MatrixMarket_TpetraNew.hpp

// @HEADER
// *****************************************************************************
//          Tpetra: Templated Linear Algebra Services Package
//
// Copyright 2008 NTESS and the Tpetra contributors.
// SPDX-License-Identifier: BSD-3-Clause
// *****************************************************************************
// @HEADER
 
#ifndef __MATRIXMARKET_TPETRA_NEW_HPP
#define __MATRIXMARKET_TPETRA_NEW_HPP
 
// Functions to read a MatrixMarket file and load it into a matrix.
// Adapted from
//    Trilinos/packages/epetraext/src/inout/EpetraExt_CrsMatrixIn.cpp
// Modified by Jon Berry and Karen Devine to make matrix reallocations
// more efficient; rather than insert each non-zero separately, we
// collect rows of non-zeros for insertion.
// Modified by Karen Devine and Steve Plimpton to prevent all processors
// from reading the same file at the same time (ouch!); chunks of the file
// are read and broadcast by processor zero; each processor then extracts
// its nonzeros from the chunk, sorts them by row, and inserts them into
// the matrix.
// The variable "chunkSize" can be changed to modify the size of the chunks
// read from the file.  Larger values of chunkSize lead to faster execution
// and greater memory use.
 
private:
template <typename global_ordinal_type, typename scalar_type>
static Teuchos::RCP<Distribution<global_ordinal_type, scalar_type> >
buildDistribution(
    std::string &distribution,             // string indicating whether to use 1D, 2D or
                                           // file-based matrix distribution
    size_t nRow,                           // Number of global matrix rows
    size_t nCol,                           // Number of global matrix rows
    const Teuchos::ParameterList &params,  // Parameters to the file reading
    const Teuchos::RCP<const Teuchos::Comm<int> > &comm
    // communicator to be used in maps
) {
  // Function to build the sets of GIDs for 1D or 2D matrix distribution.
  // Output is a Distribution object.
 
  int me = comm->getRank();
 
  using basedist_t = Distribution<global_ordinal_type, scalar_type>;
  basedist_t *retval;
 
  bool randomize = false;  // Randomly permute rows and columns before storing
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("randomize");
    if (pe != NULL)
      randomize = pe->getValue<bool>(&randomize);
  }
 
  std::string partitionFile = "";  // File to reassign rows to parts
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("partitionFile");
    if (pe != NULL)
      partitionFile = pe->getValue<std::string>(&partitionFile);
  }
 
  if (distribution == "2D") {  // Generate 2D distribution
    if (partitionFile != "") {
      // Generate 2D distribution with vector partition file
      TEUCHOS_TEST_FOR_EXCEPTION(randomize, std::logic_error,
                                 "Randomization not available for 2DVec distributions.");
      Distribution2DVec<global_ordinal_type, scalar_type> *dist =
          new Distribution2DVec<global_ordinal_type, scalar_type>(
              nRow, comm, params, partitionFile);
      retval = dynamic_cast<basedist_t *>(dist);
    } else if (randomize) {
      // Randomly assign rows/columns to processors
      Distribution2DRandom<global_ordinal_type, scalar_type> *dist =
          new Distribution2DRandom<global_ordinal_type, scalar_type>(
              nRow, comm, params);
      retval = dynamic_cast<basedist_t *>(dist);
    } else {
      // The vector will be distributed linearly, with extra vector entries
      // spread among processors to maintain balance in rows and columns.
      Distribution2DLinear<global_ordinal_type, scalar_type> *dist =
          new Distribution2DLinear<global_ordinal_type, scalar_type>(
              nRow, comm, params);
      retval = dynamic_cast<basedist_t *>(dist);
    }
  } else if (distribution == "1D") {
    if (partitionFile != "") {
      // Generate 1D row-based distribution with vector partition file
      Distribution1DVec<global_ordinal_type, scalar_type> *dist =
          new Distribution1DVec<global_ordinal_type, scalar_type>(
              nRow, comm, params, partitionFile);
      retval = dynamic_cast<basedist_t *>(dist);
    } else if (randomize) {
      // Randomly assign rows to processors.
      Distribution1DRandom<global_ordinal_type, scalar_type> *dist =
          new Distribution1DRandom<global_ordinal_type, scalar_type>(
              nRow, comm, params);
      retval = dynamic_cast<basedist_t *>(dist);
    } else {
      // Linear map similar to Trilinos default.
      Distribution1DLinear<global_ordinal_type, scalar_type> *dist =
          new Distribution1DLinear<global_ordinal_type, scalar_type>(
              nRow, comm, params);
      retval = dynamic_cast<basedist_t *>(dist);
    }
  } else if (distribution == "LowerTriangularBlock") {
    if (randomize && me == 0) {
      std::cout << "WARNING: Randomization not available for "
                << "LowerTriangularBlock distributions." << std::endl;
    }
 
