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Onur Mutlu

Publications and source records attributed to Onur Mutlu.

At least 181 records · Page 10Linked to original sources
arXiv2022

BlockHammer: Preventing RowHammer at Low Cost by Blacklisting Rapidly-Accessed DRAM Rows

Aggressive memory density scaling causes modern DRAM devices to suffer from RowHammer, a phenomenon where rapidly activating a DRAM row can cause bit-flips in physically-nearby rows. Recent studies demonstrate that modern DRAM chips, including chips previously marketed as RowHammer-safe, are even more vulnerable to RowHammer than older chips. Many works show that attackers can exploit RowHammer bit-flips to reliably mount system-level attacks to escalate privilege and leak private data. Therefore, it is critical to ensure RowHammer-safe operation on all DRAM-based systems. Unfortunately, state-of-the-art RowHammer mitigation mechanisms face two major challenges. First, they incur increasingly higher performance and/or area overheads when applied to more vulnerable DRAM chips. Second, they require either proprietary information about or modifications to the DRAM chip design. In this paper, we show that it is possible to efficiently and scalably prevent RowHammer bit-flips without knowledge of or modification to DRAM internals. We introduce BlockHammer, a low-cost, effective, and easy-to-adopt RowHammer mitigation mechanism that overcomes the two key challenges by selectively throttling memory accesses that could otherwise cause RowHammer bit-flips. The key idea of BlockHammer is to (1) track row activation rates using area-efficient Bloom filters and (2) use the tracking data to ensure that no row is ever activated rapidly enough to induce RowHammer bit-flips. By doing so, BlockHammer (1) makes it impossible for a RowHammer bit-flip to occur and (2) greatly reduces a RowHammer attack's impact on the performance of co-running benign applications. Compared to state-of-the-art RowHammer mitigation mechanisms, BlockHammer provides competitive performance and energy when the system is not under a RowHammer attack and significantly better performance and energy when the system is under attack.

cs.CR↗
arXiv2022

Understanding RowHammer Under Reduced Wordline Voltage: An Experimental Study Using Real DRAM Devices

RowHammer is a circuit-level DRAM vulnerability, where repeatedly activating and precharging a DRAM row, and thus alternating the voltage of a row's wordline between low and high voltage levels, can cause bit flips in physically nearby rows. Recent DRAM chips are more vulnerable to RowHammer: with technology node scaling, the minimum number of activate-precharge cycles to induce a RowHammer bit flip reduces and the RowHammer bit error rate increases. Therefore, it is critical to develop effective and scalable approaches to protect modern DRAM systems against RowHammer. To enable such solutions, it is essential to develop a deeper understanding of the RowHammer vulnerability of modern DRAM chips. However, even though the voltage toggling on a wordline is a key determinant of RowHammer vulnerability, no prior work experimentally demonstrates the effect of wordline voltage (VPP) on the RowHammer vulnerability. Our work closes this gap in understanding. This is the first work to experimentally demonstrate on 272 real DRAM chips that lowering VPP reduces a DRAM chip's RowHammer vulnerability. We show that lowering VPP 1) increases the number of activate-precharge cycles needed to induce a RowHammer bit flip by up to 85.8% with an average of 7.4% across all tested chips and 2) decreases the RowHammer bit error rate by up to 66.9% with an average of 15.2% across all tested chips. At the same time, reducing VPP marginally worsens a DRAM cell's access latency, charge restoration, and data retention time within the guardbands of system-level nominal timing parameters for 208 out of 272 tested chips. We conclude that reducing VPP is a promising strategy for reducing a DRAM chip's RowHammer vulnerability without requiring modifications to DRAM chips.

cs.AR↗
arXiv2022

COVIDHunter: COVID-19 pandemic wave prediction and mitigation via seasonality-aware modeling

