Cell Death Response to DNA Damage.

The cell death response to DNA damage is discussed in this Perspectives piece with cancer as the backdrop because DNA damaging agents (DDA) are widely used to treat cancer. From decades of clinical results, we learn that DDA have cured some cancers but their toxicity is temporary in most cancers due to emergence of DDA-resistant cancer cells. Investigation of DDA-activated genes, proteins, and pathways, known collectively as the DNA damage response (DDR), has uncovered the inner workings of DDR that protect the genome to sustain life. Paradoxically, however, DDR can also activate death. Current knowledge on DDA-activated death and hypotheses for how DDR may determine when and where to execute death are discussed. Given that cancer cells suffer from DDR defects, which account for their initial sensitivity to DDA, future therapeutic development may exploit those cancer-specific DDR defects to selectively create death-inducing DNA lesions, without using DDA, to kill DDA-resistant cancers

Toward Message Passing Failure Management

As machine sizes have increased and application runtimes have lengthened, research into fault tolerance has evolved alongside. Moving from result checking, to rollback recovery, and to algorithm based fault tolerance, the type of recovery being performed has changed, but the programming model in which it executes has remained virtually static since the publication of the original Message Passing Interface (MPI) Standard in 1992. Since that time, applications have used a message passing paradigm to communicate between processes, but they could not perform process recovery within an MPI implementation due to limitations of the MPI Standard. This dissertation describes a new protocol using the exiting MPI Standard called Checkpoint-on-Failure to perform limited fault tolerance within the current framework of MPI, and proposes a new platform titled User Level Failure Mitigation (ULFM) to build more complete and complex fault tolerance solutions with a true fault tolerant MPI implementation. We will demonstrate the overhead involved in using these fault tolerant solutions and give examples of applications and libraries which construct other fault tolerance mechanisms based on the constructs provided in ULFM

Automatic Software Repair: a Bibliography

This article presents a survey on automatic software repair. Automatic software repair consists of automatically finding a solution to software bugs without human intervention. This article considers all kinds of repairs. First, it discusses behavioral repair where test suites, contracts, models, and crashing inputs are taken as oracle. Second, it discusses state repair, also known as runtime repair or runtime recovery, with techniques such as checkpoint and restart, reconfiguration, and invariant restoration. The uniqueness of this article is that it spans the research communities that contribute to this body of knowledge: software engineering, dependability, operating systems, programming languages, and security. It provides a novel and structured overview of the diversity of bug oracles and repair operators used in the literature

Autonomic Approach based on Semantics and Checkpointing for IoT System Management

Le résumé en français n'a pas été communiqué par l'auteur.Le résumé en anglais n'a pas été communiqué par l'auteur

A case for resource-conscious out-of-order processors

Modern out-of-order processors tolerate long-latency memory operations by supporting a large number of in-flight instructions. This is achieved in part through proper sizing of critical resources, such as register files or instruction queues. In light of the increasing gap between processor speed and memory latency, tolerating upcoming latencies in this way would require impractical sizes of such critical resources.To tackle this scalability problem, we make a case for resource-conscious out-of-order processors. We present quantitative evidence that critical resources are increasingly underutilized in these processors. We advocate that better use of such resources should be a priority in future research in processor architectures.Peer ReviewedPostprint (published version

Middleware-based Database Replication: The Gaps between Theory and Practice

The need for high availability and performance in data management systems has been fueling a long running interest in database replication from both academia and industry. However, academic groups often attack replication problems in isolation, overlooking the need for completeness in their solutions, while commercial teams take a holistic approach that often misses opportunities for fundamental innovation. This has created over time a gap between academic research and industrial practice. This paper aims to characterize the gap along three axes: performance, availability, and administration. We build on our own experience developing and deploying replication systems in commercial and academic settings, as well as on a large body of prior related work. We sift through representative examples from the last decade of open-source, academic, and commercial database replication systems and combine this material with case studies from real systems deployed at Fortune 500 customers. We propose two agendas, one for academic research and one for industrial R&D, which we believe can bridge the gap within 5-10 years. This way, we hope to both motivate and help researchers in making the theory and practice of middleware-based database replication more relevant to each other.Comment: 14 pages. Appears in Proc. ACM SIGMOD International Conference on Management of Data, Vancouver, Canada, June 200

Transparent live migration of container deployments in userspace

En aquesta tèsis de Màster, presentem una eina per realitzar migracions de contenidors tipus runC emprant CRIU. La nostre solució és eficient en termes d utilització de recursos, memòria i disc, i minimitza el temps de migració quan comparada amb una migració basada en capturar-transferir-reiniciar i amb la migració nativa de màquines virtuals oferida pels seus proveı̈dors. En afegit, la nostra eina permet migrar aplicacions que fan ús intensiu tant de memòria com de xarxa, amb connexions TCP establertes, i namespaces externs. La implementació està acompanyada d una recerca bibliogràfica en profunditat, aixı́ com d una sèrie d experiments que motiven els nostres criteris de disseny. El codi és de lliure accés i es pot trobar a la pàgina web del projecte

Reliability models for HPC applications and a Cloud economic model

With the enormous number of computing resources in HPC and Cloud systems, failures become a major concern. Therefore, failure behaviors such as reliability, failure rate, and mean time to failure need to be understood to manage such a large system efficiently. This dissertation makes three major contributions in HPC and Cloud studies. First, a reliability model with correlated failures in a k-node system for HPC applications is studied. This model is extended to improve accuracy by accounting for failure correlation. Marshall-Olkin Multivariate Weibull distribution is improved by excess life, conditional Weibull, to better estimate system reliability. Also, the univariate method is proposed for estimating Marshall-Olkin Multivariate Weibull parameters of a system composed of a large number of nodes. Then, failure rate, and mean time to failure are derived. The model is validated by using log data from Blue Gene/L system at LLNL. Results show that when failures of nodes in the system have correlation, the system becomes less reliable. Secondly, a reliability model of Cloud computing is proposed. The reliability model and mean time to failure and failure rate are estimated based on a system of k nodes and s virtual machines under four scenarios: 1) Hardware components fail independently, and software components fail independently; 2) software components fail independently, and hardware components are correlated in failure; 3) correlated software failure and independent hardware failure; and 4) dependent software and hardware failure. Results show that if the failure of the nodes and/or software in the system possesses a degree of dependency, the system becomes less reliable. Also, an increase in the number of computing components decreases the reliability of the system. Finally, an economic model for a Cloud service provider is proposed. This economic model aims at maximizing profit based on the right pricing and rightsizing in the Cloud data center. Total cost is a key element in the model and it is analyzed by considering the Total Cost of Ownership (TCO) of the Cloud