Date: 2016-07-24T16:54:17+00:00

Actual source code: mpiaijAssemble.cu
petsc-3.7.3 2016-07-24
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      1: #define PETSC_SKIP_COMPLEX
      2: #define PETSC_SKIP_SPINLOCK

      4: #include <petscconf.h>
      5: #include <../src/mat/impls/aij/seq/aij.h>          /*I "petscmat.h" I*/
      6: #include <../src/mat/impls/aij/mpi/mpiaij.h>
      7: #include <petscbt.h>
      8: #include <../src/vec/vec/impls/dvecimpl.h>
      9: #include <petsc/private/vecimpl.h>
     10: #undef VecType
     11: #include <../src/mat/impls/aij/seq/seqcusp/cuspmatimpl.h>

     13: #include <thrust/reduce.h>
     14: #include <thrust/inner_product.h>

     16: #include <cusp/array1d.h>
     17: #include <cusp/print.h>
     18: #include <cusp/coo_matrix.h>

     20: #include <cusp/io/matrix_market.h>

     22: #include <thrust/iterator/counting_iterator.h>
     23: #include <thrust/iterator/transform_iterator.h>
     24: #include <thrust/iterator/permutation_iterator.h>
     25: #include <thrust/functional.h>
     26: #include <thrust/partition.h>
     27: #include <thrust/remove.h>

     29: // this example illustrates how to make repeated access to a range of values
     30: // examples:
     31: //   repeated_range([0, 1, 2, 3], 1) -> [0, 1, 2, 3]
     32: //   repeated_range([0, 1, 2, 3], 2) -> [0, 0, 1, 1, 2, 2, 3, 3]
     33: //   repeated_range([0, 1, 2, 3], 3) -> [0, 0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3]
     34: //   ...

     36: template <typename Iterator>
     37: class repeated_range
     38: {
     39: public:

     41:   typedef typename thrust::iterator_difference<Iterator>::type difference_type;

     43:   struct repeat_functor : public thrust::unary_function<difference_type,difference_type>
     44:   {
     45:     difference_type repeats;

     47:     repeat_functor(difference_type repeats) : repeats(repeats) {}

     49:     __host__ __device__
     50:     difference_type operator()(const difference_type &i) const
     51:     {
     52:       return i / repeats;
     53:     }
     54:   };

     56:   typedef typename thrust::counting_iterator<difference_type>                   CountingIterator;
     57:   typedef typename thrust::transform_iterator<repeat_functor, CountingIterator> TransformIterator;
     58:   typedef typename thrust::permutation_iterator<Iterator,TransformIterator>     PermutationIterator;

     60:   // type of the repeated_range iterator
     61:   typedef PermutationIterator iterator;

     63:   // construct repeated_range for the range [first,last)
     64:   repeated_range(Iterator first, Iterator last, difference_type repeats)
     65:     : first(first), last(last), repeats(repeats) {}

     67:   iterator begin(void) const
     68:   {
     69:     return PermutationIterator(first, TransformIterator(CountingIterator(0), repeat_functor(repeats)));
     70:   }

     72:   iterator end(void) const
     73:   {
     74:     return begin() + repeats * (last - first);
     75:   }

     77: protected:
     78:   difference_type repeats;
     79:   Iterator        first;
     80:   Iterator        last;

     82: };

     84: // this example illustrates how to repeat blocks in a range multiple times
     85: // examples:
     86: //   tiled_range([0, 1, 2, 3], 2)    -> [0, 1, 2, 3, 0, 1, 2, 3]
     87: //   tiled_range([0, 1, 2, 3], 4, 2) -> [0, 1, 2, 3, 0, 1, 2, 3]
     88: //   tiled_range([0, 1, 2, 3], 2, 2) -> [0, 1, 0, 1, 2, 3, 2, 3]
     89: //   tiled_range([0, 1, 2, 3], 2, 3) -> [0, 1, 0, 1 0, 1, 2, 3, 2, 3, 2, 3]
     90: //   ...

