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memory leak fix
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@DeshanPerera
DeshanPerera committed Oct 1, 2024
1 parent 893dced commit 5f00f37
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Showing 2 changed files with 105 additions and 102 deletions.
207 changes: 105 additions & 102 deletions cancer_Host.cu
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Original file line number Diff line number Diff line change
Expand Up @@ -662,7 +662,7 @@ void cancer_Host::calculate_Tajima(functions_library &functions,
cout << "Reading folder: " << sequence_Tissue_Folder << endl;
vector<pair<int, int>> indexed_Source_Folder = functions.index_sequence_Folder(sequence_Tissue_Folder);

//cout << "\nCalculating pre-requisites: \n";
// cout << "\nCalculating pre-requisites: \n";
int N = indexed_Source_Folder[indexed_Source_Folder.size() - 1].second + 1;
cout << "Total number of cells (N): " << N << endl;

Expand Down Expand Up @@ -1173,139 +1173,142 @@ void cancer_Host::migration_of_Cells(string &source_sequence_Data_folder, vector
int start_Index = last_target_Index;

int num_Sequences = tissue_cell_Index[tissue].size();
sort(tissue_cell_Index[tissue].begin(), tissue_cell_Index[tissue].end());
if (num_Sequences > 0)
{
sort(tissue_cell_Index[tissue].begin(), tissue_cell_Index[tissue].end());

cout << "Collecting " << num_Sequences << " sequence(s)\n";
int num_per_Core = num_Sequences / this->CPU_cores;
int remainder = num_Sequences % this->CPU_cores;
cout << "Collecting " << num_Sequences << " sequence(s)\n";
int num_per_Core = num_Sequences / this->CPU_cores;
int remainder = num_Sequences % this->CPU_cores;

vector<thread> threads_vec;
vector<thread> threads_vec;

for (int core_ID = 0; core_ID < this->CPU_cores; core_ID++)
{
int start_Cell = core_ID * num_per_Core;
int stop_Cell = start_Cell + num_per_Core;
for (int core_ID = 0; core_ID < this->CPU_cores; core_ID++)
{
int start_Cell = core_ID * num_per_Core;
int stop_Cell = start_Cell + num_per_Core;

threads_vec.push_back(thread{&cancer_Host::thread_find_Files_2, this, start_Cell, stop_Cell, ref(tissue_cell_Index[tissue]), ref(indexed_Source_Folder)});
}
threads_vec.push_back(thread{&cancer_Host::thread_find_Files_2, this, start_Cell, stop_Cell, ref(tissue_cell_Index[tissue]), ref(indexed_Source_Folder)});
}

if (remainder != 0)
{
int start_Cell = num_Sequences - remainder;
int stop_Cell = num_Sequences;
if (remainder != 0)
{
int start_Cell = num_Sequences - remainder;
int stop_Cell = num_Sequences;

threads_vec.push_back(thread{&cancer_Host::thread_find_Files_2, this, start_Cell, stop_Cell, ref(tissue_cell_Index[tissue]), ref(indexed_Source_Folder)});
}
threads_vec.push_back(thread{&cancer_Host::thread_find_Files_2, this, start_Cell, stop_Cell, ref(tissue_cell_Index[tissue]), ref(indexed_Source_Folder)});
}

for (thread &t : threads_vec)
{
if (t.joinable())
for (thread &t : threads_vec)
{
t.join();
if (t.joinable())
{
t.join();
}
}
}

threads_vec.clear();
threads_vec.clear();

vector<int> Tissue_files(found_Tissue_Folder_Indexes.begin(), found_Tissue_Folder_Indexes.end());
found_Tissue_Folder_Indexes.clear();
vector<int> Tissue_files(found_Tissue_Folder_Indexes.begin(), found_Tissue_Folder_Indexes.end());
found_Tissue_Folder_Indexes.clear();

sort(Tissue_files.begin(), Tissue_files.end());
sort(Tissue_files.begin(), Tissue_files.end());

cout << Tissue_files.size() << " file(s) identified\n";
cout << Tissue_files.size() << " file(s) identified\n";

vector<pair<string, string>> all_Sequences;
cout << "Retrieving sequence(s)\n";
vector<pair<string, string>> all_Sequences;
cout << "Retrieving sequence(s)\n";

fstream nfasta;
int index_Files = 0;
int line_current = 0;
nfasta.open(sequence_Tissue_Folder + "/" + to_string(indexed_Source_Folder[Tissue_files[index_Files]].first) + "_" + to_string(indexed_Source_Folder[Tissue_files[index_Files]].second) + ".nfasta", ios::in);
fstream nfasta;
int index_Files = 0;
int line_current = 0;
nfasta.open(sequence_Tissue_Folder + "/" + to_string(indexed_Source_Folder[Tissue_files[index_Files]].first) + "_" + to_string(indexed_Source_Folder[Tissue_files[index_Files]].second) + ".nfasta", ios::in);

