src/io/ifstrstream.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file ifstrstream.cpp
 * @author Teng Lin
 * @date 10/14/2004
 * @version 1.0
 */

#include "io/ifstrstream.hpp"

#ifdef IS_MPI
#include <mpi.h>
#endif

namespace OpenMD {
  
  /**  Constructs an object of class ifstream.  */
#ifdef IS_MPI
  ifstrstream::ifstrstream() 
    :  std::basic_istream<char, std::char_traits<char> >(0),
       internalStringBuf_(), isRead(false)  {    
    this->init(&internalStringBuf_);
  }
#else
  ifstrstream::ifstrstream() 
    :  std::basic_istream<char, std::char_traits<char> >(0),
       internalFileBuf_(), isRead(false)  {    
    this->init(&internalFileBuf_);
  }
#endif
  
  /**
   * Explicit constructor
   * @param filename String containing the name of the file to be opened
   * @param mode Flags describing the requested i/o mode for the file, default value is ios_base::in      
   * @param checkFilename Flags indicating checking the file name in parallel
   */
#ifdef IS_MPI
  ifstrstream::ifstrstream(const char* filename, std::ios_base::openmode mode, bool checkFilename)
    :  std::basic_istream<char, std::char_traits<char> >(0),
       internalStringBuf_(), isRead(false) {
    this->init(&internalStringBuf_);
    isRead =  internalOpen(filename,  mode | std::ios_base::in, checkFilename);
  }
#else
  ifstrstream::ifstrstream(const char* filename, std::ios_base::openmode mode, bool checkFilename)
    :  std::basic_istream<char, std::char_traits<char> >(0),
       internalFileBuf_(), isRead(false) {
    
    this->init(&internalFileBuf_);
    isRead =  internalOpen(filename,  mode | std::ios_base::in, checkFilename);
  }
#endif  
  /**
   * virtual destructor will close the file(in single mode) and clear the stream buffer
   */
  ifstrstream::~ifstrstream(){
    close();
  }
  
  /**
   * Opens a file and associats a buffer with the specified file to perform the i/o operations 
   * (single mode). Master reads a file and brocasts its content to the other slave nodes. After
   * brocasting, every nodes fall back to stringstream (parallel mode).
   * @param filename String containing the name of the file to be opened
   * @param mode Flags describing the requested i/o mode for the file
   * @param checkFilename Flags indicating checking the file name in parallel
   */
  void ifstrstream::open(const char* filename, std::ios_base::openmode mode, bool checkFilename){
    
    if (!isRead ) {
      isRead = internalOpen(filename, mode, checkFilename);
    }
  }

  /**
   * Tests if the stream is currently associated with a valid  buffer.
   * @return true if a file has successfully been opened (single mode) or the whole file is read 
   * and spreaded among all of the processors (parallel mode),  otherwise false is returned
   */
  bool ifstrstream::is_open ( ) {
#ifdef IS_MPI            
    return isRead; 
#else
    //single version fall back to ifstream
    return internalFileBuf_.is_open();
#endif
  }
  
  /**
   * In single mode, closes a file. The stream's file buffer is
   * released from its association with the currently open file. In
   * parallel mode, clean the
   */
  void ifstrstream::close() {
#ifndef IS_MPI            
    //single version fall back to ifstream
    if (!internalFileBuf_.close())
      this->setstate(std::ios_base::failbit);
#endif             
    
    isRead = false;
  }
  
  /**
   * Gets the stream buffer object associated with the stream
   * @return A pointer to the stream buffer object(filebuf in single
   * mode, stringbuf in parallel mode) associated with the stream.
   */
  std::basic_streambuf<char, std::char_traits<char> >*  ifstrstream::rdbuf() {
#ifdef IS_MPI
    return static_cast<_StringBuf*>(&internalStringBuf_); 
#else
    return static_cast<_FileBuf*>(&internalFileBuf_); 
#endif
  }  
  
  /**
     * Internal function used to open the file
     * @return true if succesfully opens a file (single mode) or gets the file content (parallel mode)
     * otherwise return false
     * @param filename String containing the name of the file to be opened
     * @param mode Flags describing the requested i/o mode for the file
     * @param checkFilename Flags indicating checking the file name in parallel
     * @todo use try - catch syntax to make the program more readable
     */

  bool ifstrstream::internalOpen(const char* filename, std::ios_base::openmode mode, bool checkFilename){
    
