Project Team Graal

Overall Objectives
Scientific Foundations
Application Domains
New Results
Partnerships and Cooperations
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Section: New Results

Scheduling Strategies and Algorithm Design for Heterogeneous Platforms

Participants : Guillaume Aupy, Anne Benoit, Marin Bougeret, Alexandru Dobrila, Fanny Dufossé, Amina Guermouche, Mathias Jacquelin, Loris Marchal, Jean-Marc Nicod, Laurent Philippe, Paul Renaud-Goud, Clément Rezvoy, Yves Robert, Mark Stillwell, Bora Uçar, Frédéric Vivien, Dounia Zaidouni.

Virtual Machine Resource Allocation for Service Hosting on Heterogeneous Distributed Platforms

We proposed algorithms for allocating multiple resources to competing services running in virtual machines on heterogeneous distributed platforms. We developped a theoretical problem formulation, designed algorithms, and compared these algorithms via simulation experiments based in part on workload data supplied by Google. Our main finding is that vector packing approaches proposed in the homogeneous case can be extended to provide high-quality solutions in the heterogeneous case, and combined to provide a single efficient algorithm. We also considered the case when there may be errors in estimates of performance-related resource needs. We provided a resource sharing algorithm and proved that for the single-resource, single-node case, when there is no bound on the error, its performance ratio relative to an omniscient optimal algorithm is 2J-1 J 2 , where J is the number of services. We also provided a heuristic approach for compensating for bounded errors in resource need estimates that performs well in simulation.

Dynamic Fractional Resource Scheduling vs. Batch Scheduling

We finalized this work in which we proposed a novel job scheduling approach for homogeneous cluster computing platforms. Its key feature is the use of virtual machine technology to share fractional node resources in a precise and controlled manner. Other VM-based scheduling approaches have focused primarily on technical issues or extensions to existing batch scheduling systems, while we take a more aggressive approach and seek to find heuristics that maximize an objective metric correlated with job performance. We derived absolute performance bounds and developped algorithms for the online, non-clairvoyant version of our scheduling problem. We further evaluated these algorithms in simulation against both synthetic and real-world HPC workloads and compared our algorithms to standard batch scheduling approaches. We found that our approach improves over batch scheduling by orders of magnitude in terms of job stretch, while leading to comparable or better resource utilization. Our results demonstrated that virtualization technology coupled with lightweight online scheduling strategies can afford dramatic improvements in performance for executing HPC workloads.

Greedy algorithms for energy minimization

This year, we have revisited the well-known greedy algorithm for scheduling independent jobs on parallel processors, with the objective of energy minimization. We have assessed the performance of the online version, as well as the performance of the offline version, which sorts the jobs by non-increasing size before execution. We have derived new approximation factors, as well as examples that show that these factors cannot be improved, thereby completely characterizing the performance of the algorithms.

Energy-aware mappings on chip multiprocessors

This year, in collaboration with Rami Melhem at Pittsburgh University (USA), we have studied the problem of mapping streaming applications that can be modeled by a series-parallel graph, onto a 2-dimensional tiled CMP architecture. The objective of the mapping is to minimize the energy consumption, using dynamic and voltage scaling techniques, while maintaining a given level of performance, reflected by the rate of processing the data streams. This mapping problem turned out to be NP-hard, but we identified simpler instances, whose optimal solution can be computed by a dynamic programming algorithm in polynomial time. Several heuristics were proposed to tackle the general problem, building upon the theoretical results. Finally, we assessed the performance of the heuristics through comprehensive simulations using the StreamIt workflow suite and various CMP grid sizes.

