sequenzo 0.1.18__cp39-cp39-macosx_10_9_universal2.whl → 0.1.19__cp39-cp39-macosx_10_9_universal2.whl

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_column_dfs.h

@@ -1,179 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-/* 
- 
- * NOTE: This file is the modified version of [s,d,c,z]column_dfs.c file in SuperLU 
- 
- * -- SuperLU routine (version 2.0) --
- * Univ. of California Berkeley, Xerox Palo Alto Research Center,
- * and Lawrence Berkeley National Lab.
- * November 15, 1997
- *
- * Copyright (c) 1994 by Xerox Corporation.  All rights reserved.
- *
- * THIS MATERIAL IS PROVIDED AS IS, WITH ABSOLUTELY NO WARRANTY
- * EXPRESSED OR IMPLIED.  ANY USE IS AT YOUR OWN RISK.
- *
- * Permission is hereby granted to use or copy this program for any
- * purpose, provided the above notices are retained on all copies.
- * Permission to modify the code and to distribute modified code is
- * granted, provided the above notices are retained, and a notice that
- * the code was modified is included with the above copyright notice.
- */
-#ifndef SPARSELU_COLUMN_DFS_H
-#define SPARSELU_COLUMN_DFS_H
-
-template <typename Scalar, typename StorageIndex> class SparseLUImpl;
-namespace Eigen {
-
-namespace internal {
-
-template<typename IndexVector, typename ScalarVector>
-struct column_dfs_traits : no_assignment_operator
-{
-  typedef typename ScalarVector::Scalar Scalar;
-  typedef typename IndexVector::Scalar StorageIndex;
-  column_dfs_traits(Index jcol, Index& jsuper, typename SparseLUImpl<Scalar, StorageIndex>::GlobalLU_t& glu, SparseLUImpl<Scalar, StorageIndex>& luImpl)
-   : m_jcol(jcol), m_jsuper_ref(jsuper), m_glu(glu), m_luImpl(luImpl)
- {}
-  bool update_segrep(Index /*krep*/, Index /*jj*/)
-  {
-    return true;
-  }
-  void mem_expand(IndexVector& lsub, Index& nextl, Index chmark)
-  {
-    if (nextl >= m_glu.nzlmax)
-      m_luImpl.memXpand(lsub, m_glu.nzlmax, nextl, LSUB, m_glu.num_expansions); 
-    if (chmark != (m_jcol-1)) m_jsuper_ref = emptyIdxLU;
-  }
-  enum { ExpandMem = true };
-  
-  Index m_jcol;
-  Index& m_jsuper_ref;
-  typename SparseLUImpl<Scalar, StorageIndex>::GlobalLU_t& m_glu;
-  SparseLUImpl<Scalar, StorageIndex>& m_luImpl;
-};
-
-
-/**
- * \brief Performs a symbolic factorization on column jcol and decide the supernode boundary
- * 
- * A supernode representative is the last column of a supernode.
- * The nonzeros in U[*,j] are segments that end at supernodes representatives. 
- * The routine returns a list of the supernodal representatives 
- * in topological order of the dfs that generates them. 
- * The location of the first nonzero in each supernodal segment 
- * (supernodal entry location) is also returned. 
- * 
- * \param m number of rows in the matrix
- * \param jcol Current column 
- * \param perm_r Row permutation
- * \param maxsuper  Maximum number of column allowed in a supernode
- * \param [in,out] nseg Number of segments in current U[*,j] - new segments appended
- * \param lsub_col defines the rhs vector to start the dfs
- * \param [in,out] segrep Segment representatives - new segments appended 
- * \param repfnz  First nonzero location in each row
- * \param xprune 
- * \param marker  marker[i] == jj, if i was visited during dfs of current column jj;
- * \param parent
- * \param xplore working array
- * \param glu global LU data 
- * \return 0 success
- *         > 0 number of bytes allocated when run out of space
- * 
- */
-template <typename Scalar, typename StorageIndex>
-Index SparseLUImpl<Scalar,StorageIndex>::column_dfs(const Index m, const Index jcol, IndexVector& perm_r, Index maxsuper, Index& nseg,
-                                                    BlockIndexVector lsub_col, IndexVector& segrep, BlockIndexVector repfnz, IndexVector& xprune,
-                                                    IndexVector& marker, IndexVector& parent, IndexVector& xplore, GlobalLU_t& glu)
-{
-  
-  Index jsuper = glu.supno(jcol); 
-  Index nextl = glu.xlsub(jcol); 
-  VectorBlock<IndexVector> marker2(marker, 2*m, m); 
-  
-  
-  column_dfs_traits<IndexVector, ScalarVector> traits(jcol, jsuper, glu, *this);
-  
-  // For each nonzero in A(*,jcol) do dfs 
-  for (Index k = 0; ((k < m) ? lsub_col[k] != emptyIdxLU : false) ; k++)
-  {
-    Index krow = lsub_col(k); 
-    lsub_col(k) = emptyIdxLU; 
-    Index kmark = marker2(krow); 
-    
-    // krow was visited before, go to the next nonz; 
-    if (kmark == jcol) continue;
-    
-    dfs_kernel(StorageIndex(jcol), perm_r, nseg, glu.lsub, segrep, repfnz, xprune, marker2, parent,
-                   xplore, glu, nextl, krow, traits);
-  } // for each nonzero ... 
