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At least 847 records · Page 47

Continuous whole-system monitoring toward rapid understanding of production HPC applications and systems

A detailed understanding of HPC applications’ resource needs and their complex interactions with each other and HPC platform resources are critical to achieving scalability and performance. Such understanding has been difficult to achieve because typical application profiling tools do not capture the behaviors of codes under the potentially wide spectrum of actual production conditions and because typical monitoring tools do not capture system resource usage information with high enough fidelity to gain sufficient insight into application performance and demands. In this paper we present both system and application profiling results based on data obtained through synchronized system wide monitoring on a production HPC cluster at Sandia National Laboratories (SNL). We demonstrate analytic and visualization techniques that we are using to characterize application and system resource usage under production conditions for better understanding of application resource needs. Furthermore, our goals are to improve application performance (through understanding application-to-resource mapping and system throughput) and to ensure that future system capabilities match their intended workloads.

97 MATHEMATICS AND COMPUTING↗

A survey of software implementations used by application codes in the Exascale Computing Project

The US Department of Energy Office of Science and the National Nuclear Security Administration initiated the Exascale Computing Project (ECP) in 2016 to prepare mission-relevant applications and scientific software for the delivery of the exascale computers starting in 2023. The ECP currently supports 24 efforts directed at specific applications and six supporting co-design projects. These 24 application projects contain 62 application codes that are implemented in three high-level languages—C, C++, and Fortran—and use 22 combinations of graphical processing unit programming models. The most common implementation language is C++, which is used in 53 different application codes. The most common programming models across ECP applications are CUDA and Kokkos, which are employed in 15 and 14 applications, respectively. This article provides a survey of the programming languages and models used in the ECP applications codebase that will be used to achieve performance on the future exascale hardware platforms.

97 MATHEMATICS AND COMPUTING↗

Application health monitoring for extreme-scale resiliency using cooperative fault management

Resiliency is and will be a critical factor in determining scientific productivity on current and exascale supercomputers, and beyond. Applications oblivious to and incapable of handling transient soft and hard errors could waste supercomputing resources or, worse, yield misleading scientific insights. In this work, we introduce a novel application-driven silent error detection and recovery strategy based on application health monitoring. Our methodology uses application output that follows known patterns, as indicators of an application's health and knowledge that violation of these patterns could be indication of faults. Information from system monitors that report hardware and software health status is used to corroborate faults. Collectively, this information is used by a fault coordinator agent to take preventive and corrective measures by applying computational steering to an application between checkpoints. This cooperative fault management system uses the Fault Tolerance Backplane as a communication channel. The benefits of this framework are demonstrated with two real application case studies, molecular dynamics, and quantum chemistry simulations, on scalable clusters with simulated memory and I/O corruptions. Lastly, the developed approach is general and can be easily applied to other applications.

97 MATHEMATICS AND COMPUTING↗

Application-Specific Fault Tolerance via Data Access Characterization

Recent trends in semiconductor technology and supercomputer design predict an increasing probability of faults during an application's execution. Designing an application that is resilient to system failures requires careful evaluation of the impact of various approaches on preserving key application state. In this paper, we present our experiences in an ongoing effort to make a large computational chemistry application fault tolerant. We construct the data access signatures of key application modules to evaluate alternative fault tolerance approaches. We present the instrumentation methodology, characterization of the application modules, and evaluation of fault tolerance techniques using the information collected. The application signatures developed capture application characteristics not traditionally revealed by performance tools. We believe these can be used in the design and evaluation of runtimes beyond fault tolerance.

