SAFARI Research Group at ETH Zurich and Carnegie Mellon University (CMU-SAFARI)

SAFARI Research Group at ETH Zurich and Carnegie Mellon University

CMU-SAFARI

Geek Repo

Site for source code and tools distribution from SAFARI Research Group at ETH Zurich and Carnegie Mellon University.

Location:ETH Zurich and Carnegie Mellon University

Home Page:https://safari.ethz.ch/

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

ramulator

A Fast and Extensible DRAM Simulator, with built-in support for modeling many different DRAM technologies including DDRx, LPDDRx, GDDRx, WIOx, HBMx, and various academic proposals. Described in the IEEE CAL 2015 paper by Kim et al. at http://users.ece.cmu.edu/~omutlu/pub/ramulator_dram_simulator-ieee-cal15.pdf

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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. (preliminary version at 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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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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SparseP

SparseP is the first open-source Sparse Matrix Vector Multiplication (SpMV) software package for real-world Processing-In-Memory (PIM) architectures. SparseP is developed to evaluate and characterize the first publicly-available real-world PIM architecture, the UPMEM PIM architecture. Described by C. Giannoula et al. [https://arxiv.org/abs/2201.05072]

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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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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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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 preprint: https://arxiv.org/abs/2111.00082

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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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. (preliminary version at https://arxiv.org/abs/2112.08687)

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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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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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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)

BlockHammer

Source code for the cycle-level simulator and RTL implementation of BlockHammer proposed in our HPCA 2021 paper: Yaglikci et. al., "BlockHammer: Preventing RowHammer at Low Cost by Blacklisting Rapidly-Accessed DRAM Rows" at https://people.inf.ethz.ch/omutlu/pub/BlockHammer_preventing-DRAM-rowhammer-at-low-cost_hpca21.pdf

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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. Four prototypes are available on different FPGA boards. Described in our preprint: https://arxiv.org/pdf/2211.05838.pdf

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COVIDHunter

COVIDHunter 🦠:construction:: An accurate and flexible COVID-19 outbreak simulation model that forecasts the strength of future mitigation measures and the numbers of cases, hospitalizations, and deaths for a given day, while considering the potential effect of environmental conditions. Described by Alser et al. (preliminary version at https://arxiv.org/abs/2102.03667 and https://doi.org/10.1101/2021.02.06.21251265).

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GenStore

GenStore is the first in-storage processing system designed for genome sequence analysis that greatly reduces both data movement and computational overheads of genome sequence analysis by exploiting low-cost and accurate in-storage filters. Described in the ASPLOS 2022 paper by Mansouri Ghiasi et al. at https://people.inf.ethz.ch/omutlu/pub/GenStore_asplos22-arxiv.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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Genome-on-Diet

Genome-on-Diet is a software tool that exemplifies sparsified genomics, which greatly reduces the amount of data used for certain genome analytics tasks to improve both performance and energy efficiency, while preserving analysis accuracy 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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DRAM-Datasheet-Survey

A survey of manufacturer-provided DRAM operating parameters and timings as specified by DRAM chip datasheets from between 1970 and 2021. This data and its analysis are described in the 2022 paper by Patel et al.: https://arxiv.org/abs/2204.10378

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Molecules2Variations

The first work to provide a comprehensive survey of a prominent set of algorithmic improvement and hardware acceleration efforts for the entire genome analysis pipeline used for the three most prominent sequencing data, short reads (Illumina), ultra-long reads (ONT), and accurate long reads (HiFi). Described in arXiv (2022) by Alser et al. https://arxiv.org/abs/2205.07957

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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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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ApHMM-GPU

ApHMM-GPU is the first GPU implementation of the Baum-Welch algorithm for profile Hidden Markov Models (pHMMs). It includes many of the software optimizations as proposed in the ApHMM paper, which is described by Firtina et al. (preliminary version at https://arxiv.org/abs/2207.09765).

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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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SNP-Selective-Hiding

An optimization-based mechanism :dna: :closed_lock_with_key: to selectively hide the minimum number of overlapping SNPs among the family members :family_man_woman_girl_boy: who participated in the genomic studies (i.e. GWAS). Our goal is to distort the dependencies among the family members in the original database for achieving better privacy without significantly degrading the data utility.

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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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