| 1 | #include "Util/types.h" |
| 2 | #include "Util/utils.h" |
| 3 | #include <mpi.h> |
| 4 | #include <stdlib.h> |
| 5 | #include <stdio.h> |
| 6 | #include <string.h> |
| 7 | #include <math.h> |
| 8 | #include <unistd.h> |
| 9 | #include "MPI_Communication/pack.h" |
| 10 | #include "MPI_Communication/unpack.h" |
| 11 | #include "Util/rng.h" |
| 12 | |
| 13 | // save the final result in XML format |
| 14 | static void result_to_XML(Result_t* result, const char* inputFileName, |
| 15 | const char* lastBinaryFileName, uint32_t p_for_dissims) |
| 16 | { |
| 17 | uint32_t nbClusters = result->nbClusters; |
| 18 | FILE* ofile = fopen("ppamResult.xml", "w"); |
| 19 | |
| 20 | fprintf(ofile, "<medoids>\n\n"); |
| 21 | |
| 22 | fprintf(ofile, " <file>"); |
| 23 | fprintf(ofile, "%s", lastBinaryFileName); |
| 24 | fprintf(ofile, "</file>\n\n"); |
| 25 | |
| 26 | fprintf(ofile, " <p_for_dissims>"); |
| 27 | fprintf(ofile, "%u", p_for_dissims); |
| 28 | fprintf(ofile, "</p_for_dissims>\n\n"); |
| 29 | |
| 30 | fprintf(ofile, " <IDs>\n"); |
| 31 | for (uint32_t i=0; i<nbClusters; i++) |
| 32 | fprintf(ofile, " <ID>%u</ID>\n", result->medoids_ID[i]); |
| 33 | fprintf(ofile, " </IDs>\n\n"); |
| 34 | |
| 35 | // medoids ranks in last binary file (human printing: 0 --> 1 ...etc) |
| 36 | fprintf(ofile, " <ranks>\n"); |
| 37 | for (uint32_t i=0; i<nbClusters; i++) |
| 38 | fprintf(ofile, " <rank>%u</rank>\n", result->medoids_ranks[i] + 1); |
| 39 | fprintf(ofile, " </ranks>\n\n"); |
| 40 | |
| 41 | fprintf(ofile, "</medoids>\n"); |
| 42 | fclose(ofile); |
| 43 | } |
| 44 | |
| 45 | static void binaryResult_to_file(Result_t* result, const char* inputFileName, |
| 46 | const char* outputFileName) |
| 47 | { |
| 48 | // Determine tsLength from inputFile |
| 49 | uint32_t tsLength = get_tsLength(inputFileName); |
| 50 | |
| 51 | FILE* ifile = fopen(inputFileName, "rb"); |
| 52 | FILE* ofile = fopen(outputFileName, "ab"); //'append binary' |
| 53 | |
| 54 | Byte tsBuffer[tsLength]; |
| 55 | for (uint32_t i = 0; i < result->nbClusters; i++) |
| 56 | { |
| 57 | // Get time-series in (binary) inputFile |
| 58 | fseek(ifile, 8 + result->medoids_ranks[i] * tsLength, SEEK_SET); |
| 59 | // Copy current serie onto ofile |
| 60 | |
| 61 | size_t lengthRead = fread(tsBuffer, 1, tsLength, ifile); |
| 62 | if (lengthRead != tsLength) |
| 63 | fprintf(stderr, "problem while copying binary series to new file.\n"); |
| 64 | fwrite(tsBuffer, 1, tsLength, ofile); |
| 65 | } |
| 66 | |
| 67 | fclose(ifile); |
| 68 | fclose(ofile); |
| 69 | } |
| 70 | |
| 71 | // fill a new unit of work suitable to be given to a slave |
| 72 | static Work_t* get_next_work(char* inputFileName, uint32_t nbSeries, uint32_t nbSeriesInChunk, |
| 73 | double idealNbSeriesInChunk, uint32_t jobsSentCount, uint32_t lastEndIndex, |
| 74 | uint32_t nbClusters, uint32_t clustOnMedoids, |
| 75 | int randomize, uint32_t p_for_dissims) |
| 76 | { |
| 77 | Work_t* work = (Work_t*) malloc(sizeof(Work_t)); |
| 78 | |
| 79 | work->inputFileName = (char*) malloc(strlen(inputFileName) + 1); |
| 80 | strcpy(work->inputFileName, inputFileName); |