     92: template <typename Iterator>
     93: class tiled_range
     94: {
     95: public:

     97:   typedef typename thrust::iterator_difference<Iterator>::type difference_type;

     99:   struct tile_functor : public thrust::unary_function<difference_type,difference_type>
    100:   {
    101:     difference_type repeats;
    102:     difference_type tile_size;

    104:     tile_functor(difference_type repeats, difference_type tile_size)
    105:       : tile_size(tile_size), repeats(repeats) {}

    107:     __host__ __device__
    108:     difference_type operator() (const difference_type &i) const
    109:     {
    110:       return tile_size * (i / (tile_size * repeats)) + i % tile_size;
    111:     }
    112:   };

    114:   typedef typename thrust::counting_iterator<difference_type>                   CountingIterator;
    115:   typedef typename thrust::transform_iterator<tile_functor, CountingIterator>   TransformIterator;
    116:   typedef typename thrust::permutation_iterator<Iterator,TransformIterator>     PermutationIterator;

    118:   // type of the tiled_range iterator
    119:   typedef PermutationIterator iterator;

    121:   // construct repeated_range for the range [first,last)
    122:   tiled_range(Iterator first, Iterator last, difference_type repeats)
    123:     : first(first), last(last), repeats(repeats), tile_size(last - first) {}

    125:   tiled_range(Iterator first, Iterator last, difference_type repeats, difference_type tile_size)
    126:     : first(first), last(last), repeats(repeats), tile_size(tile_size)
    127:   {
    128:     // ASSERT((last - first) % tile_size == 0)
    129:   }

    131:   iterator begin(void) const
    132:   {
    133:     return PermutationIterator(first, TransformIterator(CountingIterator(0), tile_functor(repeats, tile_size)));
    134:   }

    136:   iterator end(void) const
    137:   {
    138:     return begin() + repeats * (last - first);
    139:   }

    141: protected:
    142:   difference_type repeats;
    143:   difference_type tile_size;
    144:   Iterator        first;
    145:   Iterator        last;
    146: };

    148: typedef cusp::device_memory memSpace;
    149: typedef int IndexType;
    150: typedef PetscScalar ValueType;
    151: typedef cusp::array1d<IndexType, memSpace> IndexArray;
    152: typedef cusp::array1d<ValueType, memSpace> ValueArray;
    153: typedef cusp::array1d<IndexType, cusp::host_memory> IndexHostArray;
    154: typedef IndexArray::iterator IndexArrayIterator;
    155: typedef ValueArray::iterator ValueArrayIterator;

    157: struct is_diag
    158: {
    159:   IndexType first, last;

    161:   is_diag(IndexType first, IndexType last) : first(first), last(last) {}

    163:   template <typename Tuple>
    164:   __host__ __device__
    165:   bool operator()(Tuple t)
    166:   {
    167:     // Check column
    168:     IndexType row = thrust::get<0>(t);
    169:     IndexType col = thrust::get<1>(t);
    170:     return (row >= first) && (row < last) && (col >= first) && (col < last);
    171:   }
    172: };

    174: struct is_nonlocal
    175: {
    176:   IndexType first, last;

    178:   is_nonlocal(IndexType first, IndexType last) : first(first), last(last) {}

    180:   template <typename Tuple>
    181:   __host__ __device__
    182:   bool operator() (Tuple t)
    183:   {
    184:     // Check column
    185:     IndexType row = thrust::get<0>(t);
    186:     return (row < first) || (row >= last);
    187:   }
    188: };

    190: /*@C
    191:   MatMPIAIJSetValuesBatch - Set multiple blocks of values into a matrix

    193:   Not collective

    195:   Input Parameters:
    196: + J  - the assembled Mat object
    197: . Ne -  the number of blocks (elements)
    198: . Nl -  the block size (number of dof per element)
    199: . elemRows - List of block row indices, in bunches of length Nl
    200: - elemMats - List of block values, in bunches of Nl*Nl

