src/io/basic_ifstrstream.hpp

/*
 * 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.hpp
 * @author Teng Lin
 * @date 10/14/2004
 * @version 1.0
 */

#ifndef IO_IFSTRSTREAM_HPP
#define IO_IFSTRSTREAM_HPP

#include <cassert>
#include <cstring>
#include <fstream>
#include <sstream>

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

namespace OpenMD {

  /**
   * @class basic_ifstrstream basic_ifstrstream.hpp "io/basic_ifstrstream.hpp"
   * @brief basic_ifstrstream class provides a stream interface to read data from files.
   * <p>In single mode, it falls back to ifstream. Don't need to read the whole file into memory.
   * In parallel mode, the master node will read the whole file and brocast it to other slave nodes.
   * After brocasting, every node will fall back to stringstream.</p>
   *
   * @code
   *       const int MAXLEN = 1024;
   *       char buffer[MAXLEN];
   *       ifstrstream in;
   *       in.open("Shapes.frc");
   *       if (in.is_open()) {
   *           in.getline(buffer, MAXLEN);
   *       }
   *       in.close();
   * @endcode
   */
  template <class _CharT, class _Traits,  class _Alloc>
  class basic_ifstrstream : public std::basic_istream<_CharT, _Traits> {
  public:
    //traits
    typedef _CharT                     char_type;
    typedef typename _Traits::int_type int_type;
    typedef typename _Traits::pos_type pos_type;
    typedef typename _Traits::off_type off_type;
    typedef _Traits                    traits_type;

    typedef std::basic_ios<_CharT, _Traits>                _Basic_ios;
    typedef std::basic_istream<_CharT, _Traits>            _Base;

#ifdef IS_MPI
    typedef std::basic_stringbuf<_CharT, _Traits, _Alloc>  _Buf;        
#else
    typedef std::basic_filebuf<_CharT, _Traits>            _Buf;
#endif

    static  const int FileNotExists = -1;
    static const int FileIOError = -2;
        
  public:
        
    /**  Constructs an object of class ifstream.  */
    basic_ifstrstream()
      :  std::basic_istream<_CharT, _Traits>(0),
         internalBuf_(), isRead(false)  {
    
        this->init(&internalBuf_);
      }
        
    /**
     * 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
     */
    explicit basic_ifstrstream(const char* filename, std::ios_base::openmode mode = std::ios_base::in, bool checkFilename = false)
      :  std::basic_istream<_CharT, _Traits>(0),
         internalBuf_(), isRead(false) {

        this->init(&internalBuf_);
        isRead =  internalOpen(filename,  mode | std::ios_base::in, checkFilename);
      }

    /**
     * virtual destructor will close the file(in single mode) and clear the stream buffer
     */
    ~basic_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 open(const char* filename, std::ios_base::openmode mode = std::ios_base::in, bool checkFilename = false){

      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 is_open ( ) {
#ifdef IS_MPI            
      return isRead; 
#else
      //single version fall back to ifstream
      return internalBuf_.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 close() {
#ifndef IS_MPI            
      //single version fall back to ifstream
      if (!internalBuf_.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 buffe object(filebuf in single mode, stringbuf in 
     * parallel mode) associated with the stream.
     */
    _Buf* rdbuf() const{
      return static_cast<_Buf*>(&internalBuf_); 
    }

  private:

    /**
     * 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 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();      
          internalBuf_.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); 

          internalBuf_.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 (!internalBuf_.open(filename, mode)) {
        this->setstate(std::ios_base::failbit);
        return false;
      }    

#endif
      this->clear();
      return true;
    }
        
    _Buf  internalBuf_; /** internal stream buffer */        
    bool isRead;                                                                    /** file opened flag */
  };

