gargabe.hpp 17.1 KB
 incardon committed Jan 27, 2015 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 ``````/* * gargabe.hpp * * Created on: Jan 13, 2015 * Author: i-bird */ #ifndef GARGABE_HPP_ #define GARGABE_HPP_ template void optimize(size_t start_p, Graph & graph) { // We assume that Graph is the rapresentation of a cartesian graph // this mean that the direction d is at the child d // Create an Hyper-cube HyperCube hyp; // Get the number of wavefronts size_t n_wf = hyp.getNumberOfElements_R(0); // Get the number of intersecting wavefront // Get the number of sub-dimensional common wavefront // basically are a list of all the subdomain common to two or more // Create n_wf wavefront queue openfpm::vector v_w; v.reserve(n_wf); // direction of expansion size_t domain_id = 0; int exp_dir = 0; bool can_expand = true; // while is possible to expand while (can_expand) { // for each direction of expansion expand the wavefront for (int d = 0 ; d < n_wf ; d++) { // get the wavefront at direction d openfpm::vector & wf_d = v_w.get(d); // flag to indicate if the wavefront can expand bool w_can_expand = true; // for each subdomain for (size_t sub = 0 ; sub < wf_d.size() ; sub++) { // check if the adjacent domain in direction d exist // and is of the same id // get the starting subdomain size_t sub_w = wf_d.get<0>(sub); // we get the processor id of the neighborhood sub-domain on direction d size_t exp_p = graph.getChild(sub_w,d).get(); // we check if it is the same processor id if (exp_p != domain_id) { w_can_expand = false; } } // if we can expand the wavefront expand it if (w_can_expand == true) { // for each subdomain for (size_t sub = 0 ; sub < wf_d.size() ; sub++) { // update the position of the wavefront wf_d.get<0>(sub) = wf_d.get<0>(sub) + gh.stride(d); } // here we add sub-domains to all the other queues // get the face of the hyper-cube SubHyperCube sub_hyp = hyp.getSubHyperCube(d); std::vector> q_comb = sub_hyp.getCombinations_R(dim-2); } } } // For each point in the Hyper-cube check if we can move the wave front } `````` incardon committed Feb 02, 2015 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 ``````#ifndef PARALLEL_DECOMPOSITION // CreateSubspaces(); #endif #ifndef USE_METIS_GP // Here we do not use METIS // Distribute the divided domains // Get the number of processing units size_t Np = v_cl.getProcessingUnits(); // Get the ID of this processing unit // and push the subspace is taking this // processing unit for (size_t p_id = v_cl.getProcessUnitID(); p_id < Np ; p_id += Np) id_sub.push_back(p_id); #else #endif `````` incardon committed Aug 10, 2015 128 129 `````` `````` incardon committed Aug 13, 2015 130 ``````<<<<<<< HEAD `````` incardon committed Aug 10, 2015 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 `````` /////////////// DEBUG ///////////////////// // get the decomposition auto & dec = g_dist.getDecomposition(); Vcluster & v_cl = *global_v_cluster; // check the consistency of the decomposition val = dec.check_consistency(); BOOST_REQUIRE_EQUAL(val,true); // for each local volume // Get the number of local grid needed size_t n_grid = dec.getNLocalHyperCube(); size_t vol = 0; openfpm::vector> v_b; // Allocate the grids for (size_t i = 0 ; i < n_grid ; i++) { // Get the local hyper-cube SpaceBox<2,float> sub = dec.getLocalHyperCube(i); Box<2,size_t> g_box = g_dist.getCellDecomposer().convertDomainSpaceIntoGridUnits(sub); v_b.add(g_box); vol += g_box.getVolumeKey(); } v_cl.reduce(vol); v_cl.execute(); BOOST_REQUIRE_EQUAL(vol,k*k); ///////////////////////////////////// `````` incardon committed Aug 12, 2015 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 `````` // 3D test // g_dist.write(""); /* auto g_it = g_dist.getIteratorBulk(); auto g_it_halo = g_dist.getHalo(); // Let try to solve the poisson equation d2(u) = f with f = 1 and computation // comunication overlap (100 Jacobi iteration) for (int i = 0 ; i < 100 ; i++) { g_dist.ghost_get(); // Compute the bulk jacobi_iteration(g_it); g_dist.ghost_sync(); // Compute the