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root/OpenMD/trunk/src/io/ifstrstream.cpp
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Comparing:
branches/development/src/io/ifstrstream.cpp (file contents), Revision 1627 by gezelter, Tue Sep 13 22:05:04 2011 UTC vs.
trunk/src/io/ifstrstream.cpp (file contents), Revision 1962 by gezelter, Wed Jan 15 22:26:18 2014 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).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
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  
49 – #include "io/ifstrstream.hpp"
50 –
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.  */
59   #ifdef IS_MPI
60    ifstrstream::ifstrstream()
61      :  std::basic_istream<char, std::char_traits<char> >(0),
62 <       internalStringBuf_(), isRead(false)  {    
62 >    internalStringBuf_(), isRead(false)  {    
63      this->init(&internalStringBuf_);
64    }
65   #else
66    ifstrstream::ifstrstream()
67      :  std::basic_istream<char, std::char_traits<char> >(0),
68 <       internalFileBuf_(), isRead(false)  {    
68 >    internalFileBuf_(), isRead(false)  {    
69      this->init(&internalFileBuf_);
70    }
71   #endif
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,
77 >   * default value is ios_base::in
78 >   * @param checkFilename Flags indicating checking the file name in parallel
79     */
80   #ifdef IS_MPI
81    ifstrstream::ifstrstream(const char* filename, std::ios_base::openmode mode, bool checkFilename)
# Line 92 | Line 94 | namespace OpenMD {
94    }
95   #endif  
96    /**
97 <   * virtual destructor will close the file(in single mode) and clear the stream buffer
97 >   * virtual destructor will close the file (in single mode) and clear
98 >   * the stream buffer
99     */
100    ifstrstream::~ifstrstream(){
101      close();
102    }
103    
104    /**
105 <   * Opens a file and associats a buffer with the specified file to perform the i/o operations
106 <   * (single mode). Master reads a file and brocasts its content to the other slave nodes. After
107 <   * brocasting, every nodes fall back to stringstream (parallel mode).
108 <   * @filename String containing the name of the file to be opened
109 <   * @mode Flags describing the requested i/o mode for the file
110 <   * @checkFilename Flags indicating checking the file name in parallel
105 >   * Opens a file and associates a buffer with the specified file to
106 >   * perform the i/o operations (single mode). The master node reads a
107 >   * file and broadcasts its content to the other slave nodes. After
108 >   * broadcasting, all nodes fall back to stringstream (parallel
109 >   * mode).
110 >   * @param filename String containing the name of the file to be opened
111 >   * @param mode Flags describing the requested i/o mode for the file
112 >   * @param checkFilename Flags indicating checking the file name in parallel
113     */
114    void ifstrstream::open(const char* filename, std::ios_base::openmode mode, bool checkFilename){
115      
# Line 114 | Line 119 | namespace OpenMD {
119    }
120  
121    /**
122 <   * Tests if the stream is currently associated with a valid  buffer.
123 <   * @return true if a file has successfully been opened (single mode) or the whole file is read
124 <   * and spreaded among all of the processors (parallel mode),  otherwise false is returned
122 >   * Tests if the stream is currently associated with a valid buffer.
123 >   * @return true if a file has successfully been opened (single mode)
124 >   * or the whole file has been read and spread among all of the
125 >   * processors (parallel mode), otherwise false is returned
126     */
127    bool ifstrstream::is_open ( ) {
128   #ifdef IS_MPI            
# Line 130 | Line 136 | namespace OpenMD {
136    /**
137     * In single mode, closes a file. The stream's file buffer is
138     * released from its association with the currently open file. In
139 <   * parallel mode, clean the
139 >   * parallel mode, cleans up.
