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bug fix migration_2
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@DeshanPerera
DeshanPerera committed Sep 17, 2024
1 parent 48780df commit 477769a
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Showing 4 changed files with 44 additions and 29 deletions.
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64 changes: 38 additions & 26 deletions cancer_Host.cu
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Original file line number Diff line number Diff line change
Expand Up @@ -149,15 +149,15 @@ void cancer_Host::simulate_Generations(functions_library &functions,
}
}
}
}

for (int tissue = 0; tissue < num_Tissues; tissue++)
{
cout << "Tissue " << tissue_Names[tissue] << ": " << tissue_Migration_Totals[tissue] << endl;

for (int path = 0; path < tissue_migration_Targets_amount[tissue].size(); path++)
for (int tissue = 0; tissue < num_Tissues; tissue++)
{
cout << tissue_migration_Targets_amount[tissue][path].second << " cells to " << tissue_Names[tissue_migration_Targets_amount[tissue][path].first] << endl;
cout << "Tissue " << tissue_Names[tissue] << ": " << tissue_Migration_Totals[tissue] << endl;

for (int path = 0; path < tissue_migration_Targets_amount[tissue].size(); path++)
{
cout << tissue_migration_Targets_amount[tissue][path].second << " cells to " << tissue_Names[tissue_migration_Targets_amount[tissue][path].first] << endl;
}
}
}

Expand Down Expand Up @@ -379,7 +379,8 @@ void cancer_Host::simulate_Generations(functions_library &functions,
tissues_ATGC_positions_Mutation_rate_factor,
tissues_ATGC_positions_Generation_death,
tissues_ATGC_positions_Replication_prob,
tissues_ATGC_positions_Metastatic);
tissues_ATGC_positions_Metastatic,
viral_Migration);
}

// last_Progeny_written_this_Gen = indexed_Source_Folders[tissue][indexed_Source_Folders[tissue].size() - 1].second + 1;
Expand Down Expand Up @@ -1890,7 +1891,8 @@ void cancer_Host::simulate_cell_Round(functions_library &functions, string &mult
float **tissues_ATGC_positions_Mutation_rate_factor,
float **tissues_ATGC_positions_Generation_death,
float **tissues_ATGC_positions_Replication_prob,
float **tissues_ATGC_positions_Metastatic)
float **tissues_ATGC_positions_Metastatic,
string &viral_Migration)
{

sort(parents_in_Tissue + start, parents_in_Tissue + stop);
Expand All @@ -1900,7 +1902,7 @@ void cancer_Host::simulate_cell_Round(functions_library &functions, string &mult

float *parents_Elapsed = (float *)malloc(sizeof(float) * num_of_Cells);

string all_Sequences = find_Sequences_Master(start, tissue, tissue_Name, functions, this_Gen_intermediary_Sequences, parents_in_Tissue, num_of_Cells, indexed_Tissue_Folder, overall_Generations, parent_IDs, parents_Elapsed, last_index_Seq_Written, gen, tissue_Migration_Total, migration_cell_List);
string all_Sequences = find_Sequences_Master(start, tissue, tissue_Name, functions, this_Gen_intermediary_Sequences, parents_in_Tissue, num_of_Cells, indexed_Tissue_Folder, overall_Generations, parent_IDs, parents_Elapsed, last_index_Seq_Written, gen, tissue_Migration_Total, migration_cell_List, viral_Migration);
full_Write_Sequences_NEXT_Generation(max_sequences_per_File, intermediary_Tissue_folder, functions, to_write_Sequence_Store_NEXT_Gen);
// remainder_Write_Sequences_NEXT_Generation(intermediary_Tissue_folder, functions);

