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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase

Microbial genome annotation is the process of identifying structural and functional elements in DNA sequences and subsequently attaching biological information to those elements. DRAM is a tool developed to annotate bacterial, archaeal, and viral genomes derived from pure cultures or metagenomes. DRAM goes beyond traditional annotation tools by distilling multiple gene annotations to genome level summaries of functional potential. Despite these benefits, a downside of DRAM is the requirement of large computational resources, which limits its accessibility. Further, it did not integrate with downstream metabolic modeling tools that require genome annotation. To alleviate these constraints, DRAM and the viral counterpart, DRAM-v, are now available and integrated with the freely accessible KBase cyberinfrastructure. With kb_DRAM users can generate DRAM annotations and functional summaries from microbial or viral genomes in a point-and-click interface, as well as generate genome-scale metabolic models from DRAM annotations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

DRAM example narrative

DRAM example narrative DRAM on KBase let's anyone run annotations using DRAM in the cloud. DRAM is an annotation tool that can annotate bacterial, archaeal and viral genomes and distills those annotatios into represetations of the functional genomic potential of those organisms. If you want to read more about DRAM you can check out the GitHub, wiki and journal article. DRAM annotate assemblies In KBase Assembly objects contain nucleotide sequences from genomes or metagenomes. DRAM can predict genes and annotate their function from KBase Assembly objects which may be microbial isolate genomes, metagenome assembled genomes or metagenomes. This is done with the Annotate and Distill Assemblies with DRAM app. This app can also anntoate AssemblySet objects which contain collection of Assembly objects. It also generates a Genome object and a GenomeSet object which can be used for further analysis with other KBase apps. The full annotations and other DRAM files are also available for download in the app.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

KBase Narrative - kb_DRAM E. coli annotation

Here we are annotating a E. coli K-12 genome using both DRAM and RAST then using those annotations to build models. The genome is from NCBI RefSeq ID NC_000913.

Shaffer, Michael↗
DOE OSTI2022

Multifidelity DRAM Simulation in SST [Poster]

We will always want to speed up simulation. While architects are able to pick between levels of detail when designing simulation, we will find further speed-up if we can adjust the level of detail during simulation, depending on the behavior of the simulated components. We create a simple fixed-latency model for each phase. On the first execution of a phase, we record the average latency of accesses. On subsequent executions, we skip DRAMSin 3 and send the response back using the average latency.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Single-node Partitioned-Memory for Huge Graph Analytics: Cost and Performance Trade-offs

Nonvolatile memory NVDIMMs, available as Intel Optane, are less expensive than DRAM and bring large byte-addressable storage within reach to many applications. Evaluations on graph analytics have shown promising performance only when DRAM is used as a hardware cache (Memory mode). An open question is whether graph applications can exploit Optane and DRAM directly (AppDirect mode) and achieving better-than-DRAM average bandwidth and run times. We evaluate Optane as a volatile pool on two large-scale graph applications with very different computational patterns, Grappolo and Ripples. We show that AppDirect mode can deliver better-than-DRAM performance, by allocating data structures to Optane and DRAM according to their access characteristics, resulting in higher average memory bandwidth and lower average latency. Memory mode provides DRAM-competitive performance with capacity equal to persistent memory. We demonstrate occasional 4x improvement using the latest AppDirect option and frequently observe competitive performance between Optane AppDirect Memory modes and DRAM.

Ghosh, Sayan↗
DOE OSTI2025

Single-Cell Universal Logic-in-Memory Using 2T-nC FeRAM: An Area and Energy-Efficient Approach for Bulk Bitwise Computation

This work presents a novel approach to configure 2T-nC ferroelectric RAM (FeRAM) for performing single cell logic-in-memory operations, highlighting its advantages in energy-efficient computation over conventional DRAM-based approaches. Unlike conventional 1T-1C dynamic RAM (DRAM), which incurs refresh overhead, 2T-nC FeRAM offers a promising alternative as a non-volatile memory solution with low energy consumption. Our key findings include the potential of quasi-nondestructive readout (QNRO) sensing in 2T-nC FeRAM for logic-in-memory (LiM) applications, demonstrating its inherent capability to perform inverting logic without requiring external modifications, a feature absent in traditional 1T-1C DRAM. We successfully implement the MINORITY function within a single cell of 2T-nC FeRAM, enabling universal NAND and NOR logic, validated through SPICE simulations and experimental data. Additionally, the research investigates the feasibility of 3D integration with 2T-nC FeRAM, showing substantial improvements in storage and computational density, facilitating bulk-bitwise computation. Our evaluation of eight real-world, data-intensive applications reveals that 2T-nC FeRAM achieves 2× higher performance and 2.5× lower energy consumption compared to DRAM. Furthermore, the thermal stability of stacked 2T-nC FeRAM is validated, confirming its reliable operation when integrated on a compute die. These findings emphasize the advantages of 2T-nC FeRAM for LiM, offering superior performance and energy efficiency over conventional DRAM.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Application of Markov Chain Monte Carlo Methods for Uncertainty Quantification in Inverse Transport Problems

