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.
#	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			* [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			}