Expand Down Expand Up @@ -2421,7 +2423,7 @@ void cancer_Host::simulate_cell_Round(functions_library &functions, string &mult
gen, parent_IDs,
source_sequence_Data_folder,
last_Progeny_written_this_Gen,
tissue_Migration_Total, migration_cell_List);
tissue_Migration_Total, migration_cell_List, viral_Migration);

full_Write_Sequences_NEXT_Generation(max_sequences_per_File, intermediary_Tissue_folder, functions, to_write_Sequence_Store_NEXT_Gen);
// full_Write_Sequences_NEXT_Generation(max_sequences_per_File, source_sequence_Data_folder + "/" + to_string(tissue) + "/generation_" + to_string(overall_Generations), functions, to_write_Sequence_Store_THIS_Gen);
Expand Down Expand Up @@ -2682,7 +2684,7 @@ void cancer_Host::simulate_cell_Round(functions_library &functions, string &mult
gen, parent_IDs,
source_sequence_Data_folder,
last_Progeny_written_this_Gen,
tissue_Migration_Total, migration_cell_List);
tissue_Migration_Total, migration_cell_List, viral_Migration);

for (int row = 0; row < parent_Cells_Found * 2; row++)
{
Expand Down Expand Up @@ -2929,7 +2931,7 @@ vector<pair<int, int>> cancer_Host::compile_Progeny(functions_library &functions
mt19937 &gen, vector<int> &parent_IDs,
string &source_sequence_Data_folder,
int &last_Progeny_written_this_Gen,
int &tissue_Migration_Total, multiset<pair<float, int>> &migration_cell_List)
int &tissue_Migration_Total, multiset<pair<float, int>> &migration_cell_List, string &viral_Migration)
{
vector<pair<int, int>> rerun_Progeny;

Expand Down Expand Up @@ -2990,11 +2992,14 @@ vector<pair<int, int>> cancer_Host::compile_Progeny(functions_library &functions
}
to_write_Sequence_Store_NEXT_Gen.push_back(make_pair(to_string(last_index_Seq_Written) + survival_Status + to_string(progeny_Configuration_Cancer[progeny_Index][2]) + "_" + to_string(progeny_Configuration_Cancer[progeny_Index][1]) + "_" + to_string(progeny_Elapsed[progeny_Index]) + "_" + to_string(progeny_Configuration_Cancer[progeny_Index][0]) + "_" + to_string(progeny_Configuration_Cancer[progeny_Index][3]) + "_" + to_string(progeny_Configuration_Cancer[progeny_Index][4]), sequence));

int migration_Check = 0;
migration_Check = (check_Survival_Dis(gen) < progeny_Configuration_Cancer[progeny_Index][3]) ? 0 : 1;
if (migration_Check == 0)
if (viral_Migration == "YES")
{
cell_Migration_set(tissue_Migration_Total, migration_cell_List, make_pair(progeny_Configuration_Cancer[progeny_Index][3], last_index_Seq_Written));
int migration_Check = 0;
migration_Check = (check_Survival_Dis(gen) < progeny_Configuration_Cancer[progeny_Index][3]) ? 0 : 1;
if (migration_Check == 0)
{
cell_Migration_set(tissue_Migration_Total, migration_cell_List, make_pair(progeny_Configuration_Cancer[progeny_Index][3], last_index_Seq_Written));
}
}

last_index_Seq_Written++;
Expand Down Expand Up @@ -3088,11 +3093,14 @@ vector<pair<int, int>> cancer_Host::compile_Progeny(functions_library &functions
}
to_write_Sequence_Store_NEXT_Gen.push_back(make_pair(to_string(last_index_Seq_Written) + survival_Status + to_string(progeny_Configuration_Cancer[progeny_Index][2]) + "_" + to_string(progeny_Configuration_Cancer[progeny_Index][1]) + "_" + to_string(progeny_Elapsed[progeny_Index] - 1), sequence));

int migration_Check = 0;
migration_Check = (check_Survival_Dis(gen) < progeny_Configuration_Cancer[progeny_Index][3]) ? 0 : 1;
if (migration_Check == 0)
if (viral_Migration == "YES")
{
cell_Migration_set(tissue_Migration_Total, migration_cell_List, make_pair(progeny_Configuration_Cancer[progeny_Index][3], last_index_Seq_Written));
int migration_Check = 0;
migration_Check = (check_Survival_Dis(gen) < progeny_Configuration_Cancer[progeny_Index][3]) ? 0 : 1;
if (migration_Check == 0)
{
cell_Migration_set(tissue_Migration_Total, migration_cell_List, make_pair(progeny_Configuration_Cancer[progeny_Index][3], last_index_Seq_Written));
}
}