#ifdef IS_MPI         
    //int commStatus;
    long fileSize;
    char* fbuf;
    int filenameLen;
    int diffFilename;
    int error;
    int myRank;
    int masterNode;
    
    myRank =  MPI::COMM_WORLD.Get_rank();
    masterNode = 0;
    
    if (myRank == masterNode) {
      
      if (checkFilename) {
        
        //check the filename is the same
        filenameLen = strlen(filename);
        MPI::COMM_WORLD.Bcast(&filenameLen, 1, MPI::INT, masterNode);
        MPI::COMM_WORLD.Bcast((void*)filename, filenameLen, MPI::CHAR, 
                              masterNode);
        
        diffFilename = 0;
        MPI::COMM_WORLD.Allreduce(&diffFilename, &error, 1, MPI::INT, MPI::SUM);

        //if file names are different just return false
        if (error > 0)
          return false;   
      }
      
      std::ifstream fin(filename, mode);
      
      if (fin.is_open()) {
        
        fin.seekg(0, std::ios::end); 
        fileSize = fin.tellg(); 
        fin.seekg(0, std::ios::beg);
        
        // '\0' need one more char
        fbuf = new char[fileSize+1];
        
        assert(fbuf != 0);
        
        fin.read(fbuf, fileSize);
        
        if (fin.fail())
          fileSize = FileIOError;
        
        //broadcast the file size
        MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
        
        if (fileSize < 0) {
          fin.close();                    
          delete[] fbuf;
          
          return false;
        }
        
        // make a c-style  std::string and broadcast it
        fbuf[fileSize] = '\0';
        MPI::COMM_WORLD.Bcast(fbuf, fileSize + 1, MPI::CHAR, masterNode);
        
        //close the file and delete the buffer
        fin.close();      
        internalStringBuf_.str(fbuf);
        delete[] fbuf;
      }else{
        fileSize = FileNotExists;
        MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
        return false;
      }
      
    } else{ //slave nodes
      
      //check file name
      if (checkFilename) {
        MPI::COMM_WORLD.Bcast(&filenameLen, 1, MPI::INT, masterNode);
        
        char * masterFilename = new char[filenameLen];
        MPI::COMM_WORLD.Bcast(masterFilename, filenameLen, MPI::CHAR, 
                              masterNode);
        
        if( strcmp(masterFilename, filename) == 0)
          diffFilename = 0;
        else
          diffFilename = 1;
        
        delete[] masterFilename;
        
        MPI::COMM_WORLD.Allreduce(&diffFilename, &error, 1, MPI::INT, MPI::SUM);
        
        if (error > 0)
          return false;                        
      }
      //get file size
      MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
      
      if (fileSize >= 0 ) {
        fbuf = new char[fileSize+1];
        assert(fbuf);
        
        //receive file content
        MPI::COMM_WORLD.Bcast(fbuf, fileSize + 1, MPI::CHAR, masterNode);
        
        internalStringBuf_.str(fbuf);
        delete [] fbuf;
        
      } else if (fileSize == FileNotExists ) {
        return false;
        
      } else if (fileSize == FileIOError ) {
        return false;
      }
    }
    
#else
    //in single version, fall back to ifstream
    if (!internalFileBuf_.open(filename, mode)) {
      this->setstate(std::ios_base::failbit);
      return false;
    }    
    