    202:   Level: advanced

    204: .seealso MatSetValues()
    205: @*/
    208: PetscErrorCode MatSetValuesBatch_MPIAIJCUSP(Mat J, PetscInt Ne, PetscInt Nl, PetscInt *elemRows, const PetscScalar *elemMats)
    209: {
    210:   // Assumptions:
    211:   //   1) Each elemMat is square, of size Nl x Nl
    212:   //
    213:   //      This means that any nonlocal entry (i,j) where i is owned by another process is matched to
    214:   //        a) an offdiagonal entry (j,i) if j is diagonal, or
    215:   //        b) another nonlocal entry (j,i) if j is offdiagonal
    216:   //
    217:   //      No - numSendEntries: The number of on-process  diagonal+offdiagonal entries
    218:   //      numRecvEntries:      The number of off-process diagonal+offdiagonal entries
    219:   //
    220:   //  Glossary:
    221:   //     diagonal: (i,j) such that i,j in [firstRow, lastRow)
    222:   //  offdiagonal: (i,j) such that i in [firstRow, lastRow), and j not in [firstRow, lastRow)
    223:   //     nonlocal: (i,j) such that i not in [firstRow, lastRow)
    224:   //  nondiagonal: (i,j) such that i not in [firstRow, lastRow), or j not in [firstRow, lastRow)
    225:   //   on-process: entries provided by elemMats
    226:   //  off-process: entries received from other processes
    227:   MPI_Comm       comm;
    228:   Mat_MPIAIJ     *j   = (Mat_MPIAIJ*) J->data;
    229:   size_t         N    = Ne * Nl;     // Length of elemRows (dimension of unassembled space)
    230:   size_t         No   = Ne * Nl*Nl;  // Length of elemMats (total number of values)
    231:   PetscInt       Nr;                 // Size of J          (dimension of assembled space)
    232:   PetscInt       firstRow, lastRow, firstCol;
    233:   const PetscInt *rowRanges;
    234:   PetscInt       numNonlocalRows;    // Number of rows in elemRows not owned by this process
    235:   PetscInt       numSendEntries;     // Number of (i,j,v) entries sent to other processes
    236:   PetscInt       numRecvEntries;     // Number of (i,j,v) entries received from other processes
    237:   PetscInt       Nc;
    238:   PetscMPIInt    numProcs, rank;

    241:   // copy elemRows and elemMat to device
    242:   IndexArray d_elemRows(elemRows, elemRows + N);
    243:   ValueArray d_elemMats(elemMats, elemMats + No);

    246:   PetscObjectGetComm((PetscObject)J,&comm);
    247:   MPI_Comm_size(comm, &numProcs);
    248:   MPI_Comm_rank(comm, &rank);
    249:   // get matrix information
    250:   MatGetLocalSize(J, &Nr, NULL);
    251:   MatGetOwnershipRange(J, &firstRow, &lastRow);
    252:   MatGetOwnershipRanges(J, &rowRanges);
    253:   MatGetOwnershipRangeColumn(J, &firstCol, NULL);
    254:   PetscInfo3(J, "Assembling matrix of size %d (rows %d -- %d)\n", Nr, firstRow, lastRow);

    256:   // repeat elemRows entries Nl times
    257:   PetscInfo(J, "Making row indices\n");
    258:   repeated_range<IndexArrayIterator> rowInd(d_elemRows.begin(), d_elemRows.end(), Nl);

    260:   // tile rows of elemRows Nl times
    261:   PetscInfo(J, "Making column indices\n");
    262:   tiled_range<IndexArrayIterator> colInd(d_elemRows.begin(), d_elemRows.end(), Nl, Nl);

    264:   // Find number of nonlocal rows, convert nonlocal rows to procs, and send sizes of off-proc entries (could send diag and offdiag sizes)
    265:   // TODO: Ask Nathan how to do this on GPU
    266:   PetscLogEventBegin(MAT_SetValuesBatchI,0,0,0,0);
    267:   PetscMPIInt *procSendSizes, *procRecvSizes;

    269:   PetscCalloc2(numProcs, &procSendSizes, numProcs, &procRecvSizes);

    271:   numNonlocalRows = 0;
    272:   for (size_t i = 0; i < N; ++i) {
    273:     const PetscInt row = elemRows[i];

    275:     if ((row < firstRow) || (row >= lastRow)) {
    276:       numNonlocalRows++;
    277:       for (IndexType p = 0; p < numProcs; ++p) {
    278:         if ((row >= rowRanges[p]) && (row < rowRanges[p+1])) {
    279:           procSendSizes[p] += Nl;
    280:           break;
    281:         }
    282:       }
    283:     }
    284:   }
    285:   numSendEntries = numNonlocalRows*Nl;

    287:   PetscInfo2(J, "Nonlocal rows %d total entries %d\n", numNonlocalRows, No);
    288:   MPI_Alltoall(procSendSizes, 1, MPIU_INT, procRecvSizes, 1, MPIU_INT, comm);

