A detailed VM profiler for the Cog VM

International audienceCode profiling enables a user to know where in an application or function the execution time is spent. The Pharo ecosystem offers several code profilers. However, most of the publicly available profilers (MessageTally, Spy, GadgetPro-filer) largely ignore the activity carried out by the virtual machine , thus incurring inaccuracy in the gathered information and missing important information, such as the Just-in-time compiler activity. This paper describes the motivations and the latest improvements carried out in VMProfiler, a code execution pro-filer hooked into the virtual machine, that performs its analysis by monitoring the virtual machine execution. These improvements address some limitations related to assessing the activity of native functions (resulting from a Just-in-time compiler operation): as of now, VMProfiler provides more detailed profiling reports, showing for native code functions in which bytecode range the execution time is spent

Gene Context Analysis in the Integrated Microbial Genomes (IMG) Data Management System

Computational methods for determining the function of genes in newly sequenced genomes have been traditionally based on sequence similarity to genes whose function has been identified experimentally. Function prediction methods can be extended using gene context analysis approaches such as examining the conservation of chromosomal gene clusters, gene fusion events and co-occurrence profiles across genomes. Context analysis is based on the observation that functionally related genes are often having similar gene context and relies on the identification of such events across phylogenetically diverse collection of genomes. We have used the data management system of the Integrated Microbial Genomes (IMG) as the framework to implement and explore the power of gene context analysis methods because it provides one of the largest available genome integrations. Visualization and search tools to facilitate gene context analysis have been developed and applied across all publicly available archaeal and bacterial genomes in IMG. These computations are now maintained as part of IMG's regular genome content update cycle. IMG is available at: http://img.jgi.doe.gov

Object-Centric Reflection: Unifying Reflection and Bringing It Back to Objects

Reflective applications are able to query and manipulate the structure and behavior of a running system. This is essential for highly dynamic software that needs to interact with objects whose structure and behavior are not known when the application is written. Software analysis tools, like debuggers, are a typical example. Oddly, although reflection essentially concerns run-time entities, reflective applications tend to focus on static abstractions, like classes and methods, rather than objects. This is phenomenon we call the object paradox, which makes developers less effective by drawing their attention away from run-time objects. To counteract this phenomenon, we propose a purely object-centric approach to reflection. Reflective mechanisms provide object-specific capabilities as another feature. Object-centric reflection proposes to turn this around and put object-specific capabilities as the central reflection mechanism. This change in the reflection architecture allows a unification of various reflection mechanisms and a solution to the object paradox. We introduce Bifr\"ost, an object-centric reflective system based on first-class meta-objects. Through a series of practical examples we demonstrate how object-centric reflection mitigates the object paradox by avoiding the need to reflect on static abstractions. We survey existing approaches to reflection to establish key requirements in the domain, and we show that an object-centric approach simplifies the meta-level and allows a unification of the reflection field. We demonstrate how development itself is enhanced with this new approach: talents are dynamically composable units of reuse, and object-centric debugging prevents the object paradox when debugging. We also demonstrate how software analysis is benefited by object-centric reflection with Chameleon, a framework for building object-centric analysis tools and MetaSpy, a domain-specific profile

Remarkable Challenges of High-Performance Language Virtual Machines

Language Virtual Machines (VMs) are pervasive in every laptop, server, and smartphone, as is the case with Java or Javascript. They allow application portability between different platforms and better usage of resources. They are used in critical applications such as stock exchange, banking, insurance, and health [25]. Virtual machines are an important asset in companies because they allow the efficient execution of high-level programming languages. Nowadays, they even attract investments from large non-system companies, e.g., Netflix 1 , Meta 2 , Shopify 3 and Amazon 4. VMs achieve high-performance thanks to aggressive optimization techniques that observe and adapt the execution dynamically, either by doing just-in-time compilation [5] or by adapting the memory management strategies at runtime [90, 91]. For all these reasons Virtual Machines are highly-complex engineering pieces, often handcrafted by experts, that mix state-of-the-art compilation techniques with complex memory management that collaborate with the underlying operating systems and hardware. However, besides some well-known techniques that are published in research venues, most knowledge and technology around virtual machines are highly concentrated in large companies such as Microsoft, Google, and Oracle, making Virtual Machine construction difficult, and experiments difficult to reproduce and replicate. Language VMs present many multidisciplinary scientific challenges that appear at the intersection of fields such as hardware, system software, compiler, and software language engineering. This document aims to give a brief overview of the current challenges the VM community faces. To keep this document short, we selected remarkable challenges in managed execution, managed memory, performance evaluation, software engineering and security

RRS James Clark Ross Cruises JR265 and JR254D, 27 Nov-24 Dec 2011. Part 1: The Drake Passage hydrographic repeat section SR1b

