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A transcriptome software comparison for the analyses of treatments expected to give subtle gene expression responses

Background: In this comparative study we evaluate the performance of four software tools: DNAstar-D (DESeq2), DNAstar-E (edgeR), CLC Genomics and Partek Flow for identification of differentially expressed genes (DEGs) using a transcriptome of E. coli. The RNA-seq data are from the effect of below-background radiation 5.5 nGy total dose (0.2nGy/hr) on E. coli grown shielded from natural radiation 655 m below ground in a pre-World War II steel vault. The gene expression response to three supplemented sources of radiation designed to mimic natural background, 1952 – 5720 nGy in total dose (71–208 nGy/hr), are compared to this “radiation-deprived” treatment. In addition, RNA-seq data of Caenorhabditis elegans nematode from similar radiation treatments was analyzed by three of the software packages. Results: In E. coli, the four software programs identified one of the supplementary sources of radiation (KCl) to evoke about 5 times more transcribed genes than the minus-radiation treatment (69–114 differentially expressed genes, DEGs), and so the rest of the analyses used this KCl vs “Minus” comparison. After imposing a 30-read minimum cutoff, one of the DNAStar options shared two of the three steps (mapping, normalization, and statistic) with Partek Flow (they both used median of ratios to normalize and the DESeq2 statistical package), and these two programs identified the highest number of DEGs in common with each other (53). In contrast, when the programs used different approaches in each of the three steps, between 31 and 40 DEGs were found in common. Regarding the extent of expression differences, three of the four programs gave high fold-change results (15–178 fold), but one (DNAstar’s DESeq2) resulted in more conservative fold-changes (1.5–3.5). In a parallel study comparing three qPCR commercial validation software programs, these programs also gave variable results as to which genes were significantly regulated. Similarly, the C. elegans analysis showed exaggerated fold-changes in CLC and DNAstar’s edgeR while DNAstar-D was more conservative. Conclusions: Regarding the extent of expression (fold-change), and considering the subtlety of the very low level radiation treatments, in E. coli three of the four programs gave what we consider exaggerated fold-change results (15 – 178 fold), but one (DNAstar’s DESeq2) gave more realistic fold-changes (1.5–3.5). When RT-qPCR validation comparisons to transcriptome results were carried out, they supported the more conservative DNAstar-D’s expression results. When another model organism’s (nematode) response to these radiation differences was similarly analyzed, DNAstar-D also resulted in the most conservative expression patterns. Therefore, we would propose DESeq2 (“DNAstar-D”) as an appropriate software tool for differential gene expression studies for treatments expected to give subtle transcriptome responses.

59 BASIC BIOLOGICAL SCIENCES↗

TH-EF-BRA-11: Feasibility of Super-Resolution Time-Resolved 4DMRI for Multi-Breath Volumetric Motion Simulation in Radiotherapy Planning

Purpose: To develop a novel super-resolution time-resolved 4DMRI technique to evaluate multi-breath, irregular and complex organ motion without respiratory surrogate for radiotherapy planning. Methods: The super-resolution time-resolved (TR) 4DMRI approach combines a series of low-resolution 3D cine MRI images acquired during free breathing (FB) with a high-resolution breath-hold (BH) 3DMRI via deformable image registration (DIR). Five volunteers participated in the study under an IRB-approved protocol. The 3D cine images with voxel size of 5×5×5 mm{sup 3} at two volumes per second (2Hz) were acquired coronally using a T1 fast field echo sequence, half-scan (0.8) acceleration, and SENSE (3) parallel imaging. Phase-encoding was set in the lateral direction to minimize motion artifacts. The BH image with voxel size of 2×2×2 mm{sup 3} was acquired using the same sequence within 10 seconds. A demons-based DIR program was employed to produce super-resolution 2Hz 4DMRI. Registration quality was visually assessed using difference images between TR 4DMRI and 3D cine and quantitatively assessed using average voxel correlation. The fidelity of the 3D cine images was assessed using a gel phantom and a 1D motion platform by comparing mobile and static images. Results: Owing to voxel intensity similarity using the same MRI scanning sequence, accurate DIR between FB and BH images is achieved. The voxel correlations between 3D cine and TR 4DMRI are greater than 0.92 in all cases and the difference images illustrate minimal residual error with little systematic patterns. The 3D cine images of the mobile gel phantom preserve object geometry with minimal scanning artifacts. Conclusion: The super-resolution time-resolved 4DMRI technique has been achieved via DIR, providing a potential solution for multi-breath motion assessment. Accurate DIR mapping has been achieved to map high-resolution BH images to low-resolution FB images, producing 2Hz volumetric high-resolution 4DMRI. Further validation and improvement are still required prior to clinical applications. This study is in part supported by the NIH (U54CA137788/U54CA132378).