Early detection and isolation of COVID-19 patients are essential for successful implementation of mitigation strategies and eventually curbing the disease spread. With a limited number of daily COVID-19 tests performed in every country, simulating the COVID-19 spread along with the potential effect of each mitigation strategy currently remains one of the most effective ways in managing the healthcare system and guiding policy-makers. We introduce COVIDHunter, a flexible and accurate COVID-19 outbreak simulation model that evaluates the current mitigation measures that are applied to a region, predicts COVID-19 statistics (the daily number of cases, hospitalizations, and deaths), and provides suggestions on what strength the upcoming mitigation measure should be. The key idea of COVIDHunter is to quantify the spread of COVID-19 in a geographical region by simulating the average number of new infections caused by an infected person considering the effect of external factors, such as environmental conditions (e.g., climate, temperature, humidity), different variants of concern, vaccination rate, and mitigation measures. Using Switzerland as a case study, COVIDHunter estimates that we are experiencing a deadly new wave that will peak on 26 January 2022, which is very similar in numbers to the wave we had in February 2020. The policy-makers have only one choice that is to increase the strength of the currently applied mitigation measures for 30 days. Unlike existing models, the COVIDHunter model accurately monitors and predicts the daily number of cases, hospitalizations, and deaths due to COVID-19. Our model is flexible to configure and simple to modify for modeling different scenarios under different environmental conditions and mitigation measures. We release the source code of the COVIDHunter implementation at https://github.com/CMU-SAFARI/COVIDHunter.

q-bio.QM↗
arXiv2022

COVIDHunter: An Accurate, Flexible, and Environment-Aware Open-Source COVID-19 Outbreak Simulation Model

Background: Early detection and isolation of COVID-19 patients are essential for successful implementation of mitigation strategies and eventually curbing the disease spread. With a limited number of daily COVID-19 tests performed in every country, simulating the COVID-19 spread along with the potential effect of each mitigation strategy currently remains one of the most effective ways in managing the healthcare system and guiding policy-makers. Methods: We introduce COVIDHunter, a flexible and accurate COVID-19 outbreak simulation model that evaluates the current mitigation measures that are applied to a region and provides suggestions on what strength the upcoming mitigation measure should be. The key idea of COVIDHunter is to quantify the spread of COVID-19 in a geographical region by simulating the average number of new infections caused by an infected person considering the effect of external factors, such as environmental conditions (e.g., climate, temperature, humidity) and mitigation measures. Results: Using Switzerland as a case study, COVIDHunter estimates that if the policy-makers relax the mitigation measures by 50% for 30 days then both the daily capacity need for hospital beds and daily number of deaths increase exponentially by an average of 5.1x, who may occupy ICU beds and ventilators for a period of time. Unlike existing models, the COVIDHunter model accurately monitors and predicts the daily number of cases, hospitalizations, and deaths due to COVID-19. Our model is flexible to configure and simple to modify for modeling different scenarios under different environmental conditions and mitigation measures. Availability: We release the source code of the COVIDHunter implementation at https://github.com/CMU- SAFARI/COVIDHunter and show how to flexibly configure our model for any scenario and easily extend it for different measures and conditions than we account for.

q-bio.PE↗
arXiv2022

DR-STRaNGe: End-to-End System Design for DRAM-based True Random Number Generators

Random number generation is an important task in a wide variety of critical applications including cryptographic algorithms, scientific simulations, and industrial testing tools. True Random Number Generators (TRNGs) produce truly random data by sampling a physical entropy source that typically requires custom hardware and suffers from long latency. To enable high-bandwidth and low-latency TRNGs on commodity devices, recent works propose TRNGs that use DRAM as an entropy source. Although prior works demonstrate promising DRAM-based TRNGs, integration of such mechanisms into real systems poses challenges. We identify three challenges for using DRAM-based TRNGs in current systems: (1) generating random numbers can degrade system performance by slowing down concurrently-running applications due to the interference between RNG and regular memory operations in the memory controller (i.e., RNG interference), (2) this RNG interference can degrade system fairness by unfairly prioritizing applications that intensively use random numbers (i.e., RNG applications), and (3) RNG applications can experience significant slowdowns due to the high RNG latency. We propose DR-STRaNGe, an end-to-end system design for DRAM-based TRNGs that (1) reduces the RNG interference by separating RNG requests from regular requests in the memory controller, (2) improves the system fairness with an RNG-aware memory request scheduler, and (3) hides the large TRNG latencies using a random number buffering mechanism with a new DRAM idleness predictor that accurately identifies idle DRAM periods. We evaluate DR-STRaNGe using a set of 186 multiprogrammed workloads. Compared to an RNG-oblivious baseline system, DR-STRaNGe improves the average performance of non-RNG and RNG applications by 17.9% and 25.1%, respectively. DR-STRaNGe improves average system fairness by 32.1% and reduces average energy consumption by 21%.