-  
-  Index fsupc;
-  StorageIndex nsuper = glu.supno(jcol);
-  StorageIndex jcolp1 = StorageIndex(jcol) + 1;
-  Index jcolm1 = jcol - 1;
-  
-  // check to see if j belongs in the same supernode as j-1
-  if ( jcol == 0 )
-  { // Do nothing for column 0 
-    nsuper = glu.supno(0) = 0 ;
-  }
-  else 
-  {
-    fsupc = glu.xsup(nsuper); 
-    StorageIndex jptr = glu.xlsub(jcol); // Not yet compressed
-    StorageIndex jm1ptr = glu.xlsub(jcolm1); 
-    
-    // Use supernodes of type T2 : see SuperLU paper
-    if ( (nextl-jptr != jptr-jm1ptr-1) ) jsuper = emptyIdxLU;
-    
-    // Make sure the number of columns in a supernode doesn't
-    // exceed threshold
-    if ( (jcol - fsupc) >= maxsuper) jsuper = emptyIdxLU; 
-    
-    /* If jcol starts a new supernode, reclaim storage space in
-     * glu.lsub from previous supernode. Note we only store 
-     * the subscript set of the first and last columns of 
-     * a supernode. (first for num values, last for pruning)
-     */
-    if (jsuper == emptyIdxLU)
-    { // starts a new supernode 
-      if ( (fsupc < jcolm1-1) ) 
-      { // >= 3 columns in nsuper
-        StorageIndex ito = glu.xlsub(fsupc+1);
-        glu.xlsub(jcolm1) = ito; 
-        StorageIndex istop = ito + jptr - jm1ptr; 
-        xprune(jcolm1) = istop; // initialize xprune(jcol-1)
-        glu.xlsub(jcol) = istop; 
-        
-        for (StorageIndex ifrom = jm1ptr; ifrom < nextl; ++ifrom, ++ito)
-          glu.lsub(ito) = glu.lsub(ifrom); 
-        nextl = ito;  // = istop + length(jcol)
-      }
-      nsuper++; 
-      glu.supno(jcol) = nsuper; 
-    } // if a new supernode 
-  } // end else:  jcol > 0
-  
-  // Tidy up the pointers before exit
-  glu.xsup(nsuper+1) = jcolp1; 
-  glu.supno(jcolp1) = nsuper; 
-  xprune(jcol) = StorageIndex(nextl);  // Initialize upper bound for pruning
-  glu.xlsub(jcolp1) = StorageIndex(nextl); 
-  
-  return 0; 
-}
-
-} // end namespace internal
-
-} // end namespace Eigen
-
-#endif

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_copy_to_ucol.h

@@ -1,107 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-/* 
- 
- * NOTE: This file is the modified version of [s,d,c,z]copy_to_ucol.c file in SuperLU 
- 
- * -- SuperLU routine (version 2.0) --
- * Univ. of California Berkeley, Xerox Palo Alto Research Center,
- * and Lawrence Berkeley National Lab.
- * November 15, 1997
- *
- * Copyright (c) 1994 by Xerox Corporation.  All rights reserved.
- *
- * THIS MATERIAL IS PROVIDED AS IS, WITH ABSOLUTELY NO WARRANTY
- * EXPRESSED OR IMPLIED.  ANY USE IS AT YOUR OWN RISK.
- *
- * Permission is hereby granted to use or copy this program for any
- * purpose, provided the above notices are retained on all copies.
- * Permission to modify the code and to distribute modified code is
- * granted, provided the above notices are retained, and a notice that
- * the code was modified is included with the above copyright notice.
