Evaluating the performance of the allreduce collective operation on clusters. Approach and results

The performance of the collective operations provided by a communication library is important for many applications run on clusters. The communication structure of collective operations can be organized as a tree. Performance can be improved by configuring and mapping the tree to the clusters in use. We describe and demonstrate an approach for evaluating the performance of different configurations and mappings of allreduce run on clusters of different size, consisting of single-CPU hosts, and SMPs with a different number of CPUs. A breakdown of the cost of allreduce using the best configuration on different clusters is provided. For all, the broadcast part is more expensive than the reduce part. Inter-host communication contributes more to the time per allreduce than the synchronization in the allreduce components. For the small messages sizes used (4 and 256 bytes), the time spent computing the partial reductions is insignificant. Reconfiguring hierarchy aware trees improved performance up to a factor of 1.49, by avoiding scalability problems of the components on SMPs, and by finding the right balance between available concurrency, load on 'root' hosts and the number of network links in a tree. Extending a tree by adding more threads, or by combining two trees does not have a negative influence on the performance of a configuration, but increasing message size does

Large-Eddy Simulations of Flow and Heat Transfer in Complex Three-Dimensional Multilouvered Fins

The paper describes the computational procedure and results from large-eddy simulations in a complex three-dimensional louver geometry. The three-dimensionality in the louver geometry occurs along the height of the fin, where the angled louver transitions to the flat landing and joins with the tube surface. The transition region is characterized by a swept leading edge and decreasing flow area between louvers. Preliminary results show a high energy compact vortex jet forming in this region. The jet forms in the vicinity of the louver junction with the flat landing and is drawn under the louver in the transition region. Its interaction with the surface of the louver produces vorticity of the opposite sign, which aids in augmenting heat transfer on the louver surface. The top surface of the louver in the transition region experiences large velocities in the vicinity of the surface and exhibits higher heat transfer coefficients than the bottom surface.Air Conditioning and Refrigeration Project 9

Architecture--Performance Interrelationship Analysis In Single/Multiple Cpu/Gpu Computing Systems: Application To Composite Process Flow Modeling

Current developments in computing have shown the advantage of using one or more Graphic Processing Units (GPU) to boost the performance of many computationally intensive applications but there are still limits to these GPU-enhanced systems. The major factors that contribute to the limitations of GPU(s) for High Performance Computing (HPC) can be categorized as hardware and software oriented in nature. Understanding how these factors affect performance is essential to develop efficient and robust applications codes that employ one or more GPU devices as powerful co-processors for HPC computational modeling. The present work analyzes and understands the intrinsic interrelationship of both hardware and software categories on computational performance for single and multiple GPU-enhanced systems using a computationally intensive application that is representative of a large portion of challenges confronting modern HPC. The representative application uses unstructured finite element computations for transient composite resin infusion process flow modeling as the computational core, characteristics and results of which reflect many other HPC applications via the sparse matrix system used for the solution of linear system of equations. This work describes these various software and hardware factors and how they interact to affect performance of computationally intensive applications enabling more efficient development and porting of High Performance Computing applications that includes current, legacy, and future large scale computational modeling applications in various engineering and scientific disciplines

Revealing Complex Traits with Small Molecules and Naturally Recombinant Yeast Strains

SummaryHere we demonstrate that natural variants of the yeast Saccharomyces cerevisiae are a model system for the systematic study of complex traits, specifically the response to small molecules. As a complement to artificial knockout collections of S. cerevisiae widely used to study individual gene function, we used 314- and 1932-member libraries of mutant strains generated by meiotic recombination to study the cumulative, quantitative effects of natural mutations on phenotypes induced by 23 small-molecule perturbagens (SMPs). This approach reveals synthetic lethality between SMPs, and genetic mapping studies confirm the involvement of multiple quantitative trait loci in the response to two SMPs that affect respiratory processes. The systematic combination of natural variants of yeast and small molecules that modulate evolutionarily conserved cellular processes can enable a better understanding of the general features of complex traits

Is there new particle formation in the marine boundary layer of the North Sea?