cs.AR↗
arXiv2022

Exploiting Near-Data Processing to Accelerate Time Series Analysis

Time series analysis is a key technique for extracting and predicting events in domains as diverse as epidemiology, genomics, neuroscience, environmental sciences, economics, and more. Matrix profile, the state-of-the-art algorithm to perform time series analysis, computes the most similar subsequence for a given query subsequence within a sliced time series. Matrix profile has low arithmetic intensity, but it typically operates on large amounts of time series data. In current computing systems, this data needs to be moved between the off-chip memory units and the on-chip computation units for performing matrix profile. This causes a major performance bottleneck as data movement is extremely costly in terms of both execution time and energy. In this work, we present NATSA, the first Near-Data Processing accelerator for time series analysis. The key idea is to exploit modern 3D-stacked High Bandwidth Memory (HBM) to enable efficient and fast specialized matrix profile computation near memory, where time series data resides. NATSA provides three key benefits: 1) quickly computing the matrix profile for a wide range of applications by building specialized energy-efficient floating-point arithmetic processing units close to HBM, 2) improving the energy efficiency and execution time by reducing the need for data movement over slow and energy-hungry buses between the computation units and the memory units, and 3) analyzing time series data at scale by exploiting low-latency, high-bandwidth, and energy-efficient memory access provided by HBM. Our experimental evaluation shows that NATSA improves performance by up to 14.2x (9.9x on average) and reduces energy by up to 27.2x (19.4x on average), over the state-of-the-art multi-core implementation. NATSA also improves performance by 6.3x and reduces energy by 10.2x over a general-purpose NDP platform with 64 in-order cores.

cs.AR↗
arXiv2022

PiDRAM: An FPGA-based Framework for End-to-end Evaluation of Processing-in-DRAM Techniques

DRAM-based main memory is used in nearly all computing systems as a major component. One way of overcoming the main memory bottleneck is to move computation near memory, a paradigm known as processing-in-memory (PiM). Recent PiM techniques provide a promising way to improve the performance and energy efficiency of existing and future systems at no additional DRAM hardware cost. We develop the Processing-in-DRAM (PiDRAM) framework, the first flexible, end-to-end, and open source framework that enables system integration studies and evaluation of real PiM techniques using real DRAM chips. We demonstrate a prototype of PiDRAM on an FPGA-based platform (Xilinx ZC706) that implements an open-source RISC-V system (Rocket Chip). To demonstrate the flexibility and ease of use of PiDRAM, we implement two PiM techniques: (1) RowClone, an in-DRAM copy and initialization mechanism (using command sequences proposed by ComputeDRAM), and (2) D-RaNGe, an in-DRAM true random number generator based on DRAM activation-latency failures. Our end-to-end evaluation of RowClone shows up to 14.6X speedup for copy and 12.6X initialization operations over CPU copy (i.e., conventional memcpy) and initialization (i.e., conventional calloc) operations. Our implementation of D-RaNGe provides high throughput true random numbers, reaching 8.30 Mb/s throughput. Over the Verilog and C++ basis provided by PiDRAM, implementing the required hardware and software components, implementing RowClone end-to-end takes 198 (565) and implementing D-RaNGe end-to-end takes 190 (78) lines of Verilog (C++) code. PiDRAM is open sourced on Github: https://github.com/CMU-SAFARI/PiDRAM.

cs.AR↗
arXiv2022

Methodologies, Workloads, and Tools for Processing-in-Memory: Enabling the Adoption of Data-Centric Architectures

The increasing prevalence and growing size of data in modern applications have led to high costs for computation in traditional processor-centric computing systems. Moving large volumes of data between memory devices (e.g., DRAM) and computing elements (e.g., CPUs, GPUs) across bandwidth-limited memory channels can consume more than 60% of the total energy in modern systems. To mitigate these costs, the processing-in-memory (PIM) paradigm moves computation closer to where the data resides, reducing (and in some cases eliminating) the need to move data between memory and the processor. There are two main approaches to PIM: (1) processing-near-memory (PnM), where PIM logic is added to the same die as memory or to the logic layer of 3D-stacked memory; and (2) processing-using-memory (PuM), which uses the operational principles of memory cells to perform computation. Many works from academia and industry have shown the benefits of PnM and PuM for a wide range of workloads from different domains. However, fully adopting PIM in commercial systems is still very challenging due to the lack of tools and system support for PIM architectures across the computer architecture stack, which includes: (i) workload characterization methodologies and benchmark suites targeting PIM architectures; (ii) frameworks that can facilitate the implementation of complex operations and algorithms using the underlying PIM primitives; (iii) compiler support and compiler optimizations targeting PIM architectures; (iv) operating system support for PIM-aware virtual memory, memory management, data allocation, and data mapping; and (v) efficient data coherence and consistency mechanisms. Our goal in this work is to provide tools and system support for PnM and PuM architectures, aiming to ease the adoption of PIM in current and future systems.

