. In contrast to OSG, which expects each site to run and manage its own HTCondor pool, GRAPLEr allows sites to join a collaborative, distributed cluster by joining its virtual HTCondor pool via the IPOP virtual network overlay. This reduces the barrier to entry for participants to contribute nodes to the network -- e.g., by simply deploying one or more VMs on a private or public cloud. Furthermore, GRAPLEr exposes a domain-tailored Web service interface that lowers the barrier to entry for end users.
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Large scale supercomputing applications typically run on clusters using vendor message passing libraries, limiting the application to the availability of memory and CPU resources on that single machine. The ability to run inter-cluster parallel code is attractive since it allows the consolidation of multiple large scale resources for computational simulations not possible on a single machine, and it also allows the conglomeration of small subsets of CPU cores for rapid turnaround, for example, in the case of high-availability computing. MPIg is a grid-enabled implementation of the Message Passing Interface (MPI), extending the MPICH implementation of MPI to use Globus Toolkit services such as resource allocation and authentication. To achieve co-availability of resources, HARC, the Highly-Available Resource Co-allocator, is used. Here we examine two applications using MPIg: LAMMPS (Large-scale Atomic Molecular Massively Parallel Simulator), is used with a replica exchange molecular dynamics approach to enhance binding affinity calculations in HIV drug research, and HemeLB, which is a lattice-Boltzmann solver designed to address fluid flow in geometries such as the human cerebral vascular system. The cross-site scalability of both these applications is tested and compared to single-machine performance. In HemeLB, communication costs are hidden by effectively overlapping non-blocking communication with computation, essentially scaling linearly across multiple sites, and LAMMPS scales almost as well when run between two significantly geographically separated sites as it does at a single site. The Open Science Grid (OSG) provides a distributed facility where the Consortium members provide guaranteed and opportunistic access to shared computing and storage resources. OSG provides support for and evolution of the infrastructure through activities that cover operations, security, software, troubleshooting, addition of new capabilities, and support for existing and engagement with new communities. The OSG SciDAC-2 project provides specific activities to manage and evolve the distributed infrastructure and support its use. The innovative aspects of the project are the maintenance and performance of a collaborative (shared & common) petascale national facility over tens of autonomous computing sites, for many hundreds of users, transferring terabytes of data a day, executing tens of thousands of jobs a day, and providing robust and usable resources for scientific groups of all types and sizes. More information can be found at the OSG web site: www.opensciencegrid.org. Data centre applications for batch processing (e.g. map reduce frameworks) and online services (e.g. search engines) scale by distributing data and computation across many servers. They typically follow a partition aggregation pattern: tasks are first partitioned across servers that process data locally, and then those partial results are aggregated. This data aggregation step, however, shifts the performance bottleneck to the network, which typically struggles to support many-to-few, high-bandwidth traffic between servers. Instead of performing data aggregation at edge servers, we show that it can be done more efficiently along network paths. We describe NETAGG, a software platform that supports on-path aggregation for network-bound partition aggregation applications. NETAGG exploits a middlebox-like design, in which dedicated servers (agg boxes) are connected by high-bandwidth links to network switches. Agg boxes execute aggregation functions provided by applications, which alleviates network hotspots because only a fraction of the incoming traffic is forwarded at each hop. NETAGG requires only minimal application changes: it uses shim layers on edge servers to redirect application traffic transparently to the agg boxes. Our experimental results show that NETAGG improves substantially the throughput of two sample applications, the Solr distributed search engine and the Hadoop batch processing framework. Its design allows for incremental deployment in existing data centres and incurs only a modest investment cost. A key advantage of infrastructure-as-a-service (IaaS) clouds is providing users on-demand access to resources. To provide on-demand access, however, cloud providers must either significantly overprovision their infrastructure (and pay a high price for operating resources with low utilization) or reject a large proportion of user requests (in which case the access is no longer on-demand). At the same time, not all users require truly on-demand access to resources. Many applications and workflows are designed for recoverable systems where interruptions in service are expected. For instance, many scientists utilize high-throughput computing (HTC)-enabled resources, such as Condor, where jobs are dispatched to available resources and terminated when the resource is no longer available. We propose a cloud infrastructure that combines on-demand allocation of resources with opportunistic provisioning of cycles from idle cloud nodes to other processes by deploying backfill virtual machines (VMs). For demonstration and experimental evaluation, we extend the Nimbus cloud computing toolkit to deploy backfill VMs on idle cloud nodes for processing an HTC workload. Initial tests show an increase in IaaS cloud utilization from 37.5 to 100 during a portion of the evaluation trace but only 6.39 overhead cost for processing the HTC workload. We demonstrate that a shared infrastructure between IaaS cloud providers and an HTC job management system can be highly beneficial to both the IaaS cloud provider and HTC users by increasing the utilization of the cloud infrastructure (thereby decreasing the overall cost) and contributing cycles that would otherwise be idle to processing HTC jobs.