/SeisIO_paper

Downloadable benchmark tests and raw results for SeisIO:

Primary LanguagePython

SeisIO_paper

Downloadable benchmark tests and raw results from Jones et al., SeisIO: a fast, efficient geophysical data architecture for the Julia language, submitted to SRL.

How to Run Benchmarks

  1. Install Julia ≥1.1 and Python ≥3.6. We used Julia v1.1.0 and Python v3.6.8 in the manuscript.
  2. (Optional) Get restricted files; see "Data and Resources" section in paper.
    • Start Julia and run these commands: using Pkg; Pkg.add("SeisIO"); using SeisIO; SeisIO_root = dirname(pathof(SeisIO)). Save that location for the next step.
    • Place the restricted files in SeisIO_root/../test/SampleFiles/Restricted/.
  3. SAC:
    • Install SAC 101.6a from source
    • Follow example template and instructions in SAC/sac_shell.sh
    • These runs produce screen output; dump or redirect to a temporary file
    • Parse the temp file with grep -v to generate log files SAC.read_sac.log, SAC.read_suds.log
    • If carefully checking memory, repeat the process with time -v and overwrite values in run_sac_stats.jl with the medians
  4. ObsPy:
    • (Ubuntu 18.04) ensure pip is installed: sudo apt install pip
    • Modify the value of SeisIO_path in Python/ObsPy_bench1.py if you need to run the "restricted" benchmarks.
    • Install ObsPy following these instructions
      • Be sure to create and activate an ObsPy environment
    • From the bash shell: conda install pytest memory_profiler pyasdf
    • Change directory to Python/.
    • Start python3.
    • At the prompt: exec(open("ObsPy_bench1.py").read())
  5. SeisIO
    • Start Julia in the root directory of this project.
    • At the Julia prompt:
include("configure.jl")             # configure Julia portion of project
include("benchmark_file_reads.jl")  # run SeisIO benchmarks
include("benchmark_hist.jl")        # generate plots for your own benchmarks