60 APPLIED LIFE SCIENCES↗

Position Papers for the ASCR Workshop on the Management and Storage of Scientific Data

The purpose of this workshop is to identify priority research directions in the area of data management for high-performance and scientific computing above and beyond HPC’s traditional "the parallel file system is the data-management system" model. Supporting the breadth of the DOE mission, including the explosion of AI uses and the growing needs of experimental and observational science, motivates revisiting our assumptions about data management. There are many facets of this topic to explore including: (1) Interfaces for accessing data that resides on traditional persistent storage as well as memory devices; (2) Storage-system architecture design that supports scientific workflows on varied hierarchical storage and networking devices; (3) Devising metadata management infrastructure to support FAIR principles (Findability, Accessibility, Interoperability, and Reusability); (4) Capturing provenance information about scientific data; (5) Utilizing AI to learn I/O patterns of emerging workloads for efficient data management; (6) Providing data management support for AI and complex workflows; and (7) Understanding the overlap between traditional storage systems and I/O (SSIO) efforts and data management. While the program committee has identified these topics as important areas for discussion, we welcome position papers from the community that propose additional topics of interest for discussion at the workshop. The workshop agenda will include breakout sessions for discussing these and selected topic areas to inform priority research directions for data management for high-performance and scientific computing.

97 MATHEMATICS AND COMPUTING↗

Report for the ASCR Workshop on the Management and Storage of Scientific Data

The purpose of this workshop is to identify priority research directions in the area of data management for high-performance and scientific computing above and beyond HPC’s traditional "the parallel file system is the data-management system" model. Supporting the breadth of the DOE mission, including the explosion of AI uses and the growing needs of experimental and observational science, motivates revisiting our assumptions about data management. There are many facets of this topic to explore including: (1) Interfaces for accessing data that resides on traditional persistent storage as well as memory devices; (2) Storage-system architecture design that supports scientific workflows on varied hierarchical storage and networking devices; (3) Devising metadata management infrastructure to support FAIR principles (Findability, Accessibility, Interoperability, and Reusability); (4) Capturing provenance information about scientific data; (5) Utilizing AI to learn I/O patterns of emerging workloads for efficient data management; (6) Providing data management support for AI and complex workflows; and (7) Understanding the overlap between traditional storage systems and I/O (SSIO) efforts and data management. While the program committee has identified these topics as important areas for discussion, we welcome position papers from the community that propose additional topics of interest for discussion at the workshop. The workshop agenda will include breakout sessions for discussing these and selected topic areas to inform priority research directions for data management for high-performance and scientific computing.

97 MATHEMATICS AND COMPUTING↗

Endochondral bone formation in embryonic mouse pre-metatarsals

Long term exposure to a reduced gravitational environment has a deleterious effect on bone. The developmental events which occur prior to initial bone deposition will provide insight into the regulation of mature bone physiology. We have characterized a system in which the events preceding bone formation take place in an isolated in vitro organ culture environment. We show that cultured pre-metatarsal tissue parallels development of pre-metatarsal tissue in the embryo. Both undergo mesenchyme differentiation and morphogenesis to form a cartilage rod, which resembles the future bone, followed by terminal chondrocyte differentiation in a definite morphogenetic pattern. These sequential steps occur prior to osteoblast maturation and bone matrix deposition in the developing organism. Alkaline phosphatase (ALP) activity is a distinctive enzymatic marker for mineralizing tissues. We have measured this activity throughout pre-metatarsal development and show (a) where in the tissue it is predominantly found, and (b) that this is indeed the mineralizing isoform of the enzyme.

