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DOE OSTI2021

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping sequences, simplifies their layout, and creates consensus. Despite many algorithms developed in the literature, the efficient assembly of large genomes is still an open problem. In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline. Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the overlap graph to a string graph. We provide a detailed communication analysis of the main stages of our new algorithms. diBELLA 2D achieves near linear scaling with over 80% parallel efficiency for the human genome, reducing the runtime for overlap detection by 1.2-1.3× for the human genome and 1.5-1.9× for C.elegans compared to the state-of-the-art. Our transitive reduction algorithm outperforms an existing distributed-memory implementation by 10.5-13.3× for the human genome and 18-29× for the C. elegans. Our work paves the way for efficient de novo assembly of large genomes using long reads in distributed memory.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

New Total-Ionizing-Dose Resistant Data Storing Technique for NAND Flash Memory

This paper describes a new non-charge-based data storing technique in NAND flash memory called watermark that encodes read-only data in the form of physical properties of flash memory cells. Unlike traditional charge-based data storing method in flash memory, the proposed technique is resistant to total ionizing dose (TID) effects. To evaluate its resistance to irradiation effects, we analyze data stored in several commercial single-level-cell (SLC) flash memory chips from different vendors and technology nodes. These chips are irradiated using a Co-60 gamma-ray source array for up to 100 krad(Si) at Sandia National Laboratories. Experimental evaluation performed on a flash chip from Samsung shows that the intrinsic bit error rate (BER) of watermark increases from 0.8% for TID = 0 krad(Si) to 1% for TID = 100 krad(Si). Conversely, the BER of charge-based data stored on the same chip increases from 0% at TID = 0 krad(Si) to 1.5% at TID = 100 krad(Si). Overall, the results imply that the proposed technique may potentially offer significant improvements in data integrity relative to traditional charge-based data storage for very high radiation (TID > 100 krad(Si)) environments. These gains in data integrity relative to the charge-based data storage are useful in radiation-prone environments, but they come at the cost of increased write times and higher BERs before irradiation.

36 MATERIALS SCIENCE↗

DOE OSTI2025

UltraLiM: In-Memory Boolean Logic Architecture Using UltraRAM

Conventional computing architectures encounter ‘von Neumann’ and ‘memory wall’ bottlenecks which arise due to the back-and-forth data movement between the physically separate memory and processing units and the speed mismatch between them, respectively. These bottlenecks hurt both energy efficiency and the throughput of computing systems. To address these challenges, in-memory computing architectures have emerged as a promising alternative. They reduce the need for frequent data movement by executing different computing tasks inside the memory system. Here, we present UltraLiM, a logic-in-memory architecture using the UltraRAM-based memory system. UltraRAM holds the promise of developing a ‘universal memory’, overcoming the limitations of charge-based memories thanks to their non-volatile behavior with lower operating voltage. This work presents an in-memory computing architecture that integrates an UltraRAM-based memory array with a custom-designed peripheral circuitry. With this architecture, we can perform various in-memory Boolean logic operations (such as NOT, NAND, NOR, and XOR) in a single cycle. Leveraging the separate read-write paths in the UltraRAM-based memory array, we optimize read operations without encountering design conflicts. This optimization enhances the sense margin, enabling the use of simpler peripheral circuitry for in-memory logic operations.

Alam, Shamiul [University of Tennessee, Knoxville ↗

DOE OSTI2021

Columnar data analysis with ATLAS analysis formats

Future analysis of ATLAS data will involve new small-sized analysis formats to cope with the increased storage needs. The smallest of these, named DAOD_PHYSLITE, has calibrations already applied to allow fast downstream analysis and avoid the need for further analysis-specific intermediate formats. This allows for application of the "columnar analysis" paradigm where operations are applied on a per-array instead of a per-event basis. We will present methods to read the data into memory, using Uproot, and also discuss I/O aspects of columnar data and alternatives to the ROOT data format. Furthermore, we will show a representation of the event data model using the Awkward Array package and present proof of concept for a simple analysis application.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

G4VG

G4VG reads the in-memory Geant4 geometry (the volume hierarchy and physical shape descriptions defined by a user application) and produces an equivalent VecGeom representation. This provides a direct bridge between Geant4 detector descriptions and VecGeom-based applications, eliminating the need for manual export pipelines or specialized GDML workflows. The code is adapted from the Celeritas project and developed as an independent utility for broader reuse.

Johnson, SethR [Oak Ridge National Laboratory] (00↗

DOE OSTI2021

Computational processor-in-memory with enhanced strided memory access

A computational memory for a computer. The memory includes a memory bank having a selected-row buffer and being configured to store records up to a number, K. The memory also includes an accumulator connected to the memory bank, the accumulator configured to store up to K records. The memory also includes an arithmetic and logic unit (ALU) connected to the accumulator and to the selected row buffer of the memory bank, the ALU having an indirect network of 2K ports for reading and writing records in the memory bank and the accumulator, and the ALU further physically configured to operate as a sorting network. The memory also includes a controller connected to the memory bank, the ALU, and the accumulator, the controller being hardware configured to direct operation of the ALU.