Determination of the components of a radioactive source/shield system using the system’s radiation signature is of great importance in homeland security, material safeguards, and waste management. Although significant progress has been made toward solving this inverse transport problem in recent years, work remains to be done to quantify the uncertainty in reconstructed results. In this article we apply two Markov chain Monte Carlo (MCMC) approaches, the delayed rejection adaptive metropolis (DRAM) and differential evolution adaptive metropolis (DREAM) methods, to solve inverse problems and quantify uncertainty. The DRAM method uses delayed rejection combined with global adaptation of the proposal covariance matrix. Furthermore, the DREAM method hybridizes MCMC sampling with the differential evolution (DE) algorithm. In numerical test cases, the DRAM and DREAM methods are shown to be superior to a first-order inverse Hessian approach for problems with noisy data and multiple unknown quantities, with DREAM converging to the posterior distribution more quickly than DRAM. The DREAM and DRAM results indicate that a full posterior distribution is required to quantify uncertainty in many inverse transport problems.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2022

MAPredict: Static Analysis Driven Memory Access Prediction Framework for Modern CPUs

Application memory access patterns are crucial in deciding how much traffic is served by the cache and forwarded to the dynamic random-access memory (DRAM). However, predicting such memory traffic is difficult because of the interplay of prefetchers, compilers, parallel execution, and innovations in manufacturer-specific micro-architectures. This research introduced MAPredict, a static analysis-driven framework that addresses these challenges to predict last-level cache (LLC)-DRAM traffic. By exploring and analyzing the behavior of modern Intel processors, MAPredict formulates cache-aware analytical models. MAPredict invokes these models to predict LLC-DRAM traffic by combining the application model, machine model, and user-provided hints to capture dynamic information. MAPredict successfully predicts LLC-DRAM traffic for different regular access patterns and provides the means to combine static and empirical observations for irregular access patterns. Evaluating 130 workloads from six applications on recent Intel micro-architectures, MAPredict yielded an average accuracy of 99% for streaming, 91% for strided, and 92% for stencil patterns. By coupling static and empirical methods, up to 97% average accuracy was obtained for random access patterns on different micro-architectures.

Monil, M. A. H.↗
DOE OSTI2022

Persistent memory as an effective alternative to random access memory in metagenome assembly

Abstract Background The assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without laborious cultivation or single-cell metagenomics. Metagenome assembly is a process that is memory intensive and time consuming. Multi-terabyte sequences can become too large to be assembled on a single computer node, and there is no reliable method to predict the memory requirement due to data-specific memory consumption pattern. Currently, out-of-memory (OOM) is one of the most prevalent factors that causes metagenome assembly failures. Results In this study, we explored the possibility of using Persistent Memory (PMem) as a less expensive substitute for dynamic random access memory (DRAM) to reduce OOM and increase the scalability of metagenome assemblers. We evaluated the execution time and memory usage of three popular metagenome assemblers (MetaSPAdes, MEGAHIT, and MetaHipMer2) in datasets up to one terabase. We found that PMem can enable metagenome assemblers on terabyte-sized datasets by partially or fully substituting DRAM. Depending on the configured DRAM/PMEM ratio, running metagenome assemblies with PMem can achieve a similar speed as DRAM, while in the worst case it showed a roughly two-fold slowdown. In addition, different assemblers displayed distinct memory/speed trade-offs in the same hardware/software environment. Conclusions We demonstrated that PMem is capable of expanding the capacity of DRAM to allow larger metagenome assembly with a potential tradeoff in speed. Because PMem can be used directly without any application-specific code modification, these findings are likely to be generalized to other memory-intensive bioinformatics applications.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Variation Tolerant and Energy-Efficient Charge Domain Compute-in-Memory Array with Binary and Multi-Level Cell Ferroelectric FET

Here, in this work, we present a variation-tolerant and energy-efficient charge-domain Ferroelectric FET (FeFET) based Compute-in-Memory (CiM) array design that is compatible with both binary and multi-level cell memory sensing. We demonstrate that: 1) by exploiting FeFET as a nonvolatile switch, its high ON/OFF ratio in the subthreshold region can suppress the error introduced by the inaccurate ON state conductance, thus realizing robust CiM operations, unlike the current-domain CiM design where the computation results is highly sensitive to the device conductance variation; 2) by leveraging a dense dynamic random access memory (DRAM)-like 1FeFET1C cell structure, the proposed design benefits from the existing high density DRAM establishment while also significantly relaxing the capacitor retention and transistor leakage requirement; 3) the charge-domain CiM supports both binary FeFET with minimum overhead and MLC FeFET with tolerable latency for MLC state sensing, whose efficacy is validated experimentally on both cell-level and array-level; 4) the proposed CiM shows much better device variation resilience than conventional current-domain CiM, and also improves inference accuracy. Macro-level evaluation results demonstrate significantly higher energy efficiency and area efficiency compared to prior CiM works.

