Resource Modification On Multicore Server With Kernel Bypass

Technology develops very fast marked by many innovations both from hardware and software. Multicore servers with a growing number of cores require efficient software. Kernel and Hardware used to handle various operational needs have some limitations. This limitation is due to the high level of complexity especially in handling as a server such as single socket discriptor, single IRQ and lack of pooling so that it requires some modifications. The Kernel Bypass is one of the methods to overcome the deficiencies of the kernel. Modifications on this server are a combination increase throughput and decrease server latency. Modifications at the driver level with hashing rx signal and multiple receives modification with multiple ip receivers, multiple thread receivers and multiple port listener used to increase throughput. Modifications using pooling principles at either the kernel level or the program level are used to decrease the latency. This combination of modifications makes the server more reliable with an average throughput increase of 250.44% and a decrease in latency 65.83%

Multi-granular, multi-purpose and multi-Gb/s monitoring on off-the-shelf systems

This is the accepted version of the following article: [Moreno, V., Santiago del Río, P. M., Ramos, J., Muelas, D., García-Dorado, J. L., Gomez-Arribas, F. J. and Aracil, J. (2014), Multi-granular, multi-purpose and multi-Gb/s monitoring on off-the-shelf systems. Int. J. Network Mgmt., 24: 221–234. doi: 10.1002/nem.1861, which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/nem.1861/abstractAs an attempt to make network managers’ life easier, we present M3Omon, a system architecture that helps to develop monitoring applications and perform network diagnosis. M3Omon behaves as an intermediate layer between the traffic and monitoring applications that provides advanced features, high performance and low cost. Such advanced features leverage a multi-granular and multi-purpose approach to the monitoring problem. Multi-granular monitoring gives answer to tasks that use traffic aggregates to identify an event, and requires either flow records or packet data or even both to understand it and, eventually, take the convenient countermeasures. M3Omon provides a simple API to access traffic simultaneously at several different granularities—i.e., packet-level, flow-level and aggregate statistics. The multi-purposed design of M3Omon allows not only performing tasks in parallel that are specifically targeted to different traffic-related purposes (e.g., traffic classification and intrusion detection) but also sharing granularities between applications—e.g., several concurrent applications fed from flow records that are provided by M3Omon. Finally, the low-cost characteristic is brought by off-the-shelf systems (the combination of open-source software and commodity hardware) and the high performance is achieved thanks to modifications in the standard NIC driver, low-level hardware interaction, efficient memory management and programming optimization

Metallomics in environmental and health related research: Current status and perspectives

Metals and metalloids play distinct roles in human health, either beneficial or toxic, depending on their concentrations and species. There is an increasing interest in metals uptake, trafficking, function, and exertion in microorganisms to maintain and advance human health. Metallomics, an emerging research area, focuses on elucidation of metals/metalloids location, distribution, speciation, and behavior in living organisms. This paper briefly summarized the recent progress on the methodology development of metallomics including various techniques, i. e. multiple dimensional liquid chromatography-inductively coupled plasma mass spectrometry (LC-ICPMS), gel electrophoresis-laser ablation-inductively coupled plasma mass spectrometry (GE-LA-ICPMS), synchrotron X-ray fluorescent spectroscopy (XFS), and the applications of metallomics in environmental and health care. © 2012 The Author(s).published_or_final_versio

Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond

Various strategies to implement efficiently QMC simulations for large chemical systems are presented. These include: i.) the introduction of an efficient algorithm to calculate the computationally expensive Slater matrices. This novel scheme is based on the use of the highly localized character of atomic Gaussian basis functions (not the molecular orbitals as usually done), ii.) the possibility of keeping the memory footprint minimal, iii.) the important enhancement of single-core performance when efficient optimization tools are employed, and iv.) the definition of a universal, dynamic, fault-tolerant, and load-balanced computational framework adapted to all kinds of computational platforms (massively parallel machines, clusters, or distributed grids). These strategies have been implemented in the QMC=Chem code developed at Toulouse and illustrated with numerical applications on small peptides of increasing sizes (158, 434, 1056 and 1731 electrons). Using 10k-80k computing cores of the Curie machine (GENCI-TGCC-CEA, France) QMC=Chem has been shown to be capable of running at the petascale level, thus demonstrating that for this machine a large part of the peak performance can be achieved. Implementation of large-scale QMC simulations for future exascale platforms with a comparable level of efficiency is expected to be feasible

