A complete and efficient CUDA-sharing solution for HPC clusters

In this paper we detail the key features, architectural design, and implementation of rCUDA, an advanced framework to enable remote and transparent GPGPU acceleration in HPC clusters. rCUDA allows decoupling GPUs from nodes, forming pools of shared accelerators, which brings enhanced flexibility to cluster configurations. This opens the door to configurations with fewer accelerators than nodes, as well as permits a single node to exploit the whole set of GPUs installed in the cluster. In our proposal, CUDA applications can seamlessly interact with any GPU in the cluster, independently of its physical location. Thus, GPUs can be either distributed among compute nodes or concentrated in dedicated GPGPU servers, depending on the cluster administrator’s policy. This proposal leads to savings not only in space but also in energy, acquisition, and maintenance costs. The performance evaluation in this paper with a series of benchmarks and a production application clearly demonstrates the viability of this proposal. Concretely, experiments with the matrix–matrix product reveal excellent performance compared with regular executions on the local GPU; on a much more complex application, the GPU-accelerated LAMMPS, we attain up to 11x speedup employing 8 remote accelerators from a single node with respect to a 12-core CPU-only execution. GPGPU service interaction in compute nodes, remote acceleration in dedicated GPGPU servers, and data transfer performance of similar GPU virtualization frameworks are also evaluated.     

Background subtraction model based on color and depth cues

Background subtraction consists of segmenting objects in movement in a video captured by a static camera. This is typically performed using color information, but it leads to wrong estimations due to perspective and illumination issues. We show that multimodal approaches based on the integrated use of color and depth cues produce more accurate and robust results than using either data source independently. Depth is less affected by issues such as shadows or foreground objects similar to background. However, objects close to the background may not be detected when using only range information, being color information complementary in those cases. We propose an extension of a well-known background subtraction technique which fuses range and color information, as well as a post-processing mask fusion stage to get the best of each feature. We have evaluated the method proposed using a well-defined dataset and different disparity estimation algorithms, showing the benefits of our method for fusion color and depth cues.     

Rancidity development during the chilled storage of farmed Coho salmon (Oncorhynchus kisutch)

Coho salmon (Oncorhynchus kisutch) is a fatty fish species whose farming production has greatly increased in recent years. Lipid damage produced during Coho salmon chilled storage was studied for up to 24 d. Lipid hydrolysis (free fatty acids, FFA) and oxidation (conjugated dienes; peroxide value, PV; thiobarbituric acid index, TBA‐i; fluorescent compounds formation, FR; browning development) were determined and compared to lipid composition (polyene index, PI; astaxanthin, AX) changes and sensory assessment (rancid odour development) results. Most lipid damage indices developed slowly during storage; thus, values obtained for FFA, PV, TBA‐i and FR were in all cases under 1.5 g/100 g, 4.0 meq oxygen/kg lipid, 0.40 mg malondialdehyde/kg muscle and 0.40, respectively. Odour assessment showed a significant (p <0.05) rancidity development at day 10, when compared to starting fish material; then, non‐acceptable values were obtained at days 19 and 24. The PI analysis showed not many differences during the storage time, with the lowest mean value at day 19. AX analysis indicated a relatively high content in the white muscle, which was maintained till the end of the experiment. A low oxidation development is concluded for Coho salmon lipids when compared to other fatty fish species under the same chilling conditions. AX was found to contribute to the oxidation stability of Coho salmon lipids, due to its free radical scavenger properties.     

Calmodulin Supports TRPA1 Channel Association with Opioid Receptors and Glutamate NMDA Receptors in the Nervous Tissue

Transient receptor potential ankyrin member 1 (TRPA1) belongs to the family of thermo TRP cation channels that detect harmful temperatures, acids and numerous chemical pollutants. TRPA1 is expressed in nervous tissue, where it participates in the genesis of nociceptive signals in response to noxious stimuli and mediates mechanical hyperalgesia and allodynia associated with different neuropathies. The glutamate N-methyl-d-aspartate receptor (NMDAR), which plays a relevant role in allodynia to mechanical stimuli, is connected via histidine triad nucleotide-binding protein 1 (HINT1) and type 1 sigma receptor (σ1R) to mu-opioid receptors (MORs), which mediate the most potent pain relief. Notably, neuropathic pain causes a reduction in MOR antinociceptive efficacy, which can be reversed by blocking spinal NMDARs and TRPA1 channels. Thus, we studied whether TRPA1 channels form complexes with MORs and NMDARs that may be implicated in the aforementioned nociceptive signals. Our data suggest that TRPA1 channels functionally associate with MORs, delta opioid receptors and NMDARs in the dorsal root ganglia, the spinal cord and brain areas. These associations were altered in response to pharmacological interventions and the induction of inflammatory and also neuropathic pain. The MOR-TRPA1 and NMDAR-TRPA1 associations do not require HINT1 or σ1R but appear to be mediated by calcium-activated calmodulin. Thus, TRPA1 channels may associate with NMDARs to promote ascending acute and chronic pain signals and to control MOR antinociception.     

