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simulator_Master.cu
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#include "simulator_Master.cuh"
simulator_Master::simulator_Master() {}
simulator_Master::simulator_Master(string parameter_Master_Location)
{
cout << "Intializing Simulator (based on CATE's architecture)\n";
parameter_load Parameters = parameter_load();
functions_library function = functions_library();
vector<string> parameters_List = {
"\"CUDA Device IDs\"",
"\"CPU cores\"",
"\"GPU max units\"",
"\"Intermediate folders\"",
"\"Output folders\"",
"\"Multi read\"",
"\"Network profile\"",
"\"Nodes master profile\"",
"\"Sequence master profile\"",
"\"Intermediate Sequences per file\"",
"\"Process cell rate\"",
"\"Start date\"",
"\"Stop after generations\"",
"\"Enable folder management\"",
"\"First infection\""};
vector<string> found_Parameters = Parameters.get_parameters(parameter_Master_Location, parameters_List);
cout << "\nConfiguring folders:\n";
output_Folder_location = Parameters.get_STRING(found_Parameters[4]);
intermediate_Folder_location = Parameters.get_STRING(found_Parameters[3]);
max_sequences_per_File = Parameters.get_INT(found_Parameters[9]);
max_Cells_at_a_time = Parameters.get_INT(found_Parameters[10]);
start_Date = Parameters.get_STRING(found_Parameters[11]);
stop_after_generations = function.to_Upper_Case(Parameters.get_STRING(found_Parameters[12]));
first_Infection = function.to_Upper_Case(Parameters.get_STRING(found_Parameters[14]));
if (max_sequences_per_File <= 0)
{
cout << "ERROR: Intermediate Sequences per file PARAMETER MUST BE GREATER THAN ZERO.\n";
exit(-1);
}
if (max_Cells_at_a_time <= 0)
{
cout << "ERROR: Process cell rate PARAMETER MUST BE GREATER THAN ZERO.\n";
exit(-1);
}
function.config_Folder(intermediate_Folder_location, "Intermediate");
cout << "\nFolder management: ";
if (function.to_Upper_Case(Parameters.get_STRING(found_Parameters[13])) == "YES")
{
enable_Folder_management = "YES";
vector<string> folder_Management = {"\"Compress folders\""};
vector<string> folder_management_Parameters = Parameters.get_parameters(parameter_Master_Location, folder_Management);
if (function.to_Upper_Case(Parameters.get_STRING(folder_Management[0])) == "YES")
{
enable_Compression = "YES";
}
}
cout << enable_Folder_management << endl;
cout << "Folder compression: " << enable_Compression << endl;
// exit(-1);
function.config_Folder(output_Folder_location, "Output");
output_Network_location = this->output_Folder_location + "/network_Data";
function.config_Folder(output_Network_location, "Network");
output_Node_location = this->output_Folder_location + "/node_Data";
function.config_Folder(output_Node_location, "Node");
network_File_location = output_Network_location + "/node_node_Relationships.csv";
function.create_File(network_File_location, "Source\tTarget");
Host_source_target_network_location = output_Network_location + "/hosts_source_target_Relationships.csv";
function.create_File(Host_source_target_network_location, "Source\tTarget\tTime_Infection\tDate_Infection");
cout << "\nConfiguring node master profiles:\n";
node_Master_location = Parameters.get_STRING(found_Parameters[7]);
cout << "\nConfiguring sequence master profiles:\n";
sequence_Master_location = Parameters.get_STRING(found_Parameters[8]);
if (stop_after_generations == "YES")
{
cout << "\nConfiguring simulation termination by overall generations run\n";
vector<string> parameters_List_stop_Gen_Mode = {"\"Mode to stop\""};
vector<string> stop_Gen_Parameters = Parameters.get_parameters(parameter_Master_Location, parameters_List_stop_Gen_Mode);
if (function.to_Upper_Case(Parameters.get_STRING(stop_Gen_Parameters[0])) == "GENERATIONS")
{
stop_gen_Mode = 0;
cout << "Stop after given number of generations: ";
parameters_List_stop_Gen_Mode.clear();
stop_Gen_Parameters.clear();
vector<string> parameters_List_stop_Gen_Mode = {"\"Number of generations\""};
vector<string> stop_Gen_Parameters = Parameters.get_parameters(parameter_Master_Location, parameters_List_stop_Gen_Mode);
stop_generations_Count = Parameters.get_INT(stop_Gen_Parameters[0]);
