Magdalena Slawiñska

Unibus: Aspects of heterogeneity and fault tolerance in cloud computing

The paper describes our on-going project, termed Unibus, in the context of facilitating fault-tolerant executions of MPI applications on computing chunks in the cloud. In general, Unibus focuses on resource access virtualization and automatic, user-transparent resource provisioning that simplify use of heterogeneous resources available to users. In this work, we present the key Unibus concepts (the Capability Model, composite operations, mediators, soft and successive conditionings, metaapplications), and demonstrate how to employ Unibus to orchestrate resources provided by a commercial cloud provider into a fault-tolerant platform, capable of executing message passing applications. In order to support fault tolerance we use DMTCP [1] (Distributed MultiThreaded CheckPointing) that enables checkpointing at the users level. To demonstrate that the Unibus-created, FT-enabled platform allows to execute MPI applications we ran NAS Parallel Benchmarks and measured the overhead introduced by FT.

Enhancing Portability of HPC Applications across High-end Computing Platforms

Fast hardware turnover in supercomputing centers, stimulated by rapid technological progress, results in high heterogeneity among HPC platforms, and necessitates that applications are ported and adapted frequently. The cutting-edge nature of the hardware mandates customized performance tuning, which, coupled with continuously growing application complexity, makes the process inherently and increasingly challenging. In this paper, we analyze build procedures of a representative set of HPC applications, and attempt to identify commonalities that can be exploited to enhance cross-platform portability. We then propose a novel method for reducing non-portabilities while preserving high performance. The approach, based on profiles that capture and isolate non-portable features at various levels, requires only a moderate amount of changes to existing makefiles. It leverages the expertise of system designers and administrators, and reduces burdens placed on application scientists. As a proof of concept, we discuss the application of our methodology to enhancing portability of the Mile application across heterogeneous HPC platforms.

Portable builds of HPC applications on diverse target platforms

High-end machines at modern HPC centers are constantly undergoing hardware and system software upgrades - necessitating frequent rebuilds of application codes. The number of possible combinations of compilers, libraries, application build configurations, differing hardware architectures, etc, makes the process of building applications very onerous, requiring expert build knowledge from different domains. Our ongoing Harness Workbench Toolkit (HWT) project aims to foster and streamline the entire build process on heterogeneous computational platforms. This paper focuses on a key research issue of the HWT that regards facilitating and enhancement portability of build systems across multifarious machines, with particular respect to scientific software commonly used in the HPC community. The article presents a novel HWT approach based on the concept of generic build systems and profiles which encapsulate build knowledge provided independently by relevant experts. The paper describes profiles, the logistics of storing and retrieving build information, and interfacing to user-guided builds. We also report on experiences with applying the HWT approach to two scientific production codes (CPMD, GAMESS) on Cray XT4.

Unibus: a contrarian approach to grid computing

Abstract Despite maturing in many ways, heterogeneous distributed computing platforms continue to require substantial effort in terms of software installation and management for efficient use, often necessitating manual intervention by resource providers and end-users. In this paper we propose a novel model of resource sharing that is a viable alternative to that commonly adopted in the grid community. Our model, termed Unibus, shifts the resource virtualization and aggregation responsibilities to the software at the client side, taking these burdens away from resource providers. Drawing from parallels with operating systems, we argue that distributed resources may be unified and aggregated at the user’s end, in a manner similar to ordinary peripheral devices. Running on the user’s access device, the overlay system software can virtualize remote resources via dynamically deployed software mediators analogous to device drivers, reconfiguring the resources if necessary via “firmware” modules. To illustrate the feasibility of the Unibus model, we have prototyped a development toolkit automating the installation, build, run, and post-processing stages of MPI applications. Through the provided console, this toolkit can deploy and configure an MPI execution environment across a set of heterogeneous, isolated distributed resources, turning them into a coherent virtual machine with a single interface point. We conducted a series of experiments with the NAS Parallel Benchmarks. Results indicate that the toolkit preserves the application performance of “bare” MPI, while substantially reducing maintenance and configuration efforts. Overall, the results suggest that the envisioned client side overlay model for resource sharing may potentially be able to address some of long-standing obstacles in building heterogeneous HPC systems.

Unibus-managed Execution of Scientific Applications on Aggregated Clouds

Our on-going project, Unibus, aims to facilitate provisioning and aggregation of multifaceted resources from resource providers and end-users’ perspectives. To achieve that, Unibus proposes (1) the Capability Model and mediators (resource drivers) to virtualize access to diverse resources, and (2) soft and successive conditioning to enable automatic and user-transparent resource provisioning. In this paper we examine the Unibus concepts and prototype in a real situation of aggregation of two commercial clouds and execution of benchmarks on aggregated resources. We also present and discuss benchmarks’ results.

Enhancing productivity in high performance computing through systematic conditioning

In order to take full advantage of high-end computing platforms, scientific applications often require modifications to source codes, and to their build systems that generate executable files. The ever-increasing emphasis on productivity in HPC makes the efficiency of the build process an extremely important issue. Our work is motivated by the need for a systematic approach to the HPC life-cycle that encompasses build and porting tasks. In this paperwe briefly present the design of the Harness Workbench Toolkit (HWT) that addresses the porting issue through a user-assisted conversion process. We briefly describe our adaptation capability model that includes routine conversions (string substitutions) as well as more advanced transformations such as 32-64 bit changes. Next, we show and discuss results of an experiment with a production source code (the CPMD application) that examines the effort of adapting the baseline code (the Linux distribution) to specific high-end machines (IBM SP4, Cray X1E, Cray XT3/4) in terms of the number of necessary conversions. Based on the conversion capability model, we have implemented conversion assistant modules that were used in the experiment. The experimental results are promising and demonstrate that our approach takes a step towards improving the overall productivity of scientific applications on highend machines.

Towards cross-platform cloud computing

Cloud computing is becoming increasingly popular and prevalent in many domains. However, there is high variability in the programming models, access methods, and operational aspects of different clouds, diminishing the viability of cloud computing as a true utility. Our ADAPAS project attempts to analyze the commonalities and differences between cloud offerings with a view to determining the extent to which they may be unified. We propose the concept of dynamic adapters supported by runtime systems for environment preconditioning, that help facilitate cross platform deployment of cloud applications. This vision paper outlines the issues involved, and presents preliminary ideas for enhancing the executability of applications on different cloud platforms.

Zero-Force MPI: toward tractable toolkits for high performance computing

Shared HPC platforms continue to require substantial effort for software installation and management, often necessitating manual intervention and tedious procedures. We propose a novel model of resource sharing that shifts resource virtualization and aggregation responsibilities to client-side software, thus reducing the burdens on resource providers.The Zero-Force MPI toolkit automates the installation, build, run, and post-processing stages of HPC applications, thus allowing application scientists to focus on using resources instead of managing them. Through a provided console, MPI runtime systems, support libraries, application executables, and needed datafiles can be soft-installed across distributed resources with just a few commands. Built-in data synchronization capabilities simplify common HPC development tasks, saving end-user time and effort. To evaluate ZF-MPI, we conducted experiments with the NAS Parallel Benchmarks. Results demonstrate that the proposed run-not-install approach is effective and may substantially increase overall productivity.