SAFARI Research Group at ETH Zurich and Carnegie Mellon University

SAFARI Research Group at ETH Zurich and Carnegie Mellon University's repositories

MQSim

MQSim is a fast and accurate simulator modeling the performance of modern multi-queue (MQ) SSDs as well as traditional SATA based SSDs. MQSim faithfully models new high-bandwidth protocol implementations, steady-state SSD conditions, and the full end-to-end latency of requests in modern SSDs. It is described in detail in the FAST 2018 paper by Arash Tavakkol et al., "MQSim: A Framework for Enabling Realistic Studies of Modern Multi-Queue SSD Devices" (https://people.inf.ethz.ch/omutlu/pub/MQSim-SSD-simulation-framework_fast18.pdf)

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ramulator-pim

A fast and flexible simulation infrastructure for exploring general-purpose processing-in-memory (PIM) architectures. Ramulator-PIM combines a widely-used simulator for out-of-order and in-order processors (ZSim) with Ramulator, a DRAM simulator with memory models for DDRx, LPDDRx, GDDRx, WIOx, HBMx, and HMCx. Ramulator is described in the IEEE CAL 2015 paper by Kim et al. at https://people.inf.ethz.ch/omutlu/pub/ramulator_dram_simulator-ieee-cal15.pdf Ramulator-PIM is used in the DAC 2019 paper by Singh et al. at https://people.inf.ethz.ch/omutlu/pub/NAPEL-near-memory-computing-performance-prediction-via-ML_dac19.pdf

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prim-benchmarks

PrIM (Processing-In-Memory benchmarks) is the first benchmark suite for a real-world processing-in-memory (PIM) architecture. PrIM is developed to evaluate, analyze, and characterize the first publicly-available real-world PIM architecture, the UPMEM PIM architecture. Described by Gómez-Luna et al. (https://arxiv.org/abs/2105.03814).

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Pythia

A customizable hardware prefetching framework using online reinforcement learning as described in the MICRO 2021 paper by Bera et al. (https://arxiv.org/pdf/2109.12021.pdf).

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DAMOV

DAMOV is a benchmark suite and a methodical framework targeting the study of data movement bottlenecks in modern applications. It is intended to study new architectures, such as near-data processing. Described by Oliveira et al. (preliminary version at https://arxiv.org/pdf/2105.03725.pdf)

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Hermes

A speculative mechanism to accelerate long-latency off-chip load requests by removing on-chip cache access latency from their critical path, as described by MICRO 2022 paper by Bera et al. (https://arxiv.org/pdf/2209.00188.pdf)

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PiDRAM

PiDRAM is the first flexible end-to-end framework that enables system integration studies and evaluation of real Processing-using-Memory techniques. Prototype on a RISC-V rocket chip system implemented on an FPGA. Described in our paper: https://arxiv.org/abs/2111.00082

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SneakySnake

SneakySnake:snake: is the first and the only pre-alignment filtering algorithm that works efficiently and fast on modern CPU, FPGA, and GPU architectures. It greatly (by more than two orders of magnitude) expedites sequence alignment calculation for both short and long reads. Described in the Bioinformatics (2020) by Alser et al. https://arxiv.org/abs/1910.09020.

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DRAM-Bender

DRAM Bender is the first open source DRAM testing infrastructure that can be used to easily and comprehensively test state-of-the-art DDR4 modules of different form factors. Five prototypes are available on different FPGA boards. Described in our preprint: https://arxiv.org/pdf/2211.05838.pdf

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Scrooge

Scrooge is a high-performance pairwise sequence aligner based on the GenASM algorithm. Scrooge includes three novel algorithmic improvements on top of GenASM, and high-performance CPU and GPU implementations. Described by Lindegger et al. at https://doi.org/10.48550/arXiv.2208.09985

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BLEND

BLEND is a mechanism that can efficiently find fuzzy seed matches between sequences to significantly improve the performance and accuracy while reducing the memory space usage of two important applications: 1) finding overlapping reads and 2) read mapping. Described by Firtina et al. (published in NARGAB https://doi.org/10.1093/nargab/lqad004)

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RawHash

RawHash is the first mechanism that can accurately and efficiently map raw nanopore signals to large reference genomes (e.g., a human reference genome) in real-time without using powerful computational resources (e.g., GPUs). Described by Firtina et al. (published at https://academic.oup.com/bioinformatics/article/39/Supplement_1/i297/7210440)

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Sibyl

Source code for the software implementation of Sibyl proposed in our ISCA 2022 paper: Gagandeep Singh et. al., "Sibyl: Adaptive and Extensible Data Placement in Hybrid Storage Systems using Online Reinforcement Learning" at https://people.inf.ethz.ch/omutlu/pub/Sibyl_RL-based-data-placement-in-hybrid-storage-systems_isca22.pdf