halo jacobi_iteration(g_it_halo); }*/ BOOST_AUTO_TEST_CASE( grid_dist_id_poisson_test_use) { // grid size /* size_t sz[2] = {1024,1024}; // Distributed grid with id decomposition grid_dist_id<2, scalar, CartDecomposition<2,size_t>> g_dist(sz); // Create the grid on memory g_dist.Create();*/ /* auto g_it = g_dist.getIteratorBulk(); auto g_it_halo = g_dist.getHalo(); // Let try to solve the poisson equation d2(u) = f with f = 1 and computation // comunication overlap (100 Jacobi iteration) for (int i = 0 ; i < 100 ; i++) { g_dist.ghost_get(); // Compute the bulk jacobi_iteration(g_it); g_dist.ghost_sync(); // Compute the halo jacobi_iteration(g_it_halo); }*/ } template void jacobi_iteration(iterator g_it, grid_dist_id<2, float, scalar, CartDecomposition<2,float>> & g_dist) { // scalar typedef scalar S; // iterator while(g_it.isNext()) { // Jacobi update auto pos = g_it.get(); g_dist.template get(pos) = (g_dist.template get(pos.move(0,1)) + g_dist.template get(pos.move(0,-1)) + g_dist.template get(pos.move(1,1)) + g_dist.template get(pos.move(1,-1)) / 4.0); ++g_it; } } `````` incardon committed Aug 13, 2015 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 ``````======= /* * CartDecomposition.cpp * * Created on: Aug 15, 2014 * Author: Pietro Incardona */ #include "CartDecomposition.hpp" /*! \brief The the bulk part of the data set, or the data that does not depend * from the ghosts layers * * The the bulk part of the data set, or the data that does not depend from the * ghosts layers * */ /*template T CartDecomposition::getBulk(T data) { // for each element in data for (size_t i = 0; i < data.size() ; i++) { if (localSpace.isInside()) } } template T CartDecomposition::getInternal() { }*/ /*! \brief Check if is border or bulk * * \param neighboorhood define the neighboorhood of all the points * \return true if border, false if bulk * */ bool borderOrBulk(neighborhood & nb) { device::grid<1,size_t> nbr = nb.next(); // check the neighborhood // get neighborhood iterator grid_key_dx_iterator iterator_nbr = nbr.getIterator(); while (iterator_nbr.hasNext()) { grid_key_dx key_nbr = iterator_nbr.next(); // check if the neighboorhood is internal if(subspace.isBound(data.template get(key_nbr)) == false) { // it is border return true; ret.bord.push_back(key); break; } } return false; } /*! \brief This function divide the data set into bulk, border, external and internal part * * \tparam dim dimensionality of the structure storing your data * (example if they are in 3D grid, has to be 3) * \tparam T type of object we are dividing * \tparam device type of layout selected * \param data 1-dimensional grid of point * \param nb define the neighborhood of all the points * \return a structure with the set of objects divided * */ template class layout, typename Memory, template class Domain, template class data_s> dataDiv CartDecomposition::divide(device::grid<1,Point> & data, neighborhood & nb) { //! allocate the 3 subset dataDiv ret; ret.bord = new boost::shared_ptr(new T()); ret.inte = new boost::shared_ptr(new T()); ret.ext = new boost::shared_ptr(new T()); //! get grid iterator grid_key_dx_iterator iterator = data.getIterator(); //! we iterate trough all the set of objects while (iterator.hasNext()) { grid_key_dx key = iterator.next(); //! Check if the object is inside the subspace if (subspace.isBound(data.template get::x>(key))) { //! Check if the neighborhood is inside the subspace if (borderOrBulk(nb) == true) { // It is border ret.bord.push_back(key); } else { // It is bulk ret.bulk.push_back(key); } } else { //! it is external ret.ext.push_back(key); } } } >>>>>>> Jenkin script for taurus `````` Pietro Incardona committed Jan 29, 2016 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 `````` /*! \brief Allocate a set of objects * * \tparam obj * \param n number of object * * \return an object representing an array of objects * */ /* template Vcluster_object_array allocate(size_t n) { // Vcluster object array Vcluster_object_array vo; // resize the array