    DistributionLowerTriangularBlock<global_ordinal_type, scalar_type> *dist =
        new DistributionLowerTriangularBlock<global_ordinal_type, scalar_type>(
            nRow, comm, params);
    retval = dynamic_cast<basedist_t *>(dist);
  } else if (distribution == "MMFile") {
    // Generate user-defined distribution from Matrix-Market file
    if (randomize && me == 0) {
      std::cout << "WARNING: Randomization not available for MMFile "
                << "distributions." << std::endl;
    }
    DistributionMMFile<global_ordinal_type, scalar_type> *dist =
        new DistributionMMFile<global_ordinal_type, scalar_type>(
            nRow, comm, params);
    retval = dynamic_cast<basedist_t *>(dist);
  }
 
  else {
    std::cout << "ERROR:  Invalid distribution method " << distribution
              << std::endl;
    exit(-1);
  }
  return Teuchos::rcp<basedist_t>(retval);
}
 
static void
readMatrixMarket(
    const std::string &filename,  // MatrixMarket file to read
    const Teuchos::RCP<const Teuchos::Comm<int> > &comm,
    const Teuchos::ParameterList &params,
    size_t &nRow,
    size_t &nCol,
    typename Distribution<global_ordinal_type, scalar_type>::LocalNZmap_t &localNZ,
    Teuchos::RCP<Distribution<global_ordinal_type, scalar_type> > &dist) {
  bool useTimers = false;  // should we time various parts of the reader?
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("useTimers");
    if (pe != NULL)
      useTimers = pe->getValue<bool>(&useTimers);
  }
 
  Teuchos::RCP<Teuchos::TimeMonitor> timer = Teuchos::null;
  if (useTimers)
    timer = rcp(new Teuchos::TimeMonitor(
        *Teuchos::TimeMonitor::getNewTimer("RMM parameterSetup")));
 
  int me = comm->getRank();
 
  bool verbose = false;  // Print status as reading
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("verbose");
    if (pe != NULL)
      verbose = pe->getValue<bool>(&verbose);
  }
 
  size_t chunkSize = 500000;  // Number of lines to read / broadcast at once
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("chunkSize");
    if (pe != NULL)
      chunkSize = pe->getValue<size_t>(&chunkSize);
  }
 
  bool symmetrize = false;  // Symmetrize the matrix
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("symmetrize");
    if (pe != NULL)
      symmetrize = pe->getValue<bool>(&symmetrize);
  }
 
  bool transpose = false;  // Store the transpose
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("transpose");
    if (pe != NULL)
      transpose = pe->getValue<bool>(&transpose);
  }
 
  std::string diagonal = "";  // Are diagonal entries required (so add them)
                              // or ignored (so delete them) or neither?
                              // Default is neither.
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("diagonal");
    if (pe != NULL)
      diagonal = pe->getValue<std::string>(&diagonal);
  }
  bool ignoreDiagonal  = (diagonal == "exclude");
  bool requireDiagonal = (diagonal == "require");
 
  std::string distribution = "1D";  // Default distribution is 1D row-based
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("distribution");
    if (pe != NULL)
      distribution = pe->getValue<std::string>(&distribution);
  }
 
  if (useTimers) {
    timer = Teuchos::null;
    timer = rcp(new Teuchos::TimeMonitor(
        *Teuchos::TimeMonitor::getNewTimer("RMM header")));
  }
 
  if (verbose && me == 0)
    std::cout << "Reading matrix market file... " << filename << std::endl;
 
  FILE *fp      = NULL;
  size_t dim[3] = {0, 0, 0};  // nRow, nCol, nNz as read from MatrixMarket
  MM_typecode mmcode;
 
  if (me == 0) {
    fp = fopen(filename.c_str(), "r");
 
    if (fp == NULL) {
      std::cout << "Error:  cannot open file " << filename << std::endl;
    } else {
      // Read MatrixMarket banner to get type of matrix
      if (mm_read_banner(fp, &mmcode) != 0) {
        std::cout << "Error:  bad MatrixMarket banner " << std::endl;
      } else {
        // Error check for file types that this function can read
        if (!mm_is_valid(mmcode) ||
            mm_is_dense(mmcode) || mm_is_array(mmcode) ||
            mm_is_complex(mmcode) ||
            mm_is_skew(mmcode) || mm_is_hermitian(mmcode)) {
          std::cout << "Error:  matrix type is not supported by this reader\n "
                    << "This reader supports sparse, coordinate, "
                    << "real, pattern, integer, symmetric, general"
                    << std::endl;
        } else {
          // Read nRow, nCol, nNz from MatrixMarket file
          if (mm_read_mtx_crd_size(fp, &dim[0], &dim[1], &dim[2]) != 0) {
            std::cout << "Error:  bad matrix dimensions " << std::endl;
            dim[0] = dim[1] = dim[2] = 0;
          }
        }
      }
    }
  }
 
  // Broadcast relevant info
  // Bad input if dim[0] or dim[1] still is zero after broadcast;
  // all procs throw together
  Teuchos::broadcast<int, size_t>(*comm, 0, 3, dim);
  if (dim[0] == 0 || dim[1] == 0) {
    throw std::runtime_error("Error:  bad matrix header information");
  }
  Teuchos::broadcast<int, char>(*comm, 0, sizeof(MM_typecode), mmcode);
 
  nRow = dim[0];
  nCol = dim[1];
 