DeBenedictis, Erik↗

DOE OSTI2022

Techniques for storing data to enhance recovery and detection of data corruption errors

Often there are errors when reading data from computer memory. To detect and correct these errors, there are multiple types of error correction codes. Disclosed is an error correction architecture that creates a codeword having a data portion and an error correction code portion. Swizzling rearranges the order of bits and distributes the bits among different codewords. Because the data is redistributed, a potential memory error of up to N contiguous bits, where N for example equals 2 times the number of codewords swizzled together, only affects up to, at most, two bits per swizzled codeword. This keeps the error within the error detecting capabilities of the error correction architecture. Furthermore, this can allow improved error correction and detection without requiring a change to error correcting code generators and checkers.

Mills, Peter↗

DOE OSTI2023

Techniques for storing data to enhance recovery and detection of data corruption errors

Mills, Peter↗

DOE OSTI2020

Sage: parallel semi-asymmtric graph algorithms for NVRAMs

Non-volatile main memory (NVRAM) technologies provide an attractive set of features for large-scale graph analytics, including byte-addressability, low idle power, and improved memory-density. NVRAM systems today have an order of magnitude more NVRAM than traditional memory (DRAM). NVRAM systems could therefore potentially allow very large graph problems to be solved on a single machine, at a modest cost. However, a significant challenge in achieving high performance is in accounting for the fact that NVRAM writes can be much more expensive than NVRAM reads. In this paper, we propose an approach to parallel graph analytics using the Parallel Semi-Asymmetric Model (PSAM), in which the graph is stored as a read-only data structure (in NVRAM), and the amount of mutable memory is kept proportional to the number of vertices. Similar to the popular semi-external and semi-streaming models for graph analytics, the PSAM approach assumes that the vertices of the graph fit in a fast read-write memory (DRAM), but the edges do not. In NVRAM systems, our approach eliminates writes to the NVRAM, among other benefits. To experimentally study this new setting, we develop Sage, a parallel semi-asymmetric graph engine with which we implement provably-efficient (and often work-optimal) PSAM algorithms for over a dozen fundamental graph problems. We experimentally study Sage using a 48--core machine on the largest publicly-available real-world graph (the Hyperlink Web graph with over 3.5 billion vertices and 128 billion edges) equipped with Optane DC Persistent Memory, and show that Sage outperforms the fastest prior systems designed for NVRAM. Importantly, we also show that Sage nearly matches the fastest prior systems running solely in DRAM, by effectively hiding the costs of repeatedly accessing NVRAM versus DRAM.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Device and method for cache utilization aware data compression

A processing device is provided which includes memory and at least one processor. The memory includes main memory and cache memory in communication with the main memory via a link. The at least one processor is configured to receive a request for a cache line and read the cache line from main memory. The at least one processor is also configured to compress the cache line according to a compression algorithm and, when the compressed cache line includes at least one byte predicted not to be accessed, drop the at least one byte from the compressed cache line based on whether the compression algorithm is determined to successfully compress the cache line according to a compression parameter.

Das, Shomit N.↗

DOE OSTI2020

Distributed Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper (DiBELLA) v1.0.0

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous advantages for biological analysis and insight, current long read sequencing instruments have high error rates and therefore require different approaches to analysis than their short read counterparts. Our work focuses on an efficient distributed-memory parallelization of an accurate single-node algorithm for overlapping and aligning long reads. We achieve scalability of this irregular algorithm by addressing the competing issues of increasing parallelism, minimizing communication, constraining the memory footprint, and ensuring good load balance. The resulting application, DiBELLA, is the first distributed memory overlapper and aligner specifically designed for long reads and parallel scalability.

Ellis, Marquita↗

DOE OSTI2022

Register-Like Storage Block Used as Histograms, Cluster Buffers, and Hough Transform Accumulators for HEP Trigger Systems

In high energy physics experiment trigger systems, block memories are utilized for various purposes, especially in binned searching algorithms. In these algorithms, the storages are demanded to perform like a large set of registers. The writing and reading operation must be performed in single clock cycle and once an event is processed, the memory must be globally reset. These demands can be fulfilled with registers but the cost of using registers for large memory is unaffordable. Another common requirement is the boundary coverage feature during reading process. Additionally, when a memory bin is addressed, the stored contents in the addressed bin and its neighboring bin must be output simultaneously. In this paper, a register-like block storage design scheme is described, which allows updating memory locations in single clock cycle, reading two adjacent bins, and effectively refreshing entire memory within a single clock. The implementation and test results are presented.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Optical Memory, Switching, and Neuromorphic Functionality in Metal Halide Perovskite Materials and Devices

Metal halide perovskite-based materials have emerged over the past few decades as remarkable solution-processable opto-electronic materials with many intriguing properties and potential applications. Notably, these emerging materials have recently been considered for their promise in low-energy memory and information processing applications. In particular, their large optical cross-sections, high photoconductance contrast, large carrier diffusion lengths, and mixed electronic/ionic transport mechanisms are attractive for enabling memory elements and neuromorphic devices that are written and/or read in the optical domain. Here, we review recent progress towards memory and neuromorphic functionality in metal halide perovskite materials and devices where photons are used as a critical degree of freedom for switching, memory, and neuromorphic functionality.