vo.resize(n); // Create the object on memory and return a Vcluster_object_array return vo; }*/ /*template class Vcluster_object_array : public VObject { std::vector objects; public:*/ /*! \brief Constructor of object array * */ /* Vcluster_object_array() { }*/ /*! \brief Return the size of the objects array * * \return the size of the array * */ /* size_t size() const { return objects.size(); }*/ /*! \brief Return the element i * * \return a reference to the object i * */ /* T & get(unsigned int i) { return objects[i]; }*/ /*! \brief Return the element i * * \return a reference to the object i * */ /* const T & get(unsigned int i) const { return objects[i]; }*/ /*! \brief Check if this Object is an array * * \return true, it is an array * */ /* bool isArray() { return true; }*/ /*! \brief Destroy the object * */ /* virtual void destroy() { // Destroy the objects objects.clear(); }*/ /*! \brief Get the size of the memory needed to pack the object * * \return the size of the message to pack the object * */ /* size_t packObjectSize() { size_t message = 0; // Destroy each objects for (size_t i = 0 ; i < objects.size() ; i++) { message += objects[i].packObjectSize(); } return message; }*/ /*! \brief Get the size of the memory needed to pack the object * * \param Memory where to write the packed object * * \return the size of the message to pack the object * */ /* size_t packObject(void * mem) { // Pointer is zero size_t ptr = 0; unsigned char * m = (unsigned char *)mem; // pack each object for (size_t i = 0 ; i < objects.size() ; i++) { ptr += objects[i].packObject(&m[ptr]); } #ifdef DEBUG if (ptr != packObjectSize()) { std::cerr << "Error " << __FILE__ << " " << __LINE__ << " the pack object size does not match the message" << "\n"; } #endif return ptr; }*/ /*! \brief Calculate the size to pack an object in the array * * \param array object index * */ /* size_t packObjectInArraySize(size_t i) { return objects[i].packObjectSize(); }*/ /*! \brief pack the object in the array (the message produced can be used to move one) * object from one processor to another * * \param i index of the object to pack * \param p Memory of the packed object message * */ /* size_t packObjectInArray(size_t i, void * p) { return objects[i].packObject(p); }*/ /*! \brief Destroy an object from the array * * \param i object to destroy * */ /* void destroy(size_t i) { objects.erase(objects.begin() + i); }*/ /*! \brief Return the object j in the array * * \param j element j * */ /* T & operator[](size_t j) { return objects[j]; }*/ /*! \brief Return the object j in the array * * \param j element j * */ /* const T & operator[](size_t j) const { return objects[j]; }*/ /*! \brief Resize the array * * \param size * */ /* void resize(size_t n) { objects.resize(n); } };*/ /*! \brief VObject * * Any object produced by the Virtual cluster (MUST) inherit this class * */ /*class VObject { public: // Check if this Object is an array virtual bool isArray() = 0; // destroy the object virtual void destroy() = 0; // get the size of the memory needed to pack the object virtual size_t packObjectSize() = 0; // pack the object virtual size_t packObject(void *) = 0; // get the size of the memory needed to pack the object in the array virtual size_t packObjectInArraySize(size_t i) = 0; // pack the object in the array (the message produced can be used to move one) // object from one processor to another virtual size_t packObjectInArray(size_t i, void * p) = 0; // destroy an element from the array virtual void destroy(size_t n) = 0; };*/ `````` Pietro Incardona committed Apr 13, 2016 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 `````` /*! \brief Impose an operator * * This function impose an operator on a particular grid region to produce the system * * Ax = b * * ## Stokes equation, lid driven cavity with one splipping wall * * \param op Operator to impose (A term) * \param num right hand side of the term (b term) * \param id Equation id in the system that we are imposing * \param it_d iterator that define where you