GPU Concurrency: Weak Behaviours and Programming Assumptions

Concurrency is pervasive and perplexing, particularly on graphics processing units (GPUs). Current specifications of languages and hardware are inconclusive; thus programmers often rely on folklore assumptions when writing software. To remedy this state of affairs, we conducted a large empirical study of the concurrent behaviour of deployed GPUs. Armed with litmus tests (i.e. short concurrent programs), we questioned the assumptions in programming guides and vendor documentation about the guarantees provided by hardware. We developed a tool to generate thousands of litmus tests and run them under stressful workloads. We observed a litany of previously elusive weak behaviours, and exposed folklore beliefs about GPU programming---often supported by official tutorials---as false. As a way forward, we propose a model of Nvidia GPU hardware, which correctly models every behaviour witnessed in our experiments. The model is a variant of SPARC Relaxed Memory Order (RMO), structured following the GPU concurrency hierarchy

Storage and Aging Effects on Spherical Resorcinol-Formaldehyde Resin Ion Exchange Performance

Bechtel National, Inc. (BNI) is evaluating the alternate Cs ion exchanger, spherical resorcinol-formaldehyde (RF), for use in the River Protection Project-Waste Treatment Plant (RPP-WTP).( ) Previous test activities with spherical RF indicate that it has adequate capacity, selectivity, and kinetics to perform in the plant according to the flowsheet needs. It appears to have better elution and hydraulic properties than the existing alternatives: ground-gel RF and SuperLig® 644 (SL 644).( ) To date, the spherical RF performance testing has been conducted on freshly manufactured resin (within ~2 months of manufacture). The ion exchange resins will be manufactured and shipped to the WTP up to 1 year before being used in the plant. Changes in the resin properties during storage could reduce the capacity of the resin to remove Cs from low-activity waste solutions. Active sites on organic SL-644 resin have been shown to degrade during storage (Arm et al. 2004). Additional testing was needed to study the effects of storage conditions and aging on spherical RF ion exchange performance. Variables that could have a significant impact on ion exchange resins during storage include storage temperature, medium, and time. Battelle—Pacific Northwest Division (PNWD) was contracted to test the effects of various storage conditions on spherical RF resin. Data obtained from the testing will be used by the WTP operations to provide direction for suitable storage conditions and manage the spherical RF resin stock. Storage test conditions included wet and dry resin configurations under nitrogen at three temperatures. Work was initially conducted under contract number 24590-101-TSA-W000-00004 satisfying the needs defined in Appendix C of the Research and Technology Plan( ) TSS A-219 to evaluate the impact of storage conditions on RF resin performance. In February 2007, the contract mechanism was switched to Pacific Northwest National Laboratory (PNNL) Operating Contract DE-AC05-76RL01830

Results of Large-Scale Testing on Effects of Anti-Foam Agent on Gas Retention and Release

The U.S. Department of Energy (DOE) Office of River Protection’s Waste Treatment Plant (WTP) will process and treat radioactive waste that is stored in tanks at the Hanford Site. The waste treatment process in the pretreatment facility will mix both Newtonian and non-Newtonian slurries in large process tanks. Process vessels mixing non-Newtonian slurries will use pulse jet mixers (PJMs), air sparging, and recirculation pumps. An anti-foam agent (AFA) will be added to the process streams to prevent surface foaming, but may also increase gas holdup and retention within the slurry. The work described in this report addresses gas retention and release in simulants with AFA through testing and analytical studies. Gas holdup and release tests were conducted in a 1/4-scale replica of the lag storage vessel operated in the Pacific Northwest National Laboratory (PNNL) Applied Process Engineering Laboratory using a kaolin/bentonite clay and AZ-101 HLW chemical simulant with non-Newtonian rheological properties representative of actual waste slurries. Additional tests were performed in a small-scale mixing vessel in the PNNL Physical Sciences Building using liquids and slurries representing major components of typical WTP waste streams. Analytical studies were directed at discovering how the effect of AFA might depend on gas composition and predicting the effect of AFA on gas retention and release in the full-scale plant, including the effects of mass transfer to the sparge air. The work at PNNL was part of a larger program that included tests conducted at Savannah River National Laboratory (SRNL) that is being reported separately. SRNL conducted gas holdup tests in a small-scale mixing vessel using the AZ-101 high-level waste (HLW) chemical simulant to investigate the effects of different AFAs, their components, and of adding noble metals. Full-scale, single-sparger mass transfer tests were also conducted at SRNL in water and AZ-101 HLW simulant to provide data for PNNL’s WTP gas retention and release modeling

Tyrosine kinase chromosomal translocations mediate distinct and overlapping gene regulation events