99 GENERAL AND MISCELLANEOUS↗

System modeling for grid-interactive efficient building applications

Despite the abundance of research applications of system modeling in grid-interactive efficient buildings (GEBs), the transfer of those applications to real-world practices is still in its early stages. This is partially due to the lack of a summary on how system modeling should be established for a given application of GEBs. Here, we fill this gap by providing an extensive survey of the literature on system modeling for different GEBs that have been produced in the past decade. This survey involves over 300 relevant journal articles from the building community, the power system community, and the society of control. Specifically, we first identified key requirements of system modeling for GEBs based on various types of applications discussed in those publications. We then summarized the system modeling applications from those publications, in terms of their assumptions, modeling approach, and simulation. After that, we analyzed different assumptions made for various applications, the extent to which those modeling approaches satisfied the key requirements, and how those approaches can be scaled up for large-scale applications, which are quite common in GEBs. In addition, we gave insights on how to use system modeling for different applications in GEBs. At the end, we provided recommended directions for future studies to fully unleash the potentials of system modeling to support GEBs.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Implementation of a multi-threaded framework for large-scale scientific applications

The CMS experiment has recently completed the development of a multi-threaded capable application framework. In this paper, we will discuss the design, implementation and application of this framework to production applications in CMS. For the 2015 LHC run, this functionality is particularly critical for both our online and offline production applications, which depend on faster turn-around times and a reduced memory footprint relative to before. These applications are complex codes, each including a large number of physics-driven algorithms. While the framework is capable of running a mix of thread-safe and 'legacy' modules, algorithms running in our production applications need to be thread-safe for optimal use of this multi-threaded framework at a large scale. Towards this end, we discuss the types of changes, which were necessary for our algorithms to achieve good performance of our multithreaded applications in a full-scale application. Lastly performance numbers for what has been achieved for the 2015 run are presented.

97 MATHEMATICS AND COMPUTING↗

ParaOpt: Automated Application Parameterization and Optimization for the Cloud

The variety of instance types available on cloud platforms offers enormous flexibility to match the requirements of applications with available resources. However, selecting the most suitable instance type and configuring an application to optimally execute on that instance type can be complicated and time-consuming. For example, application parallelism flags must match available cores and problem sizes must be tuned to match available memory. As the search space of application configurations can be enormous, we propose an automated approach, called ParaOpt, to automatically explore and tune application configurations on arbitrary cloud instances. ParaOpt supports arbitrary applications, enables use of custom optimization methods, and can be configured with different optimization targets such as runtime and cost. We evaluate ParaOpt by optimizing genomics, molecular dynamics, and machine learning applications with four types of optimizers. We show with as few as 15 parameterized executions of an application, representing between 1.2%-26.7% of the search space, that ParaOpt is able to identify the optimal configuration in 32.7% of experiments and a near-optimal configuration in 83.2% of cases. As a result of using near-optimal configurations, ParaOpt reduces overall execution time by up to 85.8% when compared with using the default configuration.

Wu, Chaofeng↗

Autotuning in High-Performance Computing Applications

Autotuning refers to the automatic generation of a search space of possible implementations of a computation that are evaluated through models and/or empirical measurement to identify the most desirable implementation. Autotuning has the potential to dramatically improve the performance portability of petascale and exascale applications. To date, autotuning has been used primarily in high-performance applications through tunable libraries or previously tuned application code that is integrated directly into the application. This paper draws on the authors' extensive experience applying autotuning to high-performance applications, describing both successes and future challenges. If autotuning is to be widely used in the HPC community, researchers must address the software engineering challenges, manage configuration overheads, and continue to demonstrate significant performance gains and portability across architectures. In particular, tools that configure the application must be integrated into the application build process so that tuning can be reapplied as the application and target architectures evolve.

97 MATHEMATICS AND COMPUTING↗

Understanding the Performance and Potential of Cloud Computing for Scientific Applications

In this paper, commercial clouds bring a great opportunity to the scientific computing area. Scientific applications usually require significant resources, however not all scientists have access to sufficient high-end computing systems, may of which can be found in the Top500 list. Cloud Computing has gained the attention of scientists as a competitive resource to run HPC applications at a potentially lower cost. But as a different infrastructure, it is unclear whether clouds are capable of running scientific applications with a reasonable performance per money spent. This work studies the performance of public clouds and places this performance in context to price. We evaluate the raw performance of different services of AWS cloud in terms of the basic resources, such as compute, memory, network and I/O. We also evaluate the performance of the scientific applications running in the cloud. This paper aims to assess the ability of the cloud to perform well, as well as to evaluate the cost of the cloud running scientific applications. We developed a full set of metrics and conducted a comprehensive performance evlauation over the Amazon cloud. We evaluated EC2, S3, EBS and DynamoDB among the many Amazon AWS services. We evaluated the memory sub-system performance with CacheBench, the network performance with iperf, processor and network performance with the HPL benchmark application, and shared storage with NFS and PVFS in addition to S3. We also evaluated a real scientific computing application through the Swift parallel scripting system at scale. Armed with both detailed benchmarks to gauge expected performance and a detailed monetary cost analysis, we expect this paper will be a recipe cookbook for scientists to help them decide where to deploy and run their scientific applications between public clouds, private clouds, or hybrid clouds.