    290:   numRecvEntries = 0;
    291:   for (PetscInt p = 0; p < numProcs; ++p) numRecvEntries += procRecvSizes[p];
    292:   PetscInfo2(j->A, "Send entries %d Recv Entries %d\n", numSendEntries, numRecvEntries);
    293:   PetscLogEventEnd(MAT_SetValuesBatchI,0,0,0,0);
    294:   // Allocate storage for "fat" COO representation of matrix
    295:   PetscLogEventBegin(MAT_SetValuesBatchII,0,0,0,0);
    296:   PetscInfo2(j->A, "Making COO matrices, diag entries %d, nondiag entries %d\n", No-numSendEntries+numRecvEntries, numSendEntries*2);
    297:   cusp::coo_matrix<IndexType,ValueType, memSpace> diagCOO(Nr, Nr, No-numSendEntries+numRecvEntries); // ALLOC: This is oversized because I also count offdiagonal entries
    298:   IndexArray nondiagonalRows(numSendEntries+numSendEntries); // ALLOC: This is oversized because numSendEntries > on-process offdiagonal entries
    299:   IndexArray nondiagonalCols(numSendEntries+numSendEntries); // ALLOC: This is oversized because numSendEntries > on-process offdiagonal entries
    300:   ValueArray nondiagonalVals(numSendEntries+numSendEntries); // ALLOC: This is oversized because numSendEntries > on-process offdiagonal entries
    301:   IndexArray nonlocalRows(numSendEntries);
    302:   IndexArray nonlocalCols(numSendEntries);
    303:   ValueArray nonlocalVals(numSendEntries);
    304:   // partition on-process entries into diagonal and off-diagonal+nonlocal
    305:   PetscInfo(J, "Splitting on-process entries into diagonal and off-diagonal+nonlocal\n");
    306:   thrust::fill(diagCOO.row_indices.begin(), diagCOO.row_indices.end(), -1);
    307:   thrust::fill(nondiagonalRows.begin(),     nondiagonalRows.end(),     -1);
    308:   thrust::partition_copy(thrust::make_zip_iterator(thrust::make_tuple(rowInd.begin(), colInd.begin(), d_elemMats.begin())),
    309:                          thrust::make_zip_iterator(thrust::make_tuple(rowInd.end(),   colInd.end(),   d_elemMats.end())),
    310:                          thrust::make_zip_iterator(thrust::make_tuple(diagCOO.row_indices.begin(),    diagCOO.column_indices.begin(), diagCOO.values.begin())),
    311:                          thrust::make_zip_iterator(thrust::make_tuple(nondiagonalRows.begin(),        nondiagonalCols.begin(),        nondiagonalVals.begin())),
    312:                          is_diag(firstRow, lastRow));
    313:   // Current size without off-proc entries
    314:   PetscInt diagonalSize    = (diagCOO.row_indices.end() - diagCOO.row_indices.begin()) - thrust::count(diagCOO.row_indices.begin(), diagCOO.row_indices.end(), -1);
    315:   PetscInt nondiagonalSize = No - diagonalSize;
    316:   PetscInfo2(j->A, "Diagonal size %d Nondiagonal size %d\n", diagonalSize, nondiagonalSize);
    317:   ///cusp::print(diagCOO);
    318:   ///cusp::print(nondiagonalRows);
    319:   // partition on-process entries again into off-diagonal and nonlocal
    320:   PetscInfo(J, "Splitting on-process entries into off-diagonal and nonlocal\n");
    321:   thrust::stable_partition(thrust::make_zip_iterator(thrust::make_tuple(nondiagonalRows.begin(), nondiagonalCols.begin(), nondiagonalVals.begin())),
    322:                            thrust::make_zip_iterator(thrust::make_tuple(nondiagonalRows.end(),   nondiagonalCols.end(),   nondiagonalVals.end())),
    323:                            is_nonlocal(firstRow, lastRow));
    324:   PetscInt nonlocalSize    = numSendEntries;
    325:   PetscInt offdiagonalSize = nondiagonalSize - nonlocalSize;
    326:   PetscInfo2(j->A, "Nonlocal size %d Offdiagonal size %d\n", nonlocalSize, offdiagonalSize);
    327:   PetscLogEventEnd(MAT_SetValuesBatchII,0,0,0,0);
    328:   ///cusp::print(nondiagonalRows);
    329:   // send off-proc entries (pack this up later)
    330:   PetscLogEventBegin(MAT_SetValuesBatchIII,0,0,0,0);
    331:   PetscMPIInt *procSendDispls, *procRecvDispls;
    332:   PetscInt    *sendRows, *recvRows;
    333:   PetscInt    *sendCols, *recvCols;
    334:   PetscScalar *sendVals, *recvVals;