| 81 | |
| 82 | if (randomize) |
| 83 | work->nbSeries = nbSeriesInChunk; |
| 84 | else |
| 85 | { |
| 86 | double adjustedNbSeriesInNextChunk = |
| 87 | idealNbSeriesInChunk * (jobsSentCount + 1) - lastEndIndex; |
| 88 | // round to closest integer |
| 89 | work->nbSeries = (uint32_t)adjustedNbSeriesInNextChunk; |
| 90 | // stay below the upper bound (TODO: is this check required ?) |
| 91 | if (work->nbSeries > nbSeriesInChunk) |
| 92 | work->nbSeries = nbSeriesInChunk; |
| 93 | // TODO: what about this one ? (probably useless) |
| 94 | if (lastEndIndex + work->nbSeries > nbSeries) |
| 95 | work->nbSeries = nbSeries - lastEndIndex; |
| 96 | } |
| 97 | |
| 98 | //TODO: ranks on uint64_t if more than 4.3 billion series at the same place (unlikely...) |
| 99 | work->ranks = (uint32_t*) malloc(work->nbSeries * sizeof(uint32_t)); |
| 100 | for (uint32_t i = 0; i < work->nbSeries; i++) |
| 101 | work->ranks[i] = (randomize ? get_rand_int() % nbSeries : lastEndIndex + i); |
| 102 | |
| 103 | work->nbClusters = nbClusters; |
| 104 | work->clustOnMedoids = clustOnMedoids; |
| 105 | work->p_for_dissims = p_for_dissims; |
| 106 | |
| 107 | return work; |
| 108 | } |
| 109 | |
| 110 | // process all subtasks and save binary results into a new file |
| 111 | // NOTE: this file will be smaller than initial file (or DB...) |
| 112 | static void clusters_reduce(char* inputFileName, char* outputFileName, uint32_t ntasks, |
| 113 | uint32_t totalNbSeries, uint32_t nbSeriesInChunk, double idealNbSeriesInChunk, |
| 114 | uint32_t tsLength, uint32_t nbClusters, uint32_t clustOnMedoids, |
| 115 | int randomize, uint32_t p_for_dissims) |
| 116 | { |
| 117 | FILE* ofile = fopen(outputFileName, "wb"); //'write binary' |
| 118 | // Leave a blank for series' count and tsLength |
| 119 | for (uint32_t i = 0; i < 8; i++) |
| 120 | fputc(0, ofile); |
| 121 | fclose(ofile); |
| 122 | |
| 123 | uint32_t jobsSentCount = 0; //used if randomize==FALSE |
| 124 | uint32_t lastEndIndex = 0; //used if randomize==FALSE |
| 125 | |
| 126 | uint32_t sentSeriesCount = 0; //used if randomize==TRUE |
| 127 | |
| 128 | // Count series sent to binary file on output |
| 129 | uint32_t newSeriesCount = 0; |
| 130 | |
| 131 | // Expected size of a Work message in bytes: |
| 132 | uint32_t work_message_length = get_packedWork_length(nbSeriesInChunk); |
| 133 | Byte packedWork[work_message_length]; |
| 134 | |
| 135 | // Expected size of a Result message in bytes: (uint32_t is on 4 bytes) |
| 136 | uint32_t result_message_length = 4 + 4 * nbClusters + 4 * nbClusters; |
| 137 | Byte packedResult[result_message_length]; |
| 138 | |
| 139 | // Seed the slaves; send one unit of work to each slave. |
| 140 | Work_t* work; |
| 141 | int* busy_slave = (int*) malloc(ntasks * sizeof(int)); |
| 142 | for (int rank = 1; rank < ntasks; rank++) |
| 143 | busy_slave[rank] = 0; |
| 144 | for (int rank = 1; rank < ntasks; rank++) |
| 145 | { |
| 146 | // Find the next item of work to do |
| 147 | work = get_next_work(inputFileName, totalNbSeries, nbSeriesInChunk, idealNbSeriesInChunk, |
