| 1 | gezelter | 1930 | /* | 
| 2 |  |  | * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. | 
| 3 | tim | 1570 | * | 
| 4 | gezelter | 1930 | * 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. Acknowledgement of the program authors must be made in any | 
| 10 |  |  | *    publication of scientific results based in part on use of the | 
| 11 |  |  | *    program.  An acceptable form of acknowledgement is citation of | 
| 12 |  |  | *    the article in which the program was described (Matthew | 
| 13 |  |  | *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher | 
| 14 |  |  | *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented | 
| 15 |  |  | *    Parallel Simulation Engine for Molecular Dynamics," | 
| 16 |  |  | *    J. Comput. Chem. 26, pp. 252-271 (2005)) | 
| 17 |  |  | * | 
| 18 |  |  | * 2. Redistributions of source code must retain the above copyright | 
| 19 |  |  | *    notice, this list of conditions and the following disclaimer. | 
| 20 |  |  | * | 
| 21 |  |  | * 3. Redistributions in binary form must reproduce the above copyright | 
| 22 |  |  | *    notice, this list of conditions and the following disclaimer in the | 
| 23 |  |  | *    documentation and/or other materials provided with the | 
| 24 |  |  | *    distribution. | 
| 25 |  |  | * | 
| 26 |  |  | * This software is provided "AS IS," without a warranty of any | 
| 27 |  |  | * kind. All express or implied conditions, representations and | 
| 28 |  |  | * warranties, including any implied warranty of merchantability, | 
| 29 |  |  | * fitness for a particular purpose or non-infringement, are hereby | 
| 30 |  |  | * excluded.  The University of Notre Dame and its licensors shall not | 
| 31 |  |  | * be liable for any damages suffered by licensee as a result of | 
| 32 |  |  | * using, modifying or distributing the software or its | 
| 33 |  |  | * derivatives. In no event will the University of Notre Dame or its | 
| 34 |  |  | * licensors be liable for any lost revenue, profit or data, or for | 
| 35 |  |  | * direct, indirect, special, consequential, incidental or punitive | 
| 36 |  |  | * damages, however caused and regardless of the theory of liability, | 
| 37 |  |  | * arising out of the use of or inability to use software, even if the | 
| 38 |  |  | * University of Notre Dame has been advised of the possibility of | 
| 39 |  |  | * such damages. | 
| 40 | tim | 1570 | */ | 
| 41 | gezelter | 1930 |  | 
| 42 | tim | 1570 | /** | 
| 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 | tim | 1583 | #include <cassert> | 
| 53 | tim | 1572 | #include <cstring> | 
| 54 | tim | 1570 | #include <fstream> | 
| 55 |  |  | #include <sstream> | 
| 56 |  |  |  | 
| 57 | tim | 1572 | #ifdef IS_MPI | 
| 58 | tim | 1577 | #include <mpi.h> | 
| 59 | tim | 1572 | #endif | 
| 60 |  |  |  | 
| 61 | tim | 1570 | namespace oopse { | 
| 62 | gezelter | 1930 |  | 
| 63 | tim | 1570 | /** | 
| 64 |  |  | * @class basic_ifstrstream basic_ifstrstream.hpp "io/basic_ifstrstream.hpp" | 
| 65 | gezelter | 1930 | * @brief basic_ifstrstream class provides a stream interface to read data from files. | 
| 66 | tim | 1570 | * <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 | tim | 1572 | *       if (in.is_open()) { | 