NASA Discipline Number 93-10↗

Porting Gravitational Wave Signal Extraction to Parallel Virtual Machine (PVM)

Laser Interferometer Space Antenna (LISA) is a planned NASA-ESA mission to be launched around 2012. The Gravitational Wave detection is fundamentally the determination of frequency, source parameters, and waveform amplitude derived in a specific order from the interferometric time-series of the rotating LISA spacecrafts. The LISA Science Team has developed a Mock LISA Data Challenge intended to promote the testing of complicated nested search algorithms to detect the 100-1 millihertz frequency signals at amplitudes of 10E-21. However, it has become clear that, sequential search of the parameters is very time consuming and ultra-sensitive; hence, a new strategy has been developed. Parallelization of existing sequential search algorithms of Gravitational Wave signal identification consists of decomposing sequential search loops, beginning with outermost loops and working inward. In this process, the main challenge is to detect interdependencies among loops and partitioning the loops so as to preserve concurrency. Existing parallel programs are based upon either shared memory or distributed memory paradigms. In PVM, master and node programs are used to execute parallelization and process spawning. The PVM can handle process management and process addressing schemes using a virtual machine configuration. The task scheduling and the messaging and signaling can be implemented efficiently for the LISA Gravitational Wave search process using a master and 6 nodes. This approach is accomplished using a server that is available at NASA Ames Research Center, and has been dedicated to the LISA Data Challenge Competition. Historically, gravitational wave and source identification parameters have taken around 7 days in this dedicated single thread Linux based server. Using PVM approach, the parameter extraction problem can be reduced to within a day. The low frequency computation and a proxy signal-to-noise ratio are calculated in separate nodes that are controlled by the master using message and vector of data passing. The message passing among nodes follows a pattern of synchronous and asynchronous send-and-receive protocols. The communication model and the message buffers are allocated dynamically to address rapid search of gravitational wave source information in the Mock LISA data sets.

Thirumalainambi, Rajkumar↗

MTUQ: a framework for estimating moment tensors, point forces, and their uncertainties

SUMMARY We introduce MTUQ, an open-source Python package for seismic source estimation and uncertainty quantification, emphasizing flexibility and operational scalability. MTUQ provides MPI-parallelized grid search and global optimization capabilities, compatibility with 1-D and 3-D Green’s function database formats, customizable data processing, C-accelerated waveform and first-motion polarity misfit functions, and utilities for plotting seismic waveforms and visualizing misfit and likelihood surfaces. Applicability to a range of full- and constrained-moment tensor, point force, and centroid inversion problems is possible via a documented application programming interface, accompanied by example scripts and integration tests. We demonstrate the software using three different types of seismic events: (1) a 2009 intraslab earthquake near Anchorage, Alaska; (2) an episode of the 2021 Barry Arm landslide in Alaska; and (3) the 2017 Democratic People’s Republic of Korea underground nuclear test. With these events, we illustrate the well-known complementary character of body waves, surface waves, and polarities for constraining source parameters. We also convey the distinct misfit patterns that arise from each individual data type, the importance of uncertainty quantification for detecting multimodal or otherwise poorly constrained solutions, and the software’s flexible, modular design.

58 GEOSCIENCES↗

Status of DUNE Offline Computing

We summarize the status of Deep Underground Neutrino Experiment (DUNE) Offline Software and Computing program. We describe plans for the computing infrastructure needed to acquire, catalog, reconstruct, simulate and analyze the data from the DUNE experiment and its prototypes in pursuit of the experiment's physics goals of precision measurements of neutrino oscillation parameters, detection of astrophysical neutrinos, measurement of neutrino interaction properties and searches for physics beyond the Standard Model. In contrast to traditional HEP computational problems, DUNE's Liquid Argon Time Projection Chamber data consist of simple but very large (many GB) data objects which share many characteristics with astrophysical images. We have successfully reconstructed and simulated data from 4% prototype detector runs at CERN. The data volume from the full DUNE detector, when it starts commissioning late in this decade will present memory management challenges in conventional processing but significant opportunities to use advances in machine learning and pattern recognition as a frontier user of High Performance Computing facilities capable of massively parallel processing. Our goal is to develop infrastructure resources that are flexible and accessible enough to support creative software solutions as HEP computing evolves.

