Recombine ASCII output files in chunks of 24Mb

src/cluster/cluster.cpp

@@ -69,7 +69,6 @@ int cluster_jxi488_cycle(int jxi488, ScattererConfiguration *sconf, GeometryConf
 void cluster(const string& config_file, const string& data_file, const string& output_path, const mixMPI *mpidata) {
   chrono::time_point<chrono::high_resolution_clock> t_start = chrono::high_resolution_clock::now();
   chrono::duration<double> elapsed;
-  string message;
   string timing_name = output_path + "/c_timing_mpi"+ to_string(mpidata->rank) +".log";
   FILE *timing_file = fopen(timing_name.c_str(), "w");
   Logger *time_logger = new Logger(LOG_DEBG, timing_file);
@@ -260,7 +259,6 @@ void cluster(const string& config_file, const string& data_file, const string& o
 	{
 	  // thread 0 already wrote on global files, skip it and take care of appending the others
 	  for (int ri = 1; ri < ompnumthreads; ri++) {
-	    // Giovanni, please add here in this loop code to reopen the temporary files, reread them and append them respectively to the global output and tppoan, before closing them
 	    string partial_file_name = output_path + "/c_OCLU_" + to_string(mpidata->rank) + "_" + to_string(ri);
 	    string message = "Copying ASCII output in MPI process " + to_string(mpidata->rank) + " of thread " + to_string(ri) + " of " + to_string(ompnumthreads - 1) + "... ";
 	    logger->log(message, LOG_DEBG);
@@ -301,13 +299,17 @@ void cluster(const string& config_file, const string& data_file, const string& o
 	    int remotethreads;
 	    MPI_Recv(&remotethreads, 1, MPI_INT, rr, 1, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
 	    for (int ri = 0; ri < remotethreads; ri++) {
-	      // first get the ASCII local file
-	      int c = 0;
-	      MPI_Recv(&c, 1, MPI_INT, rr, 0, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-	      while (c != EOF) {
-		fputc(c, output);
-		MPI_Recv(&c, 1, MPI_INT, rr, 0, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
+	      char *chunk_buffer;
+	      int chunk_buffer_size = -1;
+	      MPI_Recv(&chunk_buffer_size, 1, MPI_INT, rr, 1, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
+	      while (chunk_buffer_size != 0) {
+		char *chunk_buffer = new char[chunk_buffer_size];
+		MPI_Recv(chunk_buffer, chunk_buffer_size, MPI_CHAR, rr, 0, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
+		fputs(chunk_buffer, output);
+		delete[] chunk_buffer;
+		MPI_Recv(&chunk_buffer_size, 1, MPI_INT, rr, 1, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
 	      }
+	      
 	      // now get the binary local file
 	      long buffer_size = 0;
 	      // get the size of the buffer
@@ -419,19 +421,39 @@ void cluster(const string& config_file, const string& data_file, const string& o
       MPI_Send(&ompnumthreads, 1, MPI_INT, 0, 1, MPI_COMM_WORLD);
       // reopen local files, send them all to MPI process 0
       for (int ri = 0; ri < ompnumthreads; ri++) {
-	// Giovanni, please add here in this loop code to reopen the temporary files, reread them and append them respectively to the global output and tppoan, before closing them
 	string partial_file_name = output_path + "/c_OCLU_" + to_string(mpidata->rank) + "_" + to_string(ri);
 	string message = "Copying ASCII output in MPI process " + to_string(mpidata->rank) + " of thread " + to_string(ri) + " of " + to_string(ompnumthreads - 1) + "... ";
 	logger->log(message, LOG_DEBG);
-	FILE *partial_output = fopen(partial_file_name.c_str(), "r");
-	int c = 0;
-	while (c != EOF) {
-	  c = fgetc(partial_output);
-	  MPI_Send(&c, 1, MPI_INT, 0, 0, MPI_COMM_WORLD);
-	}
-	fclose(partial_output);
-	remove(partial_file_name.c_str());
-	logger->log("done.\n", LOG_DEBG);
+	fstream partial_output;
+	partial_output.open(partial_file_name.c_str(), ios::in | ios::binary);
+	partial_output.seekg(0, ios::end);
+	const long partial_output_size = partial_output.tellg();
+	int chunk_buffer_size = 25165824; // Length of char array  with 24Mb size
+	char *chunk_buffer = new char[chunk_buffer_size]();
+	int full_chunks = (int)(partial_output_size / chunk_buffer_size);
+	for (int fi = 0; fi < full_chunks; fi++) {
+	  partial_output.read(chunk_buffer, chunk_buffer_size);
+	  // Send the size of the buffer that is being transmitted (Node-0 does not know whether it is full or not)
+	  MPI_Send(&chunk_buffer_size, 1, MPI_INT, 0, 1, MPI_COMM_WORLD);
+	  // Actually send the file contents to Node-0
+	  MPI_Send(chunk_buffer, chunk_buffer_size, MPI_CHAR, 0, 0, MPI_COMM_WORLD);
+	}
+	long ptr_position = partial_output.tellg();
+	if (ptr_position < partial_output_size) {
+	  // Send the last partial buffer
+	  chunk_buffer_size = partial_output_size - ptr_position;
+	  partial_output.read(chunk_buffer, chunk_buffer_size);
+	  // Send the size of the buffer that is being transmitted (Node-0 does not know whether it is full or not)
+	  MPI_Send(&chunk_buffer_size, 1, MPI_INT, 0, 1, MPI_COMM_WORLD);
+	  // Actually send the file contents to Node-0
+	  MPI_Send(chunk_buffer, chunk_buffer_size, MPI_CHAR, 0, 0, MPI_COMM_WORLD);
+	}
+	// Send a size 0 flag to inform Node-0 that the transmission is complete
+	chunk_buffer_size = 0;
+	MPI_Send(&chunk_buffer_size, 1, MPI_INT, 0, 1, MPI_COMM_WORLD);
+	partial_output.close();
+	delete[] chunk_buffer;
+
 	partial_file_name = output_path + "/c_TPPOAN_" + to_string(mpidata->rank) + "_" + to_string(ri);
 	message = "Copying binary output in MPI process " + to_string(mpidata->rank) + " of thread " + to_string(ri) + " of " + to_string(ompnumthreads - 1) + "... ";
 	logger->log(message, LOG_DEBG);