  TEUCHOS_TEST_FOR_EXCEPTION(nRow != nCol, std::logic_error,
                             "This overload of readSparseFile requires nRow == nCol "
                                 << "(nRow = " << nRow << ", nCol = " << nCol << "); "
                                 << "For now, use a different overload of readSparseFile until this "
                                 << "overload is fixed to read rectangular matrices. "
                                 << "See Trilinos github issues #7045 and #8472.");
 
  size_t nNz          = dim[2];
  bool patternInput   = mm_is_pattern(mmcode);
  bool symmetricInput = mm_is_symmetric(mmcode);
  if (symmetricInput) symmetrize = true;
 
  if (verbose && me == 0)
    std::cout << "Matrix market file... "
              << "\n  symmetrize          = " << symmetrize
              << "\n  transpose           = " << transpose
              << "\n  change diagonal     = " << diagonal
              << "\n  distribution        = " << distribution
              << std::endl;
 
  if (useTimers) {
    timer = Teuchos::null;
    timer = rcp(new Teuchos::TimeMonitor(
        *Teuchos::TimeMonitor::getNewTimer("RMM distribution")));
  }
 
  // Create distribution based on nRow, nCol, npRow, npCol
  dist = buildDistribution<global_ordinal_type, scalar_type>(distribution,
                                                             nRow, nCol, params,
                                                             comm);
  if (useTimers) {
    timer = Teuchos::null;
    timer = rcp(new Teuchos::TimeMonitor(
        *Teuchos::TimeMonitor::getNewTimer("RMM readChunks")));
  }
 
  std::set<global_ordinal_type> diagset;
  // If diagonal == require, this set keeps track of
  // which diagonal entries already existing so we can
  // add those that don't
 
  using nzindex_t =
      typename Distribution<global_ordinal_type, scalar_type>::NZindex_t;
 
  // Chunk information and buffers
  const int maxLineLength = 81;
  char *buffer            = new char[chunkSize * maxLineLength + 1];
  size_t nChunk;
  size_t nMillion = 0;
  size_t nRead    = 0;
  size_t rlen;
 
  auto timerRead   = Teuchos::TimeMonitor::getNewTimer("RMM    readNonzeros");
  auto timerSelect = Teuchos::TimeMonitor::getNewTimer("RMM    selectNonzeros");
  // Read chunks until the entire file is read
  Teuchos::RCP<Teuchos::TimeMonitor> innerTimer = Teuchos::null;
  while (nRead < nNz) {
    innerTimer = rcp(new Teuchos::TimeMonitor(*timerRead));
 
    if (nNz - nRead > chunkSize)
      nChunk = chunkSize;
    else
      nChunk = (nNz - nRead);
 
    // Processor 0 reads a chunk
    if (me == 0) {
      char *eof;
      rlen = 0;
      for (size_t i = 0; i < nChunk; i++) {
        eof = fgets(&buffer[rlen], maxLineLength, fp);
        if (eof == NULL) {
          std::cout << "Unexpected end of matrix file." << std::endl;
          std::cout.flush();
          exit(-1);
        }
        rlen += strlen(&buffer[rlen]);
      }
      buffer[rlen++] = '\n';
    }
 
    // Processor 0 broadcasts the chunk
    Teuchos::broadcast<int, size_t>(*comm, 0, 1, &rlen);
    Teuchos::broadcast<int, char>(*comm, 0, rlen, buffer);
 
    buffer[rlen++] = '\0';
    nRead += nChunk;
 
    innerTimer = Teuchos::null;
    innerTimer = rcp(new Teuchos::TimeMonitor(*timerSelect));
 
    // All processors check the received data, saving nonzeros belonging to them
    char *lineptr = buffer;
    for (rlen = 0; rlen < nChunk; rlen++) {
      char *next            = strchr(lineptr, '\n');
      global_ordinal_type I = atol(strtok(lineptr, " \t\n")) - 1;  // since MatrixMarket files are one-based
      global_ordinal_type J = atol(strtok(NULL, " \t\n")) - 1;     // since MatrixMarket files are one-based
 
      scalar_type V = (patternInput ? -1. : atof(strtok(NULL, " \t\n")));
      lineptr       = next + 1;
 
      // Special processing of nonzero
      if ((I == J) && ignoreDiagonal) continue;
 
      if (transpose) std::swap<global_ordinal_type>(I, J);
 
      // Add nonzero (I,J) to the map if it should be on this processor
      // Some file-based distributions have processor assignment stored as
      // the non-zero's value, so pass the value to Mine.
      if (dist->Mine(I, J, int(V))) {
        nzindex_t idx = std::make_pair(I, J);
        localNZ[idx]  = V;
        if (requireDiagonal && (I == J)) diagset.insert(I);
      }
 
      // If symmetrizing, add (J,I) to the map if it should be on this processor
      // Some file-based distributions have processor assignment stored as
      // the non-zero's value, so pass the value to Mine.
      if (symmetrize && (I != J) && dist->Mine(J, I, int(V))) {
        //  Add entry (J, I) if need to symmetrize
        //  This processor keeps this non-zero.
        nzindex_t idx = std::make_pair(J, I);
        localNZ[idx]  = V;
      }
    }
 
    // Status check
    if (verbose) {
      if (nRead / 1000000 > nMillion) {
        nMillion++;
        if (me == 0) std::cout << nMillion << "M ";
      }
    }
 
    innerTimer = Teuchos::null;
  }
 
  if (verbose && me == 0)
    std::cout << std::endl
              << nRead << " nonzeros read " << std::endl;
 
  if (fp != NULL) fclose(fp);
  delete[] buffer;
 
  if (useTimers) {
    timer = Teuchos::null;
    timer = rcp(new Teuchos::TimeMonitor(
        *Teuchos::TimeMonitor::getNewTimer("RMM diagonal")));
  }
 