MICRO$EC: Cost Effective, Whole-Genome Sequencing

While the feasibility of whole human genome sequencing was proven by the success of the Human Genome Project several years ago, the prevalence of personal genome sequencing in the medical industry is still elusive due to its unrealistic cost and time requirements. Micro$eq is a startup company with the goal of overcoming these limitations by sequencing a minimum of 12 complete human genomes per day at an error rate less than ten parts in million at a profitable market price of less than US$1000 per genome. To overcome the technology bottlenecks hindering current biotech companies from achieving these target throughput, error rate, and market price goals, Micro$eq has developed an innovative sequencing technique that uses shortread fragments with high coverage on a microfluidics platform. Short, amplified DNA fragments are generated from an input of customer saliva. 6 base pair(bp) sequence hybridization is used for sequencing each of the DNA fragments individually. The results are these hydridization reads are then assembled via de Bruijn graph theory and the graphical reconstructions of each fragment’s sequence are then assembled to a complete genome via shotgun sequencing with an expected error rate less than 1 in 100,000bp. Upon the completion of financial analysis, both a small-scale business model producing 72 genomes per day at US$999 per genome, and a largescale business model producing 52.2 genomes per year at a market price of US$299 per genome were found to be profitable, yielding Micro$eq investors return margins of ~90% and 300% for the small and large scale models, respectively. With a market price Micro$eq offers personal genome sequencing at one-tenth of its nearest potential competitor’s cost. Additionally, its ability for bulk-sequencing allows it to profitably venture into the previously untapped Pharmaceutical Industry market sector, enabling the creation of large-scale genome databases which are the next step forward in the quest for truly personalized

Network Traffic Processing with PFQ

This paper presents Packet Family Queue (PFQ), a high-performance framework for packet processing designed to flexibly handle network applications parallelism and making traffic processing safe and easy. PFQ is an open-source module for the Linux kernel that combines software-accelerated packet I/O to in-kernel early stage packet processing and fine-grained distribution to network applications and physical devices. PFQ does not require any modification to network device drivers and exposes programming interfaces to multi-threaded applications natively designed to run on top of it, as well as to legacy monitoring tools using the pcap library. The results show that the flexibility and the backward compatibility provided by PFQ do not impact its processing performance that, in fact, reaches line rate figures in the cases of pure speed tests and real practical monitoring use cases on 10+ Gb/s links

Microscopy Techniques for Investigating Interactions in Microbial Systems

Biological interactions occur on multiple length scales, ranging from molecular to population wide interactions. This work describes the study of two specific areas of biological interactions in microbial systems: intracellular protein-protein interactions and cell-to-cell interactions. The implementation of optical and atomic force microscopy and the methodologies developed during this study proved to be invaluable tools for investigating these systems. Identifying and characterizing protein interactions are fundamental steps toward understanding complex cellular networks. We have developed a unique methodology which combines an imaging-based protein interaction assay with a fluorescence recovery after photobleaching technique (FRAP). Protein interactions are readily detected by co-localization of two proteins of interest fused to green fluorescent protein (GFP) and DivIVA, a cell division protein from Bacillus subtilis. We demonstrate that the modified co-localization assay is sensitive enough to detect protein interactions over four orders of magnitude. FRAP data was analyzed using a combination of various image processing techniques and analytical models. This combined approach made it possible to estimate cell morphology parameters such as length, diameter, the effective laser probe volume, as well as to the mobile protein concentration in vivo, the number of bound molecules at the cellular poles, and the biophysical parameter koff. Cells not only utilize molecular interactions in the intracellular environment, but also express proteins, polysaccharides and other complex molecules to mediate interactions with the surrounding extracellular environment. In Azospirillum brasilense, cell surface properties, including exopolysaccharide production, are thought to play a direct role in promoting cell-to-cell interactions. Recently, the Che1 chemotaxis-like pathway from A. brasilense was shown to modulate flocculation, suggesting an associated modulation of cell surface properties. Using atomic force microscopy, distinct changes in the surface morphology of flocculating A. brasilense Che1 mutant strains were detected. Further analyses suggest that the extracellular matrix differs between the cheA1 and the cheY1 deletion mutants, despite similarity in the macroscopic floc structures. Collectively, these data indicate that disruption of the Che1 pathway is correlated with distinctive changes in the extracellular matrix, which likely result from changes in surface polysaccharides structure and/or composition