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, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @file basic_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
   * @filename String containing the name of the file to be opened
   * @mode Flags describing the requested i/o mode for the file, default value is ios_base::in      
   * @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).
   * @filename String containing the name of the file to be opened
   * @mode Flags describing the requested i/o mode for the file
   * @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
     * @filename String containing the name of the file to be opened
     * @mode Flags describing the requested i/o mode for the file
     * @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;
    
    commStatus = MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
    masterNode = 0;
    
    if (myRank == masterNode) {
      
      if (checkFilename) {
        
        //check the filename is the same
        filenameLen = strlen(filename);
        commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
        commStatus = MPI_Bcast((void*)filename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
        
        diffFilename = 0;
        commStatus = MPI_Allreduce(&diffFilename, &error, 1,  MPI_INT, MPI_SUM,  MPI_COMM_WORLD);             
        
        //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;
        
        //brocasting the file size
        commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);                   
        
        if (fileSize < 0) {
          fin.close();                    
          delete fbuf;
          
          return false;
        }
        
        // make a c-style  std::string and brocasting it
        fbuf[fileSize] = '\0';
        commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD); 
        
        //close the file and delete the buffer
        fin.close();      
        internalStringBuf_.str(fbuf);
        delete [] fbuf;
      }else{
        fileSize = FileNotExists;
        commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);   
        return false;
      }
      
    } else{ //slave nodes
      
      //check file name
      if (checkFilename) {
        commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
        
        char * masterFilename = new char[filenameLen];
        commStatus = MPI_Bcast(masterFilename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
        
        if( strcmp(masterFilename, filename) == 0)
          diffFilename = 0;
        else
          diffFilename = 1;
        
        delete masterFilename;
        
        commStatus = MPI_Allreduce(&diffFilename, &error, 1,  MPI_INT,  MPI_SUM, MPI_COMM_WORLD);    
        
        if (error > 0)
          return false;                        
      }
      //get file size
      commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);   
      
      if (fileSize >= 0 ) {
        fbuf = new char[fileSize+1];
        assert(fbuf);
        
        //receive file content
        commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD); 
        