#endif
    this->clear();
    return true;
  }
}
Revision:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	9957 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	Content
1	/*
2	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	*
4	* The University of Notre Dame grants you ("Licensee") a
5	* non-exclusive, royalty free, license to use, modify and
6	* redistribute this software in source and binary code form, provided
7	* that the following conditions are met:
8	*
9	* 1. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
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, 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 ifstrstream.cpp
45	* @author Teng Lin
46	* @date 10/14/2004
47	* @version 1.0
48	*/
49
50	#include "io/ifstrstream.hpp"
51
52	#ifdef IS_MPI
53	#include <mpi.h>
54	#endif
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) {
63	this->init(&internalStringBuf_);
64	}
65	#else
66	ifstrstream::ifstrstream()
67	: std::basic_istream<char, std::char_traits<char> >(0),
68	internalFileBuf_(), isRead(false) {
69	this->init(&internalFileBuf_);
70	}
71	#endif
72
73	/**
74	* Explicit constructor
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)
81	: std::basic_istream<char, std::char_traits<char> >(0),
82	internalStringBuf_(), isRead(false) {
83	this->init(&internalStringBuf_);
84	isRead = internalOpen(filename, mode \| std::ios_base::in, checkFilename);
85	}
86	#else
87	ifstrstream::ifstrstream(const char* filename, std::ios_base::openmode mode, bool checkFilename)
88	: std::basic_istream<char, std::char_traits<char> >(0),
89	internalFileBuf_(), isRead(false) {
90
91	this->init(&internalFileBuf_);
92	isRead = internalOpen(filename, mode \| std::ios_base::in, checkFilename);
93	}
94	#endif
95	/**
96	* virtual destructor will close the file(in single mode) and clear the stream buffer
97	*/
98	ifstrstream::~ifstrstream(){
99	close();
100	}
101
102	/**
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	* @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
112	if (!isRead ) {
113	isRead = internalOpen(filename, mode, checkFilename);
114	}
115	}
116
117	/**
118	* Tests if the stream is currently associated with a valid buffer.
119	* @return true if a file has successfully been opened (single mode) or the whole file is read
120	* and spreaded among all of the processors (parallel mode), otherwise false is returned
121	*/
122	bool ifstrstream::is_open ( ) {
123	#ifdef IS_MPI
124	return isRead;
125	#else
126	//single version fall back to ifstream
127	return internalFileBuf_.is_open();
128	#endif
129	}
130
131	/**
132	* In single mode, closes a file. The stream's file buffer is
133	* released from its association with the currently open file. In
134	* parallel mode, clean the
135	*/
136	void ifstrstream::close() {
137	#ifndef IS_MPI
138	//single version fall back to ifstream
139	if (!internalFileBuf_.close())
140	this->setstate(std::ios_base::failbit);
141	#endif
142
143	isRead = false;
144	}
145
146	/**
147	* Gets the stream buffer object associated with the stream
148	* @return A pointer to the stream buffer object(filebuf in single
149	* mode, stringbuf in parallel mode) associated with the stream.
150	*/
151	std::basic_streambuf<char, std::char_traits<char> >* ifstrstream::rdbuf() {
152	#ifdef IS_MPI
153	return static_cast<_StringBuf*>(&internalStringBuf_);
154	#else
155	return static_cast<_FileBuf*>(&internalFileBuf_);
156	#endif
157	}
158
159	/**
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	* @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;
173	long fileSize;
174	char* fbuf;
175	int filenameLen;
176	int diffFilename;
177	int error;
178	int myRank;
179	int masterNode;
180
181	myRank = MPI::COMM_WORLD.Get_rank();
182	masterNode = 0;
183
184	if (myRank == masterNode) {
185
186	if (checkFilename) {
187
188	//check the filename is the same
189	filenameLen = strlen(filename);
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	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;
200	}
201
202	std::ifstream fin(filename, mode);
203
204	if (fin.is_open()) {
205
206	fin.seekg(0, std::ios::end);
207	fileSize = fin.tellg();
208	fin.seekg(0, std::ios::beg);
209
210	// '\0' need one more char
211	fbuf = new char[fileSize+1];
212
213	assert(fbuf != 0);
214
215	fin.read(fbuf, fileSize);
216
217	if (fin.fail())
218	fileSize = FileIOError;
219
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;
226
227	return false;
228	}
229
230	// make a c-style std::string and broadcast it
231	fbuf[fileSize] = '\0';
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;
238	}else{
239	fileSize = FileNotExists;
240	MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
241	return false;
242	}
243
244	} else{ //slave nodes
245
246	//check file name
247	if (checkFilename) {
248	MPI::COMM_WORLD.Bcast(&filenameLen, 1, MPI::INT, masterNode);
249
250	char * masterFilename = new char[filenameLen];
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;
260
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	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	MPI::COMM_WORLD.Bcast(fbuf, fileSize + 1, MPI::CHAR, masterNode);
275
276	internalStringBuf_.str(fbuf);
277	delete [] fbuf;
278
279	} else if (fileSize == FileNotExists ) {
280	return false;
281
282	} else if (fileSize == FileIOError ) {
283	return false;
284	}
285	}
286
287	#else
288	//in single version, fall back to ifstream
289	if (!internalFileBuf_.open(filename, mode)) {
290	this->setstate(std::ios_base::failbit);
291	return false;
292	}
293
294	#endif
295	this->clear();
296	return true;
297	}
298	}