Characterization of poly(diethoxyphosphazene) by size exclusion chromatography and viscometry

Two samples of poly(diethoxyphosphazene) (PDEP) having very different molecular weights have been studied by viscometry and size exclusion chromatography in THF solution. The results obtained, together with light scattering data of these samples, allow the calculation of the Mark-Houwink constants a=0.65 and K=2.5 10^-4 in THF at 25°C. The method of calculation employed takes into account the great polydispersity of the samples. The characteristic ratio of the unperturbed dimensions was also calculated giving C_n = r²_o/n² 18, a value slightly higher than those previously reported for poly(dihexoxyphosphazene), C_n13 and poly (dichlorophosphazene), C_n13.5.     

Contribution of a disulfide bridge to the stability of 1,3-1,4-P-D-glucan 4-glucanohydrolase from Bacillus licheniformis

Bacillus 1,3-1,4-ß-glucanases possess a highly conserveddisulfide bridge connecting a ß-strand with a solventexposedloop lying on top of the extended binding site cleft The contributionof the disulfide bond and of both individual cysteines (Cys61and Cys90) in the Bacillus licheniformis enzyme to stabilityand activity has been evaluated by protein engineering methods.Reduction of the disulfide bond has no effect on kinetic parameters,has only a minor effect on the activity-temperature profileat high temperatures, and destabilizes the protein by less than0.7 kcal/mol as measured by equilibrium urea denatu ration at37°C. Replacing either of the Cys residues with Ala destabilizesthe protein and lowers the specific activity. C90A retains 70%of wild-type (wt) activity (in terms of Vmax), whereas C61Aand the double mutant C61A–C90A have 10% of wt V_max. Alarger change in free energy of unfolding is seen by equilibriumurea denaturation for the C61A mutation (loop residue, 3.2 kcal/molrelative to reduced wt) as compared with the C90A mutation (ß-strandresidue, 1.8 kcal/mol relative to reduced wt), while the doublemutant C61A–C90A is 0.8 kcal/mol less stable than thesingle C61A mutant. The effects on stability are interpretedas a result of the change in hydrophobic packing that occursupon removal of the sulfur atoms in the Cys to Ala mutations     

Effect of advanced chilling methods on lipid damage during sardine (Sardina pilchardus) storage

Slurry ice is a biphasic system consisting of small spherical ice crystals surrounded by seawater at subzero temperature. Its effect on lipid damage (hydrolysis and oxidation) was evaluated during the chilled storage of a fatty fish species, sardine (Sardina pilchardus). Slurry ice treatment was checked alone and in combination with ozone and compared to traditional flake icing during a 22‐day storage. Different lipid damage indices (free fatty acids, FFA; peroxide value, PV; thiobarbituric acid index, TBA‐i; fluorescent compounds, FR) were checked and compared to sensory assessment and nucleotide degradation (K value). According to lipid hydrolysis (FFA) and oxidation (PV and FR) developments, slurry ice showed an inhibitory effect (p <0.05) on lipid damage during storage, as well as an inhibition of nucleotide autolytic degradation. Ozonised slurry ice did not provide differences (p >0.05) from slurry ice alone when considering lipid hydrolysis, nucleotide degradation and some lipid oxidation indices (PV and FR), although a higher (p <0.05) TBA‐i was observed at day 22 of storage when compared to flake ice and slurry ice treatments. However, a lower (p <0.05) fluorescence development was observed for fish treated under ozonised slurry ice when compared to traditionally iced fish. Sensory assessment showed a higher shelf life for fish samples treated under ozonised slurry ice than for their counterparts under slurry ice (15 d versus 12 d), while flake icing led to a far shorter shelf life (5 d). According to sensory and biochemical (lipid matter and nucleotide) analysis, slurry ice has proved to be a promising technology for damage inhibition and quality retention in a fatty fish species such as sardine. Ozonised slurry ice was also shown to be useful, since a longer shelf life was obtained in the present experiment and a pro‐oxidant effect of ozone on sardine lipids was not proved.     