| 148 | jobsSentCount, lastEndIndex, nbClusters, clustOnMedoids, |
| 149 | randomize, p_for_dissims); |
| 150 | |
| 151 | if (randomize) |
| 152 | sentSeriesCount += nbSeriesInChunk; |
| 153 | else |
| 154 | { |
| 155 | lastEndIndex = lastEndIndex + work->nbSeries; |
| 156 | jobsSentCount++; |
| 157 | } |
| 158 | |
| 159 | // Send it to current rank |
| 160 | pack_work(work, nbSeriesInChunk, packedWork); |
| 161 | free_work(work); |
| 162 | fprintf(stdout, "0 / Send work %s to rank=%i / %u\n",inputFileName, rank, |
| 163 | (randomize ? sentSeriesCount : lastEndIndex)); |
| 164 | MPI_Send(packedWork, work_message_length, MPI_BYTE, rank, WORKTAG, MPI_COMM_WORLD); |
| 165 | |
| 166 | busy_slave[rank] = 1; |
| 167 | |
| 168 | if ((randomize && sentSeriesCount >= 1.5*totalNbSeries) //TODO: 1.5 = heuristic, magic number... |
| 169 | || (!randomize && lastEndIndex >= totalNbSeries)) |
| 170 | { |
| 171 | // Nothing more to read |
| 172 | break; |
| 173 | } |
| 174 | } |
| 175 | |
| 176 | // Loop over getting new work requests until there is no more work to be done |
| 177 | Result_t* result; |
| 178 | MPI_Status status; |
| 179 | while (1) |
| 180 | { |
| 181 | // If no slave is active, job is over |
| 182 | int atLeastOneSlaveActive = 0; |
| 183 | for (int rank = 1; rank < ntasks; rank++) |
| 184 | { |
| 185 | if (busy_slave[rank]) |
| 186 | { |
| 187 | atLeastOneSlaveActive = 1; |
| 188 | break; |
| 189 | } |
| 190 | } |
| 191 | if (!atLeastOneSlaveActive) |
| 192 | break; |
| 193 | |
| 194 | // Receive results from a slave |
| 195 | MPI_Recv(packedResult, result_message_length, MPI_BYTE, MPI_ANY_SOURCE, |
| 196 | WORKTAG, MPI_COMM_WORLD, &status); |
| 197 | result = unpack_result(packedResult); |
| 198 | fprintf(stdout, "0 / Receive result from rank=%i on %s\n",status.MPI_SOURCE,inputFileName); |
| 199 | |
| 200 | // 'binarize' the result (only series' values) returned by the slave |
| 201 | binaryResult_to_file(result, inputFileName, outputFileName); |
| 202 | free_result(result); |
| 203 | newSeriesCount += nbClusters; |
| 204 | |
| 205 | if ((randomize && sentSeriesCount < totalNbSeries) |
| 206 | || (!randomize && lastEndIndex < totalNbSeries)) |
| 207 | { |
| 208 | // Get the next unit of work to be done |
| 209 | work = get_next_work(inputFileName, totalNbSeries, nbSeriesInChunk, |
| 210 | idealNbSeriesInChunk, jobsSentCount, lastEndIndex, nbClusters, |
| 211 | clustOnMedoids, randomize, p_for_dissims); |
| 212 | |
| 213 | if (randomize) |
| 214 | sentSeriesCount += nbSeriesInChunk; |
| 215 | else |
| 216 | { |
| 217 | lastEndIndex = lastEndIndex + work->nbSeries; |
| 218 | jobsSentCount++; |
| 219 | } |
| 220 | |
| 221 | // Send the slave a new work unit |
| 222 | pack_work(work, nbSeriesInChunk, packedWork); |
| 223 | free_work(work); |
| 224 | fprintf(stdout, "0 / Send work %s to rank=%i / %u\n",inputFileName, status.MPI_SOURCE, |
| 225 | (randomize ? sentSeriesCount : lastEndIndex)); |
| 226 | MPI_Send(packedWork, work_message_length, MPI_BYTE, |
| 227 | status.MPI_SOURCE, WORKTAG, MPI_COMM_WORLD); |
| 228 | } |
| 229 | |
| 230 | else |
| 231 | // No more work to do |
