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
 */

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

#include "io/ifstrstream.hpp"

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 associates a buffer with the specified file to
   * perform the i/o operations (single mode). The master node reads a
   * file and broadcasts its content to the other slave nodes. After
   * broadcasting, all 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 has been read and spread 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, cleans up.
   */
  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;
    
    MPI_Comm_rank( MPI_COMM_WORLD, &myRank);
      
    masterNode = 0;
    
    if (myRank == masterNode) {
      
      if (checkFilename) {
        
        //check the filename is the same
        filenameLen = strlen(filename);
        MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
        MPI_Bcast((void*)filename, filenameLen, MPI_CHAR, 
                  masterNode, MPI_COMM_WORLD);
        
        diffFilename = 0;
        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;
        
        //broadcast the file size
        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 broadcast it
        fbuf[fileSize] = '\0';
        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;
        MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
        return false;
      }
      
    } else{ //slave nodes
      
      //check file name
      if (checkFilename) {
        MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
        
        char * masterFilename = new char[filenameLen];
        MPI_Bcast(masterFilename, filenameLen, MPI_CHAR, 
                  masterNode, MPI_COMM_WORLD);
        
        if( strcmp(masterFilename, filename) == 0)
          diffFilename = 0;
        else
          diffFilename = 1;
        
        delete[] masterFilename;
        
        MPI_Allreduce(&diffFilename, &error, 1, MPI_INT, MPI_SUM, 
                      MPI_COMM_WORLD);
        
        if (error > 0)
          return false;                        
      }
      //get file size
      MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
      
      if (fileSize >= 0 ) {
        fbuf = new char[fileSize+1];
        assert(fbuf);
        
