This project is a RISC-V CPU simulation implemented by Lior Kaplun and Idan Magram which simulates:
Wanger Fischer simulation:
    simulates calculation of 1000 WF of a read and sub-reference segment on a RISC-V simulation environment (Gem5)

    to run:
        1. first download gem5 simulator https://github.com/ppeetteerrs/gem5-RISC-V-FS-Linux
        2. riscv64-unknown-linux-gnu-g++ -std=c++17 -O3 <simulationDir>/WF_sim.cpp -static -o WF_sim
        3. cd to gem5 wd and run sudo build/riscv/gem5.opt --outdir=out_results
        <simulationDir>/multicore_with_1L2_0L3_simple.py --binary WF_sim
        4. The results will be shown at out_results/stats.txt
        5. divide by 1000 the simulation time for the time of one WF

manager simulation:
    There is a predefined list with minimizers the CPU is responsible for.
    Will find minimizers of each read.
    Calculate the read’s potential location of the minimizers from the list. (using WF)
    Send the other minimizers and the read to the DART-PIM and receive back the results.
    Decide which is the best candidate over all results
    Reconstruct the Genome

    to run:
        1. riscv64-unknown-linux-gnu-g++ -std=c++17 -O3 <simulationDir>/manager.cpp -static -o manager
        2. cd to gem5 wd and run  sudo build/riscv/gem5.opt --outdir=simple_ou
           <simulationDir>/multicore_with_1L2_0L3.py --binary wd/manager
           --args "-reads <simulationDir>/reads_R1_25.fastq  -mins <simulationDir>/riscv_cpu_mins.txt
           -pim <simulationDir>/readsMappings_090524.txt"
        3. The results will be shown at out_results/stats.txt