| 76 | tim | 1570 | *           in.getline(buffer, MAXLEN); | 
| 77 |  |  | *       } | 
| 78 |  |  | *       in.close(); | 
| 79 |  |  | * @endcode | 
| 80 |  |  | */ | 
| 81 |  |  | template <class _CharT, class _Traits,  class _Alloc> | 
| 82 | gezelter | 1930 | class basic_ifstrstream : public std::basic_istream<_CharT, _Traits> { | 
| 83 | tim | 1570 | 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 | gezelter | 1930 | typedef std::basic_ios<_CharT, _Traits>                _Basic_ios; | 
| 92 |  |  | typedef std::basic_istream<_CharT, _Traits>            _Base; | 
| 93 | tim | 1570 |  | 
| 94 |  |  | #ifdef IS_MPI | 
| 95 | gezelter | 1930 | typedef std::basic_stringbuf<_CharT, _Traits, _Alloc>  _Buf; | 
| 96 | tim | 1570 | #else | 
| 97 | gezelter | 1930 | typedef std::basic_filebuf<_CharT, _Traits>            _Buf; | 
| 98 | tim | 1570 | #endif | 
| 99 |  |  |  | 
| 100 | gezelter | 1930 | static  const int FileNotExists = -1; | 
| 101 | tim | 1570 | static const int FileIOError = -2; | 
| 102 |  |  |  | 
| 103 |  |  | public: | 
| 104 |  |  |  | 
| 105 |  |  | /**  Constructs an object of class ifstream.  */ | 
| 106 |  |  | basic_ifstrstream() | 
| 107 | gezelter | 1930 | : std::basic_ios<_CharT, _Traits>(),  std::basic_istream<_CharT, _Traits>(0), | 
| 108 | tim | 1570 | internalBuf_(NULL), isRead(false)  { | 
| 109 |  |  |  | 
| 110 |  |  | #ifdef IS_MPI | 
| 111 |  |  | //in parallel mode, fall back to istringstream | 
| 112 | gezelter | 1930 | std::basic_stringbuf<_CharT, _Traits, _Alloc>* stringBuffer = new  std::basic_stringbuf<_CharT, _Traits, _Alloc>(); | 
| 113 | tim | 1570 | internalBuf_ =  stringBuffer; | 
| 114 |  |  | #else | 
| 115 |  |  | //in single version, fall back to ifstream | 
| 116 | gezelter | 1930 | std::basic_filebuf<_CharT, _Traits>* fileBuffer = new  std::basic_filebuf<_CharT, _Traits>(); | 
| 117 | tim | 1570 | internalBuf_ =  fileBuffer; | 
| 118 |  |  | #endif | 
| 119 |  |  |  | 
| 120 |  |  | this->init(internalBuf_); | 
| 121 |  |  | isRead = false; | 
| 122 |  |  | } | 
| 123 |  |  |  | 
| 124 |  |  | /** | 
| 125 |  |  | * Explicit constructor | 
| 126 |  |  | * @filename String containing the name of the file to be opened | 
| 127 | tim | 1572 | * @mode Flags describing the requested i/o mode for the file, default value is ios_base::in | 
| 128 |  |  | * @checkFilename Flags indicating checking the file name in parallel | 
| 129 | tim | 1570 | */ | 
| 130 | gezelter | 1930 | explicit basic_ifstrstream(const char* filename, std::ios_base::openmode mode = std::ios_base::in, bool checkFilename = false) | 
| 131 |  |  | : std::basic_ios<_CharT, _Traits>(),  std::basic_istream<_CharT, _Traits>(0), | 
| 132 | tim | 1570 | internalBuf_(NULL), isRead(false) { | 
| 133 |  |  |  | 
| 134 | gezelter | 1930 | isRead =  internalOpen(filename,  mode | std::ios_base::in, checkFilename); | 
| 135 | tim | 1570 | } | 
| 136 |  |  |  | 
| 137 |  |  | /** | 
| 138 | tim | 1577 | * virtual destructor will close the file(in single mode) and clear the stream buffer | 
| 139 | tim | 1570 | */ | 
| 140 |  |  | ~basic_ifstrstream(){ | 
| 141 |  |  | close(); | 
| 142 |  |  | delete internalBuf_; | 
| 143 |  |  | internalBuf_ = NULL; | 
| 144 |  |  | } | 
| 145 |  |  |  | 
| 146 |  |  | /** | 
