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root/OpenMD/trunk/src/io/ifstrstream.cpp
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Comparing trunk/src/io/ifstrstream.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 1938 by gezelter, Thu Oct 31 15:32:17 2013 UTC

# Line 35 | Line 35
35   *                                                                      
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 < * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
39   * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   /**
44 < * @file basic_ifstrstream.cpp
44 > * @file ifstrstream.cpp
45   * @author Teng Lin
46   * @date 10/14/2004
47   * @version 1.0
48   */
49  
50 – #include "io/ifstrstream.hpp"
51 –
50   #ifdef IS_MPI
51   #include <mpi.h>
52   #endif
53  
54 + #include "io/ifstrstream.hpp"
55 +
56   namespace OpenMD {
57    
58    /**  Constructs an object of class ifstream.  */
# Line 72 | Line 72 | namespace OpenMD {
72    
73    /**
74     * Explicit constructor
75 <   * @filename String containing the name of the file to be opened
76 <   * @mode Flags describing the requested i/o mode for the file, default value is ios_base::in      
77 <   * @checkFilename Flags indicating checking the file name in parallel
75 >   * @param filename String containing the name of the file to be opened
76 >   * @param mode Flags describing the requested i/o mode for the file, default value is ios_base::in      
77 >   * @param checkFilename Flags indicating checking the file name in parallel
78     */
79   #ifdef IS_MPI
80    ifstrstream::ifstrstream(const char* filename, std::ios_base::openmode mode, bool checkFilename)
# Line 103 | Line 103 | namespace OpenMD {
103     * Opens a file and associats a buffer with the specified file to perform the i/o operations
104     * (single mode). Master reads a file and brocasts its content to the other slave nodes. After
105     * brocasting, every nodes fall back to stringstream (parallel mode).
106 <   * @filename String containing the name of the file to be opened
107 <   * @mode Flags describing the requested i/o mode for the file
108 <   * @checkFilename Flags indicating checking the file name in parallel
106 >   * @param filename String containing the name of the file to be opened
107 >   * @param mode Flags describing the requested i/o mode for the file
108 >   * @param checkFilename Flags indicating checking the file name in parallel
109     */
110    void ifstrstream::open(const char* filename, std::ios_base::openmode mode, bool checkFilename){
111      
# Line 160 | Line 160 | namespace OpenMD {
160       * Internal function used to open the file
161       * @return true if succesfully opens a file (single mode) or gets the file content (parallel mode)
162       * otherwise return false
163 <     * @filename String containing the name of the file to be opened
164 <     * @mode Flags describing the requested i/o mode for the file
163 >     * @param filename String containing the name of the file to be opened
164 >     * @param mode Flags describing the requested i/o mode for the file
165 >     * @param checkFilename Flags indicating checking the file name in parallel
166       * @todo use try - catch syntax to make the program more readable
167       */
168  
169    bool ifstrstream::internalOpen(const char* filename, std::ios_base::openmode mode, bool checkFilename){
170      
171   #ifdef IS_MPI        
172 <    int commStatus;
172 >    //int commStatus;
173      long fileSize;
174      char* fbuf;
175      int filenameLen;
# Line 177 | Line 178 | namespace OpenMD {
178      int myRank;
179      int masterNode;
180      
181 <    commStatus = MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
181 >    myRank =  MPI::COMM_WORLD.Get_rank();
182      masterNode = 0;
183      
184      if (myRank == masterNode) {
# Line 186 | Line 187 | namespace OpenMD {
187          
188          //check the filename is the same
189          filenameLen = strlen(filename);
190 <        commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
191 <        commStatus = MPI_Bcast((void*)filename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
190 >        MPI::COMM_WORLD.Bcast(&filenameLen, 1, MPI::INT, masterNode);
191 >        MPI::COMM_WORLD.Bcast((void*)filename, filenameLen, MPI::CHAR,
192 >                              masterNode);
193          
194          diffFilename = 0;
195 <        commStatus = MPI_Allreduce(&diffFilename, &error, 1,  MPI_INT, MPI_SUM,  MPI_COMM_WORLD);            
196 <        
195 >        MPI::COMM_WORLD.Allreduce(&diffFilename, &error, 1, MPI::INT, MPI::SUM);
196 >
197          //if file names are different just return false
198          if (error > 0)
199            return false;  
# Line 215 | Line 217 | namespace OpenMD {
217          if (fin.fail())
218            fileSize = FileIOError;
219          
220 <        //brocasting the file size
221 <        commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);                  
220 >        //broadcast the file size
221 >        MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
222          
223          if (fileSize < 0) {
224            fin.close();                    
225 <          delete fbuf;
225 >          delete[] fbuf;
226            
227            return false;
228          }
229          
230 <        // make a c-style  std::string and brocasting it
230 >        // make a c-style  std::string and broadcast it
231          fbuf[fileSize] = '\0';
232 <        commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
232 >        MPI::COMM_WORLD.Bcast(fbuf, fileSize + 1, MPI::CHAR, masterNode);
233          
234          //close the file and delete the buffer
235          fin.close();      
236          internalStringBuf_.str(fbuf);
237 <        delete [] fbuf;
237 >        delete[] fbuf;
238        }else{
239          fileSize = FileNotExists;
240 <        commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
240 >        MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
241          return false;
242        }
243        
# Line 243 | Line 245 | namespace OpenMD {
245        
246        //check file name
247        if (checkFilename) {
248 <        commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
248 >        MPI::COMM_WORLD.Bcast(&filenameLen, 1, MPI::INT, masterNode);
249          
250          char * masterFilename = new char[filenameLen];
251 <        commStatus = MPI_Bcast(masterFilename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
251 >        MPI::COMM_WORLD.Bcast(masterFilename, filenameLen, MPI::CHAR,
252 >                              masterNode);
253          
254          if( strcmp(masterFilename, filename) == 0)
255            diffFilename = 0;
256          else
257            diffFilename = 1;
258          
259 <        delete masterFilename;
259 >        delete[] masterFilename;
260          
261 <        commStatus = MPI_Allreduce(&diffFilename, &error, 1,  MPI_INT,  MPI_SUM, MPI_COMM_WORLD);    
261 >        MPI::COMM_WORLD.Allreduce(&diffFilename, &error, 1, MPI::INT, MPI::SUM);
262          
263          if (error > 0)
264            return false;                        
265        }
266        //get file size
267 <      commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
267 >      MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
268        
269        if (fileSize >= 0 ) {
270          fbuf = new char[fileSize+1];
271          assert(fbuf);
272          
273          //receive file content
274 <        commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
274 >        MPI::COMM_WORLD.Bcast(fbuf, fileSize + 1, MPI::CHAR, masterNode);
275          
276          internalStringBuf_.str(fbuf);
277          delete [] fbuf;

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