43 PARTICLE ACCELERATORS↗

Modelling the high-latitude ionosphere

Results of an ionospheric model program are presented which demonstrate the extreme variability of the steady state, daytime, ionospheric F region electron density and ion composition due to both neutral atmospheric changes with solar cycle, season and magnetic activity, and to the effects of ionospheric drifts caused by perpendicular electric fields. Consideration is given to the time history of the ionospheric plasma as it undergoes convective motion due to the combined effects of corotation forces and electromagnetic forces which results from the mapping of the magnetospheric cross tail electric field to the rotating ionosphere. A simple model of the convection pattern is described. The model calculates the net effect of the tendency for the plasma to corotate about the geographic pole and the E sub Bar times B sub Bar velocity induced by a perpendicular electric field mapped to a circle centered about a point 5 deg antisunward of the geomagnetic pole and oriented such that the equipotentials are parallel to the noon midnight meridian. This convection pattern shows the generally accepted features of high latitude convection, but because of the offset between the geographic and geomagnetic poles a marked universal time dependence in these features is predicted.

Raitt, W. J.↗

Reusable and Extensible High Level Data Distributions

This paper presents a reusable design of a data distribution framework for data parallel high performance applications. We are implementing the design in the context of the Chapel high productivity programming language. Distributions in Chapel are a means to express locality in systems composed of large numbers of processor and memory components connected by a network. Since distributions have a great effect on,the performance of applications, it is important that the distribution strategy can be chosen by a user. At the same time, high productivity concerns require that the user is shielded from error-prone, tedious details such as communication and synchronization. We propose an approach to distributions that enables the user to refine a language-provided distribution type and adjust it to optimize the performance of the application. Additionally, we conceal from the user low-level communication and synchronization details to increase productivity. To emphasize the generality of our distribution machinery, we present its abstract design in the form of a design pattern, which is independent of a concrete implementation. To illustrate the applicability of our distribution framework design, we outline the implementation of data distributions in terms of the Chapel language.

patterns↗

Evaluating the Performance Envelope of Axial Flow HEPA Filter Designs - 17466

Nuclear grade high efficiency particulate air (HEPA) filters are routinely employed as the final control element in confinement ventilation systems. Approximately 6000 nuclear grade HEPA filters are purchased each year for use in the Department of Energy National Nuclear Security Administration (DOE/NNSA) complex. The traditional HEPA filter utilizes a pleated filter medium of fibrous glass that has been produced in a manner analogous to manufacturing paper. Containment ventilation systems are designed to condition the air-stream (temperature, relative humidity, moisture, particle size distribution of aerosols, and aerosol concentration) to levels and conditions that fibrous glass HEPA filters can handle. Axial Flow filters can be purchased with physical separators or embossed medium to maintain proper pleat geometry. Separator-less designs use media embossed with a corrugation pattern to retain pleat geometry. At least some versions of the separator-less filter packs have demonstrated unexpected and rapid failure under slightly elevated temperature and humidity conditions. The effects of age on HEPA filter performance have been a concern for at least two decades. A combination of physical evaluation of aged filter media and a review of filter failure records resulted in Appendix C of the Nuclear Air Cleaning Handbook (NACH), Determination of HEPA Filter Life. Mississippi State University is conducting studies to more clearly identify the operating envelope of separator and separator-less designs of ASME AG-1 Section FC axial flow HEPA filters under a set of generic design basis conditions. A parallel study is also being conducted to evaluate the effects of age on fibrous glass HEPA filters. Activities described in this paper have been conducted under Institute for Clean Energy Technology (ICET's) NQA-1 nuclear quality assurance program approved by DOE-EM. Testing meets the requirements of EM Quality Assurance Program (QAP) EM-QA-001, Rev. 1, June 11, 2012 that includes the applicable requirements of NQA-1-2008/2009a and DOE Order 414.1D. (authors)

