Merge branch 'fix_io' into 'master'

Draft: fix remounting files from threads and processes, fix pycompare accordingly

See merge request giacomo.mulas/np_tmcode!34

src/cluster/cluster.cpp

@@ -13,7 +13,7 @@
    limitations under the License.
  */
 
-/*! \file cluster.cp
+/*! \file cluster.cpp
  *
  * \brief Implementation of the calculation for a cluster of spheres.
  */
@@ -388,7 +388,7 @@ 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);
 	      }
-	      fprintf(output, "\n");
+	      // if (ri<remotethreads-1) fprintf(output, "\n");
 
 	      // now get the binary local file
 	      long buffer_size = 0;
@@ -508,11 +508,11 @@ void cluster(const string& config_file, const string& data_file, const string& o
 	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);
 	fstream partial_output;
-	partial_output.open(partial_file_name.c_str(), ios::in | ios::binary);
+	partial_output.open(partial_file_name.c_str(), ios::in);
 	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);
+	partial_output.open(partial_file_name.c_str(), ios::in);
 	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);
@@ -535,7 +535,7 @@ void cluster(const string& config_file, const string& data_file, const string& o
 	  delete[] chunk_buffer;
 	  chunk_buffer = new char[chunk_buffer_size];
 	  partial_output.read(chunk_buffer, chunk_buffer_size);
-	  chunk_buffer[chunk_buffer_size - 1] = '\0';
+	  // chunk_buffer[chunk_buffer_size - 1] = '\0';
 	  // 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

src/scripts/pycompare.py

@@ -125,7 +125,7 @@ def compare_files(config):
                 return mismatch_count
             f_lines[0] = fortran_file.readline()
             c_lines[0] = c_file.readline()
-        if (c_lines[0] != ''):
+        if (c_lines[0] not in ['', '\n']):
             print("ERROR: C++ file is longer than FORTRAN file.")
             fortran_file.close()
             c_file.close()