The effect of aerosol particles on climate and the human health emphasizes the necessity to focus on the research about aerosol particles. Aerosol particles emitted due to anthropogenic activities increase the scattering and absorption of solar radiation in the atmosphere which leads to an increased cooling of the climate (direct effect). In addition, they take part in cloud formation, and thereby they affect the radiative properties of clouds, and an increase in the emission of aerosol particles in general leads to an increasing solar radiation scattering and an alteration of precipitation (indirect effect). Aerosol particles emitted directly to the atmosphere through natural or anthropogenic processes are called primary aerosol particles. Secondary aerosol particles are formed after gas to particle conversion. New particle formation (NPF) mechanism is one of the important secondary aerosol particle sources. The newly formed particles have the ability to grow to cloud activation sizes after processing in the atmosphere, and hence are important for the indirect climate effect. There are still many discussions about the theories describing nucleation process and conditions favorable for NPF, but not a single theory can be regarded as correct yet. However it is known that such components as SO2, NOx, Biogenic volatile organic compounds (BVOC), other organic compounds, and NH3 are important gaseous precursors in the NPF process. NPF events have been detected at many sites at different environments but there is no information about NPF events detected over the North Sea or over other polluted marine atmospheres. The aim of the study is to investigate whether there are NPF events over the North Sea, how frequent they are, and to identify geographical positions of the NPF events over the North Sea using the newly developed NanoMap method. The Nano Map method requires only the aerosol particle size distribution data, and air mass back trajectories from Hysplit model. For this investigation a size distributions of nano-particles were measured with the Air ion spectrometer (AIS) instrument for particles 2 – 40 nm diameter, and with the scanning mobility particle sizer (SMPS) instrument for particles 10 - 300 nm diameter during March – May 2012 at the Danish North Sea coast field station Høvsøre. This data was combined with data measured 2010-2011 at the Cabauw field site in the Netherlands and data measured 2009-2010 at the Birkenes field site in Norway. The NanoMap analysis showed that there are NPF during 27% of the days at Høvsøre and that the aerosol particles are formed close to or along major shipping lanes. Hence, SO2 from ship emissions is a possible source of NPF over the North Sea. However, also continental air pollution, continental BVOC emissions, and volatile organic carbon (VOC) emissions from oil stations at the North Sea can be contribution to NPF.Popular science There are tiny airborne particles called aerosols in atmosphere that cool climate on the Earth by reducing incoming radiation from the Sun. They play an important role in cloud formation and affect the properties of the clouds. There were no clouds without aerosol particles. Aerosol particles can enter the atmosphere due to anthropogenic and natural emissions and that is why these particles have different chemical composition, size and properties. Many questions about aerosols are poorly studied still. One of these questions is where aerosol particles are formed. There are also discussions on how the aerosol particles are formed and what conditions favor to the process. Formation of aerosol particles was detected in different environments and there are data obtained from many scientific stations. But it is needed to identify the source or the particles. With a help of NanoMap method it is possible to identify a geographical position of the place where new particles are formed. The aim of the study is to find out whether aerosol particles are formed over the North Sea, how frequent these events are, and to create maps showing where the aerosol particles were formed. A set of instruments were placed at the Danish North Sea coast field station Høvsøre during March – May 2012. This data was combined with data measured 2010-2011 at the Cabauw field site in the Netherlands and data measured 2009-2010 at the Birkenes field site in Norway. The NanoMap method showed that the aerosol particles are formed over the North Sea close to or along major shipping lanes. Probably ship emissions are a possible source of aerosols over the North Sea. However, other emissions can play an important role such as continental air pollution, emissions from oil stations and others

Growth of diesel exhaust particulate matter in a ventilated mine tunnel

The objective of this work was to study the formation and evolutionary characteristics of aerosols, originating from the exhaust plume of a diesel engine operating in a ventilated mine tunnel. To extract these characteristics, precise cross-sectional scalar exhaust maps of CO2, temperature, and aerosol concentration were generated and used to track the time averaged axial development of the plume. These maps were then used to position aerosol size distribution samples within critical regions of the plume. This approach was found to provide an efficient and thorough record of aerosol formation and evolution, as a result of naturally dispersed diesel exhaust in mine environments.;A diesel exhaust plume is made up of a complex spatial and temporally dependent array of various exhaust constituents. The state (i.e. temperature and partial pressures) of these constituents, as they travel through space, will depend on the nature of the plume and its environment. Laboratory studies usually simulate plume processes through sudden fully mixed systems. However, this approach compromises the complex path dependent processes present within natural plumes. This discrepancy can significantly affect the trends reported for the generation and transformation of diesel exhaust aerosols, which are dependent to a large extent on fuel sulfur level, temperature, species\u27 partial pressures, residence time, and dilution ratio. Some studies have been performed which preserve the natural evolution of the plume (i.e. vehicle chasing), but only demonstrate crude spatial development through the collection of relatively coarse and imprecisely positioned samples. As such, vehicle chasing studies result in relatively primitive descriptions of the formation and evolution of diesel exhaust aerosols. Consequently the following study was designed to efficiently extract detailed relationships that exist between the aerosols and other variables of a naturally occurring exhaust plume.;During this study, a digital three-axis probe placement device was developed and used to position time averaged exhaust samples precisely throughout the plume. Mapping software was also created and interfaced with the device, allowing a continued awareness of the relative probe positions with respect to the emerging plume. Scalar exhaust maps were extracted through the use of a NDIR CO2 analyzer, K-type thermocouple, and a handheld TSI CPC3007 particle counter. These maps were used to strategically position aerosol size distribution samples measured by a TSI Scanning Mobility Particle Sizer (SMPS). This approach was employed to save time without incurring any losses in the quality of trends found from aerosol size distribution samples.;The results of this study reveal the intricate 3-dimensional paths traveled by developing aerosols under natural mixing. These paths are marked by continually changing exhaust states known to affect aerosol evolution. As such, spatial trends observed in aerosol data were found highly diverse over distances spanning as little as a few inches. These trends showed growth in the nuclei mode at distances as far as 20 feet from the exhaust source. Beyond 20 feet, the nuclei mode experienced considerable losses nearing 1 order of magnitude at a distance of ∼200 feet from the exhaust source. In spite of this loss, the accumulation mode was found virtually unaffected throughout the entire 200 foot test region of the tunnel