cout << stop_generations_Count << endl;
}
else
{
cout << "Stop after given date: ";
stop_gen_Mode = 1;
parameters_List_stop_Gen_Mode.clear();
stop_Gen_Parameters.clear();
vector<string> parameters_List_stop_Gen_Mode = {"\"End date\""};
vector<string> stop_Gen_Parameters = Parameters.get_parameters(parameter_Master_Location, parameters_List_stop_Gen_Mode);
string stop_Date_String = Parameters.get_STRING(stop_Gen_Parameters[0]);
cout << stop_Date_String << endl;
vector<string> split_Date;
function.split(split_Date, stop_Date_String, '-');
stop_Date = function.date_to_Decimal(stoi(split_Date[0]), stoi(split_Date[1]), stoi(split_Date[2]));
cout << "Decimal date: " << stop_Date << endl;
}
}
else
{
cout << "\nSimulation termination by overall generations run is deactivated\n";
}
cout << "\nConfiguring hardware resources:\n\n";
this->CPU_cores = Parameters.get_INT(found_Parameters[1]);
cout << "Available CPU cores: " << this->CPU_cores << endl
<< endl;
cout << "Maximum cells processed at a time: " << this->max_Cells_at_a_time << endl
<< endl;
cout << "Maximum sequences per file (Intermediary): " << this->max_sequences_per_File << endl
<< endl;
this->multi_Read = Parameters.get_STRING(found_Parameters[5]);
transform(multi_Read.begin(), multi_Read.end(), multi_Read.begin(), ::toupper);
cout << "Multiple read and write: " << this->multi_Read << endl
<< endl;
// this->CUDA_device_number = Parameters.get_INT(found_Parameters[0]);
string cuda_IDs_String = Parameters.get_STRING(found_Parameters[0]);
vector<string> cuda_IDs;
function.split(cuda_IDs, cuda_IDs_String, ',');
if (cuda_IDs.size() > 0)
{
this->num_Cuda_devices = cuda_IDs.size();
CUDA_device_IDs = (int *)malloc(sizeof(int) * num_Cuda_devices);
tot_Blocks = (int *)malloc(sizeof(int) * num_Cuda_devices);
tot_ThreadsperBlock = (int *)malloc(sizeof(int) * num_Cuda_devices);
function.print_Cuda_devices(cuda_IDs, this->CUDA_device_IDs, num_Cuda_devices, this->tot_Blocks, this->tot_ThreadsperBlock);
}
else
{
cout << "ERROR: THERE HAS TO BE AT LEAST ONE CUDA DEVICE SELECTED\n";
exit(-1);
}
// function.print_Cuda_device(this->CUDA_device_number, this->tot_Blocks, this->tot_ThreadsperBlock);
this->gpu_Limit = Parameters.get_INT(found_Parameters[2]);
cout << "Per round GPU max unit: " << this->gpu_Limit << endl
<< endl;
configure_Network_Profile(Parameters.get_STRING(found_Parameters[6]), Parameters);
cout << "\n";
// exit(-1);
}
void simulator_Master::configure_Network_Profile(string network_Profile_File, parameter_load &Parameters)
{
cout << "Configuring network profile: " << network_Profile_File << endl;
vector<string> parameters_List = {"\"Network type\""};
vector<string> found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
transform(found_Parameters[0].begin(), found_Parameters[0].end(), found_Parameters[0].begin(), ::toupper);
// parameters_List.clear();
// found_Parameters.clear();
if (Parameters.get_STRING(found_Parameters[0]) == "BA MODEL")
{
cout << "\nBarabsi Albert model selected: \n";
network_Model = "BA";
parameters_List = {"\"BA model number of nodes\"",
"\"BA model standard new connections\""};
found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
Total_number_of_Nodes = Parameters.get_INT(found_Parameters[0]);
cout << "Number of nodes: " << Total_number_of_Nodes << endl;
connection_Model = Parameters.get_STRING(found_Parameters[1]);
transform(connection_Model.begin(), connection_Model.end(), connection_Model.begin(), ::toupper);
cout << "Node connection type: " << connection_Model << endl;
if (connection_Model == "FIXED")
{
parameters_List = {"\"BA model fixed new connections\""};
found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
BA_FIXED = Parameters.get_INT(found_Parameters[0]);
cout << "Fixed new connections: " << BA_FIXED << endl;
}
else if (connection_Model == "NEGATIVE BINOMIAL")
{
parameters_List = {"\"BA model Negative binomial sucesses\"",
"\"BA model Negative binomial probability\""};
found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
BA_NB_sucesses = Parameters.get_INT(found_Parameters[0]);