07 ISOTOPE AND RADIATION SOURCES↗

Dividing the Concentrator Target From the Genesis Mission

The Genesis spacecraft, launched in 2001, traveled to a Lagrangian point between the Earth and Sun to collect particles from the solar wind and return them to Earth. However, during the return of the spacecraft in 2004, the parachute failed to open during descent, and the Genesis spacecraft crashed into the Utah desert. Many of the solar wind collectors were broken into smaller pieces, and the field team rapidly collected the capsule and collector pieces for later assessment. On each of the next few days, the team discovered that various collectors had survived intact, including three of four concentrator targets. Within a month, the team had imaged more than 10,000 fragments and packed them for transport to the Astromaterials Acquisition and Curation Office within the ARES Directorate at JSC. Currently, the Genesis samples are curated along with the other extraterrestrial sample collections within ARES. Although they were broken and dirty, the Genesis solar wind collectors still offered the science community the opportunity to better understand our Sun and the solar system as a whole. One of the more highly prized concentrator collectors survived the crash almost completely intact. The Genesis Concentrator was designed to concentrate the solar wind by a factor of at least 20 so that solar oxygen and nitrogen isotopes could be measured. One of these materials was the Diamond-on-Silicon (DoS) concentrator target. Unfortunately, the DoS concentrator broke on impact. Nevertheless, the scientific value of the DoS concentrator target was high. The Genesis Allocation Committee received a request for approximately 1 cm(sup 2) of the DoS specimen taken near the focal point of the concentrator for the analysis of solar wind nitrogen isotopes. The largest fragment, Genesis sample 60000, was designated for this allocation and needed to be precisely cut. The requirement was to subdivide the designated sample in a manner that prevented contamination of the sample and minimized the risk of losing or breaking the precious requested sample fragment. The Genesis curator determined that the use of laser scribing techniques to "cut" a precise line and subsequently cleave the sample (in a controlled break of the sample along that line) was the best method for accomplishing the sample subdivision. However, there were risks, including excess heating of the sample, that could cause some of the implanted solar wind to be lost via thermal diffusion. Accidentally breaking the sample during the handling and cleaving process was an additional risk. Early in fiscal year 2013, to address this delicate, complicated task, the ARES Directorate assembled its top scientists to develop a cutting plan that would ensure success when applied to the actual concentrator target wafer; i.e., to produce an approximately 1 cm(sup 2) piece from the requested area of the wafer. The team, subsequently referred to as the JSC Genesis Tiger Team, spent months researching and testing parameters and techniques related to scribing, cleaving, transporting, handling, and holding (i.e., mounting) the specimen. The investigation required considerable "thinking outside the box," and many, many trials using nonflight wafer analogs. After all preliminary testing, the following method was adopted as the final cutting plan. It was used in two final end-to-end practice runs before being used on the actual flight target wafer. The wafer was oriented on the laser cutting stage with the 100 and 010 directions of the wafer parallel to the corresponding X and Y directions of the cutting stage. The laser was programed to scribe 31 lines of the appropriate length along the Y stage direction. The programed scribe lines were separated by 5 micron in the X direction. The laser parameters were set as follows: (1) The laser power was 0.5 watts; (2) each line consisted of 50 passes, with the Z position being advanced 5 micron per pass; and (3) 30 s would elapse before the next line was scribed to allow for wafer cool down from any possible heating via the laser. The ablated material that "stuck" in the "scribe-cut" was removed from the "cut" using an ultrasonic micro-tool. After all the ablated silicon was removed from the wafer, the wafer was repositioned in exactly the same orientation on the laser stage. The laser was focused using the bottom of the wafer channel, and the 31-line scribing pattern described above was reprogrammed using the Z position of the groove bottom as the starting Z value instead of the top wafer surface, which was used previously. Upon completion of the second set of scribes, the ultrasonic micro-tool was again used to clean out the cut. The wafer was remounted on the stage in exactly the same orientation as before. The laser was again focused on the bottom of the groove. This time, however, the laser was.programed to scribe only one line down the exact center of the channel. The final scribe line consisted of 100 passes with a Z advance of 5 micron per pass and with the laser power set at 0.5 watts. As mentioned above, the final cutting plan was practiced in two end-to-end trials using non-flight, triangular-shaped silicon wafers similar in size and orientation to the actual DOS 60000 target sample. The actual scribing of the triangular-shaped wafers required scribing two lines and cleaving (i.e. scribe-cleave, then scribe-cleave) to obtain the piece requested for allocation. Early in December 2012, after many months of experiments and practicing and perfecting the techniques and procedures, the team successfully subdivided the Genesis DoS 60000 target sample, one of the most scientifically important samples from the Genesis mission (figure 2). On December 17, 2012, the allocated piece of concentrator target sample was delivered to the requesting principal investigator.The cutting plan developed for the subdivision of this sample will be used as the model for subdividing future requested Genesis flight wafers (appropriately modified for different wafer types).