We are pursuing this work by investigating the routing of communications in chip multiprocessors (CMPs). The goal is to find a valid routing in the sense that the amount of data routed between two neighboring cores does not exceed the maximum link bandwidth while the power dissipated by communications is minimized. Our position is at the system level: we assume that several applications, described as task graphs, are executed on a CMP, and each task is already mapped to a core. Therefore, we consider a set of communications that have to be routed between the cores of the CMP. We consider a classical model, where the power consumed by a communication link is the sum of a static part and a dynamic part, with the dynamic part depending on the frequency of the link. This frequency is scalable and it is proportional to the throughput of the link. The most natural and widely used algorithm to handle all these communications is XY routing: for each communication, data is first forwarded horizontally, and then vertically, from source to destination. However, if it is allowed to use all Manhattan paths between the source and the destination, the consumed power can be reduced dramatically. Moreover, some solutions may be found while none existed with the XY routing. We have compared XY routing and Manhattan routing, both from a theoretical and from a practical point of view. We considered two variants of Manhattan routing: in single-path routing, only one path can be used for each communication, while multi-paths routing allows to split a communication between different routes. We established the NP-completeness of the problem of finding a Manhattan routing that minimizes the dissipated power, we exhibited the minimum upper bound of the ratio power consumed by an XY routing over power consumed by a Manhattan routing, and finally we performed simulations to assess the performance of Manhattan routing heuristics that we designed.

Power-aware replica placement

We have investigated optimal strategies to place replicas in tree networks, with the double objective to minimize the total cost of the servers, and/or to optimize power consumption. The client requests are known beforehand, and some servers are assumed to pre-exist in the tree. Without power consumption constraints, the total cost is an arbitrary function of the number of existing servers that are reused, and of the number of new servers. Whenever creating and operating a new server has higher cost than reusing an existing one (which is a very natural assumption), cost optimal strategies have to trade-off between reusing resources and load-balancing requests on new servers. We provide an optimal dynamic programming algorithm that returns the optimal cost, thereby extending known results without pre-existing servers. With power consumption constraints, we assume that servers operate under a set of M different modes depending upon the number of requests that they have to process. In practice M is a small number, typically 2 or 3, depending upon the number of allowed voltages. Power consumption includes a static part, proportional to the total number of servers, and a dynamic part, proportional to a constant exponent of the server mode, which depends upon the model for power. The cost function becomes a more complicated function that takes into account reuse and creation as before, but also upgrading or downgrading an existing server from one mode to another. We have shown that with an arbitrary number of modes, the power minimization problem is NP-complete, even without cost constraint, and without static power. Still, we have provided an optimal dynamic programming algorithm that returns the minimal power, given a threshold value on the total cost; it has exponential complexity in the number of modes M, and its practical usefulness is limited to small values of M. Still, experiments conducted with this algorithm showed that it can process large trees in reasonable time, despite its worst-case complexity.

Reclaiming the energy of a schedule

In this work, we consider a task graph to be executed on a set of processors. We assume that the mapping is given, say by an ordered list of tasks to execute on each processor, and we aim at optimizing the energy consumption while enforcing a prescribed bound on the execution time. While it is not possible to change the allocation of a task, it is possible to change its speed. Rather than using a local approach such as backfilling, we have considered the problem as a whole and studied the impact of several speed variation models on its complexity. For continuous speeds, we gave a closed-form formula for trees and series-parallel graphs, and we cast the problem into a geometric programming problem for general directed acyclic graphs. We showed that the classical dynamic voltage and frequency scaling (DVFS) model with discrete modes leads to a NP-complete problem, even if the modes are regularly distributed (an important particular case in practice, which we analyzed as the incremental model). On the contrary, the VDD-hopping model leads to a polynomial solution. Finally, we provided an approximation algorithm for the incremental model, which we extended for the general DVFS model.

Workload balancing and throughput optimization

We have investigated the problem of optimizing the throughput of streaming applications for heterogeneous platforms subject to failures. The applications are linear graphs of tasks (pipelines), and a type is associated to each task. The challenge is to map tasks onto the machines of a target platform, but machines must be specialized to process only one task type, in order to avoid costly context or setup changes. The objective is to maximize the throughput, i.e., the rate at which jobs can be processed when accounting for failures. For identical machines, we have proved that an optimal solution can be computed in polynomial time. However, the problem becomes NP-hard when two machines can compute the same task type at different speeds. Several polynomial time heuristics have been designed, and simulation results have demonstrated their efficiency.