BA_NB_probability = Parameters.get_FLOAT(found_Parameters[1]);
cout << "Negative Binomial sucesses: " << BA_NB_sucesses << endl;
cout << "Negative Binomial probability: " << BA_NB_probability << endl;
}
else if (connection_Model == "POISSON")
{
parameters_List = {"\"BA model Poisson mean\""};
found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
BA_Poisson_mean = Parameters.get_FLOAT(found_Parameters[0]);
cout << "Poisson mean: " << BA_Poisson_mean << endl;
}
}
else if (Parameters.get_STRING(found_Parameters[0]) == "SC MODEL")
{
cout << "\nStandard Caveman model selected: \n";
network_Model = "SCM";
parameters_List = {"\"SC_model number of caves\"",
"\"SC_model number of nodes per caves\""};
found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
SCM_number_of_caves = Parameters.get_INT(found_Parameters[0]);
SCM_number_of_nodes_per_cave = Parameters.get_INT(found_Parameters[1]);
cout << "Number of caves: " << SCM_number_of_caves;
cout << "\nNumber of nodes per cave: " << SCM_number_of_nodes_per_cave;
Total_number_of_Nodes = SCM_number_of_caves * SCM_number_of_nodes_per_cave;
cout << "\nTotal nodes in network: " << Total_number_of_Nodes << endl;
}
else if (Parameters.get_STRING(found_Parameters[0]) == "DC MODEL")
{
cout << "\nDynamic Caveman model selected: \n";
network_Model = "DCM";
parameters_List = {"\"DC_model number of caves\"",
"\"DC_model node distribution\"",
"\"DC_model neighbouring nodes percentage\"",
"\"DC_model global nodes percentage\""};
found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
DCM_number_of_caves = Parameters.get_INT(found_Parameters[0]);
cout << "Number of caves: " << DCM_number_of_caves << endl;
connection_Model = Parameters.get_STRING(found_Parameters[1]);
transform(connection_Model.begin(), connection_Model.end(), connection_Model.begin(), ::toupper);
DC_percent_Neighbouring = Parameters.get_FLOAT(found_Parameters[2]);
DC_percent_Global_freedom = Parameters.get_FLOAT(found_Parameters[3]);
cout << "Node connection type: " << connection_Model << endl;
if (connection_Model == "NEGATIVE BINOMIAL")
{
parameters_List = {"\"DC_model node Negative binomial sucesses\"",
"\"DC_model node Negative binomial probability\""};
found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
DC_ND_sucesses = Parameters.get_INT(found_Parameters[0]);
DC_ND_probability = Parameters.get_FLOAT(found_Parameters[1]);
cout << "Negative Binomial sucesses: " << DC_ND_sucesses << endl;
cout << "Negative Binomial probability: " << DC_ND_probability << endl;
}
else if (connection_Model == "POISSON")
{
parameters_List = {"\"DC_model node Poisson mean\""};
found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
DC_Poisson_mean = Parameters.get_FLOAT(found_Parameters[0]);
cout << "Poisson mean: " << DC_Poisson_mean << endl;
}
}
else if (Parameters.get_STRING(found_Parameters[0]) == "RANDOM MODEL")
{
cout << "\nRandom model selected: \n";
network_Model = "RANDOM";
parameters_List = {"\"Random model number of nodes\""};
found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
Total_number_of_Nodes = Parameters.get_INT(found_Parameters[0]);
}
else if (Parameters.get_STRING(found_Parameters[0]) == "ER MODEL")
{
cout << "\nErdos and Renyi Random model selected: \n";
network_Model = "ER_RANDOM";
parameters_List = {"\"ER Random model total number of nodes\"",
"\"ER Random model probability of linkage\""};
found_Parameters = Parameters.get_parameters(network_Profile_File, parameters_List);
Total_number_of_Nodes = Parameters.get_INT(found_Parameters[0]);
ER_link_probability = Parameters.get_FLOAT(found_Parameters[1]);
// exit(-1);
}
else
{
cout << "ERROR Incorrect network selected. Please check \"Network type\" in the network parameter file: \"" << network_Profile_File << "\"";
exit(-1);
}
}
void simulator_Master::ingress()
{
functions_library functions = functions_library(tot_Blocks, tot_ThreadsperBlock, CUDA_device_IDs, num_Cuda_devices, gpu_Limit, CPU_cores);
cout
<< "STEP 1: Configuring population network\n\n";
// ! Compatible for both BA and Caveman
// INT, INT = Cave_ID and Node, for BA CaveID is 0 for all.