    336:   PetscMalloc2(numProcs, &procSendDispls, numProcs, &procRecvDispls);
    337:   PetscMalloc3(numSendEntries, &sendRows, numSendEntries, &sendCols, numSendEntries, &sendVals);
    338:   PetscMalloc3(numRecvEntries, &recvRows, numRecvEntries, &recvCols, numRecvEntries, &recvVals);

    340:   procSendDispls[0] = procRecvDispls[0] = 0;
    341:   for (PetscInt p = 1; p < numProcs; ++p) {
    342:     procSendDispls[p] = procSendDispls[p-1] + procSendSizes[p-1];
    343:     procRecvDispls[p] = procRecvDispls[p-1] + procRecvSizes[p-1];
    344:   }
    345:   thrust::copy(thrust::make_zip_iterator(thrust::make_tuple(nondiagonalRows.begin(), nondiagonalCols.begin(), nondiagonalVals.begin())),
    346:                thrust::make_zip_iterator(thrust::make_tuple(nondiagonalRows.begin(), nondiagonalCols.begin(), nondiagonalVals.begin()))+nonlocalSize,
    347:                thrust::make_zip_iterator(thrust::make_tuple(sendRows,                sendCols,                sendVals)));
    348:   //   could pack into a struct and unpack
    349:   MPI_Alltoallv(sendRows, procSendSizes, procSendDispls, MPIU_INT,    recvRows, procRecvSizes, procRecvDispls, MPIU_INT,    comm);
    350:   MPI_Alltoallv(sendCols, procSendSizes, procSendDispls, MPIU_INT,    recvCols, procRecvSizes, procRecvDispls, MPIU_INT,    comm);
    351:   MPI_Alltoallv(sendVals, procSendSizes, procSendDispls, MPIU_SCALAR, recvVals, procRecvSizes, procRecvDispls, MPIU_SCALAR, comm);
    352:   PetscFree2(procSendSizes, procRecvSizes);
    353:   PetscFree2(procSendDispls, procRecvDispls);
    354:   PetscFree3(sendRows, sendCols, sendVals);
    355:   PetscLogEventEnd(MAT_SetValuesBatchIII,0,0,0,0);

    357:   PetscLogEventBegin(MAT_SetValuesBatchIV,0,0,0,0);
    358:   // Create off-diagonal matrix
    359:   cusp::coo_matrix<IndexType,ValueType, memSpace> offdiagCOO(Nr, Nr, offdiagonalSize+numRecvEntries); // ALLOC: This is oversizes because we count diagonal entries in numRecvEntries
    360:   // partition again into diagonal and off-diagonal
    361:   IndexArray d_recvRows(recvRows, recvRows+numRecvEntries);
    362:   IndexArray d_recvCols(recvCols, recvCols+numRecvEntries);
    363:   ValueArray d_recvVals(recvVals, recvVals+numRecvEntries);
    364:   thrust::copy(thrust::make_zip_iterator(thrust::make_tuple(nondiagonalRows.end(),          nondiagonalCols.end(),             nondiagonalVals.end()))-offdiagonalSize,
    365:                thrust::make_zip_iterator(thrust::make_tuple(nondiagonalRows.end(),          nondiagonalCols.end(),             nondiagonalVals.end())),
    366:                thrust::make_zip_iterator(thrust::make_tuple(offdiagCOO.row_indices.begin(), offdiagCOO.column_indices.begin(), offdiagCOO.values.begin())));
    367:   thrust::fill(diagCOO.row_indices.begin()+diagonalSize,       diagCOO.row_indices.end(),    -1);
    368:   thrust::fill(offdiagCOO.row_indices.begin()+offdiagonalSize, offdiagCOO.row_indices.end(), -1);
    369:   thrust::partition_copy(thrust::make_zip_iterator(thrust::make_tuple(d_recvRows.begin(), d_recvCols.begin(), d_recvVals.begin())),
    370:                          thrust::make_zip_iterator(thrust::make_tuple(d_recvRows.end(),   d_recvCols.end(),   d_recvVals.end())),
    371:                          thrust::make_zip_iterator(thrust::make_tuple(diagCOO.row_indices.begin()+diagonalSize, diagCOO.column_indices.begin()+diagonalSize, diagCOO.values.begin()+diagonalSize)),
    372:                          thrust::make_zip_iterator(thrust::make_tuple(offdiagCOO.row_indices.begin()+offdiagonalSize, offdiagCOO.column_indices.begin()+offdiagonalSize, offdiagCOO.values.begin()+offdiagonalSize)),
    373:                          is_diag(firstRow, lastRow));