  //  Add diagonal entries if they are required.
  //  Check to make sure they are all here; add them if they are not.
  if (requireDiagonal) {
    if (dist->DistType() == MMFile) {
      // All diagonal entries should be present in the file; we cannot create
      // them for file-based data distributions.
      // Do an error check to ensure they are all there.
      size_t localss = diagset.size();
      size_t globalss;
      Teuchos::reduceAll<int, size_t>(*comm, Teuchos::REDUCE_SUM, 1,
                                      &localss, &globalss);
      TEUCHOS_TEST_FOR_EXCEPTION(globalss != nRow, std::logic_error,
                                 "File-based nonzero distribution requires all diagonal "
                                     << "entries to be present in the file.  \n"
                                     << "Number of diagonal entries in file = " << globalss << "\n"
                                     << "Number of matrix rows = " << nRow << "\n");
    } else {
      for (global_ordinal_type i = 0;
           i < static_cast<global_ordinal_type>(nRow); i++) {
        if (dist->Mine(i, i)) {
          if (diagset.find(i) == diagset.end()) {
            nzindex_t idx = std::make_pair(i, i);
            localNZ[idx]  = 0;
          }
        }
      }
    }
  }
  // Done with diagset; free its memory
  std::set<global_ordinal_type>().swap(diagset);
 
  if (useTimers)
    timer = Teuchos::null;
}
 
//        (This format is used by the upcoming readBinary function)         //
//
// File format:
//   #vertices #edges src_1 dst_1 src_2 dst_2 ... src_#edges dst_#edges
//
// Types:
//   #edges:            unsigned long long
//   everything else:   unsigned int
//
// Base of indexing:
//   1
//
//
// A code example that converts MatrixMarket format into this format:
//
//   typedef unsigned int ord_type;
//   typedef unsigned long long size_type;
//
//   std::string line;
//   std::ifstream in(infilename);
//   std::ofstream out(outfilename,  std::ios::out | std::ios::binary);
//
//  ord_type nv, dummy, edge[2];
//  size_type ne;
//
//   do
//     std::getline (in, line);
//   while(line[0] == '%');
//
//   std::stringstream ss(line);
//   ss >> nv >> dummy >> ne;
//   out.write((char *)&nv, sizeof(ord_type));
//   out.write((char *)&ne, sizeof(size_type));
//
//   while(std::getline(in, line)) {
//     std::stringstream ss2(line);
//     ss2 >> edge[0] >> edge[1];
//     out.write((char *)edge, sizeof(ord_type)*2);
//
//    }
//   in.close();
//   out.close();
//
 
static void
readBinary(
    const std::string &filename,  // MatrixMarket file to read
    const Teuchos::RCP<const Teuchos::Comm<int> > &comm,
    const Teuchos::ParameterList &params,
    size_t &nRow,
    size_t &nCol,
    typename Distribution<global_ordinal_type, scalar_type>::LocalNZmap_t &localNZ,
    Teuchos::RCP<Distribution<global_ordinal_type, scalar_type> > &dist) {
  int me = comm->getRank();
 
  bool verbose = false;  // Print status as reading
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("verbose");
    if (pe != NULL)
      verbose = pe->getValue<bool>(&verbose);
  }
 
  size_t chunkSize = 500000;  // Number of lines to read / broadcast at once
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("chunkSize");
    if (pe != NULL)
      chunkSize = pe->getValue<size_t>(&chunkSize);
  }
 
  bool symmetrize = false;  // Symmetrize the matrix
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("symmetrize");
    if (pe != NULL)
      symmetrize = pe->getValue<bool>(&symmetrize);
  }
 
  bool transpose = false;  // Store the transpose
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("transpose");
    if (pe != NULL)
      transpose = pe->getValue<bool>(&transpose);
  }
 
  std::string diagonal = "";  // Are diagonal entries required (so add them)
                              // or ignored (so delete them) or neither?
                              // Default is neither.
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("diagonal");
    if (pe != NULL)
      diagonal = pe->getValue<std::string>(&diagonal);
  }
  bool ignoreDiagonal  = (diagonal == "exclude");
  bool requireDiagonal = (diagonal == "require");
 
  std::string distribution = "1D";  // Default distribution is 1D row-based
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("distribution");
    if (pe != NULL)
      distribution = pe->getValue<std::string>(&distribution);
  }
 
  if (verbose && me == 0)
    std::cout << "Reading binary file... " << filename << std::endl;
 
  FILE *fp      = NULL;
  size_t dim[3] = {0, 0, 0};  // Expected to read nRow and nNz, nCol = nRow
 
  if (me == 0) {
    fp = fopen(filename.c_str(), "rb");
 
    if (fp == NULL) {
      std::cout << "Error:  cannot open file " << filename << std::endl;
    } else {
      // The header in the binary file contains only numVertices and numEdges
      unsigned int nv       = 0;
      unsigned long long ne = 0;
      if (fread(&nv, sizeof(unsigned int), 1, fp) != 1)
        throw std::runtime_error("Error: bad number of read values.");
      if (fread(&ne, sizeof(unsigned long long), 1, fp) != 1)
        throw std::runtime_error("Error: bad number of read values.");
      dim[0] = nv;
      dim[1] = dim[0];
      dim[2] = ne;
    }
  }
 
