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, 2 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.
#	User	Rev	Content
1	gezelter	1627	/*
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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1627	*/
42
43			/**
44	gezelter	1879	* @file ifstrstream.cpp
45	gezelter	1627	* @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	gezelter	1938	#include "io/ifstrstream.hpp"
55
56	gezelter	1627	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	gezelter	1969	internalStringBuf_(), isRead(false) {
63	gezelter	1627	this->init(&internalStringBuf_);
64			}
65			#else
66			ifstrstream::ifstrstream()
67			: std::basic_istream<char, std::char_traits<char> >(0),
68	gezelter	1969	internalFileBuf_(), isRead(false) {
69	gezelter	1627	this->init(&internalFileBuf_);
70			}
71			#endif
72
73			/**
74			* Explicit constructor
75	gezelter	1879	* @param filename String containing the name of the file to be opened
76	gezelter	1962	* @param mode Flags describing the requested i/o mode for the file,
77			* default value is ios_base::in
78	gezelter	1879	* @param checkFilename Flags indicating checking the file name in parallel
79	gezelter	1627	*/
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	gezelter	1969	internalStringBuf_(), isRead(false) {
84	gezelter	1627	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	gezelter	1969	internalFileBuf_(), isRead(false) {
91	gezelter	1627
92			this->init(&internalFileBuf_);
93			isRead = internalOpen(filename, mode \| std::ios_base::in, checkFilename);
94			}
95			#endif
96			/**
97	gezelter	1962	* virtual destructor will close the file (in single mode) and clear
98			* the stream buffer
99	gezelter	1627	*/
100	gezelter	1969	ifstrstream::~ifstrstream(){ close();
101	gezelter	1627	}
102
103			/**
104	gezelter	1962	* 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	gezelter	1879	* @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	gezelter	1627	*/
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	gezelter	1962	* 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	gezelter	1627	*/
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	gezelter	1962	* parallel mode, cleans up.
139	gezelter	1627	*/
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	gezelter	1962	* 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	gezelter	1627
173			bool ifstrstream::internalOpen(const char* filename, std::ios_base::openmode mode, bool checkFilename){
174
175			#ifdef IS_MPI
176	gezelter	1796	//int commStatus;
177	gezelter	1627	long fileSize;
178			char* fbuf;
179			int filenameLen;
180			int diffFilename;
181			int error;
182			int myRank;
183			int masterNode;
184
185	gezelter	1969	MPI_Comm_rank( MPI_COMM_WORLD, &myRank);
186
187	gezelter	1627	masterNode = 0;
188
189			if (myRank == masterNode) {
190
191			if (checkFilename) {
192
193			//check the filename is the same
194			filenameLen = strlen(filename);
195	gezelter	1969	MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
196			MPI_Bcast((void*)filename, filenameLen, MPI_CHAR,
197			masterNode, MPI_COMM_WORLD);
198	gezelter	1627
199			diffFilename = 0;
200	gezelter	1969	MPI_Allreduce(&diffFilename, &error, 1, MPI_INT, MPI_SUM,
201			MPI_COMM_WORLD);
202	gezelter	1962
203	gezelter	1627	//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	gezelter	1796	//broadcast the file size
227	gezelter	1969	MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
228	gezelter	1627
229			if (fileSize < 0) {
230			fin.close();
231	gezelter	1879	delete[] fbuf;
232	gezelter	1627
233			return false;
234			}
235
236	gezelter	1796	// make a c-style std::string and broadcast it
237	gezelter	1627	fbuf[fileSize] = '\0';
238	gezelter	1969	MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
239	gezelter	1627
240			//close the file and delete the buffer
241			fin.close();
242			internalStringBuf_.str(fbuf);
243	gezelter	1879	delete[] fbuf;
244	gezelter	1627	}else{
245			fileSize = FileNotExists;
246	gezelter	1969	MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
247	gezelter	1627	return false;
248			}
249
250			} else{ //slave nodes
251
252			//check file name
253			if (checkFilename) {
254	gezelter	1969	MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
255	gezelter	1627
256			char * masterFilename = new char[filenameLen];
257	gezelter	1969	MPI_Bcast(masterFilename, filenameLen, MPI_CHAR,
258			masterNode, MPI_COMM_WORLD);
259	gezelter	1627
260			if( strcmp(masterFilename, filename) == 0)
261			diffFilename = 0;
262			else
263			diffFilename = 1;
264
265	gezelter	1879	delete[] masterFilename;
266	gezelter	1627
267	gezelter	1969	MPI_Allreduce(&diffFilename, &error, 1, MPI_INT, MPI_SUM,
268			MPI_COMM_WORLD);
269	gezelter	1627
270			if (error > 0)
271			return false;
272			}
273			//get file size
274	gezelter	1969	MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
275	gezelter	1627
276			if (fileSize >= 0 ) {
277			fbuf = new char[fileSize+1];
278			assert(fbuf);
279
280			//receive file content
281	gezelter	1969	MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
282	gezelter	1627
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			}