Duan, Jiahui [University of Notre Dame, IN (United↗
DOE OSTI2021

Co-design of Advanced Architectures for Graph Analytics using Machine Learning

A graph is an excellent way of representing relationships among entities. We can use graph analytics to synthesize and analyze such relational data, and extract relevant features that are useful for various tasks such as machine learning. Considering the crucial role of graph analytics in various domains, it is important and timely to investigate the right hardware configurations that can achieve optimal performance for graph workloads on future high-performance computing systems. Design space exploration studies facilitate the selection of appropriate configurations (e.g. memory) to achieve a desired system performance. Recently, the approach of accelerating graph analytics using persistent non-volatile memory has gained a lot of attention. Traditional system simulators such as Gem5 and NVMain can be used to explore the design space of these advanced memory architectures for graph workloads. However, these simulators are slow in execution thus limiting the efficiency of design space exploration studies. To overcome this challenge, we proposed a machine learning based approach to co-design advanced memory architectures for graph workloads. We tested our approach with DRAM, non-volatile memory, and hybrid memory (DRAM+NVM) using a breadth first search benchmark algorithm. Our results showed the applicability of the proposed machine learning based approach to the co-design of the advanced memory architectures. In this paper, we provide recommendations on selecting advanced memory architectures to achieve desired performance for graph workloads. We also discuss the performances of different machine learning models that were considered in this study.

Kurte, Kuldeep↗
DOE OSTI2022

Optically connected memory for disaggregated data centers

Recent advances in integrated photonics enable the implementation of reconfigurable, high-bandwidth, and low energy-per-bit interconnects in next-generation data centers. We propose and evaluate an Optically Connected Memory (OCM) architecture that disaggregates the main memory from the computation nodes in data centers. OCM is based on micro-ring resonators (MRRs), and it does not require any modification to the DRAM memory modules. We calculate energy consumption from real photonic devices and integrate them into a system simulator to evaluate performance. Here, our results show that (1) OCM is capable of interconnecting four DDR4 memory channels to a computing node using two fibers with 1.02 pJ energy-per-bit consumption and (2) OCM performs up to 5.5× faster than a disaggregated memory with 40G PCIe NIC connectors to computing nodes.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

efam: an e xpanded, metaproteome-supported HMM profile database of viral protein fam ilies

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases. Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ~24% on average (up to ~42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

A Survey on the Expanding Scope and Interdisciplinary Opportunities for Processing-in-Memory Techniques

Processing-in-Memory (PIM) is emerging as a practical path to overcome the limitations of traditional von Neumann architectures. At its core, PIM systems implement computing primitives such as logic operations and multiply-accumulate acceleration through compute-in-memory, near-memory processing, or hybrid designs. The role of memory cells varies widely across technologies, acting as inputs, outputs, or analog accumulators through bit-lines and sense amplifiers. This diversity creates trade-offs in precision, bandwidth, latency, and programmability, making it difficult to build a unified understanding on the progress of the field. In this survey, we organize recent advances of PIM into three areas. First, we discuss the progress on the architectural optimizations of PIM and its integration with both DRAM and emerging non-volatile memories. Second, we examine how PIM is being used to accelerate key computing domains, including generative AI workloads and high-performance kernels, along with new approaches. Third, we highlight the growing adoption of PIM in computational sciences, where it is being applied to solve interdisciplinary problems such as genome analysis, mRNA quantification, mass spectrometry, quantum circuit simulation, wave modeling, and secure computation. Finally, we synthesize the major challenges that continue to slow PIM adoption, including manufacturing constraints, power delivery, thermal reliability, data consistency, runtime and memory-management coordination, and the difficulty of building portable software abstractions without sacrificing commercial viability. This work provides an updated, structured perspective on PIM’s potential across computing and computational sciences and the barriers that must be solved for it to reach its full impact.

Asifuzzaman, Kazi [Oak Ridge National Laboratory (↗
DOE OSTI2026

FitCache: A Transparent Drop-In Framework for Multi-Tier Caching to Accelerate Distributed Deep Learning Workloads

Training in Deep learning (DL) remains highly compute- and data-intensive, with I/O becoming a critical bottleneck as models and datasets scale. Recent studies report that data loading can dominate training time, especially on large-scale HPC systems with shared parallel file systems (PFS). Existing caching approaches either rely on single-tier designs or require intrusive modifications to training pipelines, limiting their portability and effectiveness. In this work, we present FitCache, a transparent drop-in framework for multi-tier caching to accelerate distributed DL training by coordinating fast local memory (e.g., DRAM, Persistent Memory (PMem)) and NVMe as hierarchical caches atop PFS. Our design adapts to hardware diversity, i.e., if NVMe is missing, memory transparently acts as a caching tier, ensuring stable performance. FitCache transparently intercepts I/O requests and issues concurrent fetches across all tiers, returning data from the fastest responder without centralized metadata or static redirection paths. FitCache adapts to dynamic workloads and heterogeneous clusters while maintaining POSIX compatibility. Experiments on Frontier (2048 GPUs) and smaller research clusters show that FitCache reduces training time by up to 40% and per-batch I/O latency by up to 71.6% compared to Lustre Orion PFS, offering a drop-in solution for scalable DL training.

Hu, Guangxing [ORNL] (ORCID:0009000283203614)↗