| 232 | busy_slave[status.MPI_SOURCE] = 0; |
| 233 | } |
| 234 | |
| 235 | // There's no more work to be done, so receive all results from the slaves. |
| 236 | for (int rank = 1; rank < ntasks; rank++) |
| 237 | { |
| 238 | if (busy_slave[rank]) |
| 239 | { |
| 240 | MPI_Recv(packedResult, result_message_length, MPI_BYTE, |
| 241 | rank, WORKTAG, MPI_COMM_WORLD, &status); |
| 242 | result = unpack_result(packedResult); |
| 243 | |
| 244 | // 'binarize' the result (only series' values) returned by the slave |
| 245 | binaryResult_to_file(result, inputFileName, outputFileName); |
| 246 | free_result(result); |
| 247 | newSeriesCount += nbClusters; |
| 248 | } |
| 249 | } |
| 250 | free(busy_slave); |
| 251 | |
| 252 | // Finalize output file: write total number of series inside it, and tsLength |
| 253 | ofile = fopen(outputFileName, "r+b"); //read and write, binary |
| 254 | fseek(ofile, 0, SEEK_SET); |
| 255 | Byte intBuffer[4]; |
| 256 | write_int(newSeriesCount, 4, intBuffer); |
| 257 | fwrite(intBuffer, 1, 4, ofile); |
| 258 | write_int(tsLength, 4, intBuffer); |
| 259 | fwrite(intBuffer, 1, 4, ofile); |
| 260 | fclose(ofile); |
| 261 | } |
| 262 | |
| 263 | // generate random temporary file names |
| 264 | static char* get_unique_name() |
| 265 | { |
| 266 | size_t nbDigits = 7; //rather arbitrary |
| 267 | size_t stringLength = 5 + nbDigits; //5 for '.tmp/' |
| 268 | char* s = (char*) malloc(stringLength + 1); |
| 269 | s[0] = '.'; |
| 270 | s[1] = 't'; |
| 271 | s[2] = 'm'; |
| 272 | s[3] = 'p'; |
| 273 | s[4] = '/'; |
| 274 | for (int i=0; i<nbDigits; i++) |
| 275 | s[5+i] = '0' + get_rand_int() % 10; |
| 276 | s[stringLength] = 0; |
| 277 | return s; |
| 278 | } |
| 279 | |
| 280 | // code executed by master process |
| 281 | void master_run(char* mainInputFileName, uint32_t totalNbSeries, uint32_t nbSeriesInChunk, |
| 282 | double idealNbSeriesInChunk, uint32_t tsLength, uint32_t nbClusters, |
| 283 | int randomize, uint32_t p_for_dissims) |
| 284 | { |
| 285 | // Basic sanity check: nbClusters must be clearly less than series count per chunk |
| 286 | if (10 * nbClusters >= nbSeriesInChunk) |
| 287 | { |
| 288 | fprintf(stdout, "WARNING: cluster size (%u) may be too high compared with chunk size (%u).\n", |
| 289 | nbClusters, nbSeriesInChunk); |
| 290 | } |
| 291 | |
| 292 | // Find out how many processes there are in the default communicator |
| 293 | int ntasks; |
| 294 | MPI_Comm_size(MPI_COMM_WORLD, &ntasks); |
| 295 | if (ntasks <= 1) |
| 296 | { |
| 297 | fprintf(stderr,"No slaves available (only master running).\n"); |
| 298 | return; |
| 299 | } |
| 300 | |
| 301 | // initializations |
| 302 | char* inputFileName = mainInputFileName; |
| 303 | char* outputFileName; |
| 304 | |
| 305 | uint32_t nbSeriesInFile = totalNbSeries; |
| 306 | |
| 307 | while (nbSeriesInFile > nbSeriesInChunk) |
| 308 | { |
| 309 | outputFileName = get_unique_name(); |
| 310 | uint32_t clustOnMedoids = (nbSeriesInFile < totalNbSeries ? 1 : 0); |
| 311 | clusters_reduce(inputFileName, outputFileName, ntasks, nbSeriesInFile, nbSeriesInChunk, |
| 312 | idealNbSeriesInChunk, tsLength, nbClusters, clustOnMedoids, |