// vector<vector<pair<int, int>>> each_Nodes_Connection;
// ! Only for CAVEMAN models, to keep track of each nodes Caves
network_Manager(functions);
cout << "STEP 2: Configuring node profiles and within host mechanics\n\n";
node_Master_Manager(functions);
cout << "STEP 3: Configuring sequence profiles\n\n";
sequence_Master_Manager(functions);
cout << "STEP 4: Assigning profiles to network nodes\n\n";
vector<node_within_host> Hosts = node_Profile_assignment_Manager(functions);
// for (int host = 0; host < Total_number_of_Nodes; host++)
// {
// Hosts[host].print_All();
// }
// exit(-1);
cout << "STEP 5: Infection begins\n\n";
apollo(functions, Hosts);
}
void simulator_Master::thread_compress_Folders(int new_dead_Host, vector<node_within_host> &Hosts)
{
// for (int host = start; host < stop; host++)
//{
Hosts[new_dead_Host].compress_Folder(intermediary_Sequence_location + "/" + to_string(Hosts[new_dead_Host].get_host_Index()), enable_Compression, 1);
//}
}
void simulator_Master::apollo(functions_library &functions, vector<node_within_host> &Hosts)
{
// // TODO: host infection times
// // TODO: create an overall generational summary
// // TODO: Per individual generational summary
// // TODO: SIRS
// // TODO: Terminate after given number of generations or time
// // TODO: CHECK IF ALL ARRAYS ARE CLEARED
// Source\tTarget\tInfection_time
// Generation_Network\tGeneration_time_decimal\tDate\tSusceptible_population\tInfected\tInfectious\tDead\tRemoved
// Generation\tGeneration_time_decimal\tDate\tTissue\tParents\tParticles_produced\tDead\tTransferred\tRemaining
cout << "Configuring infection start date: " << start_Date << endl;
vector<string> split_Date;
functions.split(split_Date, start_Date, '-');
float decimal_Date = functions.date_to_Decimal(stoi(split_Date[0]), stoi(split_Date[1]), stoi(split_Date[2]));
float date_Increment = generation_Time / (float)365.25;
cout << "Decimal date: " << decimal_Date << endl;
cout << "Date incerement by generation: " << date_Increment << endl;
// cout << "Decimal date: " << (decimal_Date + date_Increment) << endl;
// int year, month, day;
// functions.decimal_to_Date(decimal_Date + date_Increment, year, month, day);
// cout << "Conversion check:\n"
// << year << endl
// << month << endl
// << day << endl;
// exit(-1);
cout << "\nConfiguring susceptible population\n\n";
vector<int> susceptible_Population;
for (size_t i = 0; i < Total_number_of_Nodes; i++)
{
susceptible_Population.push_back(i);
// removed_Population.push_back(-1);
}
cout << "Starting infection\n\n";
vector<int> infected_Population;
int first_Infected = get_first_Infected(susceptible_Population, infected_Population, functions);
Hosts[first_Infected].begin_Infection(functions, intermediary_Sequence_location, entry_tissues, entry_array, max_sequences_per_File, output_Node_location, tissue_Names, first_Infection);
cout << endl;
functions.folder_Delete(intermediate_Folder_location + "/sequence_Data/reference_Sequences");
// cout << Total_number_of_Nodes << endl;
// cout << susceptible_Population.size() << endl;
// cout << infected_Population.size() << endl;
// cout << to_string(susceptible_Population.size() + infected_Population.size()) << endl;
int stop = 0;
// test
// vector<pair<int, int>> host_Connections_TEST;
// host_Connections_TEST.push_back(make_pair(0, 88));
// host_Connections_TEST.push_back(make_pair(0, 77));
// host_Connections_TEST.push_back(make_pair(0, 1));
// Node_search(host_Connections_TEST);
// exit(-1);
random_device rd;
mt19937 gen(rd());
int overall_Generations = 0;
int removed_Count = 0;
int dead_Count = 0;
string overall_Generational_Summary = output_Network_location + "/overall_generational_Summary.csv";
functions.create_File(overall_Generational_Summary, "overall_Generation\tdecimal_Date\tDate\tsusceptible_Population\tinfected_Population\tinfectious_Population\tremoved_Population\tdead_Population");
// for (int test = 0; test < all_node_IDs.size(); test++)
// {
