Computing the expected makespan of task graphs in the presence of silent errors

International audienceApplications structured as Directed Acyclic Graphs (DAGs) of tasks correspond to a general model of parallel computation that occurs in many domains, including popular scientific workflows. DAG scheduling has received an enormous amount of attention, and several list-scheduling heuristics have been proposed and shown to be effective in practice. Many of these heuristics make scheduling decisions based on path lengths in the DAG. At large scale, however, compute platforms and thus tasks are subject to various types of failures with no longer negligible probabilities of occurrence. Failures that have recently received increasing attention are " silent errors, " which cause a task to produce incorrect results even though it ran to completion. Tolerating silent errors is done by checking the validity of the results and re-executing the task from scratch in case of an invalid result. The execution time of a task then becomes a random variable, and so are path lengths. Unfortunately, computing the expected makespan of a DAG (and equivalently computing expected path lengths in a DAG) is a computationally difficult problem. Consequently, designing effective scheduling heuristics is preconditioned on computing accurate approximations of the expected makespan. In this work we propose an algorithm that computes a first order approximation of the expected makespan of a DAG when tasks are subject to silent errors. We compare our proposed approximation to previously proposed such approximations for three classes of application graphs from the field of numerical linear algebra. Our evaluations quantify approximation error with respect to a ground truth computed via a brute-force Monte Carlo method. We find that our proposed approximation outperforms previously proposed approaches, leading to large reductions in approximation error for low (and realistic) failure rates, while executing much faster

Checkpointing vs. Migration for Post-Petascale Machines

We craft a few scenarios for the execution of sequential and parallel jobs on future generation machines. Checkpointing or migration, which technique to choose

Scheduling Computational Workflows on Failure-Prone Platforms

International audienceWe study the scheduling of computational workflows on compute resources that experience exponentially distributed failures. When a failure occurs, roll-back and recovery is used to resume the execution from the last checkpointed state. The scheduling problem is to minimize the expected execution time by deciding in which order to execute the tasks in the workflow and whether to checkpoint or not checkpoint a task after it completes. We give a polynomial-time algorithm for fork graphs and show that the problem is NP-complete with join graphs. Our main result is a polynomial-time algorithm to compute the execution time of a workflow with specified to-be-checkpointed tasks. Using this algorithm as a basis, we propose efficient heuristics for solving the scheduling problem. We evaluate these heuristics for representative workflow configurations

On the impact of process replication on executions of large-scale parallel applications with coordinated checkpointing

International audienceProcessor failures in post-petascale parallel computing platforms are common occurrences. The traditional fault-tolerance solution, checkpoint-rollback-recovery, severely limits parallel efficiency. One solution is to replicate application processes so that a processor failure does not necessarily imply an application failure. Process replication, combined with checkpoint-rollback-recovery, has been recently advocated. We first derive novel theoretical results for Exponential failure distributions, namely exact values for the Mean Number of Failures To Interruption and the Mean Time To Interruption. We then extend these results to arbitrary failure distributions, obtaining closed-form solutions for Weibull distributions. Finally, we evaluate process replica-tion in simulation using both synthetic and real-world failure traces so as to quantify average application makespan. One interesting result from these experiments is that, when process repli-cation is used, application performance is not sensitive to the checkpointing period, provided that that period is within a large neighborhood of the optimal period. More generally, our empirical results make it possible to identify regimes in which process replication is beneficial

Resource Allocation Strategies for In-Network Stream Processing

In this paper we consider the operator mapping problem for in-network stream processing applications. In-network stream processing consists in applying a tree of operators in steady-state to multiple data objects that are continually updated at various locations on a network. Examples of in-network stream processing include the processing of data in a sensor network, or of continuous queries on distributed relational databases. We study the operator mapping problem in a ``constructive'' scenario, i.e., a scenario in which one builds a platform dedicated to the application buy purchasing processing servers with various costs and capabilities. The objective is to minimize the cost of the platform while ensuring that the application achieves a minimum steady-state throughput. The first contribution of this paper is the formalization of a set of relevant operator-placement problems as linear programs, and a proof that even simple versions of the problem are NP-complete. Our second contribution is the design of several polynomial time heuristics, which are evaluated via extensive simulations and compared to theoretical bounds for optimal solutions

Cost-Optimal Execution of Boolean Query Trees with Shared Streams

International audienceThe processing of queries expressed as trees of boolean operators applied to predicates on sensor data streams has several applications in mobile computing. Sensor data must be retrieved from the sensors, which incurs a cost, e.g., an energy expense that depletes the battery of a mobile query processing device. The objective is to determine the order in which predicates should be evaluated so as to shortcut part of the query evaluation and minimize the expected cost. This problem has been studied assuming that each data stream occurs at a single predicate. In this work we remove this assumption since it does not necessarily hold for real-world queries. Our main results are an optimal algorithm for single-level trees and a proof of NP-completeness for DNF trees. For DNF trees, however, we show that there is an optimal predicate evaluation order that corresponds to a depth-first traversal. This result provides inspiration for a class of heuristics. We show that one of these heuristics largely outperforms other sensible heuristics, including a heuristic proposed in previous work