97 MATHEMATICS AND COMPUTING↗

Treatment planning of a skin-sparing conical breast brachytherapy applicator using conventional brachytherapy software

Purpose: AccuBoost is a noninvasive image-guided technique for the delivery of partial breast irradiation to the tumor bed and currently serves as an alternate to conventional electron beam boost. To irradiate the target volume while providing dose sparing to the skin, the round applicator design was augmented through the addition of an internally truncated conical shield and the reduction of the source to skin distance. Methods: Brachytherapy dose distributions for two types of conical applicators were simulated and estimated using Monte Carlo (MC) methods for radiation transport and a conventional treatment planning system (TPS). MC-derived and TPS-generated dose volume histograms (DVHs) and dose distribution data were compared for both the conical and round applicators for benchmarking purposes. Results: Agreement using the gamma-index test was {>=}99.95% for distance to agreement and dose accuracy criteria of 2 mm and 2%, respectively. After observing good agreement, TPS DVHs and dose distributions for the conical and round applicators were obtained and compared. Brachytherapy dose distributions generated using Pinnacle{sup 3} for ten CT data sets showed that the parallel-opposed beams of the conical applicators provided similar PTV coverage to the round applicators and reduced the maximum dose to skin, chest wall, and lung by up to 27%, 42%, and 43%, respectively. Conclusions: Brachytherapy dose distributions for the conical applicators have been generated using MC methods and entered into the Pinnacle{sup 3} TPS via the Tufts technique. Treatment planning metrics for the conical AccuBoost applicators were significantly improved in comparison to those for conventional electron beam breast boost.

60 APPLIED LIFE SCIENCES↗

HDR brachytherapy of rectal cancer using a novel grooved-shielding applicator design

Purpose: The aim of this work was to design a novel high-dose rate (HDR) ({sup 192}Ir) brachytherapy applicator for treatment of rectal carcinomas that uses tungsten shielding for possibly improved dosimetric results over commercial brachytherapy applicator(s).Methods: A set of 15 single-depth applicators and one dual-depth applicator were designed and simulated using Monte Carlo (MCNPX). All applicators simulated were high-density tungsten alloy cylinders, 16-mm in diameter, and 60-mm long, with longitudinal grooves within which an {sup 192}Ir source can be placed. The single-depth designs varied regarding the number and depth of these grooves, ranging from 8 to 16 and 1-mm to 3-mm, respectively. The dual-depth design had ten channels, each of which had two depths at which the source could be placed. Optimized treatment plans were generated for each design on data from 13 treated patients (36 fractions) with asymmetrical clinical target volumes (CTVs). All results were compared against the clinically treated plans which used intracavitary mold applicator (ICMA), as well as a recently designed, highly automated, and collimated intensity modulation device named dynamic modulated brachytherapy (DMBT) device.Results: All applicator designs outperformed the ICMA in every calculated dosimetric criteria, except the total dwell times (∼30% increase). There were clear, but relative, tradeoffs regarding both the number of channels and the depth of each channel. Overall, the 12-channel, 1-mm depth, and 14-channel 2-mm depth designs had the best results of the simpler designs, sparing the healthy rectal tissues the most while achieving comparable CTV coverage with the dose heterogeneity index and lateral spill doses improving by over 10% and the contralateral healthy rectum dose dropping over 30% compared to ICMA. The ten-channel dual-depth design outperformed each single-depth design, yielding the best coverage and sparing.Conclusions: New grooved tungsten HDR-brachytherapy devices have been designed and simulated. The results of this work attest to the capability of these new, highly anisotropic, intelligently shielded applicators to limit dose to healthy tissues while maintaining a conformal prescription dose to the CTV.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