Composition of phospholipids of white muscle of six tuna species

A comparative study of the phospholipids of white muscle of six of the comercially utilized tuna species, including quantitative analyses of phospholipid classes and studies of the acyl composition of the major components. Plasmalogen compounds also were identified and quantified. Choline and ethanolamine glycerophospholipids were the most abundant classes in all the samples, as well as the only molecules containing plasmalogens (16∶0, 18∶0, and 18∶1 alkenyl ether chains). The patterns of fatty acid distribution within each of the phospholipid classes showed general similarities in the species analyzed. However, ratios between certain saturated and polyunsaturated fatty acids in different phospholipid classes showed remarkable diffences. The high content of n−3 polyunsaturated fatty acids in the principal phospholipids, such as the plasmalogens, and taking into account the fatty acids possible importance in human nutrition, indicates that the white muscle of tuna species may be a potentially important dietary item.     

An empirically validated simulation for understanding the relationship between process conformance and technology skills

Software development is a fast-paced environment where developers need constant update to ever-changing technologies. Furthermore, process improvement initiatives have been proven useful in increasing the productivity of a software organization. As such, these organizations need to decide where to invest their training budget. As a result, training in technological update to their workforce or training in process conformance with its productive processes become conflicting alternatives. This paper presents a system dynamics simulation of a software factory product line. The objective of this simulation is to understand the changes in behavior when selecting either one of the above-training alternatives. The system dynamics model was validated with an expert panel, and the simulation results have been empirically validated—using statistical process control—against the performance baseline of a real software development organization. With the simulation under statistical control and performing like the baseline, the independent variables representing process conformance (process training) and technology skills (skills training) were modified to study their impact on product defects and process stability. Our results show that while both variables have positive impact on defects and process stability, investment in process training results in a process with less variation and with fewer defects.     

Biochemical,functional, and histochemical effects of essential fatty acid deficiency in rat kidney

The present study was designed to examine the effects of EFA deficiency (EFAD) on biochemical, functional, and structural aspects of the kidney in growing and adult rats fed a normal or EFAD diet for 9 wk after weaning. Food and fluid intake (FI), urine volume, and Na⁺ and K⁺ excretions were measured weekly from weeks 4 to 8 by placing the rats in individual metabolic cages for 24 h. At week 9, Li⁺ and a 5% water load, respectively, were administered at 14 and 1.5 h prior to glomerular and proximal tubular function studies, as assessed by 3-h creatinine (C_Cr) and Li⁺ (C_Li+) clearances. Hematocrit and urine volume; serum and urine [Cr], [Li⁺], [Na⁺], and [K⁺]; and renal FA distribution were also measured. Data [corrected to 100 g/body weight (bw) and presented as means ±SEM] were significant, at P<-0.05. Despite a similar ingestion of solids from weeks 4 to 7 (weeks 7 to 10 of life), the rats on the EFAD diet showed a decreased body weight from week 5. From weeks 4 to 8, Fl and urine volume were similar for both groups, but the Fl increased at week 6 in the EFAD group; 24-h Na⁺ and K⁺ excretions were similar at all weeks, except for an increase in the EFAD group for both ions at week 7. In the EFAD group, C_Cr and C_Li+ decreased by 27 and 56.3%, respectively (385.7±33.4 vs. 280±21.1, and 21.0±2.1 vs. 9.2±1.1 μL/min/100 g; n=9 vs. 10), the latter result suggesting increased proximal reabsorption. The 3-h Na⁺ and K⁺ excretions were similar, but the Li⁺ decreased (0.78±0.06×10⁻² vs. 0.32±0.03×10⁻² μeq/min/100 g) in the EFAD group, giving additional support to the suggestion. Renal structure was normal and similar for both groups, but the EFAD group showed a more prominent proximal tubule brush border, together with heavier periodic acid-Schiff staining in all specimens from weeks 5 to 9. In the EFAD group, FA of the n−9 and n−7 series were higher, but most of the n−6 series were lower as a percentage of total lipids in the medulla and cortex. Medullary levels of 20∶4n−6 were maintained, 22∶4n−6 declined twice, arachidonic acid was maintained, and 20∶5n−3 was lower. The EFAD diet affected glomerular function, proximal tubular structure and function, and FA distribution in the rat kidney.