  // Broadcast relevant info
  // Bad input if dim[0] or dim[1] still is zero after broadcast;
  // all procs throw together
  Teuchos::broadcast<int, size_t>(*comm, 0, 3, dim);
  if (dim[0] == 0 || dim[1] == 0) {
    throw std::runtime_error("Error:  bad matrix header information");
  }
 
  nRow       = dim[0];
  nCol       = dim[1];
  size_t nNz = dim[2];
 
  if (verbose && me == 0)
    std::cout << "Binary file... "
              << "\n  symmetrize          = " << symmetrize
              << "\n  transpose           = " << transpose
              << "\n  change diagonal     = " << diagonal
              << "\n  distribution        = " << distribution
              << std::endl;
 
  // Create distribution based on nRow, nCol, npRow, npCol
  dist = buildDistribution<global_ordinal_type, scalar_type>(distribution,
                                                             nRow, nCol, params,
                                                             comm);
 
  std::set<global_ordinal_type> diagset;
  // If diagonal == require, this set keeps track of
  // which diagonal entries already existing so we can
  // add those that don't
 
  using nzindex_t =
      typename Distribution<global_ordinal_type, scalar_type>::NZindex_t;
 
  // Chunk information and buffers
  unsigned int *buffer = new unsigned int[chunkSize * 2];
  size_t nChunk;
  size_t nMillion = 0;
  size_t nRead    = 0;
  size_t rlen;
  const scalar_type ONE = Teuchos::ScalarTraits<scalar_type>::one();
 
  // Read chunks until the entire file is read
  while (nRead < nNz) {
    if (nNz - nRead > chunkSize)
      nChunk = chunkSize;
    else
      nChunk = (nNz - nRead);
 
    // Processor 0 reads a chunk
    if (me == 0) {
      size_t ret = 0;
      rlen       = 0;
      for (size_t i = 0; i < nChunk; i++) {
        ret = fread(&buffer[rlen], sizeof(unsigned int), 2, fp);
        if (ret == 0) {
          std::cout << "Unexpected end of matrix file." << std::endl;
          std::cout.flush();
          exit(-1);
        }
        rlen += 2;
      }
    }
 
    // Processor 0 broadcasts the chunk
    Teuchos::broadcast<int, size_t>(*comm, 0, 1, &rlen);
    Teuchos::broadcast<int, unsigned int>(*comm, 0, rlen, buffer);
 
    nRead += nChunk;
 
    // All processors check the received data, saving nonzeros belonging to them
    for (rlen = 0; rlen < nChunk; rlen++) {
      global_ordinal_type I = buffer[2 * rlen] - 1;
      global_ordinal_type J = buffer[2 * rlen + 1] - 1;
 
      // Special processing of nonzero
      if ((I == J) && ignoreDiagonal) continue;
 
      if (transpose) std::swap<global_ordinal_type>(I, J);
 
      // Add nonzero (I,J) to the map if it should be on this processor
      // Some file-based distributions have processor assignment stored as
      // the non-zero's value, so pass the value to Mine.
      if (dist->Mine(I, J, ONE)) {
        nzindex_t idx = std::make_pair(I, J);
        localNZ[idx]  = ONE;  // For now, the input binary format does not
                              // support numeric values, so we insert one.
        if (requireDiagonal && (I == J)) diagset.insert(I);
      }
 
      // If symmetrizing, add (J,I) to the map if it should be on this processor
      // Some file-based distributions have processor assignment stored as
      // the non-zero's value, so pass the value to Mine.
      if (symmetrize && (I != J) && dist->Mine(J, I, ONE)) {
        //  Add entry (J, I) if need to symmetrize
        //  This processor keeps this non-zero.
        nzindex_t idx = std::make_pair(J, I);
        localNZ[idx]  = ONE;
      }
    }
 
    // Status check
    if (verbose) {
      if (nRead / 1000000 > nMillion) {
        nMillion++;
        if (me == 0) std::cout << nMillion << "M ";
      }
    }
  }
 
  if (verbose && me == 0)
    std::cout << std::endl
              << nRead << " nonzeros read " << std::endl;
 
  if (fp != NULL) fclose(fp);
  delete[] buffer;
 
  //  Add diagonal entries if they are required.
  //  Check to make sure they are all here; add them if they are not.
  if (requireDiagonal) {
    if (dist->DistType() == MMFile) {
      // All diagonal entries should be present in the file; we cannot create
      // them for file-based data distributions.
      // Do an error check to ensure they are all there.
      size_t localss = diagset.size();
      size_t globalss;
      Teuchos::reduceAll<int, size_t>(*comm, Teuchos::REDUCE_SUM, 1,
                                      &localss, &globalss);
      TEUCHOS_TEST_FOR_EXCEPTION(globalss != nRow, std::logic_error,
                                 "File-based nonzero distribution requires all diagonal "
                                     << "entries to be present in the file.  \n"
                                     << "Number of diagonal entries in file = " << globalss << "\n"
                                     << "Number of matrix rows = " << nRow << "\n");
    } else {
      for (global_ordinal_type i = 0;
           i < static_cast<global_ordinal_type>(nRow); i++) {
        if (dist->Mine(i, i)) {
          if (diagset.find(i) == diagset.end()) {
            nzindex_t idx = std::make_pair(i, i);
            localNZ[idx]  = 0;
          }
        }
      }
    }
  }
  // Done with diagset; free its memory
  std::set<global_ordinal_type>().swap(diagset);
}
 