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GenASM

Source code for the software implementations of the GenASM algorithms proposed in our MICRO 2020 paper: Senol Cali et. al., "GenASM: A High-Performance, Low-Power Approximate String Matching Acceleration Framework for Genome Sequence Analysis" at https://people.inf.ethz.ch/omutlu/pub/GenASM-approximate-string-matching-framework-for-genome-analysis_micro20.pdf

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AirLift

AirLift is a tool that updates mapped reads from one reference genome to another. Unlike existing tools, It accounts for regions not shared between the two reference genomes and enables remapping across all parts of the references. Described by Kim et al. (preliminary version at http://arxiv.org/abs/1912.08735)

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FastRemap

FastRemap, a C++ tool for quickly remapping reads between genome assemblies based on the commonly used CrossMap tool. Link to paper: https://arxiv.org/pdf/2201.06255.pdf

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NOCulator

NOCulator is a network-on-chip simulator providing cycle-accurate performance models for a wide variety of networks (mesh, torus, ring, hierarchical ring, flattened butterfly) and routers (buffered, bufferless, Adaptive Flow Control, minBD, HiRD).

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SPARTA

A novel spatial accelerator for horizontal diffusion weather stencil computation, as described in ICS 2023 paper by Singh et al. (https://arxiv.org/pdf/2303.03509.pdf)

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pLUTo

pLUTo is a DRAM-based Processing-using-Memory architecture that leverages the high density of DRAM to enable the massively parallel storing and querying of lookup tables (LUTs)

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pim-ml

PIM-ML is a benchmark for training machine learning algorithms on the UPMEM architecture, which is the first publicly-available real-world processing-in-memory (PIM) architecture. Described in the ISPASS 2023 paper by Gomez-Luna et al. (https://arxiv.org/pdf/2207.07886.pdf).

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SeGraM

Source code for the software implementation of SeGraM proposed in our ISCA 2022 paper: Senol Cali et. al., "SeGraM: A Universal Hardware Accelerator for Genomic Sequence-to-Graph and Sequence-to-Sequence Mapping" at https://people.inf.ethz.ch/omutlu/pub/SeGraM_genomic-sequence-mapping-universal-accelerator_isca22.pdf

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Genome-on-Diet

Genome-on-Diet is a fast and memory-frugal framework for exemplifying sparsified genomics for read mapping, containment search, and metagenomic profiling. It is much faster & more memory-efficient than minimap2 for Illumina, HiFi, and ONT reads. Described by Alser et al. (preliminary version: https://arxiv.org/abs/2211.08157).

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U-TRR

Source code of the U-TRR methodology presented in "Uncovering In-DRAM RowHammer Protection Mechanisms: A New Methodology, Custom RowHammer Patterns, and Implications", https://people.inf.ethz.ch/omutlu/pub/U-TRR-uncovering-RowHammer-protection-mechanisms_micro21.pdf

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MetaSys

Metasys is the first open-source FPGA-based infrastructure with a prototype in a RISC-V core, to enable the rapid implementation and evaluation of a wide range of cross-layer software/hardware cooperative techniques techniques in real hardware. Described in our ACM TACO paper: https://dl.acm.org/doi/full/10.1145/3505250

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QUAC-TRNG

All sources to reproduce the results presented in our paper, QUAC-TRNG, the highest-throughput DRAM-based true random number generator, described in https://people.inf.ethz.ch/omutlu/pub/QUAC-TRNG-DRAM_isca21.pdf

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TargetCall

TargetCall is the first pre-basecalling filter that is applicable to a wide range of use cases to eliminate wasted computation in basecalling. Described in our preprint: https://arxiv.org/abs/2212.04953

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transpimlib

TransPimLib is a library for transcendental (and other hard-to-calculate) functions in general-purpose PIM systems, TransPimLib provides CORDIC-based and LUT-based methods for trigonometric functions, hyperbolic functions, exponentiation, logarithm, square root, etc. Described in ISPASS'23 paper by Item et al. (https://arxiv.org/pdf/2304.01951.pdf)

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BioDynaMo

BioDynamo is a flexible and high-performance agent based simulation engine. This repository contains artifacts and materials to support the reproducibility of the paper: Breitwieser et al., "High-Performance and Scalable Agent-Based Simulation with BioDynaMo," accepted to PPoPP '23: https://arxiv.org/pdf/2301.06984.pdf

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SelfManagingDRAM

Source code for evaluating the performance and DRAM energy benefits of Self-Managing DRAM (SMD), proposed in https://arxiv.org/abs/2207.13358

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alignment-in-memory

AIM (Alignment-in-Memory), A Framework for High-throughput Sequence Alignment using Real Processing-in-Memory Systems, Bioinformatics, btad155, https://doi.org/10.1093/bioinformatics/btad155

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