lpsolver 0.1.0 → 0.2.1

data/ext/lpsolver-highs/highs/ipm/hipo/factorhighs/Analyse.cpp

@@ -0,0 +1,1367 @@
+#include "Analyse.h"
+
+#include <algorithm>
+#include <fstream>
+#include <iostream>
+#include <limits>
+#include <random>
+#include <stack>
+
+#include "DataCollector.h"
+#include "FactorHiGHSSettings.h"
+#include "ReturnValues.h"
+#include "amd/amd.h"
+#include "ipm/hipo/auxiliary/Auxiliary.h"
+#include "ipm/hipo/auxiliary/Log.h"
+#include "metis/metis.h"
+#include "rcm/rcm.h"
+
+namespace hipo {
+
+const Int64 int32_limit = std::numeric_limits<int32_t>::max();
+const Int64 int64_limit = std::numeric_limits<int64_t>::max();
+
+Analyse::Analyse(const std::vector<Int>& rows, const std::vector<Int>& ptr,
+                 const std::vector<Int>& signs, Int nb, const Log* log,
+                 DataCollector& data, const std::vector<Int>& perm)
+    : log_{log}, data_{data} {
+  // Input the symmetric matrix to be analysed in CSC format.
+  // rows contains the row indices.
+  // ptr contains the starting points of each column.
+  // Only the lower triangular part is used.
+  // signs contains the sign that each pivot should have.
+
+  n_ = ptr.size() - 1;
+  nz_ = rows.size();
+  signs_ = signs;
+  nb_ = nb;
+
+  // Create upper triangular part
+  rows_upper_.resize(nz_);
+  ptr_upper_.resize(n_ + 1);
+  transpose(ptr, rows, ptr_upper_, rows_upper_);
+
+  // Permute the matrix with identical permutation, to extract upper triangular
+  // part, if the input is not lower triangular.
+  std::vector<Int> id_perm(n_);
+  for (Int i = 0; i < n_; ++i) id_perm[i] = i;
+  permute(id_perm);
+
+  // actual number of nonzeros of only upper triangular part
+  nz_ = ptr_upper_.back();
+
+  // number of nonzeros potentially changed after Permute.
+  rows_upper_.resize(nz_);
+
+  // double transpose to sort columns
+  ptr_lower_.resize(n_ + 1);
+  rows_lower_.resize(nz_);
+  transpose(ptr_upper_, rows_upper_, ptr_lower_, rows_lower_);
+  transpose(ptr_lower_, rows_lower_, ptr_upper_, rows_upper_);
+
+  perm_ = perm;
+  iperm_.resize(n_);
+  inversePerm(perm_, iperm_);
+
+  ready_ = true;
+}
+
+void Analyse::permute(const std::vector<Int>& iperm) {
+  // Symmetric permutation of the upper triangular matrix based on inverse
+  // permutation iperm.
+  // The resulting matrix is upper triangular, regardless of the input matrix.
+
+  std::vector<Int> work(n_, 0);
+
+  // go through the columns to count the nonzeros
+  for (Int j = 0; j < n_; ++j) {
+    // get new index of column
+    const Int col = iperm[j];
+
+    // go through elements of column
+    for (Int el = ptr_upper_[j]; el < ptr_upper_[j + 1]; ++el) {
+      const Int i = rows_upper_[el];
+
+      // ignore potential entries in lower triangular part
+      if (i > j) continue;
+
+      // get new index of row
+      const Int row = iperm[i];
+
+      // since only upper triangular part is used, col is larger than row
+      Int actual_col = std::max(row, col);
+      ++work[actual_col];
+    }
+  }
+
+  std::vector<Int> new_ptr(n_ + 1);
+
+  // get column pointers by summing the count of nonzeros in each column.
+  // copy column pointers into work
+  counts2Ptr(new_ptr, work);
+
+  std::vector<Int> new_rows(new_ptr.back());
+
+  // go through the columns to assign row indices
+  for (Int j = 0; j < n_; ++j) {
+    // get new index of column
+    const Int col = iperm[j];
+
+    // go through elements of column
+    for (Int el = ptr_upper_[j]; el < ptr_upper_[j + 1]; ++el) {
+      const Int i = rows_upper_[el];
+
+      // ignore potential entries in lower triangular part
+      if (i > j) continue;
+
+      // get new index of row
+      const Int row = iperm[i];
+
+      // since only upper triangular part is used, column is larger than row
+      const Int actual_col = std::max(row, col);
+      const Int actual_row = std::min(row, col);
+
+      Int pos = work[actual_col]++;
+      new_rows[pos] = actual_row;
+    }
+  }
+
+  ptr_upper_ = std::move(new_ptr);
+  rows_upper_ = std::move(new_rows);
+}
+
+void Analyse::eTree() {
+  // Find elimination tree.
+  // It works only for upper triangular matrices.
+  // The tree is stored in the vector parent:
+  //  parent[i] = j
+  // means that j is the parent of i in the tree.
+  // For the root(s) of the tree, parent[root] = -1.