fstream sequence_Profiles_File;
sequence_Profiles_File.open(sequence_Profiles, ios::app);
fstream sequence_parent_Progeny_relationships_File;
sequence_parent_Progeny_relationships_File.open(sequence_parent_Progeny_relationships, ios::app);
fstream sequence_Profiles_File;
sequence_Profiles_File.open(sequence_Profiles, ios::app);
fstream sequence_parent_Progeny_relationships_File;
sequence_parent_Progeny_relationships_File.open(sequence_parent_Progeny_relationships, ios::app);

for (int find = 0; find < num_Sequences; find++)
{
while ((indexed_Source_Folder[Tissue_files[index_Files]].first <= tissue_cell_Index[tissue][find] && indexed_Source_Folder[Tissue_files[index_Files]].second >= tissue_cell_Index[tissue][find]) == 0)
for (int find = 0; find < num_Sequences; find++)
{
nfasta.close();
index_Files++;
nfasta.open(sequence_Tissue_Folder + "/" + to_string(indexed_Source_Folder[Tissue_files[index_Files]].first) + "_" + to_string(indexed_Source_Folder[Tissue_files[index_Files]].second) + ".nfasta", ios::in);
line_current = 0;
}
while ((indexed_Source_Folder[Tissue_files[index_Files]].first <= tissue_cell_Index[tissue][find] && indexed_Source_Folder[Tissue_files[index_Files]].second >= tissue_cell_Index[tissue][find]) == 0)
{
nfasta.close();
index_Files++;
nfasta.open(sequence_Tissue_Folder + "/" + to_string(indexed_Source_Folder[Tissue_files[index_Files]].first) + "_" + to_string(indexed_Source_Folder[Tissue_files[index_Files]].second) + ".nfasta", ios::in);
line_current = 0;
}

if (nfasta.is_open())
{
int line_t0_check = (tissue_cell_Index[tissue][find] - indexed_Source_Folder[Tissue_files[index_Files]].first) * 2;
if (nfasta.is_open())
{
int line_t0_check = (tissue_cell_Index[tissue][find] - indexed_Source_Folder[Tissue_files[index_Files]].first) * 2;

string line;
string sequence = "";
string line;
string sequence = "";

while (getline(nfasta, line))
{
if (line_t0_check == line_current)
while (getline(nfasta, line))
{
vector<string> line_Data;
functions.split(line_Data, line, '_');
if (stoi(line_Data[0].substr(1)) == tissue_cell_Index[tissue][find])
if (line_t0_check == line_current)
{
getline(nfasta, line);

all_Sequences.push_back(make_pair(to_string(last_target_Index) + "_A_" + line_Data[2] + "_" + line_Data[3] + "_" + line_Data[4] + "_" + line_Data[5] + "_" + line_Data[6] + "_" + line_Data[7], line));
sequence_Profiles_File << tissue_Names[tissue_migration_Targets_amount[tissue].first] << "_" << to_string(overall_Generations + 1) << "_" << to_string(last_target_Index) << "\t" << tissue_Names[tissue_migration_Targets_amount[tissue].first] << "\t" << line_Data[5] << "\t" << line_Data[3] << "\t" << line_Data[2] << "\t" << line_Data[6] << "\t" << line_Data[7] << endl;
sequence_parent_Progeny_relationships_File << tissue_Names[source] << "_" << to_string(overall_Generations + 1) << "_" << tissue_cell_Index[tissue][find] << "\t"
<< tissue_Names[tissue_migration_Targets_amount[tissue].first] << "_" << to_string(overall_Generations + 1) << "_" << to_string(last_target_Index)
<< "\tMigration" << endl;
last_target_Index++;
vector<string> line_Data;
functions.split(line_Data, line, '_');
if (stoi(line_Data[0].substr(1)) == tissue_cell_Index[tissue][find])
{
getline(nfasta, line);