  typedef basic_ifstrstream<char, std::char_traits<char>, std::allocator<char> > ifstrstream;
}//namespace OpenMD
#endif //IO_IFSTRSTREAM_HPP
Revision:	1465
Committed:	Fri Jul 9 23:08:25 2010 UTC (14 years, 9 months ago) by chuckv
File size:	10881 byte(s)
Log Message:	Creating busticated version of OpenMD
#	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.hpp
44	* @author Teng Lin
45	* @date 10/14/2004
46	* @version 1.0
47	*/
48
49	#ifndef IO_IFSTRSTREAM_HPP
50	#define IO_IFSTRSTREAM_HPP
51
52	#include <cassert>
53	#include <cstring>
54	#include <fstream>
55	#include <sstream>
56
57	#ifdef IS_MPI
58	#include <mpi.h>
59	#endif
60
61	namespace OpenMD {
62
63	/**
64	* @class basic_ifstrstream basic_ifstrstream.hpp "io/basic_ifstrstream.hpp"
65	* @brief basic_ifstrstream class provides a stream interface to read data from files.
66	* <p>In single mode, it falls back to ifstream. Don't need to read the whole file into memory.
67	* In parallel mode, the master node will read the whole file and brocast it to other slave nodes.
68	* After brocasting, every node will fall back to stringstream.</p>
69	*
70	* @code
71	* const int MAXLEN = 1024;
72	* char buffer[MAXLEN];
73	* ifstrstream in;
74	* in.open("Shapes.frc");
75	* if (in.is_open()) {
76	* in.getline(buffer, MAXLEN);
77	* }
78	* in.close();
79	* @endcode
80	*/
81	template <class _CharT, class _Traits, class _Alloc>
82	class basic_ifstrstream : public std::basic_istream<_CharT, _Traits> {
83	public:
84	//traits
85	typedef _CharT char_type;
86	typedef typename _Traits::int_type int_type;
87	typedef typename _Traits::pos_type pos_type;
88	typedef typename _Traits::off_type off_type;
89	typedef _Traits traits_type;
90
91	typedef std::basic_ios<_CharT, _Traits> _Basic_ios;
92	typedef std::basic_istream<_CharT, _Traits> _Base;
93
94	#ifdef IS_MPI
95	typedef std::basic_stringbuf<_CharT, _Traits, _Alloc> _Buf;
96	#else
97	typedef std::basic_filebuf<_CharT, _Traits> _Buf;
98	#endif
99
100	static const int FileNotExists = -1;
101	static const int FileIOError = -2;
102
103	public:
104
105	/** Constructs an object of class ifstream. */
106	basic_ifstrstream()
107	: std::basic_istream<_CharT, _Traits>(0),
108	internalBuf_(), isRead(false) {
109
110	this->init(&internalBuf_);
111	}
112
113	/**
114	* Explicit constructor
115	* @filename String containing the name of the file to be opened
116	* @mode Flags describing the requested i/o mode for the file, default value is ios_base::in
117	* @checkFilename Flags indicating checking the file name in parallel
118	*/
119	explicit basic_ifstrstream(const char* filename, std::ios_base::openmode mode = std::ios_base::in, bool checkFilename = false)
120	: std::basic_istream<_CharT, _Traits>(0),
121	internalBuf_(), isRead(false) {
122
123	this->init(&internalBuf_);
124	isRead = internalOpen(filename, mode \| std::ios_base::in, checkFilename);
125	}
126
127	/**
128	* virtual destructor will close the file(in single mode) and clear the stream buffer
129	*/
130	~basic_ifstrstream(){
131	close();
132	}
133
134	/**
135	* Opens a file and associats a buffer with the specified file to perform the i/o operations
136	* (single mode). Master reads a file and brocasts its content to the other slave nodes. After
137	* brocasting, every nodes fall back to stringstream (parallel mode).
138	* @filename String containing the name of the file to be opened
139	* @mode Flags describing the requested i/o mode for the file
140	* @checkFilename Flags indicating checking the file name in parallel
141	*/
142	void open(const char* filename, std::ios_base::openmode mode = std::ios_base::in, bool checkFilename = false){
143
144	if (!isRead ) {
145	isRead = internalOpen(filename, mode, checkFilename);
146	}
147	}
148
149	/**
150	* Tests if the stream is currently associated with a valid buffer.
151	* @return true if a file has successfully been opened (single mode) or the whole file is read
152	* and spreaded among all of the processors (parallel mode), otherwise false is returned
153	*/
154	bool is_open ( ) {
155	#ifdef IS_MPI
156	return isRead;
157	#else
158	//single version fall back to ifstream
159	return internalBuf_.is_open();
160	#endif
161	}
162
163	/**
164	* In single mode, closes a file. The stream's file buffer is released from its association with