+
+  parent_.resize(n_);
+  std::vector<Int> ancestor(n_);
+  Int next{};
+
+  for (Int j = 0; j < n_; ++j) {
+    // initialise parent and ancestor, which are still unknown
+    parent_[j] = -1;
+    ancestor[j] = -1;
+
+    for (Int el = ptr_upper_[j]; el < ptr_upper_[j + 1]; ++el) {
+      for (Int i = rows_upper_[el]; i != -1 && i < j; i = next) {
+        // next is used to move up the tree
+        next = ancestor[i];
+
+        // ancestor keeps track of the known part of the tree, to avoid
+        // repeating (aka path compression): from j there is a known path to i
+        ancestor[i] = j;
+
+        if (next == -1) parent_[i] = j;
+      }
+    }
+  }
+}
+
+void Analyse::postorder() {
+  // Find a postordering of the elimination tree using depth first search
+
+  postorder_.resize(n_);
+
+  // create linked list of children
+  std::vector<Int> head, next;
+  childrenLinkedList(parent_, head, next);
+
+  // Execute depth first search only for root node(s)
+  Int start{};
+  for (Int node = 0; node < n_; ++node) {
+    if (parent_[node] == -1) {
+      dfsPostorder(node, start, head, next, postorder_);
+    }
+  }
+
+  // Permute elimination tree based on postorder
+  std::vector<Int> ipost(n_);
+  inversePerm(postorder_, ipost);
+  std::vector<Int> new_parent(n_);
+  for (Int i = 0; i < n_; ++i) {
+    if (parent_[i] != -1) {
+      new_parent[ipost[i]] = ipost[parent_[i]];
+    } else {
+      new_parent[ipost[i]] = -1;
+    }
+  }
+  parent_ = std::move(new_parent);
+
+  // Permute matrix based on postorder
+  permute(ipost);
+
+  // double transpose to sort columns and compute lower part
+  transpose(ptr_upper_, rows_upper_, ptr_lower_, rows_lower_);
+  transpose(ptr_lower_, rows_lower_, ptr_upper_, rows_upper_);
+
+  // Update perm and iperm
+  permuteVector(perm_, postorder_);
+  inversePerm(perm_, iperm_);
+}
+
+void Analyse::colCount() {
+  // Columns count using skeleton matrix.
+  // Taken from Tim Davis "Direct Methods for Sparse Linear Systems".
+
+  std::vector<Int> first(n_, -1);
+  std::vector<Int> ancestor(n_, -1);
+  std::vector<Int> max_first(n_, -1);
+  std::vector<Int> prev_leaf(n_, -1);
+
+  col_count_.resize(n_);
+
+  // find first descendant
+  for (Int k = 0; k < n_; ++k) {
+    Int j = k;
+    col_count_[j] = (first[j] == -1) ? 1 : 0;
+    while (j != -1 && first[j] == -1) {
+      first[j] = k;
+      j = parent_[j];
+    }
+  }
+
+  // each node belongs to a separate set
+  for (Int j = 0; j < n_; j++) ancestor[j] = j;
+
+  for (Int k = 0; k < n_; ++k) {
+    const Int j = k;
+
+    // if not a root, decrement
+    if (parent_[j] != -1) col_count_[parent_[j]]--;
+
+    // process edges of matrix
+    for (Int el = ptr_lower_[j]; el < ptr_lower_[j + 1]; ++el) {
+      processEdge(j, rows_lower_[el], first, max_first, col_count_, prev_leaf,
+                  ancestor);
+    }
+
+    if (parent_[j] != -1) ancestor[j] = parent_[j];
+  }
+
+  // sum contributions from each child
+  for (Int j = 0; j < n_; ++j) {
+    if (parent_[j] != -1) {
+      col_count_[parent_[j]] += col_count_[j];
+    }
+  }
+
+  // compute nonzeros of L
+  dense_ops_norelax_ = 0.0;
+  nz_factor_ = 0;
+  for (Int j = 0; j < n_; ++j) {
+    nz_factor_ += col_count_[j];
+    dense_ops_norelax_ += (double)(col_count_[j] - 1) * (col_count_[j] - 1);
+  }
+}
+
+void Analyse::fundamentalSupernodes() {
+  // Find fundamental supernodes.
+
+  // isSN[i] is true if node i is the start of a fundamental supernode
+  std::vector<bool> is_sn(n_, false);
+
+  std::vector<Int> prev_nonz(n_, -1);
+
+  // compute sizes of subtrees
+  std::vector<Int> subtree_sizes(n_);
+  subtreeSize(parent_, subtree_sizes);
+
+  for (Int j = 0; j < n_; ++j) {
+    for (Int el = ptr_lower_[j]; el < ptr_lower_[j + 1]; ++el) {
+      const Int i = rows_lower_[el];
+      const Int k = prev_nonz[i];
+
+      // mark as fundamental sn, nodes which are leaf of subtrees
+      if (k < j - subtree_sizes[j] + 1) {
+        is_sn[j] = true;
+      }
+
+      // mark as fundamental sn, nodes which have more than one child
+      if (parent_[i] != -1 &&
+          subtree_sizes[i] + 1 != subtree_sizes[parent_[i]]) {
+        is_sn[parent_[i]] = true;
+      }
+
+      prev_nonz[i] = j;
+    }
+  }
+
+  // create information about fundamental supernodes
+  sn_belong_.resize(n_);
+  Int sn_number = -1;
+  for (Int i = 0; i < n_; ++i) {
+    // if isSN[i] is true, then node i is the start of a new supernode
+    if (is_sn[i]) ++sn_number;
+
+    // mark node i as belonging to the current supernode
+    sn_belong_[i] = sn_number;
+  }
+
+  // number of supernodes found
+  sn_count_ = sn_belong_.back() + 1;
+
+  // sn_start_ contains pointers to the starting node of each supernode
+  sn_start_.resize(sn_count_ + 1);
+  Int next = 0;
+  for (Int i = 0; i < n_; ++i) {
+    if (is_sn[i]) {
+      sn_start_[next] = i;
+      ++next;
+    }
+  }
+  sn_start_[next] = n_;
+
+  // build supernodal elimination tree
+  sn_parent_.resize(sn_count_);
+  for (Int i = 0; i < sn_count_ - 1; ++i) {
+    Int j = parent_[sn_start_[i + 1] - 1];
+    if (j != -1) {
+      sn_parent_[i] = sn_belong_[j];
+    } else {
+      sn_parent_[i] = -1;
+    }
+  }
+  sn_parent_.back() = -1;
+}
+
+void Analyse::relaxSupernodes() {
+  // Choose which strategy to use for supernode amalgamation.
+  // Relaxing supernodes is fast to run, so just run again the one that is
+  // chosen to set the correct information.