last_index_Seq_Written++;
Expand Down Expand Up @@ -3513,7 +3521,8 @@ vector<pair<int, int>> cancer_Host::compile_Progeny(functions_library &functions
// }

string cancer_Host::find_Sequences_Master(int &offset, int &tissue, string &tissue_Name, functions_library &functions, string &folder_Path, int *parents_in_Tissue, int &num_Sequences, vector<pair<int, int>> &indexed_Tissue_Folder, int &current_Generation, vector<int> &parent_IDs, float *parents_Elapsed, int &last_index_Seq_Written, mt19937 &gen,
int &tissue_Migration_Total, multiset<pair<float, int>> &migration_cell_List)
int &tissue_Migration_Total, multiset<pair<float, int>> &migration_cell_List,
string &viral_Migration)
{

cout << "Collecting " << num_Sequences << " sequence(s)\n";
Expand Down Expand Up @@ -3651,11 +3660,14 @@ string cancer_Host::find_Sequences_Master(int &offset, int &tissue, string &tiss
<< tissue_Name << "_" << to_string(current_Generation + 1) << "_" << to_string(last_index_Seq_Written)
<< "\tgeneration_Forward" << endl;

int migration_Check = 0;
migration_Check = (check_Survival_Dis(gen) < stof(line_Data[6])) ? 0 : 1;
if (migration_Check == 0)
if (viral_Migration == "YES")
{
cell_Migration_set(tissue_Migration_Total, migration_cell_List, make_pair(stof(line_Data[6]), last_index_Seq_Written));
int migration_Check = 0;
migration_Check = (check_Survival_Dis(gen) < stof(line_Data[6])) ? 0 : 1;
if (migration_Check == 0)
{
cell_Migration_set(tissue_Migration_Total, migration_cell_List, make_pair(stof(line_Data[6]), last_index_Seq_Written));
}
}

current_cell_load_per_Tissue[tissue] = current_cell_load_per_Tissue[tissue] + 1;
Expand Down
9 changes: 6 additions & 3 deletions cancer_Host.cuh
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Original file line number Diff line number Diff line change
Expand Up @@ -205,7 +205,8 @@ public:
float **tissues_ATGC_positions_Mutation_rate_factor,
float **tissues_ATGC_positions_Generation_death,
float **tissues_ATGC_positions_Replication_prob,
float **tissues_ATGC_positions_Metastatic);
float **tissues_ATGC_positions_Metastatic,
string &viral_Migration);

// void replication_Generation_thread(int gpu, cudaStream_t *streams,
// char *cuda_full_Char, char *full_Char,
Expand All @@ -214,7 +215,9 @@ public:
// int *CUDA_device_IDs);

string find_Sequences_Master(int &offset, int &tissue, string &tissue_Name, functions_library &functions, string &folder_Path, int *parents_in_Tissue, int &num_Sequences, vector<pair<int, int>> &indexed_Tissue_Folder, int &current_Generation, vector<int> &parent_IDs, float *parents_Elapsed, int &last_index_Seq_Written, mt19937 &gen,
int &tissue_Migration_Total, multiset<pair<float, int>> &migration_cell_List);
int &tissue_Migration_Total, multiset<pair<float, int>> &migration_cell_List,
string &viral_Migration);

void thread_find_Files(int offset, int start, int stop, int *parents_in_Tissue, vector<pair<int, int>> &indexed_Tissue_Folder);

void thread_Sequence_to_String_Cancer(int start, int stop, int **progeny_Sequences);
Expand All @@ -228,7 +231,7 @@ public:
mt19937 &gen, vector<int> &parent_IDs,
string &source_sequence_Data_folder,
int &last_Progeny_written_this_Gen,
int &tissue_Migration_Total, multiset<pair<float, int>> &migration_cell_List);
int &tissue_Migration_Total, multiset<pair<float, int>> &migration_cell_List, string &viral_Migration);

// void rerun_Progeny_THIS_gen(functions_library &functions, vector<pair<int, int>> &rerun_Progeny, vector<pair<int, int>> &start_stop_Per_GPU, int &num_Cuda_devices, int &tot_Parents,
// int **parent_sequences_INT, float *parents_Elapsed,
Expand Down
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