| 147 |  |  | * Opens a file and associats a buffer with the specified file to perform the i/o operations | 
| 148 |  |  | * (single mode). Master reads a file and brocasts its content to the other slave nodes. After | 
| 149 |  |  | * brocasting, every nodes fall back to stringstream (parallel mode). | 
| 150 |  |  | * @filename String containing the name of the file to be opened | 
| 151 |  |  | * @mode Flags describing the requested i/o mode for the file | 
| 152 | tim | 1572 | * @checkFilename Flags indicating checking the file name in parallel | 
| 153 | tim | 1570 | */ | 
| 154 | gezelter | 1930 | void open(const char* filename, std::ios_base::openmode mode = std::ios_base::in, bool checkFilename = false){ | 
| 155 | tim | 1570 |  | 
| 156 |  |  | if (!isRead ) { | 
| 157 | tim | 1572 | isRead = internalOpen(filename, mode, checkFilename); | 
| 158 | tim | 1570 | } | 
| 159 |  |  | } | 
| 160 |  |  |  | 
| 161 |  |  | /** | 
| 162 |  |  | * Tests if the stream is currently associated with a valid  buffer. | 
| 163 |  |  | * @return true if a file has successfully been opened (single mode) or the whole file is read | 
| 164 |  |  | * and spreaded among all of the processors (parallel mode),  otherwise false is returned | 
| 165 |  |  | */ | 
| 166 |  |  | bool is_open ( ) { | 
| 167 |  |  | #ifdef IS_MPI | 
| 168 |  |  | return isRead; | 
| 169 |  |  | #else | 
| 170 |  |  | //single version fall back to ifstream | 
| 171 |  |  | return this->rdbuf()->is_open(); | 
| 172 |  |  | #endif | 
| 173 |  |  | } | 
| 174 |  |  |  | 
| 175 |  |  | /** | 
| 176 |  |  | * In single mode, closes a file. The stream's file buffer is released from its association with | 
| 177 |  |  | * the currently open file. In parallel mode, clean the | 
| 178 |  |  | */ | 
| 179 |  |  | void close() { | 
| 180 |  |  | #ifndef IS_MPI | 
| 181 |  |  | //single version fall back to ifstream | 
| 182 |  |  | if (!this->rdbuf()->close()) | 
| 183 | gezelter | 1930 | this->setstate(std::ios_base::failbit); | 
| 184 | tim | 1570 | #endif | 
| 185 |  |  |  | 
| 186 |  |  | isRead = false; | 
| 187 |  |  | } | 
| 188 |  |  |  | 
| 189 |  |  | /** | 
| 190 |  |  | * Gets the stream buffer object associated with the stream | 
| 191 |  |  | * @return   A pointer to the  stream buffe object(filebuf in single mode, stringbuf in | 
| 192 |  |  | * parallel mode) associated with the stream. | 
| 193 |  |  | */ | 
| 194 |  |  | _Buf* rdbuf() const{ | 
| 195 | tim | 1582 | return static_cast<_Buf*>(internalBuf_); | 
| 196 | tim | 1570 | } | 
| 197 |  |  |  | 
| 198 |  |  | private: | 
| 199 |  |  |  | 
| 200 |  |  | /** | 
| 201 |  |  | * Internal function used to open the file | 
| 202 |  |  | * @return true if succesfully opens a file (single mode) or gets the file content (parallel mode) | 
| 203 |  |  | * otherwise return false | 
| 204 |  |  | * @filename String containing the name of the file to be opened | 
| 205 |  |  | * @mode Flags describing the requested i/o mode for the file | 
| 206 |  |  | * @todo use try - catch syntax to make the program more readable | 
| 207 |  |  | */ | 
| 208 | gezelter | 1930 | bool internalOpen(const char* filename, std::ios_base::openmode mode, bool checkFilename){ | 
| 209 | tim | 1570 |  | 
| 210 |  |  | #ifdef IS_MPI | 
