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Hi, I suggest that you send this model and request for advices either in the discussions (I will convert it to discussion anyway) or -- better -- on the mailing list. And it would be more effective if you explain what you intend to do with this grid with 25k agents: if it is only for holding values and serving as an "environment" to the agents, most can be done with fields rather than grids. If problems with GAMA are to be uncovered when measuring performances, feel free to open another issue on these problems. Thanks ! |
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Describe the bug
Creating the environment by using a matrix (https://gama-platform.org/wiki/GridSpecies#grid-from-a-matrix) is useful for defined geometries but extremely slow even with dealing with around 2000 agents. The code is very slow to the point that taking readings is not possible.
To Reproduce
Steps to reproduce the behavior:
Files
Matrix8P.csv
Desktop:
Additional context
Any recommendations for speeding up the current code are highly appreciated. The code describes the spread of a disease in a population.
model Project
/*
author: Leen Alrawas (leenr2001@gmail.com)
*/
global {
// Variables to control the grid
int matrixSize <- 500; // grid size
geometry shape <- square(matrixSize); // grid shape
file my_csv_file <- csv_file("C:/Users/leenr/Desktop/Matrix8P.csv",","); // change the location of the excel file
//file my_map <- gif_file("C:/Users/leenr/Desktop/my_map.gif"); // change the location of the gif file
matrix data <- matrix(my_csv_file);
int numOfPatches <- 8;
int numOfTunnels <- 134;
map<int, list<sir_grid>> patchesMap; // the numbered patches
map<int, list<sir_grid>> tunnelsMap; // the numbered tunnels
list<sir_grid> tunnels; // List of tunnels
list<sir_grid> entrance; // List of patch entrances
list<sir_grid> exit; // List of patch exits
list<sir_grid> patches <- []; // list of cells in all patches
map<int, int> PatchesArea; // list of areas of patches
int PatchArea; // patch area
// Variables to control the population
int neighbours_size <- 1; // agents at distace of "neighbours_size" cells are considered neighbours
float P1 <- 0.06;
float P2 <- 0.505;
float P3 <- 1 - P2 - P1;
float Cn <- 0.649;
float C <- 0.95 * Cn + 0.05;
list initialSList <- [
int(C30000.75P1),int(C30000.386P2),int(C30000.632P3),int(C30000.080P3),
int(C30000.287P3),int(C30000.25P1),int(C30000.495P2),int(C30000.119P2)
];
//list initialSList <- [90,390,550,70,250,30,500,120]; // Initial Susceptible population sizes for each patch
list initialIList <- [0, 5, 0, 5, 0, 5, 0, 5]; // Initial Infected population sizes for each patch
list initialVList; // Initial vaccinated population sizes
list sick_agents;// <- [63, 52, 83, 22, 63, 22, 63, 52]; // population with chronic or health conditions - per patch
map<int, float> crowd_index; // population density
list AgeMeanList <- [40.0, 50.0, 60.0, 60.0, 60.0, 40.0, 50.0, 50.0]; // Age mean for each patch
list AgeSDList; // Age standard deviation for each patch
map<int, float> age_index; // [agents(+60) / all agents] - per patch
map<int, float> health_index <- [1::0.173, 2::0.173, 3::0.173, 4::0.173,
5::0.173, 6::0.173, 7::0.173, 8::0.173]; // [sick_agents / all agents] - per patch
// Variables to control the mobility
list local_mobility_list <- [1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0]; // ratio of agents allowed to move locally - per patch
int stay_time <- 10; // time being in a foreign patch (in cycles)
float mobility_probability <- 1.0;
// Variables to control the disease
int safe_exposure_time <- 5; // time being exposed before becoming infectious (in cycles)
float alpha <- 0.3; // parameters in flowchart
// float betaSUS <- 0.5;
// float betaVAC <- 0.1;
map<int, float> betaSUSList; // list of betaSUS for all patches (determined by age and health indexes)
map<int, float> betaVACList; // list of betaVAC for all patches (determined by age and health indexes)
float theta <- 0.05;
float gamma <- 0.01;
int CounterofVac <- 0; // number of vaccinated people since beginning of simulation
int CounterofInf; // number of infected people since beginning of simulation
list efficacy_list <- [0.9, 0.7, 0.5, 0.5, 0.5, 0.9, 0.7, 0.7]; // list of vaccination efficacies (lambda in flowchart)
float vaccination_percentage <- 0.25; // the percentage of the whole population who are vaccinated
map<int, int> NHI_local; // number of susceptible who have been infected - per patch
map<int, int> NAI_local; // number of active infected agents - per patch