//   (This format is used by the upcoming readPerProcessBinary function)    //
//
//
// FILE FORMAT:
//     globalNumRows globalNumCols localNumNnzs row_1 col_1 ... row_n col_n,
//  where n = localNumNnzs
//
//
// ASSUMPTIONS:
//  - The nonzeros should be sorted by their row indices within each file.
//  - Nonzeros have global row and column indices.
//  - The user specifies the base <filename>, where rank i reads <filename>.i.cooBin.
//
//
// TYPES:
//  localNumNnzs:      unsigned long long
//  everything else:   unsigned int
//
//
// BASE OF INDEXING: 1
//
//
static void
readPerProcessBinary(
    const std::string &filename,
    const Teuchos::RCP<const Teuchos::Comm<int> > &comm,
    const Teuchos::ParameterList &params,
    size_t &nRow,
    size_t &nCol,
    typename Distribution<global_ordinal_type, scalar_type>::LocalNZmap_t &localNZ,
    Teuchos::RCP<Distribution<global_ordinal_type, scalar_type> > &dist,
    unsigned int *&buffer,
    size_t &nNz) {
  int me = comm->getRank();
 
  bool verbose = false;  // Print status as reading
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("verbose");
    if (pe != NULL)
      verbose = pe->getValue<bool>(&verbose);
  }
 
  std::string distribution = "1D";  // Default distribution is 1D row-based
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("distribution");
    if (pe != NULL)
      distribution = pe->getValue<std::string>(&distribution);
  }
 
  if (verbose && me == 0)
    std::cout << "Reading per-process binary files... " << filename << std::endl;
 
  std::string rankFileName = filename + "." + std::to_string(me) + ".cooBin";
  FILE *fp                 = NULL;
 
  fp = fopen(rankFileName.c_str(), "rb");
  if (fp == NULL) {
    std::cout << "Error:  cannot open file " << filename << std::endl;
    throw std::runtime_error("Error:  non-existing input file: " + rankFileName);
  }
 
  // The header in each per-process file:  globalNumRows globalNumCols localNumNonzeros
  unsigned int globalNumRows = 0, globalNumCols = 0;
  unsigned long long localNumNonzeros = 0;
  if (fread(&globalNumRows, sizeof(unsigned int), 1, fp) != 1)
    throw std::runtime_error("Error: bad number of read values.");
  if (fread(&globalNumCols, sizeof(unsigned int), 1, fp) != 1)
    throw std::runtime_error("Error: bad number of read values.");
  if (fread(&localNumNonzeros, sizeof(unsigned long long), 1, fp) != 1)
    throw std::runtime_error("Error: bad number of read values.");
 
  nRow = static_cast<size_t>(globalNumRows);
  nCol = static_cast<size_t>(globalNumCols);
  nNz  = static_cast<size_t>(localNumNonzeros);
 
  // Fill the simple buffer array instead of a std::map
  // S. Acer: With large graphs, we can't afford std::map
  buffer = new unsigned int[nNz * 2];
 
  if (nNz > 0) {
    size_t ret = fread(buffer, sizeof(unsigned int), 2 * nNz, fp);
    if (ret == 0) {
      std::cout << "Unexpected end of matrix file: " << rankFileName << std::endl;
      std::cout.flush();
      delete[] buffer;
      exit(-1);
    }
  }
  if (fp != NULL) fclose(fp);
 
  // This barrier is not necessary but useful for debugging
  comm->barrier();
  if (verbose && me == 0)
    std::cout << "All ranks finished reading their nonzeros from their individual files\n";
 
  // Create distribution based on nRow, nCol, npRow, npCol
  dist = buildDistribution<global_ordinal_type, scalar_type>(distribution,
                                                             nRow, nCol, params,
                                                             comm);
}
 
public:
// This is the default interface.
static Teuchos::RCP<sparse_matrix_type>
readSparseFile(
    const std::string &filename,  // MatrixMarket file to read
    const Teuchos::RCP<const Teuchos::Comm<int> > &comm,
    const Teuchos::ParameterList &params) {
  Teuchos::RCP<Distribution<global_ordinal_type, scalar_type> > dist;
  return readSparseFile(filename, comm, params, dist);
}
 
// This version has the Distribution object as an output parameter.
// S. Acer needs the distribution object to get the chunk cuts from
// LowerTriangularBlock distribution.
static Teuchos::RCP<sparse_matrix_type>
readSparseFile(
    const std::string &filename,  // MatrixMarket file to read
    const Teuchos::RCP<const Teuchos::Comm<int> > &comm,
    const Teuchos::ParameterList &params,
    Teuchos::RCP<Distribution<global_ordinal_type, scalar_type> > &dist) {
  bool useTimers = false;  // should we time various parts of the reader?
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("useTimers");
    if (pe != NULL)
      useTimers = pe->getValue<bool>(&useTimers);
  }
 