+
+  double flops_1{};
+  double spops_1{};
+  relaxSnMaxNz(flops_1, spops_1);
+  double ops_1 = flops_1 + kSpopsWeightSn * spops_1;
+
+  double flops_2{};
+  double spops_2{};
+  relaxSnNetOps(flops_2, spops_2);
+  double ops_2 = flops_2 + kSpopsWeightSn * spops_2;
+
+  bool total_ops_reduced = ops_2 < ops_1;
+  bool spops_reduced_enough = spops_2 < spops_1 * 0.6;
+
+  if (total_ops_reduced && spops_reduced_enough) {
+    relaxSnNetOps(flops_2, spops_2);
+  } else {
+    relaxSnMaxNz(flops_1, spops_1);
+  }
+}
+
+void Analyse::relaxSnNetOps(double& flops, double& spops) {
+  // =================================================
+  // Build information about supernodes
+  // =================================================
+  std::vector<Int> sn_size(sn_count_);
+  std::vector<Int> clique_size(sn_count_);
+  fake_nz_.assign(sn_count_, 0);
+  for (Int i = 0; i < sn_count_; ++i) {
+    sn_size[i] = sn_start_[i + 1] - sn_start_[i];
+    clique_size[i] = col_count_[sn_start_[i]] - sn_size[i];
+  }
+
+  // build linked lists of children
+  std::vector<Int> first_child, next_child;
+  childrenLinkedList(sn_parent_, first_child, next_child);
+
+  // =================================================
+  // Merge supernodes
+  // =================================================
+  merged_into_.assign(sn_count_, -1);
+  merged_sn_ = 0;
+
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    // sort children by increasing size
+    std::vector<Int> children;
+    Int child = first_child[sn];
+    while (child != -1) {
+      children.push_back(child);
+      child = next_child[child];
+    }
+    std::sort(children.begin(), children.end(),
+              [&](Int a, Int b) { return sn_size[a] < sn_size[b]; });
+
+    for (Int child : children) {
+      // how many zero rows would become nonzero
+      const Int rows_filled =
+          sn_size[sn] + clique_size[sn] - clique_size[child];
+
+      // how many zero entries would become nonzero
+      const Int64 nz_added = (Int64)rows_filled * sn_size[child];
+
+      // how many artificial nonzeros would the merged supernode have
+      const Int64 total_art_nz = nz_added + fake_nz_[sn] + fake_nz_[child];
+
+      const double flops_added =
+          rows_filled * rows_filled * sn_size[child] +
+          2 * rows_filled *
+              (sn_size[child] * (sn_size[child] + clique_size[child]) -
+               sn_size[child] * (sn_size[child] + 1) / 2);
+
+      const double spops_removed =
+          clique_size[child] * (clique_size[child] + 1) / 2;
+
+      const double net_ops = flops_added - kSpopsWeightSn * spops_removed;
+
+      if (net_ops < 0) {
+        // merge child with parent
+        sn_size[sn] += sn_size[child];
+        fake_nz_[sn] = total_art_nz;
+        ++merged_sn_;
+        merged_into_[child] = sn;
+      }
+    }
+  }
+
+  flops = 0.0;
+  spops = 0.0;
+  for (Int i = 0; i < sn_count_; ++i) {
+    if (merged_into_[i] == -1) {
+      spops += snSpops(clique_size[i]);
+      flops += snFlops(sn_size[i], clique_size[i]);
+    }
+  }
+}
+
+double Analyse::doRelaxSnMaxNz(double& flops, double& spops,
+                               Int64 max_artificial_nz) {
+  // =================================================
+  // Build information about supernodes
+  // =================================================
+  std::vector<Int> sn_size(sn_count_);
+  std::vector<Int> clique_size(sn_count_);
+  fake_nz_.assign(sn_count_, 0);
+  for (Int i = 0; i < sn_count_; ++i) {
+    sn_size[i] = sn_start_[i + 1] - sn_start_[i];
+    clique_size[i] = col_count_[sn_start_[i]] - sn_size[i];
+    fake_nz_[i] = 0;
+  }
+
+  // build linked lists of children
+  std::vector<Int> first_child, next_child;
+  childrenLinkedList(sn_parent_, first_child, next_child);
+
+  // =================================================
+  // Merge supernodes
+  // =================================================
+  merged_into_.assign(sn_count_, -1);
+  merged_sn_ = 0;
+
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    // keep iterating through the children of the supernode, until there's no
+    // more child to merge with
+
+    while (true) {
+      Int child = first_child[sn];
+
+      // info for first criterion
+      Int64 nz_fakenz = int64_limit;
+      Int size_fakenz = 0;
+      Int child_fakenz = -1;
+
+      while (child != -1) {
+        // how many zero rows would become nonzero
+        const Int rows_filled =
+            sn_size[sn] + clique_size[sn] - clique_size[child];
+
+        // how many zero entries would become nonzero
+        const Int64 nz_added = (Int64)rows_filled * sn_size[child];
+
+        // how many artificial nonzeros would the merged supernode have
+        const Int64 total_art_nz = nz_added + fake_nz_[sn] + fake_nz_[child];
+
+        // Save child with smallest number of artificial zeros created.
+        // Ties are broken based on size of child.