Lauer, H. V., Jr.↗

Hydration Mechanisms in Nanoparticle Interaction and Surface Energetics

Work on the project advanced molecular level understanding, prediction and control of nanoscale hydration in salt solutions under electric stimuli or ionic patterning. Permeation of nanoporous electrodes at preset voltage underlies the function of ultracapacitors. Transitory regulation of wetting in nanoporous media by electric field spans an array of applications in materials, energy storage, and separation sciences. The physically related modulation of nanoparticle solubility by surface charges can significantly extend the range of the nanomaterial applications, improve processing techniques, and potentially alleviate environmental concerns. Pore/solution equilibria, and activated kinetics of liquid gating by nanoconfined electrolytes are challenging problems at the forefront of experimental and theoretical research. Addressing these problems from a molecular perspective required the development of state-of-the-art simulation algorithms in statistical mechanics to capture complex processes in open systems under electric control. Parallel studies of wetting and dispersibility of polar and ionizing particles aim to uncover predictive relations between electrowetting, chemical functionalization, and geometry of nanomaterial particles. By nonequilibrium dynamic modeling, we elucidated electrolyte flow in nanochanels and associated electrokinetic energy conversion. Research on the program provided training opportunities for the next generation of scientists in computational chemistry. Insights, and methods from the project implicate broad segment of researchers in energy and nanosciences, materials and surface chemistry.

74 ATOMIC AND MOLECULAR PHYSICS↗

Automated rendezvous and docking with video imagery

For rendezvous and docking, assessing and tracking relative orientation is necessary within a minimum approach distance. Special target light patterns have previously been considered for use with video sensors for ease of determining relative orientation. A generalization of those approaches is addressed. At certain ranges, the entire structure of the target vehicle constitutes an acceptable target; at closer ranges, substructures will suffice. Acting on the same principle as the human intelligence, these structures can be compared with a memory model to assess the relative orientation and range. Models for comparison are constructed from a CAD facet model and current imagery. This approach requires fast image handling, projection, and comparison techniques which rely on rapidly developing parallel processing technology. Relative orientation and range assessment consists of successful comparison of the perceived target aspect with a known aspect. Generating a known projection from a model within required times, say subsecond times, is only now approaching feasibility. With this capability, rates of comparison used by the human brain can be approached and arbitrary known structures can be compared in reasonable times. Future space programs will have access to powerful computation devices which far exceed even this capability. For example, the possibility will exist to assess unknown structures and then control rendezvous and docking, all at very fast rates. The first step which has the current utility, namely applying this to known structures, is taken.

Rodgers, Mike↗

Automatic Differentiation for Adjoint Stencil Loops

Stencil loops are a common motif in computations including convolutional neural networks, structured-mesh solvers for partial differential equations, and image processing. Stencil loops are easy to parallelise, and their fast execution is aided by compilers, libraries, and domain-specific languages. Reverse-mode automatic differentiation, also known as algorithmic differentiation, autodiff, adjoint differentiation, or back-propagation, is sometimes used to obtain gradients of programs that contain stencil loops. Unfortunately, conventional automatic differentiation results in a memory access pattern that is not stencil-like and not easily parallelisable. In this paper we present a novel combination of automatic differentiation and loop transformations that preserves the structure and memory access pattern of stencil loops, while computing fully consistent derivatives. The generated loops can be parallelised and optimised for performance in the same way and using the same tools as the original computation. We have implemented this new technique in the Python tool PerforAD, which we release with this paper along with test cases derived from seismic imaging and computational fluid dynamics applications.

Automatic Differentiation↗

Data Locality Enhancement of Dynamic Simulations for Exascale Computing (Final Report)