// for (size_t i = 0; i < each_Nodes_Connection_INT[test].size(); i++)
// {
// cout << all_node_IDs[each_Nodes_Connection_INT[test][i]].first << "_" << all_node_IDs[each_Nodes_Connection_INT[test][i]].second << ", ";
// }
// cout << endl;
// }
cout << "\nWriting node index information\n";
functions.create_File(intermediary_Index_location + "/node_Index.csv", "node_Index\tnode_ID");
fstream index_Data_file;
index_Data_file.open(intermediary_Index_location + "/node_Index.csv", ios::app);
if (index_Data_file.is_open())
{
for (int node = 0; node < all_node_IDs.size(); node++)
{
index_Data_file << node << "\t" << all_node_IDs[node].first << "_" << all_node_IDs[node].second << "\n";
}
index_Data_file.close();
}
else
{
cout << "\nERROR: INDEX DATA FILE CANNOT BE OPENED: " << intermediary_Index_location << "/node_Index.csv\n";
}
// exit(-1);
fstream time_Track;
functions.create_File(output_Folder_location + "/run_Time_track.csv", "Generation\tTime");
time_Track.open(output_Folder_location + "/run_Time_track.csv", ios::app);
do
{
auto start_Time = chrono::high_resolution_clock::now();
// check dead and remove from infected
cout << "\nDetermining removed/ dead and newly infectious hosts\n";
vector<int> temp;
vector<int> infectious_Population;
vector<int> new_dead_Population;
for (int host = 0; host < infected_Population.size(); host++)
{
if (Hosts[infected_Population[host]].get_Status() == "Dead")
{
cout << "Node " << Hosts[infected_Population[host]].get_Name() << " is dead\n";
dead_Count++;
// removed_Population.push_back(infected_Population[host]);
}
else if (Hosts[infected_Population[host]].get_Status() == "Removed")
{
cout << "Node " << Hosts[infected_Population[host]].get_Name() << " removed\n";
removed_Count++;
}
else if (Hosts[infected_Population[host]].terminal_status(terminal_tissues, terminal_array) == 1)
{
cout << "Node " << Hosts[infected_Population[host]].get_Name() << " is dead\n";
new_dead_Population.push_back(infected_Population[host]);
dead_Count++;
}
else if (Hosts[infected_Population[host]].get_Status() != "Susceptible")
{
temp.push_back(infected_Population[host]);
if (Hosts[infected_Population[host]].get_Status() == "Infectious" || Hosts[infected_Population[host]].infectious_status(infectious_tissues, infectious_array) == 1)
{
cout << "Node " << Hosts[infected_Population[host]].get_Name() << " is infectious\n";
infectious_Population.push_back(infected_Population[host]);
}
}
}
infected_Population = temp;
temp.clear();
// // TODO: Compress all dead at once if multiread is available or else one by one
if (new_dead_Population.size() > 0 && enable_Folder_management == "YES")
{
cout << "\nCompressing " << new_dead_Population.size() << " dead host(s)\n";
// intermediary_Sequence_location + "/" + to_string(Hosts[infected_Population[host]].get_host_Index()), enable_Folder_management, enable_Compression
if (multi_Read == "NO")
{
cout << "Single thread compression\n";
for (int host = 0; host < new_dead_Population.size(); host++)
{
Hosts[new_dead_Population[host]].compress_Folder(intermediary_Sequence_location + "/" + to_string(Hosts[new_dead_Population[host]].get_host_Index()), enable_Compression);
}
}
else
{
cout << "Multi threaded compression\n";
// int num_per_Core = new_dead_Population.size() / CPU_cores;
// int remainder = new_dead_Population.size() % CPU_cores;
vector<thread> threads_vec;
int current_thread_Usage = 0;
for (int host = 0; host < new_dead_Population.size(); host++)
{
threads_vec.push_back(thread{&simulator_Master::thread_compress_Folders, this, new_dead_Population[host], ref(Hosts)});
current_thread_Usage++;
if (current_thread_Usage >= CPU_cores)
{
for (thread &t : threads_vec)
{
if (t.joinable())
{
t.join();
}
}
threads_vec.clear();
current_thread_Usage = 0;
}
}
for (thread &t : threads_vec)
{
if (t.joinable())
{
t.join();
}
}
// for (int core_ID = 0; core_ID < CPU_cores; core_ID++)
// {
// int start_Node = core_ID * num_per_Core;
// int stop_Node = start_Node + num_per_Core;