all_Sequences.push_back(make_pair(to_string(last_target_Index) + "_A_" + line_Data[2] + "_" + line_Data[3] + "_" + line_Data[4] + "_" + line_Data[5] + "_" + line_Data[6] + "_" + line_Data[7], line));
sequence_Profiles_File << tissue_Names[tissue_migration_Targets_amount[tissue].first] << "_" << to_string(overall_Generations + 1) << "_" << to_string(last_target_Index) << "\t" << tissue_Names[tissue_migration_Targets_amount[tissue].first] << "\t" << line_Data[5] << "\t" << line_Data[3] << "\t" << line_Data[2] << "\t" << line_Data[6] << "\t" << line_Data[7] << endl;
sequence_parent_Progeny_relationships_File << tissue_Names[source] << "_" << to_string(overall_Generations + 1) << "_" << tissue_cell_Index[tissue][find] << "\t"
<< tissue_Names[tissue_migration_Targets_amount[tissue].first] << "_" << to_string(overall_Generations + 1) << "_" << to_string(last_target_Index)
<< "\tMigration" << endl;
last_target_Index++;
line_current++;
}
else
{
cout << "ERROR: CORRECT SEQUENCE NOT FOUND AT INDEX\n";
cout << "Looking for: " << tissue_cell_Index[tissue][find] << endl
<< "Sequence ID at location: " << line << endl
<< "File: " << sequence_Tissue_Folder << "/" << indexed_Source_Folder[Tissue_files[index_Files]].first
<< "_" << indexed_Source_Folder[Tissue_files[index_Files]].second << ".nfasta" << endl;
exit(-1);
}
line_current++;
}
else
{
cout << "ERROR: CORRECT SEQUENCE NOT FOUND AT INDEX\n";
cout << "Looking for: " << tissue_cell_Index[tissue][find] << endl
<< "Sequence ID at location: " << line << endl
<< "File: " << sequence_Tissue_Folder << "/" << indexed_Source_Folder[Tissue_files[index_Files]].first
<< "_" << indexed_Source_Folder[Tissue_files[index_Files]].second << ".nfasta" << endl;
exit(-1);
break;
}
line_current++;
break;
}
line_current++;
}
else
{
cout << "ERROR UNABLE TO OPEN NFATSA FILE: " << sequence_Tissue_Folder << "/" << indexed_Source_Folder[Tissue_files[index_Files]].first << "_" << indexed_Source_Folder[Tissue_files[index_Files]].second << ".nfasta" << endl;
exit(-1);
}
}
else
{
cout << "ERROR UNABLE TO OPEN NFATSA FILE: " << sequence_Tissue_Folder << "/" << indexed_Source_Folder[Tissue_files[index_Files]].first << "_" << indexed_Source_Folder[Tissue_files[index_Files]].second << ".nfasta" << endl;
exit(-1);
}
}
nfasta.close();
nfasta.close();

sequence_Profiles_File.close();
sequence_parent_Progeny_relationships_File.close();
sequence_Profiles_File.close();
sequence_parent_Progeny_relationships_File.close();

cout << "Found " << all_Sequences.size() << " sequences\nWriting migrating sequences: ";
fstream write_Migration;
write_Migration.open(sequence_target_Folder + "/" + to_string(start_Index) + "_" + to_string(last_target_Index - 1) + ".nfasta", ios::out);
cout << "Found " << all_Sequences.size() << " sequences\nWriting migrating sequences: ";
fstream write_Migration;
write_Migration.open(sequence_target_Folder + "/" + to_string(start_Index) + "_" + to_string(last_target_Index - 1) + ".nfasta", ios::out);

if (write_Migration.is_open())
{
for (int sequence = 0; sequence < all_Sequences.size(); sequence++)
if (write_Migration.is_open())
{
write_Migration << ">" << all_Sequences[sequence].first << endl
<< all_Sequences[sequence].second << endl;
for (int sequence = 0; sequence < all_Sequences.size(); sequence++)
{
write_Migration << ">" << all_Sequences[sequence].first << endl
<< all_Sequences[sequence].second << endl;
}
write_Migration.close();
cout << "Complete\n";
}
else
{
cout << "ERROR: UNABLE TO CREATE METASTIC SEQUENCES FILE: " << sequence_target_Folder << "/" << to_string(start_Index) << "_" << to_string(last_target_Index - 1) << ".nfasta" << endl;
exit(-1);
}
write_Migration.close();
cout << "Complete\n";
}
else
{
cout << "ERROR: UNABLE TO CREATE METASTIC SEQUENCES FILE: " << sequence_target_Folder << "/" << to_string(start_Index) << "_" << to_string(last_target_Index - 1) << ".nfasta" << endl;
exit(-1);
}
}
}
Expand Down Expand Up @@ -2866,7 +2869,7 @@ void cancer_Host::simulate_cell_Round(functions_library &functions, string &mult

} while (rerun_Progeny.size() > 0);

for (int row = 0; row < tot_Parents * 2; row++)
for (int row = 0; row < parent_Cells_Found * 2; row++)
{
free(progeny_Sequences[row]);
}
Expand Down Expand Up @@ -2909,7 +2912,7 @@ void cancer_Host::simulate_cell_Round(functions_library &functions, string &mult
// remainder_Write_Sequences_NEXT_Generation(intermediary_Tissue_folder, functions);
// cout << "Check 1\n";
// functions.clear_Array_int_CPU(progeny_Sequences, parent_Cells_Found * 2);
for (int row = 0; row < parent_Cells_Found; row++)
for (int row = 0; row < parent_Cells_Found * 2; row++)
{
free(progeny_Sequences[row]);
}
Expand Down
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