+        if (total_art_nz < nz_fakenz ||
+            (total_art_nz == nz_fakenz && size_fakenz < sn_size[child])) {
+          nz_fakenz = total_art_nz;
+          size_fakenz = sn_size[child];
+          child_fakenz = child;
+        }
+
+        child = next_child[child];
+      }
+
+      if (nz_fakenz <= max_artificial_nz) {
+        // merging creates fewer nonzeros than the maximum allowed
+
+        // update information of parent
+        sn_size[sn] += size_fakenz;
+        fake_nz_[sn] = nz_fakenz;
+
+        // count number of merged supernodes
+        ++merged_sn_;
+
+        // save information about merging of supernodes
+        merged_into_[child_fakenz] = sn;
+
+        // remove child from linked list of children
+        child = first_child[sn];
+        if (child == child_fakenz) {
+          // child_smallest is the first child
+          first_child[sn] = next_child[child_fakenz];
+        } else {
+          while (next_child[child] != child_fakenz) {
+            child = next_child[child];
+          }
+          // now child is the previous child of child_smallest
+          next_child[child] = next_child[child_fakenz];
+        }
+
+      } else {
+        // no more children can be merged with parent
+        break;
+      }
+    }
+  }
+
+  flops = 0.0;
+  spops = 0.0;
+  for (Int i = 0; i < sn_count_; ++i) {
+    if (merged_into_[i] == -1) {
+      spops += snSpops(clique_size[i]);
+      flops += snFlops(sn_size[i], clique_size[i]);
+    }
+  }
+
+  // compute total number of artificial nonzeros and artificial ops for this
+  // value of max_artificial_nz
+  double temp_art_nz{};
+  double temp_art_ops{};
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    if (merged_into_[sn] == -1) {
+      temp_art_nz += fake_nz_[sn];
+      temp_art_ops += snFlops(sn_size[sn], clique_size[sn]);
+    }
+  }
+  temp_art_ops -= dense_ops_norelax_;
+
+  // if enough fake nz or ops have been added, stop.
+  const double ratio_fake = temp_art_ops / (temp_art_ops + dense_ops_norelax_);
+
+  return ratio_fake;
+}
+
+void Analyse::relaxSnMaxNz(double& flops, double& spops) {
+  // Child which produces smallest number of fake nonzeros is merged if
+  // resulting sn has fewer than max_artificial_nz fake nonzeros.
+  // Multiple values of max_artificial_nz are tried, chosen with bisection
+  // method, until the percentage of artificial nonzeros is in the range [1,2]%.
+
+  Int64 max_artificial_nz = kStartThreshRelax;
+  Int64 largest_below = -1;
+  Int64 smallest_above = -1;
+
+  double best_dist_ratio = kHighsInf;
+  Int64 best_max_art_nz = -1;
+
+  for (Int iter = 0; iter < kMaxIterRelax; ++iter) {
+    // relax the supernodes and obtain the ratio of how many new ops have been
+    // added with the current value of max_artificial_nz
+    const double ratio_fake = doRelaxSnMaxNz(flops, spops, max_artificial_nz);
+
+    // store the best ratio, in case a good ratio is never found
+    double dist_ratio_fake = std::min(std::abs(ratio_fake - kLowerRatioRelax),
+                                      std::abs(ratio_fake - kUpperRatioRelax));
+    if (dist_ratio_fake < best_dist_ratio) {
+      best_dist_ratio = dist_ratio_fake;
+      best_max_art_nz = max_artificial_nz;
+    }
+
+    // try to find ratio in interval [0.01,0.02] using bisection
+    if (ratio_fake < kLowerRatioRelax) {
+      // ratio too small
+      largest_below = max_artificial_nz;
+      if (smallest_above == -1) {
+        max_artificial_nz *= 2;
+      } else {
+        max_artificial_nz = (largest_below + smallest_above) / 2;
+      }
+    } else if (ratio_fake > kUpperRatioRelax) {
+      // ratio too large
+      smallest_above = max_artificial_nz;
+      if (largest_below == -1) {
+        max_artificial_nz /= 2;
+      } else {
+        max_artificial_nz = (largest_below + smallest_above) / 2;
+      }
+    } else {
+      // good ratio
+      return;
+    }
+  }
+
+  // If reach here, no good ratio was found within kMaxIterRelax
+  // To avoid having a catastrophically bad ratio in pathological problems,
+  // choose the best ratio found
+
+  doRelaxSnMaxNz(flops, spops, best_max_art_nz);
+}
+
+void Analyse::afterRelaxSn() {
+  // number of new supernodes
+  const Int new_snCount = sn_count_ - merged_sn_;
+
+  // keep track of number of row indices needed for each supernode
+  sn_indices_.assign(new_snCount, 0);
+
+  // =================================================
+  // Create supernodal permutation
+  // =================================================
+
+  // permutation of supernodes needed after merging
+  std::vector<Int> sn_perm(sn_count_);
+
+  // number of new sn that includes the old sn
+  std::vector<Int> new_id(sn_count_);
+
+  // new sn pointer vector
+  std::vector<Int> new_snStart(new_snCount + 1);
+
+  // keep track of the children merged into a given supernode
+  std::vector<std::vector<Int>> received_from(sn_count_, std::vector<Int>());
+
+  // index to write into sn_perm
+  Int start_perm{};
+
+  // index to write into new_snStart
+  Int snStart_ind{};
+
+  // next available number for new sn numbering
+  Int next_id{};
+
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    if (merged_into_[sn] > -1) {
+      // Current sn was merged into its parent.
+      // Save information about which supernode sn was merged into
+      received_from[merged_into_[sn]].push_back(sn);
+    } else {
+      // Current sn was not merged into its parent.
+      // It is one of the new sn.
+
+      // Add merged supernodes to the permutation, recursively.
+
+      ++snStart_ind;
+
+      std::stack<Int> toadd;
+      toadd.push(sn);
+
+      while (!toadd.empty()) {
+        const Int current = toadd.top();
+
+        if (!received_from[current].empty()) {
+          for (Int i : received_from[current]) toadd.push(i);
+          received_from[current].clear();
+        } else {
+          toadd.pop();
+          sn_perm[start_perm++] = current;
+          new_id[current] = next_id;
+
+          // count number of nodes in each new supernode
+          new_snStart[snStart_ind] +=
+              sn_start_[current + 1] - sn_start_[current];
+        }
+      }
+
+      // keep track of total number of artificial nonzeros
+      artificial_nz_ += fake_nz_[sn];
+
+      // Compute number of indices for new sn.
+      // This is equal to the number of columns in the new sn plus the clique
+      // size of the original supernode where the children where merged.
+      sn_indices_[next_id] = new_snStart[snStart_ind] +
+                             col_count_[sn_start_[sn]] - sn_start_[sn + 1] +
+                             sn_start_[sn];
+
+      ++next_id;
+    }
+  }
+
+  // new_snStart contain the number of cols in each new sn.