<p>Abstract</p> <p>Background</p> <p>Leukemia is a heterogeneous disease commonly associated with recurrent chromosomal translocations that involve tyrosine kinases including BCR-ABL, TEL-PDGFRB and TEL-JAK2. Most studies on the activated tyrosine kinases have focused on proximal signaling events, but little is known about gene transcription regulated by these fusions.</p> <p>Methods</p> <p>Oligonucleotide microarray was performed to compare mRNA changes attributable to BCR-ABL, TEL-PDGFRB and TEL-JAK2 after 1 week of activation of each fusion in Ba/F3 cell lines. Imatinib was used to control the activation of BCR-ABL and TEL-PDGFRB, and TEL-JAK2-mediated gene expression was examined 1 week after Ba/F3-TEL-JAK2 cells were switched to factor-independent conditions.</p> <p>Results</p> <p>Microarray analysis revealed between 800 to 2000 genes induced or suppressed by two-fold or greater by each tyrosine kinase, with a subset of these genes commonly induced or suppressed among the three fusions. Validation by Quantitative PCR confirmed that eight genes (Dok2, Mrvi1, Isg20, Id1, gp49b, Cxcl10, Scinderin, and collagen Vα1(Col5a1)) displayed an overlapping regulation among the three tested fusion proteins. Stat1 and Gbp1 were induced uniquely by TEL-PDGFRB.</p> <p>Conclusions</p> <p>Our results suggest that BCR-ABL, TEL-PDGFRB and TEL-JAK2 regulate distinct and overlapping gene transcription profiles. Many of the genes identified are known to be involved in processes associated with leukemogenesis, including cell migration, proliferation and differentiation. This study offers the basis for further work that could lead to an understanding of the specificity of diseases caused by these three chromosomal translocations.</p

Technical Basis of Scaling Relationships for the Pretreatment Engineering Platform

Pacific Northwest National Laboratory has been tasked by Bechtel National Inc. (BNI) on the River Protection Project-Waste Treatment Plant (RPP-WTP) project to perform research and development activities. The Pretreatment Engineering Platform (PEP) is being designed and constructed as part of a plan to respond to an issue raised by the WTP External Flowsheet Review Team (EFRT) entitled “Undemonstrated Leaching Processes” and numbered M12. The PEP replicates the WTP leaching process using prototypic equipment and control strategies. The approach for scaling PEP performance data to predict WTP performance is critical to the successful resolution of the EFRT issue. This report describes the recommended PEP scaling approach, PEP data interpretation and provides recommendations on test conduct and data requirements

Recent Improvements In Interface Management For Hanfords Waste Treatment And Immobilization Plant - 13263

The U.S. Department of Energy (DOE), Office of River Protection (ORP) is responsible for management and completion of the River Protection Project (RPP) mission, which comprises both the Hanford Site tank farms operations and the Waste Treatment and Immobilization Plant (WTP). The RPP mission is to store, retrieve and treat Hanford&#x27;s tank waste; store and dispose of treated wastes; and close the tank farm waste management areas and treatment facilities by 2047. The WTP is currently being designed and constructed by Bechtel National Inc. (BNI) for DOE-ORP. BNI relies on a number oftechnical services from other Hanford contractors for WTP&#x27;s construction and commissioning. These same services will be required of the future WTP operations contractor. The WTP interface management process has recently been improved through changes in organization and technical issue management documented in an Interface Management Plan. Ten of the thirteen active WTP Interface Control Documents (ICDs) have been revised in 2012 using the improved process with the remaining three in progress. The value of the process improvements is reflected by the ability to issue these documents on schedule

Correction: Molecular Subsets in the Gene Expression Signatures of Scleroderma Skin

Background: Scleroderma is a clinically heterogeneous disease with a complex phenotype. The disease is characterized by vascular dysfunction, tissue fibrosis, internal organ dysfunction, and immune dysfunction resulting in autoantibody production. Methodology and Findings: We analyzed the genome-wide patterns of gene expression with DNA microarrays in skin biopsies from distinct scleroderma subsets including 17 patients with systemic sclerosis (SSc) with diffuse scleroderma (dSSc), 7 patients with SSc with limited scleroderma (lSSc), 3 patients with morphea, and 6 healthy controls. 61 skin biopsies were analyzed in a total of 75 microarray hybridizations. Analysis by hierarchical clustering demonstrates nearly identical patterns of gene expression in 17 out of 22 of the forearm and back skin pairs of SSc patients. Using this property of the gene expression, we selected a set of ‘intrinsic’ genes and analyzed the inherent data-driven groupings. Distinct patterns of gene expression separate patients with dSSc from those with lSSc and both are easily distinguished from normal controls. Our data show three distinct patient groups among the patients with dSSc and two groups among patients with lSSc. Each group can be distinguished by unique gene expression signatures indicative of proliferating cells, immune infiltrates and a fibrotic program. The intrinsic groups are statistically significant (p , 0.001) and each has been mapped to clinical covariates of modified Rodnan skin score, interstitial lung disease, gastrointestinal involvement, digital ulcers, Raynaud’s phenomenon and disease duration. We report a 177-gene signature that is associated with severity of skin disease in dSSc. Conclusions and Significance: Genome-wide gene expression profiling of skin biopsies demonstrates that the heterogeneity in scleroderma can be measured quantitatively with DNA microarrays. The diversity in gene expression demonstrates multiple distinct gene expression programs in the skin of patients with scleroderma