// threads_vec.push_back(thread{&simulator_Master::thread_compress_Folders, this, start_Node, stop_Node, new_dead_Population, ref(Hosts)});
// }
// if (remainder != 0)
// {
// int start_Node = new_dead_Population.size() - remainder;
// int stop_Node = new_dead_Population.size();
// threads_vec.push_back(thread{&simulator_Master::thread_compress_Folders, this, start_Node, stop_Node, new_dead_Population, ref(Hosts)});
// }
// for (thread &t : threads_vec)
// {
// if (t.joinable())
// {
// t.join();
// }
// }
threads_vec.clear();
}
cout << endl;
// exit(-1);
}
new_dead_Population.clear();
// // TODO WRITE to overall generational summary
fstream overall_Generational_summary_File;
overall_Generational_summary_File.open(overall_Generational_Summary, ios::app);
if (overall_Generational_summary_File.is_open())
{
cout << "Writing generation " << overall_Generations << " summary: " << overall_Generational_Summary << endl;
int year, month, day;
functions.decimal_to_Date(decimal_Date, year, month, day);
overall_Generational_summary_File << to_string(overall_Generations)
<< "\t" << to_string(decimal_Date)
<< "\t" << to_string(year) << "-" << to_string(month) << "-" << to_string(day)
<< "\t" << to_string(susceptible_Population.size() - infected_Population.size() - removed_Count - dead_Count)
<< "\t" << to_string(infected_Population.size())
<< "\t" << to_string(infectious_Population.size())
<< "\t" << to_string(removed_Count)
<< "\t" << to_string(dead_Count) << endl;
overall_Generational_summary_File.close();
}
else
{
cout << "ERROR: UNABLE TO OPEN OVERALL GENERATIONAL SUMMARY FILE: " << overall_Generational_Summary << endl;
exit(-1);
}
// TEST BLOCKS
// if (overall_Generations == 1)
// {
// cout << "\n******DONE UPTO HERE********\n";
// exit(-1);
// }
// infect
if (infectious_Population.size() > 0)
{
cout << "\nNew host to host infections\n";
for (int host = 0; host < infectious_Population.size(); host++)
{
float infection_probability = Hosts[infectious_Population[host]].get_infection_probability();
int go_for_Infection = 0;
if (infection_probability == 1)
{
go_for_Infection = 1;
}
else if (infection_probability > 0)
{
bernoulli_distribution infection_draw(infection_probability);
bool result = infection_draw(gen);
if (result)
{
go_for_Infection = 1;
}
}
if (go_for_Infection == 1)
{
cout << "\nNode: " << Hosts[infectious_Population[host]].get_Name() << " is infecting new nodes\n";
int node_Profile = Hosts[infectious_Population[host]].get_Profile();
vector<int> host_Connections = each_Nodes_Connection_INT[infectious_Population[host]];
// Node_search(host_Connections);
// test
// cout << Hosts[infectious_Population[host]].get_Name() << endl
// << endl;
// for (int test = 0; test < host_Connections.size(); test++)
// {
// cout << host_Connections[test].first << "_" << host_Connections[test].second << endl;
// }
// cout << "\ncheck\n";
// for (int test = 0; test < host_Connections.size(); test++)
// {
// cout << Hosts[search_Indexes[test]].get_Name() << endl;
// }
// exit(-1);
cout << "Checking index search\n";
vector<int> possible_Infections;
vector<int> new_Hosts_Indexes;
if (reinfection_Availability == 0)
{
cout << "Preventing reinfection of infeceted hosts\n";
// index and position in host_Connections
for (int host = 0; host < host_Connections.size(); host++)
{
// if (search_Indexes[host] == -1)
// {
// cout << "ERROR: ID MISSING\n";
// exit(-1);
// }
// if (host_Connections[host] != -1)
// {
if (Hosts[host_Connections[host]].get_Status() == "Susceptible")
{
possible_Infections.push_back(host_Connections[host]);
}
// }
}
// search_Indexes.clear();
// overall_Found = 0;
if (possible_Infections.size() > 0)
{
new_Hosts_Indexes = get_new_Hosts_Indexes(node_Profile, gen, possible_Infections);
}
else
{
cout << "No new infection from node as all surrounding nodes have already been infected.\n";
}
}
else
{
cout << "Reinfection of infected hosts can occur\n";
// vector<pair<int, int>> host_Connections = each_Nodes_Connection[infectious_Population[host]];
// Node_search(host_Connections);