  Teuchos::RCP<Teuchos::TimeMonitor> timer = Teuchos::null;
  if (useTimers)
    timer = rcp(new Teuchos::TimeMonitor(
        *Teuchos::TimeMonitor::getNewTimer("RSF parameterSetup")));
 
  int me = comm->getRank();
 
  // Check parameters to determine how to process the matrix while reading
  // TODO:  Add validators for the parameters
 
  bool verbose = false;  // Print status as reading
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("verbose");
    if (pe != NULL)
      verbose = pe->getValue<bool>(&verbose);
  }
 
  bool callFillComplete = true;  // should we fillComplete the new CrsMatrix?
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("callFillComplete");
    if (pe != NULL)
      callFillComplete = pe->getValue<bool>(&callFillComplete);
  }
 
  // Don't want to use MatrixMarket's coordinate reader, because don't want
  // entire matrix on one processor.
  // Instead, Proc 0 reads nonzeros in chunks and broadcasts chunks to all
  // processors.
  // All processors insert nonzeros they own into a std::map
 
  // Storage for this processor's nonzeros.
  using localNZmap_t =
      typename Distribution<global_ordinal_type, scalar_type>::LocalNZmap_t;
  localNZmap_t localNZ;
 
  bool binary = false;  // should we read a binary file?
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("binary");
    if (pe != NULL)
      binary = pe->getValue<bool>(&binary);
  }
 
  bool readPerProcess = false;  // should we read a separate file per process?
  {
    const Teuchos::ParameterEntry *pe = params.getEntryPtr("readPerProcess");
    if (pe != NULL)
      readPerProcess = pe->getValue<bool>(&readPerProcess);
  }
 
  if (useTimers) {
    const char *timername = (binary ? "RSF readBinary" : "RSF readMatrixMarket");
    timer                 = Teuchos::null;
    timer                 = rcp(new Teuchos::TimeMonitor(
                        *Teuchos::TimeMonitor::getNewTimer(timername)));
  }
 
  // Read nonzeros from the given file(s)
  size_t nRow = 0, nCol = 0;
  unsigned int *buffer = 0;
  size_t nNz           = 0;
  if (binary) {
    if (readPerProcess)
      readPerProcessBinary(filename, comm, params, nRow, nCol, localNZ, dist, buffer, nNz);
    else
      readBinary(filename, comm, params, nRow, nCol, localNZ, dist);
  } else
    readMatrixMarket(filename, comm, params, nRow, nCol, localNZ, dist);
 
  if (readPerProcess == false) {
    // Redistribute nonzeros as needed to satisfy the Distribution
    // For most Distributions, this is a no-op
    if (useTimers) {
      timer = Teuchos::null;
      timer = rcp(new Teuchos::TimeMonitor(
          *Teuchos::TimeMonitor::getNewTimer("RSF redistribute")));
    }
 
    dist->Redistribute(localNZ);
  }
 
  if (useTimers) {
    timer = Teuchos::null;
    timer = rcp(new Teuchos::TimeMonitor(
        *Teuchos::TimeMonitor::getNewTimer("RSF nonzerosConstruction")));
  }
 
  //  Now construct the matrix.
  //  Count number of entries in each row for best use of StaticProfile
  if (verbose && me == 0)
    std::cout << std::endl
              << "Constructing the matrix" << std::endl;
 
  Teuchos::Array<global_ordinal_type> rowIdx;
  Teuchos::Array<size_t> nnzPerRow;
  Teuchos::Array<global_ordinal_type> colIdx;
  Teuchos::Array<scalar_type> val;
  Teuchos::Array<size_t> offsets;
 
  if (readPerProcess) {
    global_ordinal_type prevI = std::numeric_limits<global_ordinal_type>::max();
    for (size_t it = 0; it < nNz; it++) {
      global_ordinal_type I = buffer[2 * it] - 1;
      global_ordinal_type J = buffer[2 * it + 1] - 1;
      if (prevI != I) {
        prevI = I;
        rowIdx.push_back(I);
        nnzPerRow.push_back(0);
      }
      nnzPerRow.back()++;
      colIdx.push_back(J);
    }
    delete[] buffer;
  } else {
    // Exploit fact that map has entries sorted by I, then J
    global_ordinal_type prevI = std::numeric_limits<global_ordinal_type>::max();
    for (auto it = localNZ.begin(); it != localNZ.end(); it++) {
      global_ordinal_type I = it->first.first;
      global_ordinal_type J = it->first.second;
      scalar_type V         = it->second;
      if (prevI != I) {
        prevI = I;
        rowIdx.push_back(I);
        nnzPerRow.push_back(0);
      }
      nnzPerRow.back()++;
      colIdx.push_back(J);
      val.push_back(V);
    }
 
    // Done with localNZ map; free it.
    localNZmap_t().swap(localNZ);
  }
 
  // Compute prefix sum in offsets array
  offsets.resize(rowIdx.size() + 1);
  offsets[0] = 0;
  for (size_t row = 0; row < static_cast<size_t>(rowIdx.size()); row++)
    offsets[row + 1] = offsets[row] + nnzPerRow[row];
 
  if (useTimers) {
    timer = Teuchos::null;
    timer = rcp(new Teuchos::TimeMonitor(
        *Teuchos::TimeMonitor::getNewTimer("RSF insertNonzeros")));
  }
 