The development of modern processors exhibits two trends that complicate the optimizations of modern software. The first is the increasing sensitivity of processors' throughput to irregularities in computation. With more processors produced through a massive integration of simple cores, future systems will increasingly favor regular data-level parallel computations, but deviate from the needs of applications with complex patterns. Some evidences are already shown on Graphic Processing Units (GPU): Irregular data accesses (e.g., indirect references A[D[i]]) and conditional branches are limiting many GPU applications' performance at a level an order of magnitude lower than the peak of GPU. The second hardware trend is the growing gap between memory bandwidth and the aggregate speed—that is, the sum of all cores' computing power—of a Chip Multiprocessor (CMP). Despite the capped growth of the peak CPU speed, the aggregate speed of a CMP keeps increasing as more cores get into a single chip. It is expected that by 2018, node concurrency in an exascale system will increase by hundreds of times, whereas, memory bandwidth will expand by only 10 to 20 times. Consequently, data movement and storage is expected to consume more than 70% of the total system power. Bridging this gap is difficult; the complexities of modern CMP memory hierarchy make it even harder: Data cache becomes shared among computing units, and the sharing is often non-uniform—whether two computing units share a cache depends on their proximity and the level of the cache. On the recent IBM Power7 architecture, for instance, four hardware contexts (or SMT threads) in a core share the entire memory hierarchy, all cores in one chip share an on-chip L3 cache, and cores across chips share L3 and main memory through off-chip connections. These two trends complicate the translation of computing power into performance, especially for a program with either intensive data accesses or complex patterns in data accesses or control flow paths. Unfortunately, both attributes present and will persist in a class of important applications. For instance, many scientific simulations deal with a large volume of data. And meanwhile, as most real-world processes are non-uniform and evolving (e.g., the evolution of a galaxy or the process of a drug injection), both the computations and data accesses of these programs tend to be irregular and dynamically changing. Currently, the lack of support to these applications on modern CMP severely limits their performance. On GPU, as our recent study shows and other studies echo, performance enhancement of a factor of integers is possible when memory accesses or control flows are streamlined for a set of GPU applications. On multicore CPU, our studies show that traditional locality enhancement, for being oblivious to the new features of multicore memory hierarchy, may even cause large slowdown to data-intensive dynamic applications. The severity of the issues is expected to worsen as the two hardware trends continue. Some recent studies try to match software with the trends, but in a limited scope or manner. For irregularities on GPU, most studies focus on irregularities analyzable through static analysis (e.g., data accesses in regular loops). Dynamic irregularities are harder to address because the needed analysis and transformations typically have to happen at run time. Some other research resorts to hardware extensions, an actual adoption of which is unclear for the entailed space cost and complexity. For data locality, recent years have seen some exploitations of the new memory hierarchy on multicore for performance, but most of them are on process or thread scheduling, rather than program transformations. Our recent study reveals that program-level transformations may magnify the scheduling benefits by a factor of seven, concluding that program-level transformation should play a central role for data locality enhancement on modern CMP. But research in this direction has been sparse, and most have focused on data layout or cache performance modeling, rather than program transformations to match with the new memory hierarchy features. Overall, it is still an open question how to bridge the gap between dynamic computations and the two prominent properties of modern processors. The goal of this project is to develop a set of techniques and software tools to enhance the matching between memory accesses in dynamic simulations and the prominent features of modern and future CMP, alleviating the memory performance issues for petascale and exascale computing. This report summarizes the discoveries and products produced throughout this project. It includes free launch, a new software approach to overcoming the shortcomings of both methods; coherence-free multiview, an approach that allows multiple views of a single data object to co-exist on GPU memory during a GPU kernel execution; algorithmic optimizations to data analytics problems, especially those that involve lots of distance calculations. Supporting dynamic parallelism is important for GPU to benefit a broad range of applications. There are currently two fundamental ways for programs to exploit dynamic parallelism on GPU: a software-based approach with software-managed worklists, and a hardware-based approach through dynamic subkernel launches. Neither is satisfactory. The former is complicated to program and is often subject to some load imbalance; the latter suffers large runtime overhead. In this work, we propose free launch, a new software approach to overcoming the shortcomings of both methods. It allows programmers to use subkernel launches to express dynamic parallelism. It employs a novel compiler-based code transformation named subkernel launch removal to replace the subkernel launches with the reuse of parent threads. Coupled with an adaptive task assignment mechanism, the transformation reassigns the tasks in the subkernels to the parent threads with a good load balance. The technique requires no hardware extensions, immediately deployable on existing GPUs. It keeps the programming convenience of the subkernel launch-based approach while avoiding its large runtime overhead. Meanwhile, its superior load balancing makes it outperform manual worklist-based techniques by 3X on average. The work was published at the 48th Annual IEEE/ACM International Symposium on Microarchitecture (Micro'2015). A Graphic Processing Unit (GPU) system is typically equipped with many types of memory (e.g., global, constant, texture, shared, cache). Data placement determines what data are placed on which type of memory, essential for GPU memory performance. Prior optimizations of data placement always require a single view of a data object on memory, which limits the optimization effectiveness. In this work, we propose coherence-free multiview, an approach that allows multiple views of a single data object to co-exist on GPU memory during a GPU kernel execution. We demonstrate that under certain conditions, the multiple views can remain incoherent while facilitating enhanced data placement. We present a theorem and some compiler support to ensure the soundness of the usage of coherence-free multiview. We further develop reference-discerning data placement, a new way to enhance data placements on GPU. It enables more flexible data placements by using coherence-free multiview to leverage the slack in coherence requirement of some GPU programs. Experiments on three types of GPU systems show that, with less than 200KB space cost, the new data placement technique can provide a 1.6X average (up to 4.27X) speedup. In addition, we have examined algorithmic optimizations to data analytics problems, especially those that involve lots of distance calculations. Computing distances among data points is an essential part of many important algorithms in data analytics, graph analysis, and other domains. In each of these domains, developers have spent significant manual effort optimizing algorithms, often through novel applications of the triangle equality, in order to minimize the number of distance computations in the algorithms. In this work, we observe that many algorithms across these domains can be generalized as an instance of a generic distance-related abstraction. Based on this abstraction, we derive seven principles for correctly applying the triangular inequality to optimize distance-related algorithms. Guided by the findings, we develop Triangular OPtimizer (TOP), the first software framework that is able to automatically produce optimized algorithms that either matches or outperforms manually designed algorithms for solving distance-related problems. TOP achieves up to 237x speedups and 2.5X on average. The work has been published at the 32nd International Conference on Machine Learning (ICML'15) and the 41st International Conference on Very Large Data Bases (VLDB'15).