// cout << "Checking index search\n";
// vector<int> possible_Infections;
for (int host = 0; host < host_Connections.size(); host++)
{
// if (search_Indexes[host] == -1)
// {
// cout << "ERROR: ID MISSING\n";
// exit(-1);
// }
// if (host_Connections[host] != -1)
// {
if (Hosts[host_Connections[host]].get_Status() != "Dead" && Hosts[host_Connections[host]].get_Status() != "Removed")
{
possible_Infections.push_back(host_Connections[host]);
}
//}
}
// search_Indexes.clear();
// overall_Found = 0;
if (possible_Infections.size() > 0)
{
new_Hosts_Indexes = get_new_Hosts_Indexes(node_Profile, gen, possible_Infections);
}
else
{
cout << "No new infection from node as all surrounding nodes are dead or removed.\n";
}
}
if (new_Hosts_Indexes.size() > 0)
{
cout << "\nNovel host(s) recognised\n\n";
//// DO: 1 Make document to host to target, then sequence/ sequences of infection, TEST above code
int num_viruses_to_transfer = (int)transmission_parameters[1];
string source_Target_file_Location = intermediary_Sequence_location + "/" + to_string(Hosts[infectious_Population[host]].get_host_Index());
int source_Index = Hosts[infectious_Population[host]].get_host_Index();
int source_Generation = Hosts[infectious_Population[host]].get_Generation();
string source_Name = Hosts[infectious_Population[host]].get_Name();
//// INDEX FOLDER of Source HOST
vector<vector<pair<int, int>>> indexed_Source_Folders = functions.index_sequence_Folders(source_Target_file_Location, num_tissues_per_Node, source_Generation, multi_Read);
// for (int test = 0; test < num_tissues_per_Node; test++)
// {
// cout << "tissue: " << test << endl;
// for (size_t i = 0; i < indexed_Source_Folders[test].size(); i++)
// {
// cout << indexed_Source_Folders[test][i].first << "_" << indexed_Source_Folders[test][i].second << endl;
// }
// cout << endl;
// }
// exit(-1);
for (int target_Host = 0; target_Host < new_Hosts_Indexes.size(); target_Host++)
{
if (transmission_parameters[0] == 1)
{
binomial_distribution<int> viruses_to_transfer_distribution(transmission_parameters[1], transmission_parameters[2]);
num_viruses_to_transfer = viruses_to_transfer_distribution(gen);
}
string status = Hosts[new_Hosts_Indexes[target_Host]].transfer_Infection(functions, intermediary_Sequence_location, source_Target_file_Location,
source_Index, source_Generation, source_Name, Hosts[infectious_Population[host]].get_current_Viral_load_per_Tissue(),
num_viruses_to_transfer,
entry_tissues, entry_array, Hosts[infectious_Population[host]].get_Load(exit_tissues, exit_array), exit_tissues, exit_array,
Hosts[infectious_Population[host]].removed_by_Transfer_Indexes,
max_sequences_per_File,
indexed_Source_Folders,
decimal_Date,
Host_source_target_network_location,
output_Node_location, tissue_Names,
gen);
// exit(-1);
if (status == "Infected")
{
infected_Population.push_back(new_Hosts_Indexes[target_Host]);
}
}
}
}
}
// // TEST BLOCKS
// if (overall_Generations == 1)
// {
// cout << "\n******DONE UPTO HERE********\n";
// exit(-1);
// }
}
if (infected_Population.size() > 0)
{
cout << "\nAttempting to simulate " << infected_Population.size() << " hosts\n";
for (int host = 0; host < infected_Population.size(); host++)
{
// string source_Target_file_Location = intermediary_Sequence_location + "/" + to_string(Hosts[infectious_Population[host]].get_host_Index());
Hosts[infected_Population[host]].run_Generation(functions, this->multi_Read, this->max_Cells_at_a_time, this->gpu_Limit, CUDA_device_IDs, this->num_Cuda_devices, this->genome_Length,
CPU_cores, max_sequences_per_File,
intermediary_Sequence_location + "/" + to_string(Hosts[infected_Population[host]].get_host_Index()), output_Node_location,
tissue_Names,
num_replication_phases, tissue_replication_data, tissue_param_profile_Stride,
terminal_tissues, terminal_array,
cell_Distribution_Type, ALL_profiles_Tissue_cell_disribution[Hosts[infected_Population[host]].get_Profile()],
Reference_fitness_survivability_proof_reading,