Estudio sobre la adherencia de armaduras pretesas y su influencia en el fallo a cortante

En elements de formigó pretesat, l'adherència entre armadura pretesa i el formigó és una propietat fonamental per assegurar la integritat estructural. L'acer pretensat té una doble funcionalitat, per una banda, es fa servir la tensió de tracció de l'acer disponible fins a arribar al límit elàstic per comprimir el formigó, i per altra banda, la resistència a tracció dels cordons d'acer s'utilitza per col·laborar amb el formigó en la resistència de les càrregues externes millorant així el comportament de les estructures i podent fer dissenys estructurals molt més complexos, amb llums majors i més esvelts. Al introduir aquesta tensió longitudinal de compressió a la biga, es modifiquen els estats tensionals i deformacions que pateix l'element estructural, la forma de trencament, els modes de fallada, etc. Aquest document es centra amb el desenvolupament d’un nou model per determinar la resistència a tallant de bigues de formigó pretensat quan aquestes pateixen pèrdua per adherència. Aquest model proposat és vàlid per a bigues amb seccions rectangulars, amb I i T sense armadura transversal. Es tracta d'una modificació del model CCCM original, desenvolupat recentment a la UPC i la UIB. Es verifica a partir d'assajos reals la modificació d'aquest model per determinar si és vàlid o no, és a dir, per veure si aplicant aquest nou model quan una biga pateix pèrdua per adherència es millora el resultat obtingut pel model original o no. Es determina que si ho fa, el model modificat és més realista en aquesta situació encara que s'hauria de continuar estudiant sobre ell ja que la quantitat de bigues que fallen per ancoratge en aquesta base de dades són mínimes.En elementos de hormigón pretensado, la adherencia entre armadura pretesa y el hormigón es una propiedad fundamental para asegurar la integridad estructural. El acero pretensado tiene una doble funcionalidad, por un lado, se usa la tensión de tracción del acero disponible hasta llegar a su límite elástico para comprimir el hormigón, y por otro lado, la resistencia a tracción de los cordones de acero se utiliza para colaborar con el hormigón en la resistencia de las cargas externas mejorando así el comportamiento de las estructuras y pudiendo hacer diseños estructurales mucho más complejos, con mayores luces y más esbeltos. Al introducir esta tensión longitudinal de compresión a la viga, se modifican los estados tensionales y deformaciones que sufre el elemento estructural, la forma de rotura, los modos de fallo, etc. El presente documento se centra en desarrollar un nuevo modelo para determinar la resistencia a cortante de vigas de hormigón pretensado cuando estas sufren pérdida por adherencia. Este modelo propuesto es válido para vigas con secciones rectangulares, en I y en T sin armadura transversal. Se trata de una modificación del modelo CCCM original, desarrollado recientemente en la UPC y la UIB. Se verifica a partir de ensayos reales la modificación de este modelo para determinar si es válido o no, es decir, para ver si aplicando este nuevo modelo cuando una viga sufre pérdida por adherencia se mejora el resultado obtenido por el modelo original o no. Se determina que si lo hace, el modelo modificado es más realista en esta situación aunque se debería seguir estudiando sobre él ya que la cantidad de vigas que fallan por anclaje en esta base de datos son mínimas.In pre-stressed concrete elements, the bond between pre-tensed reinforcement and concrete is a fundamental property to ensure structural integrity. Pre-stressed steel has a double functionality: on the one hand, the tensile stress of the available steel is used until it reaches its elastic limit to compress the concrete, and on the other hand, the tensile strength of the steel strands is used to work with the concrete in resisting external loads, thus improving the behavior of the structures and allowing for much more complex structural designs, with longer spans and slenderness. By introducing this longitudinal compressive stress to the beam, the stress states and deformations suffered by the structural element, the form of rupture, the failure modes, etc., are modified. This paper focuses on developing a new model to determine the shear strength of prestressed concrete beams when they suffer bond loss. This proposed model is valid for beams with rectangular, I- and T-sections without transverse reinforcement. It is a modification of the original CCCM model, recently developed at UPC and UIB. The modification of this model is verified from real tests to determine if it is valid or not, that is, to see if applying this new model when a beam suffers adhesion loss improves the result obtained by the original model or not. It is determined that if it does, the modified model is more realistic in this situation although further study should be done on it since the number of beams that fail by anchorage in this database are minimal