14 SOLAR ENERGY↗

DOE OSTI2021

Determining diagnostic coverage for memory using redundant execution

Memory, used by a computer to store data, is generally prone to faults, including permanent faults (i.e. relating to a lifetime of the memory hardware), and also transient faults (i.e. relating to some external cause) which are otherwise known as soft errors. Since soft errors can change the state of the data in the memory and thus cause errors in applications reading and processing the data, there is a desire to characterize the degree of vulnerability of the memory to soft errors. In particular, once the vulnerability for a particular memory to soft errors has been characterized, cost/reliability trade-offs can be determined, or soft error detection mechanisms (e.g. parity) may be selectively employed for the memory. In some cases, memory faults can be diagnosed by redundant execution and a diagnostic coverage may be determined.

Bramley, Richard Gavin↗

DOE OSTI2023

Liveness as a factor to evaluate memory vulnerability to soft errors

Bramley, Richard Gavin↗

DOE OSTI2020

Performance Potential of Mixed Data Management Modes for Heterogeneous Memory Systems

Many high-performance systems now include different types of memory devices within the same compute platform to meet strict performance and cost constraints. Such heterogeneous memory systems often include an upper-level tier with better performance, but limited capacity, and lower-level tiers with higher capacity, but less bandwidth and longer latencies for reads and writes. To utilize the different memory layers efficiently, current systems rely on hardware-directed, memory -side caching or they provide facilities in the operating system (OS) that allow applications to make their own data-tier assignments. Since these data management options each come with their own set of trade-offs, many systems also include mixed data management configurations that allow applications to employ hardware- and software-directed management simultaneously, but for different portions of their address space. Despite the opportunity to address limitations of stand-alone data management options, such mixed management modes are under-utilized in practice, and have not been evaluated in prior studies of complex memory hardware. In this work, we develop custom program profiling, configurations, and policies to study the potential of mixed data management modes to outperform hardware- or software-based management schemes alone. Our experiments, conducted on an Intel ® Knights Landing platform with high-bandwidth memory, demonstrate that the mixed data management mode achieves the same or better performance than the best stand-alone option for five memory intensive benchmark applications (run separately and in isolation), resulting in an average speedup compared to the best stand-alone policy of over 10 %, on average.

Effler, Chad↗

DOE OSTI2022

ECRAM Materials, Devices, Circuits and Architectures: A Perspective

Abstract Non‐von‐Neumann computing using neuromorphic systems based on two‐terminal resistive nonvolatile memory elements has emerged as a promising approach, but its full potential has not been realized due to the lack of materials and devices with the appropriate attributes. Unlike memristors, which require large write currents to drive phase transformations or filament growth, electrochemical random access memory (ECRAM) decouples the “write” and “read” operations using a “gate” electrode to tune the conductance state through charge‐transfer reactions, and every electron transferred through the external circuit in ECRAM corresponds to the migration of ≈1 ion used to store analogue information. Like static dopants in traditional semiconductors, electrochemically inserted ions modulate the conductivity by locally perturbing a host's electronic structure; however, ECRAM does so in a dynamic and reversible manner. The resulting change in conductance can span orders of magnitude, from gradual increments needed for analog elements, to large, abrupt changes for dynamically reconfigurable adaptive architectures. In this in‐depth perspective, the history of ECRAM, the recent progress in devices spanning organic, inorganic, and 2D materials, circuits, architectures, the rich portfolio of challenging, fundamental questions, and how ECRAM can be harnessed to realize a new paradigm for low‐power neuromorphic computing are discussed.

Talin, A. Alec↗

DOE OSTI2025

Benchmarking Operators in Deep Neural Networks for Improving Performance Portability of SYCL

SYCL is a portable programming model for heterogeneous computing, so it is important to obtain reasonable performance portability of SYCL. Towards the goal of better understanding and improving performance portability of SYCL for machine learning workloads, we have been developing benchmarks for basic operators in deep neural networks (DNNs). These operators could be offloaded to heterogeneous computing devices such as graphics processing units (GPUs) to speed up computation. In this paper, we introduce the benchmarks, evaluate the performance of the operators on GPU-based systems, and describe the causes of the performance gap between the SYCL and Compute Unified Device Architecture (CUDA) kernels. We find that the causes are related to the utilization of the texture cache for read-only data, optimization of the memory accesses with strength reduction, use of local memory, and register usage per thread. We hope that the efforts of developing benchmarks for studying performance portability will stimulate discussion and interactions within the community.

Jin, Zheming [ORNL] (ORCID:000000027197780X)↗