- */
-#ifndef SPARSELU_COPY_TO_UCOL_H
-#define SPARSELU_COPY_TO_UCOL_H
-
-namespace Eigen {
-namespace internal {
-
-/**
- * \brief Performs numeric block updates (sup-col) in topological order
- * 
- * \param jcol current column to update
- * \param nseg Number of segments in the U part
- * \param segrep segment representative ...
- * \param repfnz First nonzero column in each row  ...
- * \param perm_r Row permutation 
- * \param dense Store the full representation of the column
- * \param glu Global LU data. 
- * \return 0 - successful return 
- *         > 0 - number of bytes allocated when run out of space
- * 
- */
-template <typename Scalar, typename StorageIndex>
-Index SparseLUImpl<Scalar,StorageIndex>::copy_to_ucol(const Index jcol, const Index nseg, IndexVector& segrep,
-                                                      BlockIndexVector repfnz ,IndexVector& perm_r, BlockScalarVector dense, GlobalLU_t& glu)
-{  
-  Index ksub, krep, ksupno; 
-    
-  Index jsupno = glu.supno(jcol);
-  
-  // For each nonzero supernode segment of U[*,j] in topological order 
-  Index k = nseg - 1, i; 
-  StorageIndex nextu = glu.xusub(jcol); 
-  Index kfnz, isub, segsize; 
-  Index new_next,irow; 
-  Index fsupc, mem; 
-  for (ksub = 0; ksub < nseg; ksub++)
-  {
-    krep = segrep(k); k--; 
-    ksupno = glu.supno(krep); 
-    if (jsupno != ksupno ) // should go into ucol(); 
-    {
-      kfnz = repfnz(krep); 
-      if (kfnz != emptyIdxLU)
-      { // Nonzero U-segment 
-        fsupc = glu.xsup(ksupno); 
-        isub = glu.xlsub(fsupc) + kfnz - fsupc; 
-        segsize = krep - kfnz + 1; 
-        new_next = nextu + segsize; 
-        while (new_next > glu.nzumax) 
-        {
-          mem = memXpand<ScalarVector>(glu.ucol, glu.nzumax, nextu, UCOL, glu.num_expansions); 
-          if (mem) return mem; 
-          mem = memXpand<IndexVector>(glu.usub, glu.nzumax, nextu, USUB, glu.num_expansions); 
-          if (mem) return mem; 
-          
-        }
-        
-        for (i = 0; i < segsize; i++)
-        {
-          irow = glu.lsub(isub); 
-          glu.usub(nextu) = perm_r(irow); // Unlike the L part, the U part is stored in its final order
-          glu.ucol(nextu) = dense(irow); 
-          dense(irow) = Scalar(0.0); 
-          nextu++;
-          isub++;
-        }
-        
-      } // end nonzero U-segment 
-      
-    } // end if jsupno 
-    
-  } // end for each segment
-  glu.xusub(jcol + 1) = nextu; // close U(*,jcol)
-  return 0; 
-}
-
-} // namespace internal
-} // end namespace Eigen
-
-#endif // SPARSELU_COPY_TO_UCOL_H

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_gemm_kernel.h

@@ -1,280 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Gael Guennebaud <gael.guennebaud@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-#ifndef EIGEN_SPARSELU_GEMM_KERNEL_H
-#define EIGEN_SPARSELU_GEMM_KERNEL_H
-
-namespace Eigen {
-
-namespace internal {
-
-
-/** \internal
-  * A general matrix-matrix product kernel optimized for the SparseLU factorization.