This report describes the 17th complete occupation of the Drake Passage CTD section, established during the World Ocean Circulation Experiment as repeat section SR1b. It wasfirst occupied by National Oceanography Centre (previously IOSDL and then SOC) in collaboration with the British Antarctic Survey in 1993, and has been re-occupied most years since then. Thirty two full depth stations were performed during JR265: two test stations, and all 30 of the nominal stations for the SR1b Drake Passage section. An initial result is that the estimated total transport measured across the section was 133 Sv which compares well to an average transport measured from the 16 previous UK cruises of 135 Sv (standard deviation of 7 Sv). In conjunction with the hydrographic cruise, a "Waves Aerosol and Gas Exchange Study" (WAGES) intensive observation cruise JR245D was also carried out. WAGES involves continuous measurement of the air-sea turbulent fluxes of CO2, sea spray aerosol, momentum and sensible and latent heat fluxes, plus directional sea-state and whitecap parameters using systems installed on the ship in May 2010. In addition to the continuous measurements, a number of intensive observation periods (IOPs) have been carried out by WAGES staff on board the ship. These involve deployments of a spar buoy to measure wave breaking and an aerial camera system to measure whitecap fraction. The activities of JR254D are summarised here, but are described in detail in a separate cruise report. Cruise JR264 was carried out by NOC-L staff at the same time as JR265 and JR254D. JR264 is also the subject of a separate cruise report. The CTD was an underwater SBE 9 plus unit equipped with the following sensors: dual temperature and conductivity sensors, a pressure sensor encased in the SBE underwater unit, a SBE-43 oxygen probe, an Aquatracka MKIII fluorometer, a transmissometer, an upwardlooking downwelling PAR sensor, and an altimeter. A downward-looking LADCP (RDI Workhorse Monitor 300 kHz) was deployed on all stations. Various underway measurements were obtained, including navigation, VM-ADCP, sea surface temperature and salinity, water depth and various meteorological parameters. A practical aim during this cruise was to update the detailed guides for each of the hydrographic data streams which were first written duringJR195 in 2009. The hydrographic data analysis was performed using "MSTAR", a suite of Matlab programs developed at NOCS by Brian King and used on the JCR for the first time during JR195

Complete genome sequence and description of Salinispira pacifica gen. nov., sp. nov., a novel spirochaete isolated form a hypersaline microbial mat

During a study of the anaerobic microbial community of a lithifying hypersaline microbial mat of Lake 21 on the Kiritimati atoll (Kiribati Republic, Central Pacific) strain L21-RPul-D2(T) was isolated. The closest phylogenetic neighbor was Spirochaeta africana Z-7692(T) that shared a 16S rRNA gene sequence identity value of 90% with the novel strain and thus was only distantly related. A comprehensive polyphasic study including determination of the complete genome sequence was initiated to characterize the novel isolate. Cells of strain L21-RPul-D2(T) had a size of 0.2 - 0.25 x 8-9 mu m, were helical, motile, stained Gram-negative and produced an orange carotenoid-like pigment. Optimal conditions for growth were 35 degrees C, a salinity of 50 g/l NaCl and a pH around 7.0. Preferred substrates for growth were carbohydrates and a few carboxylic acids. The novel strain had an obligate fermentative metabolism and produced ethanol, acetate, lactate, hydrogen and carbon dioxide during growth on glucose. Strain L21-RPul-D2(T) was aerotolerant, but oxygen did not stimulate growth. Major cellular fatty acids were C-14:0, iso-C-15:0, C-16:0 and C-18:0. The major polar lipids were an unidentified aminolipid, phosphatidylglycerol, an unidentified phospholipid and two unidentified glycolipids. Whole cell hydrolysates contained L-ornithine as diagnostic diamino acid of the cell wall peptidoglycan. The complete genome sequence was determined and annotated. The genome comprised one circular chromosome with a size of 3.78 Mbp that contained 3450 protein-coding genes and 50 RNA genes, including 2 operons of ribosomal RNA genes. The DNA G + C content was determined from the genome sequence as 51.9 mol%. There were no predicted genes encoding cytochromes or enzymes responsible for the biosynthesis of respiratory lipoquinones. Based on significant differences to the uncultured type species of the genus Spirochaeta, S. plicatilis, as well as to any other phylogenetically related cultured species it is suggested to place strain L21-RPul-D2(T) (=DSM 27196(T) = JCM 18663(T)) in a novel species and genus, for which the name Salinispira pacifica gen. nov., sp. nov. is proposed

The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota

<p>Abstract</p> <p>Background</p> <p><it>Staphylothermus marinus </it>is an anaerobic, sulfur-reducing peptide fermenter of the archaeal phylum Crenarchaeota. It is the third heterotrophic, obligate sulfur reducing crenarchaeote to be sequenced and provides an opportunity for comparative analysis of the three genomes.</p> <p>Results</p> <p>The 1.57 Mbp genome of the hyperthermophilic crenarchaeote <it>Staphylothermus marinus </it>has been completely sequenced. The main energy generating pathways likely involve 2-oxoacid:ferredoxin oxidoreductases and ADP-forming acetyl-CoA synthases. <it>S. marinus </it>possesses several enzymes not present in other crenarchaeotes including a sodium ion-translocating decarboxylase likely to be involved in amino acid degradation. <it>S. marinus </it>lacks sulfur-reducing enzymes present in the other two sulfur-reducing crenarchaeotes that have been sequenced – <it>Thermofilum pendens </it>and <it>Hyperthermus butylicus</it>. Instead it has three operons similar to the <it>mbh </it>and <it>mbx </it>operons of <it>Pyrococcus furiosus</it>, which may play a role in sulfur reduction and/or hydrogen production. The two marine organisms, <it>S. marinus </it>and <it>H. butylicus</it>, possess more sodium-dependent transporters than <it>T. pendens </it>and use symporters for potassium uptake while <it>T. pendens </it>uses an ATP-dependent potassium transporter. <it>T. pendens </it>has adapted to a nutrient-rich environment while <it>H. butylicus </it>is adapted to a nutrient-poor environment, and <it>S. marinus </it>lies between these two extremes.</p> <p>Conclusion</p> <p>The three heterotrophic sulfur-reducing crenarchaeotes have adapted to their habitats, terrestrial vs. marine, via their transporter content, and they have also adapted to environments with differing levels of nutrients. Despite the fact that they all use sulfur as an electron acceptor, they are likely to have different pathways for sulfur reduction.</p