  // Create a new RowMap with only rows having non-zero entries.
  size_t dummy = Teuchos::OrdinalTraits<Tpetra::global_size_t>::invalid();
  Teuchos::RCP<const Tpetra::Map<> > rowMap =
      Teuchos::rcp(new Tpetra::Map<>(dummy, rowIdx(), 0, comm));
 
  Teuchos::RCP<sparse_matrix_type> A =
      rcp(new sparse_matrix_type(rowMap, nnzPerRow()));
 
  //  Insert the global values into the matrix row-by-row.
  if (verbose && me == 0)
    std::cout << "Inserting global values" << std::endl;
 
  if (readPerProcess) {
    const scalar_type ONE = Teuchos::ScalarTraits<scalar_type>::one();
    for (int i = 0; i < rowIdx.size(); i++) {
      size_t nnz = nnzPerRow[i];
      size_t off = offsets[i];
      val.assign(nnz, ONE);
      // ReadPerProcess routine does not read any numeric values from the file,
      // So we insert dummy values here.
      A->insertGlobalValues(rowIdx[i], colIdx(off, nnz), val());
    }
  } else {
    for (int i = 0; i < rowIdx.size(); i++) {
      size_t nnz = nnzPerRow[i];
      size_t off = offsets[i];
      A->insertGlobalValues(rowIdx[i], colIdx(off, nnz), val(off, nnz));
    }
  }
 
  // free memory that is no longer needed
  Teuchos::Array<size_t>().swap(nnzPerRow);
  Teuchos::Array<size_t>().swap(offsets);
  Teuchos::Array<global_ordinal_type>().swap(rowIdx);
  Teuchos::Array<global_ordinal_type>().swap(colIdx);
  Teuchos::Array<scalar_type>().swap(val);
 
  if (useTimers)
    timer = Teuchos::null;
 
  if (callFillComplete) {
    if (verbose && me == 0)
      std::cout << "Building vector maps" << std::endl;
 
    if (useTimers) {
      timer = Teuchos::null;
      timer = rcp(new Teuchos::TimeMonitor(
          *Teuchos::TimeMonitor::getNewTimer("RSF buildVectorMaps")));
    }
 
    // Build domain map that corresponds to distribution
    Teuchos::Array<global_ordinal_type> vectorSet;
    for (global_ordinal_type i = 0;
         i < static_cast<global_ordinal_type>(nCol); i++)
      if (dist->VecMine(i)) vectorSet.push_back(i);
 
    dummy = Teuchos::OrdinalTraits<Tpetra::global_size_t>::invalid();
    Teuchos::RCP<const Tpetra::Map<> > domainMap =
        Teuchos::rcp(new Tpetra::Map<>(dummy, vectorSet(), 0, comm));
 
    Teuchos::Array<global_ordinal_type>().swap(vectorSet);
 
    // Build range map that corresponds to distribution
    for (global_ordinal_type i = 0;
         i < static_cast<global_ordinal_type>(nRow); i++)
      if (dist->VecMine(i)) vectorSet.push_back(i);
 
    dummy = Teuchos::OrdinalTraits<Tpetra::global_size_t>::invalid();
    Teuchos::RCP<const Tpetra::Map<> > rangeMap =
        Teuchos::rcp(new Tpetra::Map<>(dummy, vectorSet(), 0, comm));
 
    Teuchos::Array<global_ordinal_type>().swap(vectorSet);
 
    // FillComplete the matrix
    if (useTimers) {
      timer = Teuchos::null;
      timer = rcp(new Teuchos::TimeMonitor(
          *Teuchos::TimeMonitor::getNewTimer("RSF fillComplete")));
    }
 
    if (verbose && me == 0)
      std::cout << "Calling fillComplete" << std::endl;
 
    A->fillComplete(domainMap, rangeMap);
 
    if (useTimers)
      timer = Teuchos::null;
 
    if (verbose) {
      std::cout << "\nRank " << A->getComm()->getRank()
                << "  nRows " << A->getLocalNumRows()
                << "  minRow " << A->getRowMap()->getMinGlobalIndex()
                << "  maxRow " << A->getRowMap()->getMaxGlobalIndex()
                << "\nRank " << A->getComm()->getRank()
                << "  nCols " << A->getLocalNumCols()
                << "  minCol " << A->getColMap()->getMinGlobalIndex()
                << "  maxCol " << A->getColMap()->getMaxGlobalIndex()
                << "\nRank " << A->getComm()->getRank()
                << "  nDomain " << A->getDomainMap()->getLocalNumElements()
                << "  minDomain " << A->getDomainMap()->getMinGlobalIndex()
                << "  maxDomain " << A->getDomainMap()->getMaxGlobalIndex()
                << "\nRank " << A->getComm()->getRank()
                << "  nRange " << A->getRangeMap()->getLocalNumElements()
                << "  minRange " << A->getRangeMap()->getMinGlobalIndex()
                << "  maxRange " << A->getRangeMap()->getMaxGlobalIndex()
                << "\nRank " << A->getComm()->getRank()
                << "  nEntries " << A->getLocalNumEntries()
                << std::endl;
    }
  }
 
  return A;
}
 
#endif