want to impose * */ template void impose(const T & op , typename Sys_eqs::stype num ,long int id ,grid_dist_iterator_sub it_d, bool skip_first = false) { //////////////////////// DEBUG ///////////////// SparseMatrix Al; Al.load("debug_matrix_single_processor"); // Construct the map 3 processors 1 processors std::unordered_map map_row; auto it2 = g_map.getDomainGhostIterator(); auto ginfo = g_map.getGridInfoVoid(); while (it2.isNext()) { auto key = it2.get(); auto key_g = g_map.getGKey(key); key_g += pd.getKP1(); // To linearize must be positive bool is_negative = false; for (size_t i = 0 ; i < Sys_eqs::dims ; i++) { if (key_g.get(i) < 0) is_negative = true; } if (is_negative == true) { ++it2; continue; } // Carefull g map is extended, so the original (0,0) is shifted in g_map by if (g_map.template get<0>(key) == 7) { int debug = 0; debug++; } map_row[g_map.template get<0>(key)] = ginfo.LinId(key_g); ++it2; } //////////////////////////////////////////////// Vcluster & v_cl = *global_v_cluster; openfpm::vector & trpl = A.getMatrixTriplets(); auto it = it_d; grid_sm gs = g_map.getGridInfoVoid(); std::unordered_map cols; // resize b if needed b.resize(Sys_eqs::nvar * g_map.size()); bool is_first = skip_first; // iterate all the grid points while (it.isNext()) { if (is_first == true && v_cl.getProcessUnitID() == 0) { ++it; is_first = false; continue; } else is_first = false; // get the position auto key = it.get(); // Calculate the non-zero colums T::value(g_map,key,gs,spacing,cols,1.0); //////////// DEBUG ////////////////// auto g_calc_pos = g_map.getGKey(key); g_calc_pos += pd.getKP1(); ///////////////////////////////////// // create the triplet for ( auto it = cols.begin(); it != cols.end(); ++it ) { trpl.add(); trpl.last().row() = g_map.template get<0>(key)*Sys_eqs::nvar + id; trpl.last().col() = it->first; trpl.last().value() = it->second; ///////////// DEBUG /////////////////////// auto ginfo = g_map.getGridInfoVoid(); size_t r = (trpl.last().row() / Sys_eqs::nvar); size_t r_rest = (trpl.last().row() % Sys_eqs::nvar); size_t c = (trpl.last().col() / Sys_eqs::nvar); size_t c_rest = (trpl.last().col() % Sys_eqs::nvar); double val = trpl.last().value(); // Transform size_t rf = map_row[r] * 3 + r_rest; size_t cf = map_row[c] * 3 + c_rest; auto position_row = ginfo.InvLinId(rf / 3); auto position_col = ginfo.InvLinId(cf / 3); double valf = Al.getValue(rf,cf); if (val != valf) { int debug = 0; debug++; } /////////////////////////////////////////// // std::cout << "(" << trpl.last().row() << "," << trpl.last().col() << "," << trpl.last().value() << ")" << "\n"; } b(g_map.template get<0>(key)*Sys_eqs::nvar + id) = num; cols.clear(); // std::cout << "\n"; // if SE_CLASS1 is defined check the position #ifdef SE_CLASS1 // T::position(key,gs,s_pos); #endif ++row; ++row_b; ++it; } } typename Sys_eqs::SparseMatrix_type A; /*! \brief produce the Matrix * * \return the Sparse matrix produced * */ typename Sys_eqs::SparseMatrix_type & getA() { #ifdef SE_CLASS1 consistency(); #endif A.resize(g_map.size()*Sys_eqs::nvar,g_map.size()*Sys_eqs::nvar); ///////////////// DEBUG SAVE ////////////////// // A.save("debug_matrix_single_processor"); //////////////////////////////////////////////// return A; } typename Sys_eqs::SparseMatrix_type A; /*! \brief produce the Matrix * * \return the Sparse matrix produced * */ typename Sys_eqs::SparseMatrix_type & getA() { #ifdef SE_CLASS1 consistency(); #endif A.resize(g_map.size()*Sys_eqs::nvar,g_map.size()*Sys_eqs::nvar); ///////////////// DEBUG SAVE ////////////////// // A.save("debug_matrix_single_processor"); //////////////////////////////////////////////// return A; } /*! \brief produce the B vector * * \return the vector produced * */ typename Sys_eqs::Vector_type & getB() { #ifdef SE_CLASS1 consistency(); #endif // size of the matrix // B.resize(g_map.size()*Sys_eqs::nvar); // copy the vector // for (size_t i = 0; i < row_b; i++) // B.insert(i,b.get(i)); return b; } }; `````` incardon committed Jan 27, 2015 862 ``#endif /* GARGABE_HPP_ */``