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;
    
    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:	1962
Committed:	Wed Jan 15 22:26:18 2014 UTC (11 years, 3 months ago) by gezelter
File size:	9977 byte(s)
Log Message:	Some potential bug fixes.
#	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	1962	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	1962	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			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	gezelter	1962	* virtual destructor will close the file (in single mode) and clear
98			* the stream buffer
99	gezelter	1627	*/
100			ifstrstream::~ifstrstream(){
101			close();
102			}
103
104			/**
105	gezelter	1962	* 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	gezelter	1879	* @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	gezelter	1627	*/
114			void ifstrstream::open(const char* filename, std::ios_base::openmode mode, bool checkFilename){
115
116			if (!isRead ) {
117			isRead = internalOpen(filename, mode, checkFilename);
118			}
119			}
120
121			/**
122	gezelter	1962	* 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	gezelter	1627	*/
127			bool ifstrstream::is_open ( ) {
128			#ifdef IS_MPI
129			return isRead;
130			#else
131			//single version fall back to ifstream
132			return internalFileBuf_.is_open();
133			#endif
134			}
135
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	gezelter	1962	* parallel mode, cleans up.
140	gezelter	1627	*/
141			void ifstrstream::close() {
142			#ifndef IS_MPI
143			//single version fall back to ifstream
144			if (!internalFileBuf_.close())
145			this->setstate(std::ios_base::failbit);
146			#endif
147
148			isRead = false;
149			}
150
151			/**
152			* Gets the stream buffer object associated with the stream
153			* @return A pointer to the stream buffer object(filebuf in single
154			* mode, stringbuf in parallel mode) associated with the stream.
155			*/
156			std::basic_streambuf<char, std::char_traits<char> >* ifstrstream::rdbuf() {
157			#ifdef IS_MPI
158			return static_cast<_StringBuf*>(&internalStringBuf_);
159			#else
160			return static_cast<_FileBuf*>(&internalFileBuf_);
161			#endif
162			}
163
164			/**
165	gezelter	1962	* 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	gezelter	1627
174			bool ifstrstream::internalOpen(const char* filename, std::ios_base::openmode mode, bool checkFilename){
175
176			#ifdef IS_MPI
177	gezelter	1796	//int commStatus;
178	gezelter	1627	long fileSize;
179			char* fbuf;
180			int filenameLen;
181			int diffFilename;
182			int error;
183			int myRank;
184			int masterNode;
185
186	gezelter	1796	myRank = MPI::COMM_WORLD.Get_rank();
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	1796	MPI::COMM_WORLD.Bcast(&filenameLen, 1, MPI::INT, masterNode);
196			MPI::COMM_WORLD.Bcast((void*)filename, filenameLen, MPI::CHAR,
197			masterNode);
198	gezelter	1627
199			diffFilename = 0;
200	gezelter	1796	MPI::COMM_WORLD.Allreduce(&diffFilename, &error, 1, MPI::INT, MPI::SUM);
201	gezelter	1962
202	gezelter	1627	//if file names are different just return false
203			if (error > 0)
204			return false;
205			}
206
207			std::ifstream fin(filename, mode);
208
209			if (fin.is_open()) {
210
211			fin.seekg(0, std::ios::end);
212			fileSize = fin.tellg();
213			fin.seekg(0, std::ios::beg);
214
215			// '\0' need one more char
216			fbuf = new char[fileSize+1];
217
218			assert(fbuf != 0);
219
220			fin.read(fbuf, fileSize);
221
222			if (fin.fail())
223			fileSize = FileIOError;
224
225	gezelter	1796	//broadcast the file size
226			MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
227	gezelter	1627
228			if (fileSize < 0) {
229			fin.close();
230	gezelter	1879	delete[] fbuf;
231	gezelter	1627
232			return false;
233			}
234
235	gezelter	1796	// make a c-style std::string and broadcast it
236	gezelter	1627	fbuf[fileSize] = '\0';
237	gezelter	1796	MPI::COMM_WORLD.Bcast(fbuf, fileSize + 1, MPI::CHAR, masterNode);
238	gezelter	1627
239			//close the file and delete the buffer
240			fin.close();
241			internalStringBuf_.str(fbuf);
242	gezelter	1879	delete[] fbuf;
243	gezelter	1627	}else{
244			fileSize = FileNotExists;
245	gezelter	1796	MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
246	gezelter	1627	return false;
247			}
248
249			} else{ //slave nodes
250
251			//check file name
252			if (checkFilename) {
253	gezelter	1796	MPI::COMM_WORLD.Bcast(&filenameLen, 1, MPI::INT, masterNode);
254	gezelter	1627
255			char * masterFilename = new char[filenameLen];
256	gezelter	1796	MPI::COMM_WORLD.Bcast(masterFilename, filenameLen, MPI::CHAR,
257			masterNode);
258	gezelter	1627
259			if( strcmp(masterFilename, filename) == 0)
260			diffFilename = 0;
261			else
262			diffFilename = 1;
263
264	gezelter	1879	delete[] masterFilename;
265	gezelter	1627
266	gezelter	1796	MPI::COMM_WORLD.Allreduce(&diffFilename, &error, 1, MPI::INT, MPI::SUM);
267	gezelter	1627
268			if (error > 0)
269			return false;
270			}
271			//get file size
272	gezelter	1796	MPI::COMM_WORLD.Bcast(&fileSize, 1, MPI::LONG, masterNode);
273	gezelter	1627
274			if (fileSize >= 0 ) {
275			fbuf = new char[fileSize+1];
276			assert(fbuf);
277
278			//receive file content
279	gezelter	1796	MPI::COMM_WORLD.Bcast(fbuf, fileSize + 1, MPI::CHAR, masterNode);
280	gezelter	1627
281			internalStringBuf_.str(fbuf);
282			delete [] fbuf;
283
284			} else if (fileSize == FileNotExists ) {
285			return false;
286
287			} else if (fileSize == FileIOError ) {
288			return false;
289			}
290			}
291
292			#else
293			//in single version, fall back to ifstream
294			if (!internalFileBuf_.open(filename, mode)) {
295			this->setstate(std::ios_base::failbit);
296			return false;
297			}
298
299			#endif
300			this->clear();
301			return true;
302			}
303			}