Comparing archival policies for BlueWaters

In this work, we focus on the archive system which will be used in the BlueWaters supercomputer. We have introduced two new tape archival policies that can improve tape archive performance in certain regimes, compared to the classical RAIT (Redundant Array of Independent Tapes) policy. The first policy, PARALLEL, still requires as many parallel tape drives as RAIT but pre-computes large data stripes that are written contiguously on tapes to increase write/read performance. The second policy, VERTICAL, writes contiguous data into a single tape, while updating error correcting information on the fly and delaying its archival until enough data has been archived. This second approach reduces the number of tape drives used for every user request to one. The performance of the three RAIT, PARALLEL and VERTICAL policies have been assessed through extensive simulations, using a hardware configuration and a distribution of I/O requests similar to these expected on the BlueWaters system. These simulations have shown that VERTICAL is the most suitable policy for small files, whereas PARALLEL must be used for files larger than 1 GB. We have also demonstrated that RAIT never outperforms both proposed policies, and that a heterogeneous policy mixing VERTICAL and PARALLEL performs 10 times better than any other policy.

Using Virtualization and Job Folding for Batch Scheduling

In this work we study the problem of batch scheduling within a homogeneous cluster. In this context, the problem is that the more processors the job requires the more difficult it is to find an idle slot to run it on. As a consequence the resources are often inefficiently used as some of them remain unallocated in the final schedule. To address this issue we propose a technique called job folding that uses virtualization to reduce the number of processors allocated to a parallel job and thus allows to execute it earlier. Our goal is to optimize the resource use. We propose several heuristics based on job folding and we compare their performance with classical on-line scheduling algorithms as FCFS or backfilling. The contributions of this work are both the design of the job folding algorithms and their performance analysis.

A Genetic Algorithm with Communication Costs to Schedule Workflows on a SOA-Grid

We propose in this work to study the problem of scheduling a collection of workflows, identical or not, on a SOA (Service Oriented Architecture) grid . A workflow (job) is represented by a directed acyclic graph (DAG) with typed tasks. All of the grid hosts are able to process a set of typed tasks with unrelated processing costs and are able to transmit files through communication links for which the communication times are not negligible. The goal of our study is to minimize the maximum completion time (makespan) of the workflows. To solve this problem we propose a genetic approach. The contributions of this paper are both the design of a Genetic Algorithm taking the communication costs into account and its performance analysis.

Checkpointing policies for post-petascale supercomputers

In this work, we provided an analysis of checkpointing strategies for minimizing expected job execution times in an environment that is subject to processor failures. In the case of both sequential and parallel jobs, we gave the optimal solution for exponentially distributed failure inter-arrival times, which, to the best of our knowledge, is the first rigorous proof that periodic checkpointing is optimal. For non-exponentially distributed failures, we developped a dynamic programming algorithm to maximize the amount of work completed before the next failure, which provides a good heuristic for minimizing the expected execution time. Our work considers various models of job parallelism and of parallel checkpointing overhead. We first performed extensive simulation experiments assuming that failures follow Exponential or Weibull distributions, the latter being more representative of real-world systems. The obtained results not only corroborate our theoretical findings, but also show that our dynamic programming algorithm significantly outperforms previously proposed solutions in the case of Weibull failures. We then performed simulation experiments that use failure logs from production clusters. These results confirmed that our dynamic programming algorithm significantly outperforms existing solutions for real-world clusters.

We have also showed an unexpected result: in some cases, when (i) the platform is sufficiently large, and (ii) the checkpointing costs are sufficiently expensive, or the failures are frequent enough, then one should limit the application parallelism and duplicate tasks, rather than fully parallelize the application on the whole platform. In other words, the expectation of the job duration is smaller with fewer processors! To establish this result we have derived and analyzed several scheduling heuristics.

Scheduling parallel iterative applications on volatile resources

In this work we study the efficient execution of iterative applications onto volatile resources. We studied a master-worker scheduling scheme that trades-off between the speed and the (expected) reliability and availability of enrolled workers. A key feature of this approach is that it uses a realistic communication model that bounds the capacity of the master to serve the workers, which requires the design of sophisticated resource selection strategies. The contribution of this work is twofold. On the theoretical side, we assess the complexity of the problem in its off-line version, i.e., when processor availability behaviors are known in advance. Even with this knowledge, the problem is NP-hard. On the pragmatic side, we proposed several on-line heuristics that were evaluated in simulation while a Markovian model of processor availabilities.

We have started this study with the simple case of iterations composed of independent tasks that can execute asynchronously. Then we have investigated a much more challenging scenario, that of a tightly-coupled application whose tasks steadily communicate throughout the iteration. In this latter scenario, if one processor computing some task fails, all the work executed for current iteration is lost, and the computation of all tasks has to be restarted. Similarly, if one processor of the current configuration is preempted, the computation of all tasks is interrupted. Changing the configuration within an iteration becomes a much riskier decision than with independent tasks.