42 ENGINEERING↗

GPU-Based Static Data-Flow Analysis for Fast and Scalable Android App Vetting

Many popular vetting tools for Android applications use static code analysis techniques. In particular, Interprocedural Data-Flow Graph (IDFG) construction is the computation at the core of Android static data-flow analysis and consumes most of the analysis time. Many analysis tools use a worklist algorithm, an iterative fixed-point approach, to construct the IDFG. In this paper, we observe that a straightforward GPU parallelization of the worklist algorithm leads to significant underutilization of the GPU resources. We identify four performance bottlenecks, namely, frequent dynamic memory allocations, high branch divergence, workload imbalance, and irregular memory access patterns. Accordingly, we propose GDroid, a GPU-based worklist algorithm implementation with multiple fine-grained optimizations tailored to common characteristics of Android applications. The optimizations considered are: matrix-based data structure, memory access-based node grouping, and worklist merging. Our experimental evaluation, performed on 1000 Android applications, shows that the proposed optimizations are beneficial to performance, and GDroid can achieve up to 128X speedups against a plain GPU implementation.

Android security↗

Pulmonary function in microgravity: KC-135 experience

We have commenced a KC-135 program that parallels and proceeds our Spacelab (SLS-1) pulmonary function experiment. Our first task was to elucidate the affect of normal gravitation on the shape of the maximum expiratory flow volume (MEFV) curve. Nine normal subjects performed multiple MEFV maneuvers at 0-G, 1-G, and approximately 1.7-G. The MEFV curves for each subject were filtered, aligned at RV, and ensemble-averaged to produce an average MEFV curve for each state, allowing differences to be studied. Most subjects showed a decrease in the FVC at 0-G, which we attribute to an increased intrathoracic blood volume. In most of these subjects, the mean lung volume associated with a given flow was lower at 0-G, over about the upper half of the vital capacity. This is similar to the change previously reported during heat out immersion and is consistent with the known affect of engorgement of the lung with blood, on elastic recoil. There were also consistent but highly individual changes in the position and magnitude of detailed features of the curve, the individual patterns being similar to those previously reported on transition from the erect to the supine position. This supports the idea that the location and motion of choke points which determine the detailed individual configuration of MEFV curves, can be significantly influenced by gravitational forces, presumably via the effects of change in longitudinal tension on local airway pressure-diameter behavior and wave speed. We have developed a flight mass spectrometer and have commenced a study of single breath gradients in gas exchange, inert gas washouts, and rebreathing cardiac outputs and lung volumes at 0-G, 1-G, and 1.7-G. Comparison of our results with those from SLS-1 should identify the opportunities and limitations of the KC-135 as an accessible microgravity resource.

Guy, Harold J.↗