Rewind ASCII files after getting their size and skip EOF character transmission

src/cluster/cluster.cpp

@@ -13,7 +13,7 @@
    limitations under the License.
  */
 
-/*! \file cluster.cpp
+/*! \file cluster.cp
  *
  * \brief Implementation of the calculation for a cluster of spheres.
  */
@@ -82,6 +82,7 @@ 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);
@@ -271,39 +272,34 @@ void cluster(const string& config_file, const string& data_file, const string& o
 #pragma omp barrier
 	{
 	  // thread 0 already wrote on global files, skip it and take care of appending the others
-	  for (int ri = 0; ri < ompnumthreads; ri++) {
-	    // still, we need to remove all c_OCLU_RANK_0 files
+	  for (int ri = 1; ri < ompnumthreads; ri++) {
 	    string partial_file_name = output_path + "/c_OCLU_" + to_string(mpidata->rank) + "_" + to_string(ri);
-	    if (ri == 0) {
-	      remove(partial_file_name.c_str());
-	    } else {
-	      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 = fgetc(partial_output);
-	      while (c != EOF) {
-		fputc(c, output);
-		c = fgetc(partial_output);
-	      }
-	      fclose(partial_output);
-	      remove(partial_file_name.c_str());
-	      logger->log("done.\n", LOG_DEBG);
-	      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);
-	      fstream partial_tppoan;
-	      partial_tppoan.open(partial_file_name.c_str(), ios::in | ios::binary);
-	      partial_tppoan.seekg(0, ios::end);
-	      long buffer_size = partial_tppoan.tellg();
-	      char *binary_buffer = new char[buffer_size];
-	      partial_tppoan.seekg(0, ios::beg);
-	      partial_tppoan.read(binary_buffer, buffer_size);
-	      tppoan.write(binary_buffer, buffer_size);
-	      partial_tppoan.close();
-	      delete[] binary_buffer;
-	      remove(partial_file_name.c_str());
-	      logger->log("done.\n", LOG_DEBG);
+	    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 = fgetc(partial_output);
+	    while (c != EOF) {
+	      fputc(c, output);
+	      c = fgetc(partial_output);
 	    }
+	    fclose(partial_output);
+	    remove(partial_file_name.c_str());
+	    logger->log("done.\n", LOG_DEBG);
+	    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);
+	    fstream partial_tppoan;
+	    partial_tppoan.open(partial_file_name.c_str(), ios::in | ios::binary);
+	    partial_tppoan.seekg(0, ios::end);
+	    long buffer_size = partial_tppoan.tellg();
+	    char *binary_buffer = new char[buffer_size];
+	    partial_tppoan.seekg(0, ios::beg);
+	    partial_tppoan.read(binary_buffer, buffer_size);
+	    tppoan.write(binary_buffer, buffer_size);
+	    partial_tppoan.close();
+	    delete[] binary_buffer;
+	    remove(partial_file_name.c_str());
+	    logger->log("done.\n", LOG_DEBG);
 	  }
 	}
 #endif
@@ -311,12 +307,13 @@ void cluster(const string& config_file, const string& data_file, const string& o
 #ifdef MPI_VERSION
 	if (mpidata->mpirunning) {
 	  // only go through this if MPI has been actually used
-	  for (int rr=1; rr < mpidata->nprocs; rr++) {
+	  for (int rr=1; rr<mpidata->nprocs; rr++) {
 	    // get the data from process rr
 	    // how many openmp threads did process rr use?
 	    int remotethreads;
 	    MPI_Recv(&remotethreads, 1, MPI_INT, rr, 1, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
-	    for (int ri = 0; ri < remotethreads; ri++) {
+	    for (int ri=0; ri<remotethreads; ri++) {
+	      // first get the ASCII local file
 	      char *chunk_buffer;
 	      int chunk_buffer_size = -1;
 	      MPI_Recv(&chunk_buffer_size, 1, MPI_INT, rr, 1, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
@@ -327,7 +324,8 @@ void cluster(const string& config_file, const string& data_file, const string& o
 		delete[] chunk_buffer;
 		MPI_Recv(&chunk_buffer_size, 1, MPI_INT, rr, 1, MPI_COMM_WORLD, MPI_STATUS_IGNORE);
 	      }
-	      
+	      fputc(10, output);
+
 	      // now get the binary local file
 	      long buffer_size = 0;
 	      // get the size of the buffer
@@ -446,11 +444,18 @@ void cluster(const string& config_file, const string& data_file, const string& o
 	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();
+	partial_output.close();
+	partial_output.open(partial_file_name.c_str(), ios::in | ios::binary);
 	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);
+	  // If EOF is reached, do not send EOF character.
+	  long ptr_position = partial_output.tellg();
+	  if (ptr_position == partial_output_size) {
+	    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
@@ -459,7 +464,7 @@ void cluster(const string& config_file, const string& data_file, const string& o
 	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;
+	  chunk_buffer_size = partial_output_size - ptr_position - 1;
 	  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);
@@ -472,7 +477,8 @@ void cluster(const string& config_file, const string& data_file, const string& o
 	partial_output.close();
 	delete[] chunk_buffer;
 	remove(partial_file_name.c_str());
-
+	logger->log("done.\n", LOG_DEBG);
+	
 	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);