cs.AR↗
arXiv2022

SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping

A critical step of genome sequence analysis is the mapping of sequenced DNA fragments (i.e., reads) collected from an individual to a known linear reference genome sequence (i.e., sequence-to-sequence mapping). Recent works replace the linear reference sequence with a graph-based representation of the reference genome, which captures the genetic variations and diversity across many individuals in a population. Mapping reads to the graph-based reference genome (i.e., sequence-to-graph mapping) results in notable quality improvements in genome analysis. Unfortunately, while sequence-to-sequence mapping is well studied with many available tools and accelerators, sequence-to-graph mapping is a more difficult computational problem, with a much smaller number of practical software tools currently available. We analyze two state-of-the-art sequence-to-graph mapping tools and reveal four key issues. We find that there is a pressing need to have a specialized, high-performance, scalable, and low-cost algorithm/hardware co-design that alleviates bottlenecks in both the seeding and alignment steps of sequence-to-graph mapping. To this end, we propose SeGraM, a universal algorithm/hardware co-designed genomic mapping accelerator that can effectively and efficiently support both sequence-to-graph mapping and sequence-to-sequence mapping, for both short and long reads. To our knowledge, SeGraM is the first algorithm/hardware co-design for accelerating sequence-to-graph mapping. SeGraM consists of two main components: (1) MinSeed, the first minimizer-based seeding accelerator; and (2) BitAlign, the first bitvector-based sequence-to-graph alignment accelerator. We demonstrate that SeGraM provides significant improvements for multiple steps of the sequence-to-graph and sequence-to-sequence mapping pipelines.

cs.AR↗
arXiv2022

Heterogeneous Data-Centric Architectures for Modern Data-Intensive Applications: Case Studies in Machine Learning and Databases

Today's computing systems require moving data back-and-forth between computing resources (e.g., CPUs, GPUs, accelerators) and off-chip main memory so that computation can take place on the data. Unfortunately, this data movement is a major bottleneck for system performance and energy consumption. One promising execution paradigm that alleviates the data movement bottleneck in modern and emerging applications is processing-in-memory (PIM), where the cost of data movement to/from main memory is reduced by placing computation capabilities close to memory. Naively employing PIM to accelerate data-intensive workloads can lead to sub-optimal performance due to the many design constraints PIM substrates impose. Therefore, many recent works co-design specialized PIM accelerators and algorithms to improve performance and reduce the energy consumption of (i) applications from various application domains; and (ii) various computing environments, including cloud systems, mobile systems, and edge devices. We showcase the benefits of co-designing algorithms and hardware in a way that efficiently takes advantage of the PIM paradigm for two modern data-intensive applications: (1) machine learning inference models for edge devices and (2) hybrid transactional/analytical processing databases for cloud systems. We follow a two-step approach in our system design. In the first step, we extensively analyze the computation and memory access patterns of each application to gain insights into its hardware/software requirements and major sources of performance and energy bottlenecks in processor-centric systems. In the second step, we leverage the insights from the first step to co-design algorithms and hardware accelerators to enable high-performance and energy-efficient data-centric architectures for each application.

cs.AR↗
arXiv2022

SparseP: Towards Efficient Sparse Matrix Vector Multiplication on Real Processing-In-Memory Systems