map<int, float> R0_local; // Basic Reproduction Number - defined as the max of NHI/NAI - per patch
float R0_global <- 0.0; // defined as the average of R0_local values
map<int, int> I_of_peak_local; // peak of infection is maximum number of infected agents
int I_of_peak_global <- 0;
map<int, int> time_of_peak_local;
int time_of_peak_global <- 0;
map<int, int> R0_max_time; // time of each R0_local
float R01; // individual R0 values of patches
float R02;
float R03;
float R04;
float R05;
float R06;
float R07;
float R08;
// Set colors in grid
ask sir_grid {
grid_value <- float(data[grid_x, grid_y]);
do setColor;
}
// Set patch color
list<sir_grid> patchCell <- (sir_grid where (each.grid_value = i));
ask patchCell {
color <- #black;
}
// Initialize values
add patchCell at: i to: patchesMap; //number the patches
add 0.0 at: i to: NHI_local;
add 0.0 at: i to: NAI_local;
add 0.0 at: i to: I_of_peak_local;
add 0.0 at: i to: R0_local;
add 0 at: i to: R0_max_time;
add 0 at: i to: time_of_peak_local;
//add 50 to: AgeMeanList; // uniform mean age for all patches
add 15 to: AgeSDList; // age standard deviation for all patches
// Set tunnel color
ask tunnelCell {
color <- #slategrey;
}
// Initiate population
loop i from: 1 to: numOfPatches {
create Host number: (initialSList at (i - 1)) { //create initial Susceptible agents
is_susceptible <- true;
is_exposed <- false;
is_infected <- false;
is_immune <- false;
is_vac <- false;
color <- #green;
currentPatch <- (patchesMap at i);
originalPatch <- (patchesMap at i);
local_mobility <- (local_mobility_list at (i - 1));
time_in_patch <- 0;
efficacy <- (efficacy_list at (i - 1));
mean_age <- (AgeMeanList at (i - 1));
SD_age <- (AgeSDList at (i - 1));
}
//Grid used to discretize space
grid sir_grid width: matrixSize height: matrixSize neighbors: 8 {
// Set entrance color
action setColor {
if (grid_value = numOfTunnels + numOfPatches + 5) {
color <- #orange;
}
// Set exit color
if (grid_value = numOfTunnels + numOfPatches + 6) {
color <- #brown;
}
}
}
}
// Species host which represents the host of the disease
species Host skills: [moving] {
// Varibales to control agent state and age
bool is_susceptible <- true;
bool is_exposed <- false;
bool is_infected <- false;
bool is_immune <- false;
bool is_vac <- false;
bool infectious <- false; // exposed can be infectious after some defined time
bool active <- false; // number of infectious agents
rgb color <- #green;
float mean_age;
float SD_age;
int age;
float age_risk;
// Variables to control agent location
list<sir_grid> originalPatch;
list<sir_grid> currentPatch;
sir_grid myPlace;
list<sir_grid> myEntrance;
list<sir_grid> current_tunnel;
sir_grid targetEntrance;
int time_in_patch;
bool Leave <- false;
// Variables to control agent mobility
float local_mobility;
float travel_status;
// Variables to control agent neighbours
int ngb_infectious_number function: self neighbors_at (neighbours_size) count (each.is_infected or each.infectious);
int ngb_susceptible_number function: self neighbors_at (neighbours_size + 1) count (each.is_susceptible);
int ngb_exposed_number function: self neighbors_at (neighbours_size) count (each.is_exposed);
list ngb_susceptible function: self neighbors_at (neighbours_size) where (each.is_susceptible);
list ngb_infected function: self neighbors_at (neighbours_size) where (each.is_infected or each.infectious);
list ngb_exposed function: self neighbors_at (neighbours_size + 1) where (each.is_exposed);
// Variables to control the disease
int time_being_exposed; // the time an agent spends being exposed
float efficacy;
int patch_of_vac; // index to vaccinate an agent randomly
float betaSUS;
float betaVAC;
// Shape of agents
aspect basic {
draw circle(0.5) color: color;
}
// ACTIONS to describe mobility
// leave patch when the time in patch reaches the stay time
reflex LeavePatch when: (time_in_patch >= stay_time) and (currentPatch!=originalPatch) and (myPlace in patches) {
if(!is_infected){ // leave only if not infected
Leave <- true;
do moveToExit;
}
}
// REFLEXES to control the disease state
/* reflex has_infected when: is_infected { // reflex of infected who infect other agents
if (ngb_exposed_number > 0) {
list new_exposed <- ngb_exposed where (each.time_being_exposed <= 1);
if (new_exposed != nil) {
active <- true;
}
}
} */ // Alternative definition for active
}
experiment Simulation_SA_Project type: gui {
}
experiment Optimization type: batch repeat: 2 until: (Host count (each.is_infected) <= 5 or cycle=2) {
}
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