Cost-Optimal Execution of Trees of Boolean Operators with Shared Streams

The processing of queries expressed as trees of boolean operators applied to predicates on sensor data streams has several applications in mobile computing. Sensor data must be retrieved from the sensors to a query processing device, such as a smartphone, over one or more network interfaces. Retrieving a data item incurs a cost, e.g., an energy expense that depletes the smartphone's battery. Since the query tree contains boolean operators, part of the tree can be shortcircuited depending on the retrieved sensor data. An interesting problem is to determine the order in which predicates should be evaluated so as to minimize the expected query processing cost. This problem has been studied in previous work assuming that each data stream occurs in a single predicate. In this work we remove this assumption since it does not necessarily hold for real-world queries. Our main results are an optimal algorithm for single-level trees and a proof of NP-completeness for DNF trees. For DNF trees, however, we show that there is an optimal predicate evaluation order that corresponds to a depth-first traversal. This result provides inspiration for a class of heuristics. We show that one of these heuristics largely outperforms other sensible heuristics, including the one heuristic proposed in previous work for our general version of the query processing problem.Le traitement de requêtes, exprimées sous forme d'arbres d'opérateurs booléens appliqués à des prédicats sur des flux de données de senseurs, a de nombreuses applications dans le domaine du calcul mobile. Les données doivent être transférées des senseurs vers l'appareil de traitement des données, par exemple un {smartphone}. Transférer une donnée induit un coût, par exemple une consommation énergétique qui diminuera la charge de la batterie du smartphone. Comme l'arbre de requêtes contient des opérateurs booléens, des pans de l'arbre peuvent être court-circuités en fonction des données récupérées. Un problème intéressant est de déterminer l'ordre dans lequel les prédicats doivent être évalués afin de minimiser l'espérance du coût du traitement de la requête. Ce problème a déjà été étudié sous l'hypothèse que chaque flux apparaît dans un seul prédicat. Dans le présent travail nous éliminons cette hypothèse qui ne correspond pas forcément à la réalité. Nos principaux résultats sont un algorithme optimal pour les arbres avec un seul niveau, et une preuve de NP-complétude pour les arbres sous forme normale disjonctive. Pour les arbres sous forme normale disjonctive, cependant, nous montrons qu'il existe un ordre optimal d'évaluation des prédicats qui correspond à un parcours en profondeur d'abord. Ce résultat nous sert à concevoir toute une classe d'heuristiques. Nous montrons que l'une de ces heuristiques a de bien meilleurs résultats que les autres heuristiques et, entre autres, que la seule heuristique précédemment proposée pour le cadre général

Sex and Gender in Medical Education, and proceedings from the 2015 Sex and Gender Education Summit

The Sex and Gender Medical Education Summit: a roadmap for curricular innovation was a collaborative initiative of the American Medical Women\u27s Association, Laura W. Bush Institute for Women’s Health, Mayo Clinic, and Society for Women\u27s Health Research (www.sgbmeducationsummit.com). It was held on October 18–19, 2015 to provide a unique venue for collaboration among nationally and internationally renowned experts in developing a roadmap for the incorporation of sex and gender based concepts into medical education curricula. The Summit engaged 148 in-person attendees for the 1 1/2-day program. Pre- and post-Summit surveys assessed the impact of the Summit, and workshop discussions provided a framework for informal consensus building. Sixty-one percent of attendees indicated that the Summit had increased their awareness of the importance of sex and gender specific medicine. Other comments indicate that the Summit had a significant impact for motivating a call to action among attendees and provided resources to initiate change in curricula within their home institutions. These educational efforts will help to ensure a sex and gender basis for delivery of health care in the future

Bacterial artificial chromosomes improve recombinant protein production in mammalian cells

<p>Abstract</p> <p>Background</p> <p>The development of appropriate expression vectors for large scale protein production constitutes a critical step in recombinant protein production. The use of conventional expression vectors to obtain cell lines is a cumbersome procedure. Often, stable cell lines produce low protein yields and production is not stable over the time. These problems are due to silencing of randomly integrated expression vectors by the surrounding chromatin. To overcome these chromatin effects, we have employed a Bacterial Artificial Chromosome (BAC) as expression vector to obtain stable cell lines suitable for protein production.</p> <p>Results</p> <p>In this work, we explore the efficacy of a Bacterial Artificial Chromosome based vector applied to production of the constant region of the human IgG1. Direct comparison of bulk HEK 293 cell cultures generated with a "conventional" vector or with a BAC-based vector showed that the BAC-based vector improved the protein yield by a factor of 10. Further analysis of stable cell clones harboring the BAC-based vector showed that the protein production was directly proportional to the number of integrated BAC copies and that the protein production was stable for at least 30 passages.</p> <p>Conclusion</p> <p>Generation of stable cell clones for protein production using Bacterial Artificial Chromosomes offers a clear advantage over the use of conventional vectors. First, protein production is increased by a factor of 10; second, protein production is stable overtime and third, generation of BAC-based expression vectors does not imply a significant amount of work compare to a conventional vector. Therefore, BAC-based vectors may become an attractive tool for protein production.</p