+  // sum them to obtain the sn pointers.
+  for (Int i = 0; i < new_snCount; ++i) {
+    new_snStart[i + 1] += new_snStart[i];
+  }
+
+  // include artificial nonzeros in the nonzeros of the factor
+  nz_factor_ += artificial_nz_;
+
+  // compute number of flops needed for the factorisation
+  dense_ops_ = 0.0;
+  for (Int sn = 0; sn < new_snCount; ++sn) {
+    const double colcount_sn = (double)sn_indices_[sn];
+    for (Int i = 0; i < new_snStart[sn + 1] - new_snStart[sn]; ++i) {
+      dense_ops_ += (colcount_sn - i - 1) * (colcount_sn - i - 1);
+    }
+  }
+
+  // =================================================
+  // Create nodal permutation
+  // =================================================
+  // Given the supernodal permutation, find the nodal permutation needed after
+  // sn merging.
+
+  // permutation to apply to the existing one
+  std::vector<Int> new_perm(n_);
+
+  // index to write into new_perm
+  Int start{};
+
+  for (Int i = 0; i < sn_count_; ++i) {
+    const Int sn = sn_perm[i];
+    for (Int j = sn_start_[sn]; j < sn_start_[sn + 1]; ++j) {
+      new_perm[start++] = j;
+    }
+  }
+
+  // obtain inverse permutation
+  std::vector<Int> new_iperm(n_);
+  inversePerm(new_perm, new_iperm);
+
+  // =================================================
+  // Create new sn elimination tree
+  // =================================================
+  std::vector<Int> new_snParent(new_snCount, -1);
+  for (Int i = 0; i < sn_count_; ++i) {
+    if (sn_parent_[i] == -1) continue;
+
+    const Int ii = new_id[i];
+    const Int pp = new_id[sn_parent_[i]];
+
+    if (ii == pp) continue;
+
+    new_snParent[ii] = pp;
+  }
+
+  // =================================================
+  // Save new information
+  // =================================================
+
+  // build new snBelong, i.e., the sn to which each column belongs
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    for (Int i = sn_start_[sn]; i < sn_start_[sn + 1]; ++i) {
+      sn_belong_[i] = new_id[sn];
+    }
+  }
+  permuteVector(sn_belong_, new_perm);
+
+  permuteVector(col_count_, new_perm);
+
+  // Overwrite previous data
+  sn_parent_ = std::move(new_snParent);
+  sn_start_ = std::move(new_snStart);
+  sn_count_ = new_snCount;
+
+  // Permute matrix based on new permutation
+  permute(new_iperm);
+
+  // double transpose to sort columns and compute lower part
+  transpose(ptr_upper_, rows_upper_, ptr_lower_, rows_lower_);
+  transpose(ptr_lower_, rows_lower_, ptr_upper_, rows_upper_);
+
+  // Update perm and iperm
+  permuteVector(perm_, new_perm);
+  inversePerm(perm_, iperm_);
+}
+
+void Analyse::snPattern() {
+  // number of total indices needed
+  Int64 indices{};
+
+  for (Int64 i : sn_indices_) indices += i;
+
+  // allocate space for sn pattern
+  rows_sn_.resize(indices);
+  ptr_sn_.resize(sn_count_ + 1);
+
+  // keep track of visited supernodes
+  std::vector<Int> mark(sn_count_, -1);
+
+  // compute column pointers of L
+  std::vector<Int64> work(sn_indices_.size());
+  for (Int i = 0; i < static_cast<Int>(sn_indices_.size()); ++i)
+    work[i] = sn_indices_[i];
+  counts2Ptr(ptr_sn_, work);
+
+  // consider each row
+  for (Int i = 0; i < n_; ++i) {
+    // for all entries in the row of lower triangle
+    for (Int el = ptr_upper_[i]; el < ptr_upper_[i + 1]; ++el) {
+      // there is nonzero (i,j)
+      const Int j = rows_upper_[el];
+
+      // supernode to which column j belongs to
+      Int snj = sn_belong_[j];
+
+      // while supernodes are not yet considered
+      while (snj != -1 && mark[snj] != i) {
+        // we may end up too far
+        if (sn_start_[snj] > i) break;
+
+        // supernode snj is now considered for row i
+        mark[snj] = i;
+
+        // there is a nonzero entry in supernode snj at row i
+        rows_sn_[work[snj]++] = i;
+
+        // go up the elimination tree
+        snj = sn_parent_[snj];
+      }
+    }
+  }
+}
+
+void Analyse::relativeIndCols() {
+  // Find the relative indices of the original column wrt the frontal matrix of
+  // the corresponding supernode
+
+  relind_cols_.resize(nz_);
+
+  // go through the supernodes
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    const Int64 ptL_start = ptr_sn_[sn];
+    const Int64 ptL_end = ptr_sn_[sn + 1];
+
+    // go through the columns of the supernode
+    for (Int col = sn_start_[sn]; col < sn_start_[sn + 1]; ++col) {
+      // go through original column and supernodal column
+      Int ptA = ptr_lower_[col];
+      Int64 ptL = ptL_start;
+
+      // offset wrt ptrLower[col]
+      Int index{};
+
+      // size of the column of the original matrix
+      Int col_size = ptr_lower_[col + 1] - ptr_lower_[col];
+
+      while (ptL < ptL_end) {
+        // if found all the relative indices that are needed, stop
+        if (index == col_size) {
+          break;
+        }
+
+        // check if indices coincide
+        if (rows_sn_[ptL] == rows_lower_[ptA]) {
+          // yes: save relative index and move pointers forward
+          // NB: difference fits into Int
+          relind_cols_[ptr_lower_[col] + index] = ptL - ptL_start;
+          ++index;
+          ++ptL;
+          ++ptA;
+        } else {
+          // no: move pointer of L forward
+          ++ptL;
+        }
+      }
+    }
+  }
+}
+
+void Analyse::relativeIndClique() {
+  // Find the relative indices of the child clique wrt the frontal matrix of the
+  // parent supernode
+
+  relind_clique_.resize(sn_count_);
+  consecutive_sums_.resize(sn_count_);
+
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    // if there is no parent, skip supernode