    375:   PetscFree3(recvRows, recvCols, recvVals);

    377:   diagonalSize    = (diagCOO.row_indices.end()    - diagCOO.row_indices.begin())    - thrust::count(diagCOO.row_indices.begin(),    diagCOO.row_indices.end(),    -1);
    378:   offdiagonalSize = (offdiagCOO.row_indices.end() - offdiagCOO.row_indices.begin()) - thrust::count(offdiagCOO.row_indices.begin(), offdiagCOO.row_indices.end(), -1);

    380:   // sort COO format by (i,j), this is the most costly step
    381:   PetscInfo(J, "Sorting rows and columns\n");
    382:   diagCOO.sort_by_row_and_column();
    383:   offdiagCOO.sort_by_row_and_column();
    384:   PetscInt diagonalOffset    = (diagCOO.row_indices.end()    - diagCOO.row_indices.begin())    - diagonalSize;
    385:   PetscInt offdiagonalOffset = (offdiagCOO.row_indices.end() - offdiagCOO.row_indices.begin()) - offdiagonalSize;

    387:   // print the "fat" COO representation
    388:   if (PetscLogPrintInfo) {
    389: #if !defined(PETSC_USE_COMPLEX)
    390:     cusp::print(diagCOO);
    391:     cusp::print(offdiagCOO);
    392: #endif
    393:   }

    395:   // Figure out the number of unique off-diagonal columns
    396:   Nc = thrust::inner_product(offdiagCOO.column_indices.begin()+offdiagonalOffset,
    397:                              offdiagCOO.column_indices.end()   - 1,
    398:                              offdiagCOO.column_indices.begin()+offdiagonalOffset + 1,
    399:                              size_t(1), thrust::plus<size_t>(), thrust::not_equal_to<IndexType>());

    401:   // compute number of unique (i,j) entries
    402:   //   this counts the number of changes as we move along the (i,j) list
    403:   PetscInfo(J, "Computing number of unique entries\n");
    404:   size_t num_diag_entries = thrust::inner_product
    405:                               (thrust::make_zip_iterator(thrust::make_tuple(diagCOO.row_indices.begin(), diagCOO.column_indices.begin())) + diagonalOffset,
    406:                               thrust::make_zip_iterator(thrust::make_tuple(diagCOO.row_indices.end(),   diagCOO.column_indices.end())) - 1,
    407:                               thrust::make_zip_iterator(thrust::make_tuple(diagCOO.row_indices.begin(), diagCOO.column_indices.begin())) + diagonalOffset + 1,
    408:                               size_t(1),
    409:                               thrust::plus<size_t>(),
    410:                               thrust::not_equal_to< thrust::tuple<IndexType,IndexType> >());
    411:   size_t num_offdiag_entries = thrust::inner_product
    412:                                  (thrust::make_zip_iterator(thrust::make_tuple(offdiagCOO.row_indices.begin(), offdiagCOO.column_indices.begin())) + offdiagonalOffset,
    413:                                  thrust::make_zip_iterator(thrust::make_tuple(offdiagCOO.row_indices.end(),   offdiagCOO.column_indices.end())) - 1,
    414:                                  thrust::make_zip_iterator(thrust::make_tuple(offdiagCOO.row_indices.begin(), offdiagCOO.column_indices.begin())) + offdiagonalOffset + 1,
    415:                                  size_t(1),
    416:                                  thrust::plus<size_t>(),
    417:                                  thrust::not_equal_to< thrust::tuple<IndexType,IndexType> >());