A complete software application for automatic registration of x-ray mammography and magnetic resonance images

Purpose: This work presents a complete and automatic software application to aid radiologists in breast cancer diagnosis. The application is a fully automated method that performs a complete registration of magnetic resonance (MR) images and x-ray (XR) images in both directions (from MR to XR and from XR to MR) and for both x-ray mammograms, craniocaudal (CC), and mediolateral oblique (MLO). This new approximation allows radiologists to mark points in the MR images and, without any manual intervention, it provides their corresponding points in both types of XR mammograms and vice versa. Methods: The application automatically segments magnetic resonance images and x-ray images using the C-Means method and the Otsu method, respectively. It compresses the magnetic resonance images in both directions, CC and MLO, using a biomechanical model of the breast that distinguishes the specific biomechanical behavior of each one of its three tissues (skin, fat, and glandular tissue) separately. It makes a projection of both compressions and registers them with the original XR images using affine transformations and nonrigid registration methods. Results: The application has been validated by two expert radiologists. This was carried out through a quantitative validation on 14 data sets in which the Euclidean distance between points marked by the radiologists and the corresponding points obtained by the application were measured. The results showed a mean error of 4.2 ± 1.9 mm for the MRI to CC registration, 4.8 ± 1.3 mm for the MRI to MLO registration, and 4.1 ± 1.3 mm for the CC and MLO to MRI registration. Conclusions: A complete software application that automatically registers XR and MR images of the breast has been implemented. The application permits radiologists to estimate the position of a lesion that is suspected of being a tumor in an imaging modality based on its position in another different modality with a clinically acceptable error. The results show that the application can accelerate the mammographic screening process for high risk populations or for dense breasts.

60 APPLIED LIFE SCIENCES↗

MO-E-12A-01: Quantitative Imaging: Techniques, Applications, and Challenges

The first symposium in the Quantitative Imaging Track focused on the introduction of quantitative imaging (QI) by illustrating the potential of QI in diagnostic and therapeutic applications in research and patient care, highlighting key challenges in implementation of such QI applications, and reviewing QI efforts of selected national and international agencies and organizations, including the FDA, NCI, NIST, and RSNA. This second QI symposium will focus more specifically on the techniques, applications, and challenges of QI. The first talk of the session will focus on modalityagnostic challenges of QI, beginning with challenges of the development and implementation of QI applications in single-center, single-vendor settings and progressing to the challenges encountered in the most general setting of multi-center, multi-vendor settings. The subsequent three talks will focus on specific QI challenges and opportunities in the modalityspecific settings of CT, PET/CT, and MR. Each talk will provide information on modality-specific QI techniques, applications, and challenges, including current efforts focused on solutions to such challenges. Learning Objectives: Understand key general challenges of QI application development and implementation, regardless of modality. Understand selected QI techniques and applications in CT, PET/CT, and MR. Understand challenges, and potential solutions for such challenges, for the applications presented for each modality.

60 APPLIED LIFE SCIENCES↗

TH-A-17A-01: Innovation in PET Instrumentation and Applications

Innovation in PET instrumentation has led to the new millennium revolutionary imaging applications for diagnosis, therapeutic guidance, and development of new molecular imaging probes, etc. However, after several decades innovations, will the advances of PET technology and applications continue with the same trend and pace? What will be the next big thing beyond the PET/CT, PET/MRI, and Time-of-flight PET? How will the PET instrumentation and imaging performance be further improved by novel detector research and advanced imaging system development? Or will the development of new algorithms and methodologies extend the limit of current instrumentation and leapfrog the imaging quality and quantification for practical applications? The objective of this session is to present an overview of current status and advances in the PET instrumentation and applications with speakers from leading academic institutes and a major medical imaging company. Presenting with both academic research projects and commercial technology developments, this session will provide a glimpse of some latest advances and challenges in the field, such as using semiconductor photon-sensor based PET detectors to improve performance and enable new applications, as well as the technology trend that may lead to the next breakthrough in PET imaging for clinical and preclinical applications. Both imaging and image-guided therapy subjects will be discussed. Learning Objectives: Describe the latest innovations in PET instrumentation and applications Understand the driven force behind the PET instrumentation innovation and development Learn the trend of PET technology development for applications.