| 211 |  |  | int commStatus; | 
| 212 |  |  | long fileSize; | 
| 213 |  |  | char* fbuf; | 
| 214 |  |  | int filenameLen; | 
| 215 |  |  | int diffFilename; | 
| 216 |  |  | int error; | 
| 217 | tim | 1572 | int myRank; | 
| 218 |  |  | int masterNode; | 
| 219 | tim | 1570 |  | 
| 220 | tim | 1572 | commStatus = MPI_Comm_rank(MPI_COMM_WORLD, &myRank); | 
| 221 |  |  | masterNode = 0; | 
| 222 |  |  |  | 
| 223 |  |  | if (myRank == masterNode) { | 
| 224 | tim | 1570 |  | 
| 225 | tim | 1572 | if (checkFilename) { | 
| 226 | tim | 1570 |  | 
| 227 | tim | 1572 | //check the filename is the same | 
| 228 |  |  | filenameLen = strlen(filename); | 
| 229 | tim | 1583 | commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD); | 
| 230 |  |  | commStatus = MPI_Bcast((void*)filename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD); | 
| 231 | tim | 1570 |  | 
| 232 | tim | 1572 | diffFilename = 0; | 
| 233 | tim | 1583 | commStatus = MPI_Allreduce(&diffFilename, &error, 1,  MPI_INT, MPI_SUM,  MPI_COMM_WORLD); | 
| 234 | tim | 1572 |  | 
| 235 |  |  | //if file names are different just return false | 
| 236 |  |  | if (error > 0) | 
| 237 | tim | 1570 | return false; | 
| 238 | tim | 1572 | } | 
| 239 | tim | 1570 |  | 
| 240 | gezelter | 1930 | std::ifstream fin(filename, mode); | 
| 241 |  |  | std::basic_stringbuf<_CharT, _Traits, _Alloc>* sbuf; | 
| 242 | tim | 1570 |  | 
| 243 |  |  | if (fin.is_open()) { | 
| 244 |  |  |  | 
| 245 | gezelter | 1930 | fin.seekg(0, std::ios::end); | 
| 246 | tim | 1570 | fileSize = fin.tellg(); | 
| 247 | gezelter | 1930 | fin.seekg(0, std::ios::beg); | 
| 248 | tim | 1583 |  | 
| 249 | tim | 1570 | // '\0' need one more char | 
| 250 |  |  | fbuf = new char[fileSize+1]; | 
| 251 |  |  |  | 
| 252 |  |  | assert(fbuf != 0); | 
| 253 |  |  |  | 
| 254 |  |  | fin.read(fbuf, fileSize); | 
| 255 |  |  |  | 
| 256 |  |  | if (fin.fail()) | 
| 257 |  |  | fileSize = FileIOError; | 
| 258 |  |  |  | 
| 259 |  |  | //brocasting the file size | 
| 260 |  |  | commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); | 
| 261 |  |  |  | 
| 262 |  |  | if (fileSize < 0) { | 
| 263 |  |  | fin.close(); | 
| 264 |  |  | delete fbuf; | 
| 265 |  |  |  | 
| 266 |  |  | return false; | 
| 267 |  |  | } | 
| 268 |  |  |  | 
| 269 | gezelter | 1930 | // make a c-style  std::string and brocasting it | 
| 270 | tim | 1570 | fbuf[fileSize] = '\0'; | 
| 271 |  |  | commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD); | 
| 272 |  |  |  | 
| 273 |  |  | //it is safe to delete null pointer | 
| 274 |  |  | delete internalBuf_; | 
| 275 |  |  |  | 
| 276 |  |  | //initilaize istream | 
| 277 | gezelter | 1930 | internalBuf_  = new std::basic_stringbuf<_CharT, _Traits, _Alloc>(fbuf, mode); | 
| 278 | tim | 1570 | assert(internalBuf_); | 
| 279 |  |  | this->init(internalBuf_); | 
| 280 |  |  |  | 
| 281 |  |  | //close the file and delete the buffer | 
| 282 |  |  | fin.close(); | 
| 283 |  |  | delete fbuf; | 
| 284 |  |  | }else{ | 
| 285 | gezelter | 1930 | fileSize = FileNotExists; | 
| 286 | tim | 1570 | commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); | 
| 287 |  |  | return false; | 
| 288 |  |  | } | 
| 289 |  |  |  | 
| 290 | gezelter | 1930 | } else{ //slave nodes | 