    419:   // allocate COO storage for final matrix
    420:   PetscInfo(J, "Allocating compressed matrices\n");
    421:   cusp::coo_matrix<IndexType, ValueType, memSpace> A(Nr, Nr, num_diag_entries);
    422:   cusp::coo_matrix<IndexType, ValueType, memSpace> B(Nr, Nc, num_offdiag_entries);

    424:   // sum values with the same (i,j) index
    425:   // XXX thrust::reduce_by_key is unoptimized right now, so we provide a SpMV-based one in cusp::detail
    426:   //     the Cusp one is 2x faster, but still not optimal
    427:   // This could possibly be done in-place
    428:   PetscInfo(J, "Compressing matrices\n");
    429:   thrust::reduce_by_key(thrust::make_zip_iterator(thrust::make_tuple(diagCOO.row_indices.begin(), diagCOO.column_indices.begin())) + diagonalOffset,
    430:                         thrust::make_zip_iterator(thrust::make_tuple(diagCOO.row_indices.end(),   diagCOO.column_indices.end())),
    431:                         diagCOO.values.begin() + diagonalOffset,
    432:                         thrust::make_zip_iterator(thrust::make_tuple(A.row_indices.begin(), A.column_indices.begin())),
    433:                         A.values.begin(),
    434:                         thrust::equal_to< thrust::tuple<IndexType,IndexType> >(),
    435:                         thrust::plus<ValueType>());

    437:   thrust::reduce_by_key(thrust::make_zip_iterator(thrust::make_tuple(offdiagCOO.row_indices.begin(), offdiagCOO.column_indices.begin())) + offdiagonalOffset,
    438:                         thrust::make_zip_iterator(thrust::make_tuple(offdiagCOO.row_indices.end(),   offdiagCOO.column_indices.end())),
    439:                         offdiagCOO.values.begin() + offdiagonalOffset,
    440:                         thrust::make_zip_iterator(thrust::make_tuple(B.row_indices.begin(), B.column_indices.begin())),
    441:                         B.values.begin(),
    442:                         thrust::equal_to< thrust::tuple<IndexType,IndexType> >(),
    443:                         thrust::plus<ValueType>());

    445:   // Convert row and column numbers
    446:   if (firstRow) {
    447:     thrust::transform(A.row_indices.begin(), A.row_indices.end(), thrust::make_constant_iterator(firstRow), A.row_indices.begin(), thrust::minus<IndexType>());
    448:     thrust::transform(B.row_indices.begin(), B.row_indices.end(), thrust::make_constant_iterator(firstRow), B.row_indices.begin(), thrust::minus<IndexType>());
    449:   }
    450:   if (firstCol) {
    451:     thrust::transform(A.column_indices.begin(), A.column_indices.end(), thrust::make_constant_iterator(firstCol), A.column_indices.begin(), thrust::minus<IndexType>());
    452:   }

    454:   // print the final matrix
    455:   if (PetscLogPrintInfo) {
    456: #if !defined(PETSC_USE_COMPLEX)
    457:     cusp::print(A);
    458:     cusp::print(B);
    459: #endif
    460:   }

    462:   PetscInfo(J, "Converting to PETSc matrix\n");
    463:   MatSetType(J, MATMPIAIJCUSP);
    464:   CUSPMATRIX *Agpu = new CUSPMATRIX;
    465:   CUSPMATRIX *Bgpu = new CUSPMATRIX;
    466:   cusp::convert(A, *Agpu);
    467:   cusp::convert(B, *Bgpu);
    468:   if (PetscLogPrintInfo) {
    469: #if !defined(PETSC_USE_COMPLEX)
    470:     cusp::print(*Agpu);
    471:     cusp::print(*Bgpu);
    472: #endif
    473:   }
    474:   {
    475:     PetscInfo(J, "Copying to CPU matrix");
    476:     MatCUSPCopyFromGPU(j->A, Agpu);
    477:     MatCUSPCopyFromGPU(j->B, Bgpu);
    478:   }
    479:   PetscLogEventEnd(MAT_SetValuesBatchIV,0,0,0,0);
    480:   return(0);
    481: }