+    if (sn_parent_[sn] == -1) continue;
+
+    // number of nodes in the supernode
+    const Int sn_size = sn_start_[sn + 1] - sn_start_[sn];
+
+    // column of the first node in the supernode
+    const Int j = sn_start_[sn];
+
+    // size of the first column of the supernode
+    const Int sn_column_size = ptr_sn_[sn + 1] - ptr_sn_[sn];
+
+    // size of the clique of the supernode
+    const Int sn_clique_size = sn_column_size - sn_size;
+
+    // count number of assembly operations during factorise
+    sparse_ops_ += snSpops(sn_clique_size);
+
+    relind_clique_[sn].resize(sn_clique_size);
+
+    // iterate through the clique of sn
+    Int64 ptr_current = ptr_sn_[sn] + sn_size;
+
+    // iterate through the full column of parent sn
+    Int64 ptr_parent = ptr_sn_[sn_parent_[sn]];
+
+    // keep track of start and end of parent sn column
+    const Int64 ptr_parent_start = ptr_parent;
+    const Int64 ptr_parent_end = ptr_sn_[sn_parent_[sn] + 1];
+
+    // where to write into relind
+    Int index{};
+
+    // iterate though the column of the parent sn
+    while (ptr_parent < ptr_parent_end) {
+      // if found all the relative indices that are needed, stop
+      if (index == sn_clique_size) {
+        break;
+      }
+
+      // check if indices coincide
+      if (rows_sn_[ptr_current] == rows_sn_[ptr_parent]) {
+        // yes: save relative index and move pointers forward
+        // NB: difference fits into Int
+        relind_clique_[sn][index] = ptr_parent - ptr_parent_start;
+        ++index;
+        ++ptr_parent;
+        ++ptr_current;
+      } else {
+        // no: move pointer of parent forward
+        ++ptr_parent;
+      }
+    }
+
+    // Difference between consecutive relative indices.
+    // Useful to detect chains of consecutive indices.
+    consecutive_sums_[sn].resize(sn_clique_size);
+    for (Int i = 0; i < sn_clique_size - 1; ++i) {
+      consecutive_sums_[sn][i] =
+          relind_clique_[sn][i + 1] - relind_clique_[sn][i];
+    }
+
+    // Number of consecutive sums that can be done in one blas call.
+    consecutive_sums_[sn].back() = 1;
+    for (Int i = sn_clique_size - 2; i >= 0; --i) {
+      if (consecutive_sums_[sn][i] > 1) {
+        consecutive_sums_[sn][i] = 1;
+      } else if (consecutive_sums_[sn][i] == 1) {
+        consecutive_sums_[sn][i] = consecutive_sums_[sn][i + 1] + 1;
+      } else {
+        if (log_) log_->printDevInfo("Error in consecutiveSums\n");
+      }
+    }
+  }
+}
+
+void Analyse::computeStorage(Int fr, Int sz, Int64& fr_entries,
+                             Int64& cl_entries) const {
+  // compute storage required by frontal and clique, based on the format used
+
+  const Int cl = fr - sz;
+
+  Int n_blocks = (sz - 1) / nb_ + 1;
+  std::vector<Int64> temp;
+  fr_entries = getDiagStart(fr, sz, nb_, n_blocks, temp);
+
+  // clique is stored as a collection of rectangles
+  n_blocks = (cl - 1) / nb_ + 1;
+  Int64 schur_size{};
+  for (Int j = 0; j < n_blocks; ++j) {
+    const Int jb = std::min(nb_, cl - j * nb_);
+    schur_size += (Int64)(cl - j * nb_) * jb;
+  }
+  cl_entries = schur_size;
+}
+
+void Analyse::computeCriticalPath() {
+  // Compute the critical path within the supernodal elimination tree, and the
+  // number of operations along the path. This is the number of operations that
+  // need to be done sequentially while doing tree parallelism.
+
+  std::vector<double> critical_ops(sn_count_);
+
+  // linked lists of children
+  std::vector<Int> head, next;
+  childrenLinkedList(sn_parent_, head, next);
+
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    // supernode size
+    const Int sz = sn_start_[sn + 1] - sn_start_[sn];
+
+    // frontal size
+    const Int fr = ptr_sn_[sn + 1] - ptr_sn_[sn];
+
+    critical_ops[sn] = snFlops(sz, fr - sz);
+  }
+
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    // leaf nodes
+    if (head[sn] == -1) continue;
+
+    double max_ops{};
+    Int child = head[sn];
+    while (child != -1) {
+      // critical_ops of this supernode is max over children of
+      // (ops_of_this_sn + critical_ops_of_child)
+      max_ops = std::max(max_ops, critical_ops[sn] + critical_ops[child]);
+      child = next[child];
+    }
+    critical_ops[sn] = max_ops;
+  }
+
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    critical_ops_ = std::max(critical_ops_, critical_ops[sn]);
+  }
+}
+
+void Analyse::reorderChildren() {
+  std::vector<Int64> clique_entries(sn_count_);
+  std::vector<Int64> frontal_entries(sn_count_);
+  std::vector<double> storage(sn_count_);
+  std::vector<double> storage_factors(sn_count_);
+
+  // initialise data of supernodes
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    // supernode size
+    const Int sz = sn_start_[sn + 1] - sn_start_[sn];
+
+    // frontal size
+    const Int fr = col_count_[sn_start_[sn]];
+
+    // compute storage based on format used
+    computeStorage(fr, sz, frontal_entries[sn], clique_entries[sn]);
+
+    // compute number of entries in factors within the subtree
+    storage_factors[sn] += frontal_entries[sn];
+    if (sn_parent_[sn] != -1)
+      storage_factors[sn_parent_[sn]] += storage_factors[sn];
+  }
+
+  // linked lists of children
+  std::vector<Int> head, next;
+  childrenLinkedList(sn_parent_, head, next);
+
+  // go through the supernodes
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    // leaf node
+    if (head[sn] == -1) {
+      storage[sn] = frontal_entries[sn] + clique_entries[sn];
+      continue;
+    }
+
+    // save children and values to sort