        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:	1627
Committed:	Tue Sep 13 22:05:04 2011 UTC (13 years, 7 months ago) by gezelter
File size:	9968 byte(s)
Log Message:	Splitting out ifstrstream into a header and an implementation. This means that much of the code that depends on it can be compiled only once and the parallel I/O is concentrated into a few files. To do this, a number of files that relied on basic_ifstrstream to load the mpi header had to be modified to manage their own headers.
#	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, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	/**
43	* @file basic_ifstrstream.cpp
44	* @author Teng Lin
45	* @date 10/14/2004
46	* @version 1.0
47	*/
48
49	#include "io/ifstrstream.hpp"
50
51	#ifdef IS_MPI
52	#include <mpi.h>
53	#endif
54
55	namespace OpenMD {
56
57	/** Constructs an object of class ifstream. */
58	#ifdef IS_MPI
59	ifstrstream::ifstrstream()
60	: std::basic_istream<char, std::char_traits<char> >(0),
61	internalStringBuf_(), isRead(false) {
62	this->init(&internalStringBuf_);
63	}
64	#else
65	ifstrstream::ifstrstream()
66	: std::basic_istream<char, std::char_traits<char> >(0),
67	internalFileBuf_(), isRead(false) {
68	this->init(&internalFileBuf_);
69	}
70	#endif
71
72	/**
73	* Explicit constructor
74	* @filename String containing the name of the file to be opened
75	* @mode Flags describing the requested i/o mode for the file, default value is ios_base::in
76	* @checkFilename Flags indicating checking the file name in parallel
77	*/
78	#ifdef IS_MPI
79	ifstrstream::ifstrstream(const char* filename, std::ios_base::openmode mode, bool checkFilename)
80	: std::basic_istream<char, std::char_traits<char> >(0),
81	internalStringBuf_(), isRead(false) {
82	this->init(&internalStringBuf_);
83	isRead = internalOpen(filename, mode \| std::ios_base::in, checkFilename);
84	}
85	#else
86	ifstrstream::ifstrstream(const char* filename, std::ios_base::openmode mode, bool checkFilename)
87	: std::basic_istream<char, std::char_traits<char> >(0),
88	internalFileBuf_(), isRead(false) {
89
90	this->init(&internalFileBuf_);
91	isRead = internalOpen(filename, mode \| std::ios_base::in, checkFilename);
92	}
93	#endif
94	/**
95	* virtual destructor will close the file(in single mode) and clear the stream buffer
96	*/
97	ifstrstream::~ifstrstream(){
98	close();
99	}
100
101	/**
102	* Opens a file and associats a buffer with the specified file to perform the i/o operations
103	* (single mode). Master reads a file and brocasts its content to the other slave nodes. After
104	* brocasting, every nodes fall back to stringstream (parallel mode).
105	* @filename String containing the name of the file to be opened
106	* @mode Flags describing the requested i/o mode for the file
107	* @checkFilename Flags indicating checking the file name in parallel
108	*/
109	void ifstrstream::open(const char* filename, std::ios_base::openmode mode, bool checkFilename){
110
111	if (!isRead ) {
112	isRead = internalOpen(filename, mode, checkFilename);
113	}
114	}
115
116	/**
117	* Tests if the stream is currently associated with a valid buffer.
118	* @return true if a file has successfully been opened (single mode) or the whole file is read
119	* and spreaded among all of the processors (parallel mode), otherwise false is returned
120	*/
121	bool ifstrstream::is_open ( ) {
122	#ifdef IS_MPI
123	return isRead;
124	#else
125	//single version fall back to ifstream
126	return internalFileBuf_.is_open();
127	#endif
128	}
129
130	/**
131	* In single mode, closes a file. The stream's file buffer is
132	* released from its association with the currently open file. In
133	* parallel mode, clean the
134	*/
135	void ifstrstream::close() {
136	#ifndef IS_MPI
137	//single version fall back to ifstream
138	if (!internalFileBuf_.close())
139	this->setstate(std::ios_base::failbit);
140	#endif
141
142	isRead = false;
143	}
144
145	/**
146	* Gets the stream buffer object associated with the stream
147	* @return A pointer to the stream buffer object(filebuf in single
148	* mode, stringbuf in parallel mode) associated with the stream.
149	*/
150	std::basic_streambuf<char, std::char_traits<char> >* ifstrstream::rdbuf() {
151	#ifdef IS_MPI
152	return static_cast<_StringBuf*>(&internalStringBuf_);
153	#else
154	return static_cast<_FileBuf*>(&internalFileBuf_);
155	#endif
156	}
157
158	/**
159	* Internal function used to open the file
160	* @return true if succesfully opens a file (single mode) or gets the file content (parallel mode)
161	* otherwise return false
162	* @filename String containing the name of the file to be opened
163	* @mode Flags describing the requested i/o mode for the file
164	* @todo use try - catch syntax to make the program more readable
165	*/
166
167	bool ifstrstream::internalOpen(const char* filename, std::ios_base::openmode mode, bool checkFilename){
168
169	#ifdef IS_MPI
170	int commStatus;
171	long fileSize;
172	char* fbuf;
173	int filenameLen;
174	int diffFilename;
175	int error;
176	int myRank;
177	int masterNode;
178
179	commStatus = MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
180	masterNode = 0;
181
182	if (myRank == masterNode) {
183
184	if (checkFilename) {
185
186	//check the filename is the same
187	filenameLen = strlen(filename);
188	commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
189	commStatus = MPI_Bcast((void*)filename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD);
190
191	diffFilename = 0;
192	commStatus = MPI_Allreduce(&diffFilename, &error, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
193
194	//if file names are different just return false
195	if (error > 0)
196	return false;
197	}
198
199	std::ifstream fin(filename, mode);
200
201	if (fin.is_open()) {
202
203	fin.seekg(0, std::ios::end);
204	fileSize = fin.tellg();
205	fin.seekg(0, std::ios::beg);
206
207	// '\0' need one more char
208	fbuf = new char[fileSize+1];
209
210	assert(fbuf != 0);
211
212	fin.read(fbuf, fileSize);
213
214	if (fin.fail())
215	fileSize = FileIOError;
216
217	//brocasting the file size
218	commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
219
220	if (fileSize < 0) {
221	fin.close();
222	delete fbuf;
223
224	return false;
225	}
226
227	// make a c-style std::string and brocasting it
228	fbuf[fileSize] = '\0';
229	commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
230
231	//close the file and delete the buffer
232	fin.close();
233	internalStringBuf_.str(fbuf);
234	delete [] fbuf;
235	}else{
236	fileSize = FileNotExists;
237	commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
238	return false;
239	}
240
241	} else{ //slave nodes
242
243	//check file name
244	if (checkFilename) {
245	commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
246
247	char * masterFilename = new char[filenameLen];
248	commStatus = MPI_Bcast(masterFilename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD);
249
250	if( strcmp(masterFilename, filename) == 0)
251	diffFilename = 0;
252	else
253	diffFilename = 1;
254
255	delete masterFilename;
256
257	commStatus = MPI_Allreduce(&diffFilename, &error, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
258
259	if (error > 0)
260	return false;
261	}
262	//get file size
263	commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
264
265	if (fileSize >= 0 ) {
266	fbuf = new char[fileSize+1];
267	assert(fbuf);
268
269	//receive file content
270	commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
271
272	internalStringBuf_.str(fbuf);
273	delete [] fbuf;
274
275	} else if (fileSize == FileNotExists ) {
276	return false;
277
278	} else if (fileSize == FileIOError ) {
279	return false;
280	}
281	}
282
283	#else
284	//in single version, fall back to ifstream
285	if (!internalFileBuf_.open(filename, mode)) {
286	this->setstate(std::ios_base::failbit);
287	return false;
288	}
289
290	#endif
291	this->clear();
292	return true;
293	}
294	}