60 APPLIED LIFE SCIENCES↗

SU-E-T-232: Custom High-Dose-Rate Brachytherapy Surface Mold Applicators: The Importance Source to Skin Distance

Purpose: Surface mold applicators can be customized to fit irregular skin surfaces that are difficult to treat with other radiation therapy techniques. Optimal design of customized HDR skin brachytherapy is not well-established. We evaluated the impact of applicator thickness (source to skin distance) on target dosimetry. Methods: 27 patients had 34 treated sites: scalp 4, face 13, extremity 13, and torso 4. Custom applicators were constructed from 5–15 mm thick thermoplastic bolus molded over the skin lesion. A planar array of plastic brachytherapy catheters spaced 5–10 mm apart was affixed to the bolus. CT simulation was used to contour the target volume and to determine the prescription depth. Inverse planning simulated annealing followed by graphical optimization was used to plan and deliver 40–56 Gy in 8–16 fractions. Target coverage parameters (D90, Dmean, and V100) and dose uniformity (V110–200, D0.1cc, D1cc, and D2cc) were studied according to target depth (<5mm vs. ≥5mm) and applicator thickness (5–10mm vs. ≥10mm). Results: The average prescription depth was 4.2±1.5mm. The average bolus thickness was 9.2±2.4mm. The median CTV volume was 10.0 cc (0.2–212.4 cc). Similar target coverage was achieved with prescription depths of <5mm and ≥5mm (Dmean = 113.8% vs. 112.4% and D90 = 100.2% vs. 98.3%). The <5mm prescription depth plans were more uniform (D0.1cc = 131.8% vs. 151.8%). Bolus thickness <10mm vs. ≥10mm plans also had similar target coverage (Dmean = 118.2% vs. 110.7% and D90 = 100.1% vs. 99.0%). Applicators ≥10mm thick, however, provide more uniform target dosimetry (D0.1cc = 146.9% vs. 139.5%). Conclusion: Prescription depth is based upon the thickness of the lesion and upon the clinical needs of the patient. Applicators ≥10mm thick provide more dose uniformity than 5–10mm thick applicators. Applicator thickness is an important variable that should be considered during treatment planning to achieve optimal dose uniformity.

60 APPLIED LIFE SCIENCES↗

SU-E-T-352: Effects of Skull Attenuation and Missing Backscatter On Brain Dose in HDR Treatment of the Head with Surface Applicators

Purpose: To calculate the effect of lack of backscatter from air and attenuation of bone on dose distributions in brachytherapy surface treatment of head. Existing treatment planning systems based on TG43 do not account for heterogeneities, and thus may overestimate the dose to the brain. While brachytherapy generally has rapid dose falloff, the dose to the deeper tissues (in this case, the brain) can become significant when treating large curved surfaces. Methods: Applicator geometries representing a range of clinical cases were simulated in MCNP5. An Ir-192 source was modeled using the energy spectrum presented by TG-43. The head phantom was modeled as a 7.5-cm radius water sphere, with a 7 -mm thick skull embedded 5-mm beneath the surface. Dose values were calculated at 20 points inside the head, in which 10 of them were on the central axis and the other 10 on the axis connecting the central of the phantom with the second to last source from the applicator edge. Results: Central and peripheral dose distributions for a range of applicator and head sizes are presented. The distance along the central axis at which the dose falls to 80% of the prescribed dose (D80) was 7 mm for a representative small applicator and 9 mm for a large applicator. Corresponding D50 and D30 for the same small applicator were 17 mm and 32 mm respectively. D50 and D30 for the larger applicator were 32 mm and 60 mm respectively. These results reflect the slower falloff expected for larger applicators on a curved surface. Conclusion: Our results can provide guidance for clinicians to calculate the dose reduction effect due to bone attenuation and the lack of backscatter from air to estimate the brain dose for the HDR treatments of surface lesions.