Several manufacturers have already started to commercialize near-bank Processing-In-Memory (PIM) architectures. Near-bank PIM architectures place simple cores close to DRAM banks and can yield significant performance and energy improvements in parallel applications by alleviating data access costs. Real PIM systems can provide high levels of parallelism, large aggregate memory bandwidth and low memory access latency, thereby being a good fit to accelerate the widely-used, memory-bound Sparse Matrix Vector Multiplication (SpMV) kernel. This paper provides the first comprehensive analysis of SpMV on a real-world PIM architecture, and presents SparseP, the first SpMV library for real PIM architectures. We make three key contributions. First, we implement a wide variety of software strategies on SpMV for a multithreaded PIM core and characterize the computational limits of a single multithreaded PIM core. Second, we design various load balancing schemes across multiple PIM cores, and two types of data partitioning techniques to execute SpMV on thousands of PIM cores: (1) 1D-partitioned kernels to perform the complete SpMV computation only using PIM cores, and (2) 2D-partitioned kernels to strive a balance between computation and data transfer costs to PIM-enabled memory. Third, we compare SpMV execution on a real-world PIM system with 2528 PIM cores to state-of-the-art CPU and GPU systems to study the performance and energy efficiency of various devices. SparseP software package provides 25 SpMV kernels for real PIM systems supporting the four most widely used compressed matrix formats, and a wide range of data types. Our extensive evaluation provides new insights and recommendations for software designers and hardware architects to efficiently accelerate SpMV on real PIM systems.

cs.AR↗
arXiv2022

Going From Molecules to Genomic Variations to Scientific Discovery: Intelligent Algorithms and Architectures for Intelligent Genome Analysis

We now need more than ever to make genome analysis more intelligent. We need to read, analyze, and interpret our genomes not only quickly, but also accurately and efficiently enough to scale the analysis to population level. There currently exist major computational bottlenecks and inefficiencies throughout the entire genome analysis pipeline, because state-of-the-art genome sequencing technologies are still not able to read a genome in its entirety. We describe the ongoing journey in significantly improving the performance, accuracy, and efficiency of genome analysis using intelligent algorithms and hardware architectures. We explain state-of-the-art algorithmic methods and hardware-based acceleration approaches for each step of the genome analysis pipeline and provide experimental evaluations. Algorithmic approaches exploit the structure of the genome as well as the structure of the underlying hardware. Hardware-based acceleration approaches exploit specialized microarchitectures or various execution paradigms (e.g., processing inside or near memory) along with algorithmic changes, leading to new hardware/software co-designed systems. We conclude with a foreshadowing of future challenges, benefits, and research directions triggered by the development of both very low cost yet highly error prone new sequencing technologies and specialized hardware chips for genomics. We hope that these efforts and the challenges we discuss provide a foundation for future work in making genome analysis more intelligent. The analysis script and data used in our experimental evaluation are available at: https://github.com/CMU-SAFARI/Molecules2Variations

q-bio.GN↗
arXiv2022

Benchmarking a New Paradigm: An Experimental Analysis of a Real Processing-in-Memory Architecture

Many modern workloads, such as neural networks, databases, and graph processing, are fundamentally memory-bound. For such workloads, the data movement between main memory and CPU cores imposes a significant overhead in terms of both latency and energy. A major reason is that this communication happens through a narrow bus with high latency and limited bandwidth, and the low data reuse in memory-bound workloads is insufficient to amortize the cost of main memory access. Fundamentally addressing this data movement bottleneck requires a paradigm where the memory system assumes an active role in computing by integrating processing capabilities. This paradigm is known as processing-in-memory (PIM). Recent research explores different forms of PIM architectures, motivated by the emergence of new 3D-stacked memory technologies that integrate memory with a logic layer where processing elements can be easily placed. Past works evaluate these architectures in simulation or, at best, with simplified hardware prototypes. In contrast, the UPMEM company has designed and manufactured the first publicly-available real-world PIM architecture. This paper provides the first comprehensive analysis of the first publicly-available real-world PIM architecture. We make two key contributions. First, we conduct an experimental characterization of the UPMEM-based PIM system using microbenchmarks to assess various architecture limits such as compute throughput and memory bandwidth, yielding new insights. Second, we present PrIM, a benchmark suite of 16 workloads from different application domains (e.g., linear algebra, databases, graph processing, neural networks, bioinformatics).

cs.AR↗
arXiv2022

Enabling High-Performance and Energy-Efficient Hybrid Transactional/Analytical Databases with Hardware/Software Cooperation