Tiled QR factorization algorithms

In this work, we have revisited existing algorithms for the QR factorization of rectangular matrices composed of p×q tiles, where pq. We target a shared-memory multi-core processor. Within this framework, we study the critical paths and performance of algorithms such as Fibonacci and Greedy , and those found within PLASMA. Although neither is optimal, both are shown to be asymptotically optimal for all matrices of size p=q 2 f(q), where f is any function such that lim + f=0. This novel and important complexity result applies to all matrices where p and q are proportional, p=λq, with λ1, thereby encompassing many important situations in practice (least squares). We provide an extensive set of experiments that show the superiority of the new algorithms for tall matrices.

We have then extended this work to a distributed-memory environment, that corresponds to clusters of multi-core processors. These platforms make the present and the foreseeable future of high-performance computing. In the context of a cluster of multicores, in order to minimize the number of inter-processor communications (aka, “communication-avoiding” algorithm), it is natural to consider two-level hierarchical reduction trees composed of an “inter-node” tree which acts on top of “intra-node” trees. At the intra-node level, we propose a hierarchical tree made of three levels: (0) “TS level” for cache-friendliness, (1) “low level” for decoupled highly parallel inter-node reductions, (2) “coupling level” to efficiently resolve interactions between local reductions and global reductions. Our hierarchical algorithm and its implementation are flexible and modular, and can accommodate several kernel types, different distribution layouts, and a variety of reduction trees at all levels, both inter-cluster and intra-cluster. Numerical experiments on a cluster of multicore nodes (1) confirm that each of the four levels of our hierarchical tree contributes to build up performance and (2) build insights on how these levels influence performance and interact within each other. Our implementation of the new algorithm with the Dague scheduling tool significantly outperforms currently available QR factorization softwares for all matrix shapes, thereby bringing a new advance in numerical linear algebra for petascale and exascale platforms.

Scheduling malleable tasks and minimizing total weighted flow

Malleable tasks are jobs that can be scheduled with preemptions on a varying number of resources. In this work, we have focused on the special case of work-preserving malleable tasks, for which the area of the allocated resources does not depend on the allocation and is equal to the sequential processing time. Moreover, we have assumed that the number of resources allocated to each task at each time instant is bounded. Although this study concerns malleable task scheduling, we have shown that this is equivalent to the problem of minimizing the makespan of independent tasks distributed among processors, when the data corresponding to tasks is sent using network flows sharing the same bandwidth.

We have considered both the clairvoyant and non-clairvoyant cases, and we have focused on minimizing the weighted sum of completion times. In the weighted non-clairvoyant case, we have proposed an approximation algorithm whose ratio (2) is the same as in the unweighted non-clairvoyant case. In the clairvoyant case, we have provided a normal form for the schedule of such malleable tasks, and proved that any valid schedule can be turned into this normal form, based only on the completion times of the tasks. We have shown that in these normal form schedules, the number of preemptions per task is bounded by 3 on average. At last, we have analyzed the performance of greedy schedules, and proved that optimal schedules are greedy for a special case of homogeneous instances. We conjecture that there exists an optimal greedy schedule for all instances, which would greatly simplify the study of this problem.

Parallelizing the construction of the ProDom database

ProDom is a protein domain family database automatically built from a comprehensive analysis of all known protein sequences. ProDom development is headed by Daniel Kahn (Inria project-team BAMBOO, formerly HELIX). With the protein sequence databases increasing in size at an exponential pace, the parallelization of MkDom2, the algorithm used to build ProDom, has become mandatory (the original sequential version of MkDom2 took 15 months to build the 2006 version of ProDom).

When protein domain families and protein families are built independently, the result may be inconsistent. In order to solve this inconsistency problem, we designed a new algorithm, MPI_MkDom3, that simultaneously builds a clustering in protein domain families and one in protein families. This algorithm mixes the principles of MP_MkDom2 and that of the building of Hogenom. As a proof of concept, we successfully processed all the sequences included in the April 2010 version of the UniProt database, namely 6 118 869 sequences and 2 194 382 846 amino-acids.