Freezing time emulating new and faster devices with virtual machines

Recent proposals of emerging data storage devices make it necessary to reevaluate all levels of the storage hierarchy to optimize the software stack performance. However, these new devices are not always widely available and therefore early experiments may be impossible. Emulators aim at mimicking as close as possible the behavior of a component, nonetheless, emulating new and fast storage devices is a challenging task due to time perception. In this work, we propose an approach to emulate storage devices using virtual machines (VMs) allowing the evaluation of a new device within a real system. We use a technique called freezing time, which pauses a VM to manipulate its clock and hide the real I/O completion time. Our approach is implemented at the hypervisor level and it is transparent to the guest operating system or application. We evaluate the technique under a real system using regular magnetic disks to emulate faster storage devices. Our method presented a latency error of 6.5% compared to a real device. Moreover, decoupled experiment between two laboratories, at the Barcelona Super Computing Center (BSC) in Spain, and the Center of Computer Science and Free Software (C3SL) in Brazil, demonstrated that our approach is reproducible and promising to allow the virtual evaluation of next-gen storage devices.This work was partially supported by the Spanish Ministry of Science and Innovation under the TIN2015-65316 Grant, the Generalitat de Catalunya under contract 2014-SGR-1051, the Serrapilheira Institute (Grant number Serra-1709-16621), as well as the European Union’s Horizon 2020 Research and Innovation Programme, under Grant Agreement no. 671951 (NEXTGenIO) for the extensions added after the MASCOTS paper.Peer ReviewedPostprint (author's final draft

Freezing Time: a new approach for emulating fast storage devices using VM

© 2018 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Recently we are seeing a considerable effort from both academy and industry in proposing new technologies for storage devices. Often these devices are not readily available for evaluation and methods to allow performing their tests just from their performance parameters are an important tool for system administrators. Simulators are a traditional approach for carrying out such evaluations, however, they are more suitable for evaluating the storage device as an isolate component, mostly due to time constraints. In this paper, we propose an approach based on virtual machine technology that is capable of emulate storage devices transparently for the operating system allowing evaluation of simulating devices within a real system using any synthetic or real workload. To emulate devices in real environments it is necessary to use the currently available devices as a storage medium which creates a difficulty when the device to be emulated is faster than this storage medium. To circumvent this limitation we introduce a new technique called Freezing Time, which takes advantage of virtual machine pausing mechanism to manipulate the virtual machine clock and hide the real I/O completion time. Our approach can be implemented just requiring the hypervisor to be modified, providing a high degree of compatibility and flexibility since it is not necessary to modify neither the operating system nor the application. We evaluate our tool under a real system using old magnetic disks to emulate faster storage devices. Experiments using our technique presented an average latency error of 6.08% for read operations and 6.78% for write operations when comparing a real to device.This work was partially supported by the Spanish Ministry of Science and Innovation under the TIN2015–65316 grant, the Generalitat de Catalunya under contract 2014–SGR–1051.Peer ReviewedPostprint (author's final draft

Freezing Time: a new approach for emulating fast storage devices using VM

© 2018 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.Recently we are seeing a considerable effort from both academy and industry in proposing new technologies for storage devices. Often these devices are not readily available for evaluation and methods to allow performing their tests just from their performance parameters are an important tool for system administrators. Simulators are a traditional approach for carrying out such evaluations, however, they are more suitable for evaluating the storage device as an isolate component, mostly due to time constraints. In this paper, we propose an approach based on virtual machine technology that is capable of emulate storage devices transparently for the operating system allowing evaluation of simulating devices within a real system using any synthetic or real workload. To emulate devices in real environments it is necessary to use the currently available devices as a storage medium which creates a difficulty when the device to be emulated is faster than this storage medium. To circumvent this limitation we introduce a new technique called Freezing Time, which takes advantage of virtual machine pausing mechanism to manipulate the virtual machine clock and hide the real I/O completion time. Our approach can be implemented just requiring the hypervisor to be modified, providing a high degree of compatibility and flexibility since it is not necessary to modify neither the operating system nor the application. We evaluate our tool under a real system using old magnetic disks to emulate faster storage devices. Experiments using our technique presented an average latency error of 6.08% for read operations and 6.78% for write operations when comparing a real to device.This work was partially supported by the Spanish Ministry of Science and Innovation under the TIN2015–65316 grant, the Generalitat de Catalunya under contract 2014–SGR–1051.Peer Reviewe

NEOTROPICAL ALIEN MAMMALS: a data set of occurrence and abundance of alien mammals in the Neotropics

Biological invasion is one of the main threats to native biodiversity. For a species to become invasive, it must be voluntarily or involuntarily introduced by humans into a nonnative habitat. Mammals were among first taxa to be introduced worldwide for game, meat, and labor, yet the number of species introduced in the Neotropics remains unknown. In this data set, we make available occurrence and abundance data on mammal species that (1) transposed a geographical barrier and (2) were voluntarily or involuntarily introduced by humans into the Neotropics. Our data set is composed of 73,738 historical and current georeferenced records on alien mammal species of which around 96% correspond to occurrence data on 77 species belonging to eight orders and 26 families. Data cover 26 continental countries in the Neotropics, ranging from Mexico and its frontier regions (southern Florida and coastal-central Florida in the southeast United States) to Argentina, Paraguay, Chile, and Uruguay, and the 13 countries of Caribbean islands. Our data set also includes neotropical species (e.g., Callithrix sp., Myocastor coypus, Nasua nasua) considered alien in particular areas of Neotropics. The most numerous species in terms of records are from Bos sp. (n = 37,782), Sus scrofa (n = 6,730), and Canis familiaris (n = 10,084); 17 species were represented by only one record (e.g., Syncerus caffer, Cervus timorensis, Cervus unicolor, Canis latrans). Primates have the highest number of species in the data set (n = 20 species), partly because of uncertainties regarding taxonomic identification of the genera Callithrix, which includes the species Callithrix aurita, Callithrix flaviceps, Callithrix geoffroyi, Callithrix jacchus, Callithrix kuhlii, Callithrix penicillata, and their hybrids. This unique data set will be a valuable source of information on invasion risk assessments, biodiversity redistribution and conservation-related research. There are no copyright restrictions. Please cite this data paper when using the data in publications. We also request that researchers and teachers inform us on how they are using the data

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field