+    std::vector<std::pair<Int, double>> children{};
+    Int child = head[sn];
+    while (child != -1) {
+      double value =
+          storage[child] - clique_entries[child] - storage_factors[child];
+      children.push_back({child, value});
+      child = next[child];
+    }
+
+    // sort children in decreasing order of the values
+    std::sort(children.begin(), children.end(),
+              [&](std::pair<Int, double>& a, std::pair<Int, double>& b) {
+                return a.second > b.second;
+              });
+
+    // modify linked lists with new order of children
+    head[sn] = children.front().first;
+    for (Int i = 0; i < static_cast<Int>(children.size()) - 1; ++i) {
+      next[children[i].first] = children[i + 1].first;
+    }
+    next[children.back().first] = -1;
+  }
+
+  // =================================================
+  // Create supernodal permutation
+  // =================================================
+  // build supernodal permutation with dfs
+  std::vector<Int> sn_perm(sn_count_);
+  Int start{};
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    if (sn_parent_[sn] == -1) dfsPostorder(sn, start, head, next, sn_perm);
+  }
+
+  // =================================================
+  // Create nodal permutation
+  // =================================================
+  // Given the supernodal permutation, find the nodal permutation
+
+  // permutation to apply to the existing one
+  std::vector<Int> new_perm(n_);
+
+  // index to write into new_perm
+  start = 0;
+
+  for (Int i = 0; i < sn_count_; ++i) {
+    const Int sn = sn_perm[i];
+    for (Int j = sn_start_[sn]; j < sn_start_[sn + 1]; ++j) {
+      new_perm[start++] = j;
+    }
+  }
+
+  // obtain inverse permutation
+  std::vector<Int> new_iperm(n_);
+  inversePerm(new_perm, new_iperm);
+
+  // =================================================
+  // Create new sn elimination tree
+  // =================================================
+  std::vector<Int> isn_perm(sn_count_);
+  inversePerm(sn_perm, isn_perm);
+  std::vector<Int> new_sn_parent(sn_count_);
+  for (Int i = 0; i < sn_count_; ++i) {
+    if (sn_parent_[i] != -1) {
+      new_sn_parent[isn_perm[i]] = isn_perm[sn_parent_[i]];
+    } else {
+      new_sn_parent[isn_perm[i]] = -1;
+    }
+  }
+
+  // =================================================
+  // Create new snBelong
+  // =================================================
+
+  // build new snBelong, i.e., the sn to which each colum belongs
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    for (Int i = sn_start_[sn]; i < sn_start_[sn + 1]; ++i) {
+      sn_belong_[i] = isn_perm[sn];
+    }
+  }
+  permuteVector(sn_belong_, new_perm);
+
+  // permute other vectors that may be needed
+  permuteVector(col_count_, new_perm);
+  permuteVector(sn_indices_, sn_perm);
+
+  // =================================================
+  // Create new snStart
+  // =================================================
+  std::vector<Int> cols_per_sn(sn_count_);
+
+  // compute size of each supernode
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    cols_per_sn[sn] = sn_start_[sn + 1] - sn_start_[sn];
+  }
+
+  // permute according to new order of supernodes
+  permuteVector(cols_per_sn, sn_perm);
+
+  // sum number of columns to obtain pointers
+  for (Int i = 0; i < sn_count_ - 1; ++i) {
+    cols_per_sn[i + 1] += cols_per_sn[i];
+  }
+
+  for (Int i = 0; i < sn_count_; ++i) {
+    sn_start_[i + 1] = cols_per_sn[i];
+  }
+
+  // =================================================
+  // Save new data
+  // =================================================
+
+  // Overwrite previous data
+  sn_parent_ = std::move(new_sn_parent);
+
+  // Permute matrix based on new permutation
+  permute(new_iperm);
+
+  // double transpose to sort columns and compute lower part
+  transpose(ptr_upper_, rows_upper_, ptr_lower_, rows_lower_);
+  transpose(ptr_lower_, rows_lower_, ptr_upper_, rows_upper_);
+
+  // Update perm and iperm
+  permuteVector(perm_, new_perm);
+  inversePerm(perm_, iperm_);
+}
+
+void Analyse::computeBlockStart() {
+  clique_block_start_.resize(sn_count_);
+  // compute starting position of each block of columns in the clique, for
+  // each supernode
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    const Int sn_size = sn_start_[sn + 1] - sn_start_[sn];
+    const Int ldf = ptr_sn_[sn + 1] - ptr_sn_[sn];
+    const Int ldc = ldf - sn_size;
+    const Int n_blocks = (ldc - 1) / nb_ + 1;
+
+    Int64 schur_size =
+        getDiagStart(ldc, ldc, nb_, n_blocks, clique_block_start_[sn]);
+    clique_block_start_[sn].push_back(schur_size);
+  }
+}
+
+Int Analyse::checkOverflow() const {
+  // In order to use 32-bit BLAS, any data accessed by BLAS must be addressable
+  // using 32-bit integer offset. If BLAS is given a pointer double* A, the
+  // distance between the first and last entry of A used by BLAS needs to be
+  // smaller than int32_limit. Since the matrices are stored in blocked data
+  // structures, and BLAS only uses contiguous data from a given block of
+  // columns, we need to impose that:
+  //   front_size * min(block_size, sn_size) <= int32_limit
+
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    const Int sn_size = sn_start_[sn + 1] - sn_start_[sn];
+    const Int front_size = ptr_sn_[sn + 1] - ptr_sn_[sn];
+
+    if ((Int64)front_size * std::min(sn_size, nb_) > int32_limit) return 1;
+  }
+
+  return 0;
+}
+
+void Analyse::computeStackSize() {
+  // Compute the minimum size of the stack to process the elimination tree
+  // serially.