165	* the currently open file. In parallel mode, clean the
166	*/
167	void close() {
168	#ifndef IS_MPI
169	//single version fall back to ifstream
170	if (!internalBuf_.close())
171	this->setstate(std::ios_base::failbit);
172	#endif
173
174	isRead = false;
175	}
176
177	/**
178	* Gets the stream buffer object associated with the stream
179	* @return A pointer to the stream buffe object(filebuf in single mode, stringbuf in
180	* parallel mode) associated with the stream.
181	*/
182	_Buf* rdbuf() const{
183	return static_cast<_Buf*>(&internalBuf_);
184	}
185
186	private:
187
188	/**
189	* Internal function used to open the file
190	* @return true if succesfully opens a file (single mode) or gets the file content (parallel mode)
191	* otherwise return false
192	* @filename String containing the name of the file to be opened
193	* @mode Flags describing the requested i/o mode for the file
194	* @todo use try - catch syntax to make the program more readable
195	*/
196	bool internalOpen(const char* filename, std::ios_base::openmode mode, bool checkFilename){
197
198	#ifdef IS_MPI
199	int commStatus;
200	long fileSize;
201	char* fbuf;
202	int filenameLen;
203	int diffFilename;
204	int error;
205	int myRank;
206	int masterNode;
207
208	commStatus = MPI_Comm_rank(MPI_COMM_WORLD, &myRank);
209	masterNode = 0;
210
211	if (myRank == masterNode) {
212
213	if (checkFilename) {
214
215	//check the filename is the same
216	filenameLen = strlen(filename);
217	commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
218	commStatus = MPI_Bcast((void*)filename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD);
219
220	diffFilename = 0;
221	commStatus = MPI_Allreduce(&diffFilename, &error, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
222
223	//if file names are different just return false
224	if (error > 0)
225	return false;
226	}
227
228	std::ifstream fin(filename, mode);
229
230	if (fin.is_open()) {
231
232	fin.seekg(0, std::ios::end);
233	fileSize = fin.tellg();
234	fin.seekg(0, std::ios::beg);
235
236	// '\0' need one more char
237	fbuf = new char[fileSize+1];
238
239	assert(fbuf != 0);
240
241	fin.read(fbuf, fileSize);
242
243	if (fin.fail())
244	fileSize = FileIOError;
245
246	//brocasting the file size
247	commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
248
249	if (fileSize < 0) {
250	fin.close();
251	delete fbuf;
252
253	return false;
254	}
255
256	// make a c-style std::string and brocasting it
257	fbuf[fileSize] = '\0';
258	commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
259
260	//close the file and delete the buffer
261	fin.close();
262	internalBuf_.str(fbuf);
263	delete [] fbuf;
264	}else{
265	fileSize = FileNotExists;
266	commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
267	return false;
268	}
269
270	} else{ //slave nodes
271
272	//check file name
273	if (checkFilename) {
274	commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
275
276	char * masterFilename = new char[filenameLen];
277	commStatus = MPI_Bcast(masterFilename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD);
278
279	if( strcmp(masterFilename, filename) == 0)
280	diffFilename = 0;
281	else
282	diffFilename = 1;
283
284	delete masterFilename;
285
286	commStatus = MPI_Allreduce(&diffFilename, &error, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
287
288	if (error > 0)
289	return false;
290	}
291	//get file size
292	commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);
293
294	if (fileSize >= 0 ) {
295	fbuf = new char[fileSize+1];
296	assert(fbuf);
297
298	//receive file content
299	commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD);
300
301	internalBuf_.str(fbuf);
302	delete [] fbuf;
303
304	} else if (fileSize == FileNotExists ) {
305	return false;
306
307	} else if (fileSize == FileIOError ) {
308	return false;
309	}
310	}
311
312	#else
313	//in single version, fall back to ifstream
314	if (!internalBuf_.open(filename, mode)) {
315	this->setstate(std::ios_base::failbit);
316	return false;
317	}
318
319	#endif
320	this->clear();
321	return true;
322	}
323
324	_Buf internalBuf_; /** internal stream buffer */
325	bool isRead; /** file opened flag */
326	};
327
328	typedef basic_ifstrstream<char, std::char_traits<char>, std::allocator<char> > ifstrstream;
329	}//namespace OpenMD
330	#endif //IO_IFSTRSTREAM_HPP