A growth in data volume, combined with increasing demand for real-time analysis (using the most recent data), has resulted in the emergence of database systems that concurrently support transactions and data analytics. These hybrid transactional and analytical processing (HTAP) database systems can support real-time data analysis without the high costs of synchronizing across separate single-purpose databases. Unfortunately, for many applications that perform a high rate of data updates, state-of-the-art HTAP systems incur significant losses in transactional (up to 74.6%) and/or analytical (up to 49.8%) throughput compared to performing only transactional or only analytical queries in isolation, due to (1) data movement between the CPU and memory, (2) data update propagation from transactional to analytical workloads, and (3) the cost to maintain a consistent view of data across the system. We propose Polynesia, a hardware-software co-designed system for in-memory HTAP databases that avoids the large throughput losses of traditional HTAP systems. Polynesia (1) divides the HTAP system into transactional and analytical processing islands, (2) implements new custom hardware that unlocks software optimizations to reduce the costs of update propagation and consistency, and (3) exploits processing-in-memory for the analytical islands to alleviate data movement overheads. Our evaluation shows that Polynesia outperforms three state-of-the-art HTAP systems, with average transactional/analytical throughput improvements of 1.7x/3.7x, and reduces energy consumption by 48% over the prior lowest-energy HTAP system.

cs.AR↗
arXiv2022

A Case for Transparent Reliability in DRAM Systems

Today's systems have diverse needs that are difficult to address using one-size-fits-all commodity DRAM. Unfortunately, although system designers can theoretically adapt commodity DRAM chips to meet their particular design goals (e.g., by reducing access timings to improve performance, implementing system-level RowHammer mitigations), we observe that designers today lack sufficient insight into commodity DRAM chips' reliability characteristics to implement these techniques in practice. In this work, we make a case for DRAM manufacturers to provide increased transparency into key aspects of DRAM reliability (e.g., basic chip design properties, testing strategies). Doing so enables system designers to make informed decisions to better adapt commodity DRAM to meet modern systems' needs while preserving its cost advantages. To support our argument, we study four ways that system designers can adapt commodity DRAM chips to system-specific design goals: (1) improving DRAM reliability; (2) reducing DRAM refresh overheads; (3) reducing DRAM access latency; and (4) mitigating RowHammer attacks. We observe that adopting solutions for any of the four goals requires system designers to make assumptions about a DRAM chip's reliability characteristics. These assumptions discourage system designers from using such solutions in practice due to the difficulty of both making and relying upon the assumption. We identify DRAM standards as the root of the problem: current standards rigidly enforce a fixed operating point with no specifications for how a system designer might explore alternative operating points. To overcome this problem, we introduce a two-step approach that reevaluates DRAM standards with a focus on transparency of DRAM reliability so that system designers are encouraged to make the most of commodity DRAM technology for both current and future DRAM chips.

cs.AR↗
arXiv2022

Towards Efficient Sparse Matrix Vector Multiplication on Real Processing-In-Memory Systems

Several manufacturers have already started to commercialize near-bank Processing-In-Memory (PIM) architectures. Near-bank PIM architectures place simple cores close to DRAM banks and can yield significant performance and energy improvements in parallel applications by alleviating data access costs. Real PIM systems can provide high levels of parallelism, large aggregate memory bandwidth and low memory access latency, thereby being a good fit to accelerate the widely-used, memory-bound Sparse Matrix Vector Multiplication (SpMV) kernel. This paper provides the first comprehensive analysis of SpMV on a real-world PIM architecture, and presents SparseP, the first SpMV library for real PIM architectures. We make two key contributions. First, we design efficient SpMV algorithms to accelerate the SpMV kernel in current and future PIM systems, while covering a wide variety of sparse matrices with diverse sparsity patterns. Second, we provide the first comprehensive analysis of SpMV on a real PIM architecture. Specifically, we conduct our rigorous experimental analysis of SpMV kernels in the UPMEM PIM system, the first publicly-available real-world PIM architecture. Our extensive evaluation provides new insights and recommendations for software designers and hardware architects to efficiently accelerate the SpMV kernel on real PIM systems. For more information about our thorough characterization on the SpMV PIM execution, results, insights and the open-source SparseP software package [26], we refer the reader to the full version of the paper [3, 4]. The SparseP software package is publicly and freely available at https://github.com/CMU-SAFARI/SparseP.

cs.AR↗
arXiv2022

Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities

Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging, virtualization, and containerization are different approaches to satisfy this need by wrapping omics tools in additional software that makes the omics tools easier to install and use. Here, we systematically review practices across prominent packaging, virtualization, and containerization platforms. We outline the challenges, advantages, and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers, and system administrators. We also propose principles to make packaging, virtualization, and containerization of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.

q-bio.GN↗