GMT: Enabling easy development and efficient execution of irregular applications on commodity clusters

In this poster we introduce GMT (Global Memory and Threading library), a custom runtime library that enables efficient execution of irregular applications on commodity clusters. GMT only requires a cluster with x86 nodes supporting MPI. GMT integrates the Partititioned Global Address Space (PGAS) locality-aware global data model with a fork/join control model common in single node multithreaded environments. GMT supports lightweight software multithreading to tolerate latencies for accessing data on remote nodes, and is built around data aggregation to maximize network bandwidth utilization.Peer ReviewedPostprint (author's final draft

High level synthesis of RDF queries for graph analytics

In this paper we present a set of techniques that enable the synthesis of efficient custom accelerators for memory intensive, irregular applications. To address the challenges of irregular applications (large memory footprint, unpredictable fine-grained data accesses, and high synchronization intensity), and exploit their opportunities (thread level parallelism, memory level parallelism), we propose a novel accelerator design that employs an adaptive and Distributed Controller (DC) architecture, and a Memory Interface Controller (MIC) that supports concurrent and atomic memory operations on a multi-ported/multi-banked shared memory. Among the multitude of algorithms that may benefit from our solution, we focus on the acceleration of graph analytics applications and, in particular, on the synthesis of SPARQL queries on Resource Description Framework (RDF) databases. We achieve this objective by incorporating the synthesis techniques into Bambu, an Open Source high-level synthesis tools, and interfacing it with GEMS, the Graph database Engine for Multithreaded Systems. The GEMS' front-end generates optimized C implementations of the input queries, modeled as graph pattern matching algorithms, which are then automatically synthesized by Bambu. We validate our approach by synthesizing several SPARQL queries from the Lehigh University Benchmark (LUBM)

HPC system software for regular and irregular parallel applications

The upcoming generation of system software for High Performance Computing is expected to provide a richer set of functionalities without compromising application performance. This Ph.D. thesis addresses the problem of designing scalable system software for both regular and irregular applications. The contributions are two-fold. First, we evaluate the drawbacks of current HPC system software for regular applications. We describe a methodology to precisely measure jitter on a general-purpose OS. Considering a lightweight operating system (IBM CNK), we analyze the overhead of adding support for a missing feature such as dynamic memory management. Second, we focus on irregular applications and build a specialized runtime system to enhance this kind of applications on common HPC flop intensive systems. The proposed runtime system provides a global address space abstraction of a distributed memory machine combined with a transparent fork/join execution model and it also includes lightweight multithreading and network message aggregation.Peer Reviewe

Genetic deletion of Rhes or pharmacological blockade of mTORC1 prevent striato-nigral neurons activation in levodopa-induced dyskinesia

Ras homolog enriched in striatum (Rhes) is a small GTP-binding protein that modulates signal transduction at dopamine receptors, and also activates mammalian target of rapamycin complex 1 (mTORC1). Rhes binding to mTORC1 is hypothesized to play a role in motor disorders such as levodopa-induced dyskinesia. Here, we investigate the behavioral and in vivo neurocircuitry changes associated with genetic deletion of Rhes or inhibition of mTORC1 signaling in the mouse model of levodopa-induced dyskinesia. 6-Hydroxydopamine-hemilesioned Rhes knockout mice and wild-type littermates were chronically treated with levodopa. In parallel, 6-hydroxydopamine-hemilesioned naïve mice were chronically treated with levodopa or levodopa plus rapamycin, to block mTORC1 pathway activation. Dyskinetic movements were monitored during levodopa treatment along with motor activity on the rotarod. Finally, dyskinetic mice underwent microdialysis probe implantation in the dopamine-depleted striatum and ipsilateral substantia nigra reticulata, and GABA and glutamate levels were monitored upon acute challenge with levodopa. Both Rhes knockouts and rapamycin-treated mice developed less dyskinesia than controls, although only rapamycin-treated mice fully preserved rotarod performance on levodopa. Levodopa elevated nigral GABA and glutamate in controls but not in Rhes knockouts or rapamycin-treated mice. Levodopa also stimulated striatal glutamate in controls and Rhes knockouts but not in rapamycin-treated mice. We conclude that both genetic deletion of Rhes and pharmacological blockade of mTORC1 significantly attenuate dyskinesia development by reducing the sensitization of striato-nigral medium-sized spiny neurons to levodopa. However, mTORC1 blockade seems to provide a more favorable behavioral outcome and a wider effect on neurochemical correlates of dyskinesia