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Performance issues, memory leak, high cpu usage?

Open alext-extracellular opened this issue 6 months ago • 2 comments

Hi there, I am not sure if this is because I am using the package wrong, but when I try and make the most simple possible script to run a simulation, I am getting very high memory and CPU usage, and it seems to hang and not produce any results. When I had save_points set to nothing, the memory usage climbed to 5.9 GB and then it got OOM killed. I tried with save_points set as below, and this took me to 533 MB and 12.4% CPU usage, and stayed there for a while before I killed it as well. Any tips would be appreciated!

 using BioSimulator, Plots
  
  # initialize
  network = Network("BDI")
 
  # species definitions; add components with <=
  network <= Species("X", 5)
  
  # reaction definitions
  network <= Reaction("birth", 2.0, "X --> X + X")
  network <= Reaction("death", 1.0, "X --> 0")
  network <= Reaction("immigration", 0.5, "0 --> X")
  state, model = parse_model(network)
  result = simulate(state, model, EnhancedDirect(),
             tfinal = 100.0,
             save_points = 0:10:100)
  
  plot(result, summary = :trajectory,
      xlabel = "time", ylabel = "count",
      label = ["X"])

alext-extracellular avatar Aug 05 '24 10:08 alext-extracellular