PaRiS: Causally Consistent Transactions with Non-blocking Reads and Partial Replication

Geo-replicated data platforms are at the backbone of several large-scale online services. Transactional Causal Consistency (TCC) is an attractive consistency level for building such platforms. TCC avoids many anomalies of eventual consistency, eschews the synchronization costs of strong consistency, and supports interactive read-write transactions. Partial replication is another attractive design choice for building geo-replicated platforms, as it increases the storage capacity and reduces update propagation costs. This paper presents PaRiS, the first TCC system that supports partial replication and implements non-blocking parallel read operations, whose latency is paramount for the performance of read-intensive applications. PaRiS relies on a novel protocol to track dependencies, called Universal Stable Time (UST). By means of a lightweight background gossip process, UST identifies a snapshot of the data that has been installed by every DC in the system. Hence, transactions can consistently read from such a snapshot on any server in any replication site without having to block. Moreover, PaRiS requires only one timestamp to track dependencies and define transactional snapshots, thereby achieving resource efficiency and scalability. We evaluate PaRiS on a large-scale AWS deployment composed of up to 10 replication sites. We show that PaRiS scales well with the number of DCs and partitions, while being able to handle larger data-sets than existing solutions that assume full replication. We also demonstrate a performance gain of non-blocking reads vs. a blocking alternative (up to 1.47x higher throughput with 5.91x lower latency for read-dominated workloads and up to 1.46x higher throughput with 20.56x lower latency for write-heavy workloads)

Fast and Compact Distributed Verification and Self-Stabilization of a DFS Tree

We present algorithms for distributed verification and silent-stabilization of a DFS(Depth First Search) spanning tree of a connected network. Computing and maintaining such a DFS tree is an important task, e.g., for constructing efficient routing schemes. Our algorithm improves upon previous work in various ways. Comparable previous work has space and time complexities of $O(n\log \Delta)$ bits per node and $O(nD)$ respectively, where $\Delta$ is the highest degree of a node, $n$ is the number of nodes and $D$ is the diameter of the network. In contrast, our algorithm has a space complexity of $O(\log n)$ bits per node, which is optimal for silent-stabilizing spanning trees and runs in $O(n)$ time. In addition, our solution is modular since it utilizes the distributed verification algorithm as an independent subtask of the overall solution. It is possible to use the verification algorithm as a stand alone task or as a subtask in another algorithm. To demonstrate the simplicity of constructing efficient DFS algorithms using the modular approach, We also present a (non-sielnt) self-stabilizing DFS token circulation algorithm for general networks based on our silent-stabilizing DFS tree. The complexities of this token circulation algorithm are comparable to the known ones

Automated performance attack discovery in distributed system implementations

Security and performance are critical goals for distributed systems. The increased complexity in design, incomplete expertise of developers, and limited functionality of existing testing tools often result in implementations with vulnerabilities and make the debugging process difficult and costly. The deployed vulnerabilities are often exploited by adversaries preventing the system from achieving its design goals. We refer to attacks that slow down the performance of a system as performance attacks. In the past, finding performance attacks has been a painstaking manual process that involved an expert of the target implementation. Given the cost associated with each vulnerability that occurs in the production, there is a need for tools to automatically check that the implementation of a protocol achieves its performance goals with respect to malicious components in the system. In this dissertation, we find performance attacks automatically from implementations of distributed systems. We do not try to show that an implementation is free from all attacks. Our goal is to find attacks and report them to the user in a timely manner. We first investigate how to find attacks automatically from implementations under a simulated environment. A simulated approach, however, has a fundamental limitation in terms of applicable target systems, as certain assumptions are made about languages, operating systems or libraries used. Therefore, we next investigate challenges and requirements to automatically find attacks in implementations of distributed systems under an emulated environment where no limiting assumptions are made

A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases.

African trypanosomiasis occurs in 36 countries in sub-Saharan Africa with 10,000 reported cases annually. No definitive remedy is currently available and if left untreated, the disease becomes fatal. Structural and biochemical studies of trypanosomal terminal uridylyl transferases (TUTases) demonstrated their functional role in extensive uridylate insertion/deletion of RNA. Trypanosoma brucei RNA Editing TUTase 1 (TbRET1) is involved in guide RNA 3' end uridylation and maturation, while TbRET2 is responsible for U-insertion at RNA editing sites. Two additional TUTases called TbMEAT1 and TbTUT4 have also been reported to share similar function. TbRET1 and TbRET2 are essential enzymes for the parasite viability making them potential drug targets. For this study, we clustered molecular dynamics (MD) trajectories of four TUTases based on active site shape measured by Pocket Volume Measurer (POVME) program. Among the four TUTases, TbRET1 exhibited the largest average pocket volume, while TbMEAT1's and TbTUT4's active sites displayed the most flexibility. A side pocket was also identified within the active site in all TUTases with TbRET1 having the most pronounced. Our results indicate that TbRET1's larger side pocket can be exploited to achieve selective inhibitor design as FTMap identifies it as a druggable pocket

Tractable reliable communication in compromised networks

Reliable communication is a fundamental primitive in distributed systems prone to Byzantine (i.e. arbitrary, and possibly malicious) failures to guarantee the integrity, delivery, and authorship of the messages exchanged between processes. Its practical adoption strongly depends on the system assumptions. Several solutions have been proposed so far in the literature implementing such a primitive, but some lack in scalability and/or demand topological network conditions computationally hard to be verified. This thesis aims to investigate and address some of the open problems and challenges implementing such a communication primitive. Specifically, we analyze how a reliable communication primitive can be implemented in 1) a static distributed system where a subset of processes is compromised, 2) a dynamic distributed system where part of the processes is Byzantine faulty, and 3) a static distributed system where every process can be compromised and recover. We define several more efficient protocols and we characterize alternative network conditions guaranteeing their correctness

Mechanistic Insight into the Enzymatic Reduction of Truncated Hemoglobin N of Mycobacterium tuberculosis: role of the CD loop and pre-A Motif in electron cycling

Background: The HbN of Mycobacterium tuberculosis carries a potent nitric-oxide dioxygenase activity despite lacking a reductase domain. Results: The NADH-ferredoxin reductase system acts as an efficient partner for the reduction of HbN. Conclusion: The interactions of HbN with the reductase are modulated by its CD loop and the Pre-A region. Significance: The present study provides new insights into the mechanism of electron transfer during nitric oxide detoxification by HbN.Fil: Singh, Sandeep. Institute of Microbial Technology; IndiaFil: Thakur, Naveen. Institute of Microbial Technology; IndiaFil: Oliveira, Ana. Universidad de Barcelona; EspañaFil: Petruk, Ariel Alcides. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Hade, Mangesh Dattu. Institute of Microbial Technology; IndiaFil: Sethi, Deepti. Institute of Microbial Technology; IndiaFil: Bidon Chanal, Axel. Universidad de Barcelona; EspañaFil: Marti, Marcelo Adrian. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Datta, H.. Institute of Microbial Technology; IndiaFil: Parkesh, R.. Institute of Microbial Technology; IndiaFil: Estrin, Dario Ariel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química, Física de los Materiales, Medioambiente y Energía. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química, Física de los Materiales, Medioambiente y Energía; ArgentinaFil: Luque, F. Javier. Universidad de Barcelona; EspañaFil: Dikshit, Kanak L.. Institute of Microbial Technology; Indi