mutation_recombination_proof_Reading_availability,
num_effect_Segregating_sites,
sequence_Fitness_changes,
sequence_Survivability_changes,
sequence_Proof_reading_changes,
mutation_Hotspots,
mutation_hotspot_parameters,
A_0_mutation,
T_1_mutation,
G_2_mutation,
C_3_mutation,
recombination_Hotspots,
recombination_hotspot_parameters,
tot_prob_selectivity,
recombination_prob_Stride,
recombination_select_Stride,
recombination_Prob_matrix,
recombination_Select_matrix,
progeny_distribution_parameters_Array,
viral_Migration,
viral_Migration_Values,
migration_start_Generation,
overall_Generations,
infected_to_Recovered,
enable_Folder_management,
enable_Compression,
gen);
}
cout << "\nCompleted simulating hosts\n";
decimal_Date = decimal_Date + date_Increment;
auto stop_Time = chrono::high_resolution_clock::now();
// Calculate the duration
auto duration_Time = chrono::duration_cast<chrono::milliseconds>(stop_Time - start_Time);
time_Track << to_string(overall_Generations) << "\t" << to_string(duration_Time.count()) << "\n";
overall_Generations++;
cout << "\nMoved generation forward\n";
// // TEST BLOCKS
// if (overall_Generations == 1)
// {
// cout << "\n******DONE UPTO HERE********\n";
// exit(-1);
// }
if (trials_Sampling != -1)
{
cout << "\nSampling infected hosts\n";
binomial_distribution<int> sequences_to_Sample(sampling_trials, sampling_probability);
int num_Nodes_to_Sample = sequences_to_Sample(gen);
uniform_int_distribution<> distribution_Indexes(0, infected_Population.size() - 1);
set<int> nodes_Indexes;
for (int host = 0; host < num_Nodes_to_Sample; host++)
{
int node_Index = distribution_Indexes(gen);
if (resampling == -1)
{
auto it = sampled_Nodes.find(infected_Population[node_Index]);
if (it == sampled_Nodes.end())
{
nodes_Indexes.insert(node_Index);
sampled_Nodes.insert(infected_Population[node_Index]);
}
}
else
{
nodes_Indexes.insert(node_Index);
}
}
if (nodes_Indexes.size() > 0)
{
vector<int> indexes_of_Sampling_Nodes(nodes_Indexes.begin(), nodes_Indexes.end());
nodes_Indexes.clear();
cout << "Attempting to sample " << indexes_of_Sampling_Nodes.size() << " hosts\n";
int num_Samples = per_Node_sampling[1];
// // TODO: FIX
int success_Sampling = 0;
for (int host = 0; host < indexes_of_Sampling_Nodes.size(); host++)
{
if (Hosts[infected_Population[indexes_of_Sampling_Nodes[host]]].get_Status() != "Dead" && Hosts[infected_Population[indexes_of_Sampling_Nodes[host]]].get_Status() != "Removed")
{
cout << "\nSampling host " << Hosts[infected_Population[indexes_of_Sampling_Nodes[host]]].get_Name() << endl;
for (int tissue = 0; tissue < sampling_tissues; tissue++)
{
cout << "Attempting to sample " << tissue_Names[sampling_array[tissue]] << " tissue\n";
if (per_Node_sampling[0] == 1)
{
binomial_distribution<int> num_samples_Obtained(per_Node_sampling[1], per_Node_sampling[2]);
num_Samples = num_samples_Obtained(gen);
}
if (num_Samples > 0)
{
success_Sampling = Hosts[infected_Population[indexes_of_Sampling_Nodes[host]]].sample_Host(functions, decimal_Date,
tissue_Names,
intermediary_Sequence_location + "/" + to_string(Hosts[infected_Population[indexes_of_Sampling_Nodes[host]]].get_host_Index()), sampling_array[tissue], num_Samples,
sampled_sequences_Folder,
gen);
}
}
// REMOVE
// exit(-1);
if (Hosts[infected_Population[indexes_of_Sampling_Nodes[host]]].get_infection_probability() <= 0)
{
Hosts[infected_Population[indexes_of_Sampling_Nodes[host]]].set_Infection_prob_Zero(intermediary_Sequence_location + "/" + to_string(Hosts[infected_Population[indexes_of_Sampling_Nodes[host]]].get_host_Index()), enable_Folder_management, enable_Compression);
}
}
}
if (success_Sampling == 1)
{
count_Sampling_instances++;
}
}
else
{
cout << "No new hosts to sample\n";
}
if (limit_Sampled != -1)
{
if (count_Sampling_instances >= limit_Sampled)
{
stop = 3;
}
}
}
// REMOVE
// exit(-1);
// TEST BLOCKS
// if (overall_Generations == 2)
// {
// cout << "\n******DONE UPTO HERE********\n";
// exit(-1);
// }
}
else
{
stop = 2;
}
if (stop_after_generations == "YES")