+
+  std::vector<Int64> clique_entries(sn_count_);
+  std::vector<Int64> stack_subtrees(sn_count_);
+  Int64 total_frontal{};
+
+  // initialise data of supernodes
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    // supernode size
+    const Int sz = sn_start_[sn + 1] - sn_start_[sn];
+
+    // frontal size
+    const Int fr = ptr_sn_[sn + 1] - ptr_sn_[sn];
+
+    Int64 frontal_entries{};
+
+    // compute storage based on format used
+    computeStorage(fr, sz, frontal_entries, clique_entries[sn]);
+
+    total_frontal += frontal_entries;
+  }
+
+  // linked lists of children
+  std::vector<Int> head, next;
+  childrenLinkedList(sn_parent_, head, next);
+
+  // go through the supernodes
+  for (Int sn = 0; sn < sn_count_; ++sn) {
+    // leaf node
+    if (head[sn] == -1) {
+      stack_subtrees[sn] = clique_entries[sn];
+      continue;
+    }
+
+    // Compute storage
+    // storage is found as max(storage_1,storage_2), where
+    // storage_1 = max_j stack_size[j] + \sum_{k up to j-1} clique_entries[k]
+    // storage_2 = clique_total_entries (including node itself)
+
+    Int64 clique_partial_entries{};
+    Int64 storage_1{};
+
+    Int child = head[sn];
+    while (child != -1) {
+      Int64 current = stack_subtrees[child] + clique_partial_entries;
+
+      clique_partial_entries += clique_entries[child];
+      storage_1 = std::max(storage_1, current);
+
+      child = next[child];
+    }
+
+    Int64 storage_2 = clique_partial_entries + clique_entries[sn];
+
+    stack_subtrees[sn] = std::max(storage_1, storage_2);
+    max_stack_size_ = std::max(max_stack_size_, stack_subtrees[sn]);
+  }
+
+  // minimum storage in serial is equal to the space needed to store the
+  // factorisation and the maximum size of the stack. Times 8 to obtain the
+  // number of bytes.
+  serial_storage_ = (total_frontal + max_stack_size_) * 8;
+}
+
+Int Analyse::run(Symbolic& S) {
+  // Perform analyse phase and store the result into the symbolic object S.
+  // After Run returns, the Analyse object is not valid.
+
+  if (!ready_) return kRetGeneric;
+
+  HIPO_CLOCK_CREATE;
+
+  HIPO_CLOCK_START(2);
+  permute(iperm_);
+  eTree();
+  postorder();
+  HIPO_CLOCK_STOP(2, data_, kTimeAnalyseTree);
+
+  HIPO_CLOCK_START(2);
+  colCount();
+  HIPO_CLOCK_STOP(2, data_, kTimeAnalyseCount);
+
+  HIPO_CLOCK_START(2);
+  fundamentalSupernodes();
+  relaxSupernodes();
+  afterRelaxSn();
+  HIPO_CLOCK_STOP(2, data_, kTimeAnalyseSn);
+
+  HIPO_CLOCK_START(2);
+  reorderChildren();
+  HIPO_CLOCK_STOP(2, data_, kTimeAnalyseReorder);
+
+  HIPO_CLOCK_START(2);
+  snPattern();
+  HIPO_CLOCK_STOP(2, data_, kTimeAnalysePattern);
+
+  HIPO_CLOCK_START(2);
+  relativeIndCols();
+  relativeIndClique();
+  HIPO_CLOCK_STOP(2, data_, kTimeAnalyseRelInd);
+
+  computeBlockStart();
+  computeCriticalPath();
+  computeStackSize();
+
+  // move relevant stuff into S
+  S.n_ = n_;
+  S.sn_ = sn_count_;
+  S.nz_ = nz_factor_;
+  S.fillin_ = (double)nz_factor_ / nz_;
+  S.artificial_nz_ = artificial_nz_;
+  S.artificial_ops_ = dense_ops_ - dense_ops_norelax_;
+  S.spops_ = sparse_ops_;
+  S.critops_ = critical_ops_;
+  S.largest_front_ = *std::max_element(sn_indices_.begin(), sn_indices_.end());
+  S.serial_storage_ = serial_storage_;
+  S.flops_ = dense_ops_;
+  S.block_size_ = nb_;
+  S.max_stack_size_ = max_stack_size_;
+  S.tree_depth_ = maxDepthTree(sn_parent_);
+
+  // compute largest supernode
+  std::vector<Int> sn_size(sn_start_.begin() + 1, sn_start_.end());
+  for (Int i = sn_count_ - 1; i > 0; --i) sn_size[i] -= sn_size[i - 1];
+  S.largest_sn_ = *std::max_element(sn_size.begin(), sn_size.end());
+
+  // build statistics about supernodes size
+  for (Int i : sn_size) {
+    if (i == 1) S.sn_size_1_++;
+    if (i <= 10) S.sn_size_10_++;
+    if (i <= 100) S.sn_size_100_++;
+  }
+
+  if (checkOverflow()) {
+    if (log_) log_->printe("Integer overflow in analyse phase\n");
+    return kRetIntOverflow;
+  }
+
+  // permute signs of pivots
+  S.pivot_sign_ = std::move(signs_);
+  permuteVector(S.pivot_sign_, perm_);
+
+  S.iperm_ = std::move(iperm_);
+  S.rows_ = std::move(rows_sn_);
+  S.ptr_ = std::move(ptr_sn_);
+  S.sn_parent_ = std::move(sn_parent_);
+  S.sn_start_ = std::move(sn_start_);
+  S.relind_cols_ = std::move(relind_cols_);
+  S.relind_clique_ = std::move(relind_clique_);
+  S.consecutive_sums_ = std::move(consecutive_sums_);
+  S.clique_block_start_ = std::move(clique_block_start_);
+
+  HIPO_CLOCK_STOP(1, data_, kTimeAnalyse);
+
+  return kRetOk;
+}
+
+}  // namespace hipo