| 313 | randomize, p_for_dissims); |
| 314 | |
| 315 | // read nbSeries in outputFile |
| 316 | nbSeriesInFile = get_nbSeries(outputFileName); |
| 317 | |
| 318 | // update file names |
| 319 | if (strcmp(mainInputFileName, inputFileName) != 0) |
| 320 | { |
| 321 | // No need to keep every intermediate binary |
| 322 | unlink(inputFileName); |
| 323 | free(inputFileName); |
| 324 | } |
| 325 | inputFileName = outputFileName; |
| 326 | } |
| 327 | |
| 328 | // read nbSeries in inputFileName (the last one) |
| 329 | // we know that there is at most 'nbSeriesInChunk' series in it |
| 330 | nbSeriesInFile = get_nbSeries(inputFileName); |
| 331 | |
| 332 | // Expected size of a Work message in bytes: |
| 333 | uint32_t work_message_length = get_packedWork_length(nbSeriesInChunk); |
| 334 | Byte packedWork[work_message_length]; |
| 335 | |
| 336 | // Expected size of a Result message in bytes: (uint32_t is on 4 bytes) |
| 337 | uint32_t result_message_length = get_packedResult_length(nbClusters); |
| 338 | Byte packedResult[result_message_length]; |
| 339 | |
| 340 | // Run a last task by some slave, and get final result |
| 341 | Work_t* work = get_next_work(inputFileName, nbSeriesInFile, nbSeriesInChunk, |
| 342 | (double)nbSeriesInFile, 0, 0, nbClusters, 1, 0, p_for_dissims); |
| 343 | |
| 344 | // Send the slave a new work unit |
| 345 | pack_work(work, nbSeriesInChunk, packedWork); |
| 346 | free_work(work); |
| 347 | int selectedSlaveRank = get_rand_int() % (ntasks - 1) + 1; |
| 348 | fprintf(stdout, "0 / Send final work %s to rank=%i / %u\n", |
| 349 | inputFileName, selectedSlaveRank, nbSeriesInFile); |
| 350 | MPI_Send(packedWork, work_message_length, MPI_BYTE, selectedSlaveRank, |
| 351 | WORKTAG, MPI_COMM_WORLD); |
| 352 | |
| 353 | MPI_Status status; |
| 354 | // Wait for him to finish |
| 355 | MPI_Recv(packedResult, result_message_length, MPI_BYTE, selectedSlaveRank, |
| 356 | WORKTAG, MPI_COMM_WORLD, &status); |
| 357 | Result_t* finalResult = unpack_result(packedResult); |
| 358 | fprintf(stdout, "0 / Receive final result from rank=%i on %s\n",status.MPI_SOURCE,inputFileName); |
| 359 | |
| 360 | //Tell all the slaves to exit by sending an empty message with the DIETAG. |
| 361 | for (int rank = 1; rank < ntasks; ++rank) |
| 362 | MPI_Send(0, 0, MPI_BYTE, rank, DIETAG, MPI_COMM_WORLD); |
| 363 | |
| 364 | const char finalBinaryName[] = "ppamFinalSeries.bin"; |
| 365 | result_to_XML(finalResult, inputFileName, finalBinaryName, p_for_dissims); |
| 366 | free_result(finalResult); |
| 367 | |
| 368 | // free memory |
| 369 | if (strcmp(mainInputFileName, inputFileName)) |
| 370 | { |
| 371 | // Keep last input binary, but rename it |
| 372 | rename(inputFileName, finalBinaryName); |
| 373 | free(inputFileName); |
| 374 | } |
| 375 | else |
| 376 | { |
| 377 | // just symlink mainInputFileName |
| 378 | if (!access(finalBinaryName, F_OK)) |
| 379 | unlink(finalBinaryName); |
| 380 | if (symlink(mainInputFileName, finalBinaryName)) |
| 381 | fprintf(stderr,"Cannot create symlink to initial binary file.\n"); |
| 382 | } |
| 383 | } |