140     */
141    void ifstrstream::close() {
142   #ifndef IS_MPI            
# Line 156 | Line 162 | namespace OpenMD {
162    }  
163    
164    /**
165 <     * Internal function used to open the file
166 <     * @return true if succesfully opens a file (single mode) or gets the file content (parallel mode)
167 <     * otherwise return false
168 <     * @filename String containing the name of the file to be opened
169 <     * @mode Flags describing the requested i/o mode for the file
170 <     * @todo use try - catch syntax to make the program more readable
171 <     */
165 >   * Internal function used to open the file
166 >   * @return true if succesfully opens a file (single mode) or gets
167 >   * the file content (parallel mode) otherwise return false
168 >   * @param filename String containing the name of the file to be opened
169 >   * @param mode Flags describing the requested i/o mode for the file
170 >   * @param checkFilename Flags indicating checking the file name in parallel
171 >   * @todo use try - catch syntax to make the program more readable
172 >   */
173  
174    bool ifstrstream::internalOpen(const char* filename, std::ios_base::openmode mode, bool checkFilename){
175      
176   #ifdef IS_MPI        
177 <    int commStatus;
177 >    //int commStatus;
178      long fileSize;
179      char* fbuf;
180      int filenameLen;
# Line 176 | Line 183 | namespace OpenMD {
183      int myRank;
184      int masterNode;
185      
186 <    commStatus = MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
186 >    myRank =  MPI::COMM_WORLD.Get_rank();
187      masterNode = 0;
188      
189      if (myRank == masterNode) {
# Line 185 | Line 192 | namespace OpenMD {
192          
193          //check the filename is the same
194          filenameLen = strlen(filename);
195 <        commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
196 <        commStatus = MPI_Bcast((void*)filename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
195 >        MPI::COMM_WORLD.Bcast(&filenameLen, 1, MPI::INT, masterNode);
196 >        MPI::COMM_WORLD.Bcast((void*)filename, filenameLen, MPI::CHAR,
197 >                              masterNode);
198          
199          diffFilename = 0;
200 <        commStatus = MPI_Allreduce(&diffFilename, &error, 1,  MPI_INT, MPI_SUM,  MPI_COMM_WORLD);            
200 >        MPI::COMM_WORLD.Allreduce(&diffFilename, &error, 1, MPI::INT, MPI::SUM);
201          
202          //if file names are different just return false
203          if (error > 0)
# Line 214 | Line 222 | namespace OpenMD {
222          if (fin.fail())
223            fileSize = FileIOError;
224          
225 <        //brocasting the file size
226 <        commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);                  
225 >        //broadcast the file size
226 >        MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
227          
228          if (fileSize < 0) {
229            fin.close();                    
230 <          delete fbuf;
230 >          delete[] fbuf;
231            
232            return false;
233          }
234          
235 <        // make a c-style  std::string and brocasting it
235 >        // make a c-style  std::string and broadcast it
236          fbuf[fileSize] = '\0';
237 <        commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
237 >        MPI::COMM_WORLD.Bcast(fbuf, fileSize + 1, MPI::CHAR, masterNode);
238          
239          //close the file and delete the buffer
240          fin.close();      
241          internalStringBuf_.str(fbuf);
242 <        delete [] fbuf;
242 >        delete[] fbuf;
243        }else{
244          fileSize = FileNotExists;
245 <        commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
245 >        MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
246          return false;
247        }
248        
# Line 242 | Line 250 | namespace OpenMD {
250        
251        //check file name
252        if (checkFilename) {
253 <        commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);    
253 >        MPI::COMM_WORLD.Bcast(&filenameLen, 1, MPI::INT, masterNode);
254          
255          char * masterFilename = new char[filenameLen];
256 <        commStatus = MPI_Bcast(masterFilename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD);    
256 >        MPI::COMM_WORLD.Bcast(masterFilename, filenameLen, MPI::CHAR,
257 >                              masterNode);
258          
259          if( strcmp(masterFilename, filename) == 0)
260            diffFilename = 0;
261          else
262            diffFilename = 1;
263          
264 <        delete masterFilename;
264 >        delete[] masterFilename;
265          
266 <        commStatus = MPI_Allreduce(&diffFilename, &error, 1,  MPI_INT,  MPI_SUM, MPI_COMM_WORLD);    
266 >        MPI::COMM_WORLD.Allreduce(&diffFilename, &error, 1, MPI::INT, MPI::SUM);
267          
268          if (error > 0)
269            return false;                        
270        }
271        //get file size
272 <      commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);  
272 >      MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
273        
274        if (fileSize >= 0 ) {
275          fbuf = new char[fileSize+1];
276          assert(fbuf);
277          
278          //receive file content
279 <        commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
279 >        MPI::COMM_WORLD.Bcast(fbuf, fileSize + 1, MPI::CHAR, masterNode);
280          
281          internalStringBuf_.str(fbuf);
282          delete [] fbuf;

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