60 APPLIED LIFE SCIENCES↗

SU-F-J-163: In Vivo Quantification of Sequence Parameter Effect On Geometric Distortion Caused by Implanted Titanium Brachytherapy Applicator

Purpose: The use of MR to plan and evaluate brachytherapy treatment for cervical cancer is increasing given the availability of MR conditional or safe applicators and MRI’s proven superiority to CT for characterizing soft tissue lesions. The titanium applicators, however, cause geometric distortions or imaging artifacts, which reduce the utility of MRI for dosimetry. We sought to quantify the observed volume of the same applicator on a previously optimized T2 sequence in comparison to the conventional T2 sequence and CT obtained for brachytherapy planning. Methods: Prior work with testing in phantoms showed that increases in readout bandwidth yielded reductions in artifact area and distortion measurements even with voxel increases. Following IRB approval, nine patients with titanium tandem & ovoid applicator (Varian Medical Systems) in place were scanned with a standard periprocedural protocol which included sagittal T2 fast spin echo (FSE) acquisition (res 0.98×0.78×4.0 mm{sup 3}; BW 200Hz). An additional T2-weighted FSE sequence (res 0.98×0.98×3–4 mm{sup 3}; BW500Hz) with increased readout bandwidth, readout voxel size, and echo train length was added to the protocol. Volume measurements of the applicator (from tip to cervical stop) were hand-segmented in Velocity AI 3.1 (Velocity Medical Solutions) for the two T2 FSE sequences and a planning CT obtained shortly after MRI. Differences were analyzed using a paired t-test. Results: Average apparent volumes of the applicator on standard T2 sequence, decreased bandwidth T2 sequence and CT were 5.922±1.283 cm{sup 3}, 4.544±1.524 cm3, and 2.304±0.509 cm{sup 3} respectively. Conclusion: Apparent volumes of a brachytherapy applicator can be compared in vivo. The modified sequence results in decreased apparent size of the cervical applicator. Both MR sequence volumes were larger than the planning CT, which was expected. Future work will focus on the diagnostic quality of the new sequence and quantifying any geometric shifts after CT to MRI registration based on anatomical landmarks.

60 APPLIED LIFE SCIENCES↗

SU-F-T-21: A Novel Beam-Light View, Collimating Applicator for HDR Ocular Conjunctiva Brachytherapy-Treatments

Purpose: We propose the use of a HDR X-ray source collimator to apply a conformal, relatively small, radiation suitable for a single fraction with short delivery time. In addition, this technique can be applied using a radioactive source. Methods: We have built a stainless steel 1.5 mm thick applicator, to accommodate the needle applicator of the Intra-Beam X-ray source. Additional cavity is created in the applicator to allow the hosting/nesting/positioning of a LED diode. This LED is allowing a pre-irradiation beam marking on the tissue. The visible light emitted from the opening of the collimated applicator will delineate/verify the aperture of the kV beam to be applied, as well as serve as distance indicator and will assist in the determination of dose to be delivered. For the evaluation of the collimated spatial dose distribution we have performed water tank measurements using (IBA Dosimetry) with a 0.4 cc ion chamber (IBA Dosimetry). We have scanned a two dimensional array with 1mm pitch in depth and 0.3 mm step size laterally. Additional verifications were conducted using Gaf-Chromic film for PDD measurements and Optical Stimulated Luminescence Dosimetry (OSLD, Landauer inc.) for absolute dosimetry. Results: The collimated applicator enables a conformal irradiated cross-section of about 3 mm square at the applicator surface was used in this study. A 180 seconds of 50 kVp delivery yielded 29 Gy, 20.6 Gy and 14.5 Gy at 5, 10 and 15 mm depths respectively. These results are in good agreement with the needle applicator depth dose curve published data. Conclusion: We have demonstrated the feasibility of focal HDR brachytherapy for conjunctival and ocular tumors, using the Intra-Beam needle applicator with in-house developed collimator. The delivery time was found to be several minutes- suitable for an intra-operative procedure and will allow dose fractionation deliveries.

61 RADIATION PROTECTION AND DOSIMETRY↗