| 291 |  |  |  | 
| 292 | tim | 1570 | //check file name | 
| 293 | tim | 1572 | if (checkFilename) { | 
| 294 | tim | 1583 | commStatus = MPI_Bcast(&filenameLen, 1, MPI_INT, masterNode, MPI_COMM_WORLD); | 
| 295 | tim | 1570 |  | 
| 296 | tim | 1572 | char * masterFilename = new char[filenameLen]; | 
| 297 |  |  | commStatus = MPI_Bcast(masterFilename, filenameLen, MPI_CHAR, masterNode, MPI_COMM_WORLD); | 
| 298 |  |  |  | 
| 299 |  |  | if( strcmp(masterFilename, filename) == 0) | 
| 300 |  |  | diffFilename = 0; | 
| 301 |  |  | else | 
| 302 |  |  | diffFilename = 1; | 
| 303 | tim | 1570 |  | 
| 304 | tim | 1572 | delete masterFilename; | 
| 305 |  |  |  | 
| 306 | tim | 1583 | commStatus = MPI_Allreduce(&diffFilename, &error, 1,  MPI_INT,  MPI_SUM, MPI_COMM_WORLD); | 
| 307 | tim | 1570 |  | 
| 308 | tim | 1572 | if (error > 0) | 
| 309 |  |  | return false; | 
| 310 |  |  | } | 
| 311 | tim | 1570 | //get file size | 
| 312 |  |  | commStatus = MPI_Bcast(&fileSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD); | 
| 313 |  |  |  | 
| 314 |  |  | if (fileSize >= 0 ) { | 
| 315 |  |  | fbuf = new char[fileSize+1]; | 
| 316 |  |  | assert(fbuf); | 
| 317 |  |  |  | 
| 318 |  |  | //receive file content | 
| 319 |  |  | commStatus = MPI_Bcast(fbuf, fileSize + 1, MPI_CHAR, masterNode, MPI_COMM_WORLD); | 
| 320 |  |  |  | 
| 321 |  |  | //it is safe to delete null pointer | 
| 322 |  |  | delete internalBuf_; | 
| 323 |  |  |  | 
| 324 |  |  | //initilaize istream | 
| 325 | gezelter | 1930 | internalBuf_  = new std::basic_stringbuf<_CharT, _Traits, _Alloc>(fbuf, mode); | 
| 326 | tim | 1570 | assert(internalBuf_); | 
| 327 |  |  | this->init(internalBuf_); | 
| 328 |  |  |  | 
| 329 |  |  | delete fbuf; | 
| 330 |  |  |  | 
| 331 | gezelter | 1930 | } else if (fileSize == FileNotExists ) { | 
| 332 | tim | 1570 | return false; | 
| 333 |  |  |  | 
| 334 |  |  | } else if (fileSize == FileIOError ) { | 
| 335 |  |  | return false; | 
| 336 |  |  | } | 
| 337 |  |  | } | 
| 338 |  |  |  | 
| 339 |  |  | #else | 
| 340 |  |  | //in single version, fall back to ifstream | 
| 341 | gezelter | 1930 | std::basic_filebuf<_CharT, _Traits>* fileBuffer = new  std::basic_filebuf<_CharT, _Traits>(); | 
| 342 | tim | 1570 |  | 
| 343 | gezelter | 1930 | //it is safe to delete null pointer | 
| 344 |  |  | delete internalBuf_; | 
| 345 |  |  | internalBuf_ =  fileBuffer; | 
| 346 | tim | 1570 |  | 
| 347 | gezelter | 1930 | this->init(internalBuf_); | 
| 348 |  |  | if (!fileBuffer->open(filename, mode)) { | 
| 349 |  |  | this->setstate(std::ios_base::failbit); | 
| 350 |  |  | return false; | 
| 351 |  |  | } | 
| 352 |  |  |  | 
| 353 | tim | 1570 | #endif | 
| 354 |  |  |  | 
| 355 |  |  | return true; | 
| 356 |  |  | } | 
| 357 |  |  |  | 
| 358 | gezelter | 1930 | std::basic_streambuf<_CharT, _Traits>*  internalBuf_; /** internal stream buffer */ | 
| 359 | tim | 1570 | bool isRead;                                                                    /** file opened flag */ | 
| 360 |  |  | }; | 
| 361 |  |  |  | 
| 362 | gezelter | 1930 | typedef basic_ifstrstream<char, std::char_traits<char>, std::allocator<char> > ifstrstream; | 
| 363 | tim | 1570 | }//namespace oopse | 
| 364 |  |  | #endif //IO_IFSTRSTREAM_HPP |