        //receive file content
        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:	1969
Committed:	Wed Feb 26 14:14:50 2014 UTC (11 years, 8 months ago) by gezelter
File size:	10033 byte(s)
Log Message:	Fixes to deal with deprecation of MPI C++ bindings. We've reverted back to the C calls.
#	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	#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) {
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,
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)
82	: std::basic_istream<char, std::char_traits<char> >(0),
83	internalStringBuf_(), isRead(false) {
84	this->init(&internalStringBuf_);
85	isRead = internalOpen(filename, mode \| std::ios_base::in, checkFilename);
86	}
87	#else
88	ifstrstream::ifstrstream(const char* filename, std::ios_base::openmode mode, bool checkFilename)
89	: std::basic_istream<char, std::char_traits<char> >(0),
90	internalFileBuf_(), isRead(false) {
91
92	this->init(&internalFileBuf_);
93	isRead = internalOpen(filename, mode \| std::ios_base::in, checkFilename);
94	}
95	#endif
96	/**
97	* virtual destructor will close the file (in single mode) and clear
98	* the stream buffer
99	*/
100	ifstrstream::~ifstrstream(){ close();
101	}
102
103	/**
104	* Opens a file and associates a buffer with the specified file to
105	* perform the i/o operations (single mode). The master node reads a
106	* file and broadcasts its content to the other slave nodes. After
107	* broadcasting, all nodes fall back to stringstream (parallel
108	* mode).
109	* @param filename String containing the name of the file to be opened
110	* @param mode Flags describing the requested i/o mode for the file
111	* @param checkFilename Flags indicating checking the file name in parallel
112	*/
113	void ifstrstream::open(const char* filename, std::ios_base::openmode mode, bool checkFilename){
114
115	if (!isRead ) {
116	isRead = internalOpen(filename, mode, checkFilename);
117	}
118	}
119
120	/**
121	* Tests if the stream is currently associated with a valid buffer.
122	* @return true if a file has successfully been opened (single mode)
123	* or the whole file has been read and spread among all of the
124	* processors (parallel mode), otherwise false is returned
125	*/
126	bool ifstrstream::is_open ( ) {
127	#ifdef IS_MPI
128	return isRead;
129	#else
130	//single version fall back to ifstream
131	return internalFileBuf_.is_open();
132	#endif
133	}
134
135	/**
136	* In single mode, closes a file. The stream's file buffer is
137	* released from its association with the currently open file. In
138	* parallel mode, cleans up.
139	*/
140	void ifstrstream::close() {
141	#ifndef IS_MPI
142	//single version fall back to ifstream
143	if (!internalFileBuf_.close())
144	this->setstate(std::ios_base::failbit);
145	#endif
146
147	isRead = false;
148	}
149
150	/**
151	* Gets the stream buffer object associated with the stream
152	* @return A pointer to the stream buffer object(filebuf in single
153	* mode, stringbuf in parallel mode) associated with the stream.
154	*/
155	std::basic_streambuf<char, std::char_traits<char> >* ifstrstream::rdbuf() {
156	#ifdef IS_MPI
157	return static_cast<_StringBuf*>(&internalStringBuf_);
158	#else
159	return static_cast<_FileBuf*>(&internalFileBuf_);
160	#endif
161	}
162
163	/**
164	* Internal function used to open the file
165	* @return true if succesfully opens a file (single mode) or gets
166	* the file content (parallel mode) otherwise return false
167	* @param filename String containing the name of the file to be opened
168	* @param mode Flags describing the requested i/o mode for the file
169	* @param checkFilename Flags indicating checking the file name in parallel
170	* @todo use try - catch syntax to make the program more readable
171	*/
172
173	bool ifstrstream::internalOpen(const char* filename, std::ios_base::openmode mode, bool checkFilename){
174
175	#ifdef IS_MPI
176	//int commStatus;
177	long fileSize;
178	char* fbuf;
179	int filenameLen;
180	int diffFilename;
181	int error;
182	int myRank;
183	int masterNode;
184
185	MPI_Comm_rank( MPI_COMM_WORLD, &myRank);
186
187	masterNode = 0;
188
189	if (myRank == masterNode) {
190
191	if (checkFilename) {
192
193	//check the filename is the same
194	filenameLen = strlen(filename);
195	MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
196	MPI_Bcast((void*)filename, filenameLen, MPI_CHAR,
197	masterNode, MPI_COMM_WORLD);
198
199	diffFilename = 0;
200	MPI_Allreduce(&diffFilename, &error, 1, MPI_INT, MPI_SUM,
201	MPI_COMM_WORLD);
202
203	//if file names are different just return false
204	if (error > 0)
205	return false;
206	}
207
208	std::ifstream fin(filename, mode);
209
210	if (fin.is_open()) {
211
212	fin.seekg(0, std::ios::end);
213	fileSize = fin.tellg();
214	fin.seekg(0, std::ios::beg);
215
216	// '\0' need one more char
217	fbuf = new char[fileSize+1];
218
219	assert(fbuf != 0);
220
221	fin.read(fbuf, fileSize);
222
223	if (fin.fail())
224	fileSize = FileIOError;
225
226	//broadcast the file size
227	MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
228
229	if (fileSize < 0) {
230	fin.close();
231	delete[] fbuf;
232
233	return false;
234	}
235
236	// make a c-style std::string and broadcast it
237	fbuf[fileSize] = '\0';
238	MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
239
240	//close the file and delete the buffer
241	fin.close();
242	internalStringBuf_.str(fbuf);
243	delete[] fbuf;
244	}else{
245	fileSize = FileNotExists;
246	MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
247	return false;
248	}
249
250	} else{ //slave nodes
251
252	//check file name
253	if (checkFilename) {
254	MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
255
256	char * masterFilename = new char[filenameLen];
257	MPI_Bcast(masterFilename, filenameLen, MPI_CHAR,
258	masterNode, MPI_COMM_WORLD);
259
260	if( strcmp(masterFilename, filename) == 0)
261	diffFilename = 0;
262	else
263	diffFilename = 1;
264
265	delete[] masterFilename;
266
267	MPI_Allreduce(&diffFilename, &error, 1, MPI_INT, MPI_SUM,
268	MPI_COMM_WORLD);
269
270	if (error > 0)
271	return false;
272	}
273	//get file size
274	MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
275
276	if (fileSize >= 0 ) {
277	fbuf = new char[fileSize+1];
278	assert(fbuf);
279
280	//receive file content
281	MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
282
283	internalStringBuf_.str(fbuf);
284	delete [] fbuf;
285
286	} else if (fileSize == FileNotExists ) {
287	return false;
288
289	} else if (fileSize == FileIOError ) {
290	return false;
291	}
292	}
293
294	#else
295	//in single version, fall back to ifstream
296	if (!internalFileBuf_.open(filename, mode)) {
297	this->setstate(std::ios_base::failbit);
298	return false;
299	}
300
301	#endif
302	this->clear();
303	return true;
304	}
305	}