-  *  - A, B, and C must be column major
-  *  - lda and ldc must be multiples of the respective packet size
-  *  - C must have the same alignment as A
-  */
-template<typename Scalar>
-EIGEN_DONT_INLINE
-void sparselu_gemm(Index m, Index n, Index d, const Scalar* A, Index lda, const Scalar* B, Index ldb, Scalar* C, Index ldc)
-{
-  using namespace Eigen::internal;
-  
-  typedef typename packet_traits<Scalar>::type Packet;
-  enum {
-    NumberOfRegisters = EIGEN_ARCH_DEFAULT_NUMBER_OF_REGISTERS,
-    PacketSize = packet_traits<Scalar>::size,
-    PM = 8,                             // peeling in M
-    RN = 2,                             // register blocking
-    RK = NumberOfRegisters>=16 ? 4 : 2, // register blocking
-    BM = 4096/sizeof(Scalar),           // number of rows of A-C per chunk
-    SM = PM*PacketSize                  // step along M
-  };
-  Index d_end = (d/RK)*RK;    // number of columns of A (rows of B) suitable for full register blocking
-  Index n_end = (n/RN)*RN;    // number of columns of B-C suitable for processing RN columns at once
-  Index i0 = internal::first_default_aligned(A,m);
-  
-  eigen_internal_assert(((lda%PacketSize)==0) && ((ldc%PacketSize)==0) && (i0==internal::first_default_aligned(C,m)));
-  
-  // handle the non aligned rows of A and C without any optimization:
-  for(Index i=0; i<i0; ++i)
-  {
-    for(Index j=0; j<n; ++j)
-    {
-      Scalar c = C[i+j*ldc];
-      for(Index k=0; k<d; ++k)
-        c += B[k+j*ldb] * A[i+k*lda];
-      C[i+j*ldc] = c;
-    }
-  }
-  // process the remaining rows per chunk of BM rows
-  for(Index ib=i0; ib<m; ib+=BM)
-  {
-    Index actual_b = std::min<Index>(BM, m-ib);                 // actual number of rows
-    Index actual_b_end1 = (actual_b/SM)*SM;                   // actual number of rows suitable for peeling
-    Index actual_b_end2 = (actual_b/PacketSize)*PacketSize;   // actual number of rows suitable for vectorization
-    
-    // Let's process two columns of B-C at once
-    for(Index j=0; j<n_end; j+=RN)
-    {
-      const Scalar* Bc0 = B+(j+0)*ldb;
-      const Scalar* Bc1 = B+(j+1)*ldb;
-      
-      for(Index k=0; k<d_end; k+=RK)
-      {
-        
-        // load and expand a RN x RK block of B
-        Packet b00, b10, b20, b30, b01, b11, b21, b31;
-                  { b00 = pset1<Packet>(Bc0[0]); }
-                  { b10 = pset1<Packet>(Bc0[1]); }
-        if(RK==4) { b20 = pset1<Packet>(Bc0[2]); }
-        if(RK==4) { b30 = pset1<Packet>(Bc0[3]); }
-                  { b01 = pset1<Packet>(Bc1[0]); }
-                  { b11 = pset1<Packet>(Bc1[1]); }
-        if(RK==4) { b21 = pset1<Packet>(Bc1[2]); }
-        if(RK==4) { b31 = pset1<Packet>(Bc1[3]); }
-        
-        Packet a0, a1, a2, a3, c0, c1, t0, t1;
-        
-        const Scalar* A0 = A+ib+(k+0)*lda;
-        const Scalar* A1 = A+ib+(k+1)*lda;
-        const Scalar* A2 = A+ib+(k+2)*lda;
-        const Scalar* A3 = A+ib+(k+3)*lda;
-        
-        Scalar* C0 = C+ib+(j+0)*ldc;
-        Scalar* C1 = C+ib+(j+1)*ldc;
-        
-                  a0 = pload<Packet>(A0);
-                  a1 = pload<Packet>(A1);
-        if(RK==4)
-        {
-          a2 = pload<Packet>(A2);
-          a3 = pload<Packet>(A3);
-        }
-        else
-        {
-          // workaround "may be used uninitialized in this function" warning
-          a2 = a3 = a0;
-        }
-        
-#define KMADD(c, a, b, tmp) {tmp = b; tmp = pmul(a,tmp); c = padd(c,tmp);}
-#define WORK(I)  \
-                     c0 = pload<Packet>(C0+i+(I)*PacketSize);    \
-                     c1 = pload<Packet>(C1+i+(I)*PacketSize);    \
-                     KMADD(c0, a0, b00, t0)                      \
-                     KMADD(c1, a0, b01, t1)                      \
-                     a0 = pload<Packet>(A0+i+(I+1)*PacketSize);  \
-                     KMADD(c0, a1, b10, t0)                      \
-                     KMADD(c1, a1, b11, t1)                      \
-                     a1 = pload<Packet>(A1+i+(I+1)*PacketSize);  \
-          if(RK==4){ KMADD(c0, a2, b20, t0)                     }\
-          if(RK==4){ KMADD(c1, a2, b21, t1)                     }\
-          if(RK==4){ a2 = pload<Packet>(A2+i+(I+1)*PacketSize); }\
-          if(RK==4){ KMADD(c0, a3, b30, t0)                     }\
-          if(RK==4){ KMADD(c1, a3, b31, t1)                     }\
-          if(RK==4){ a3 = pload<Packet>(A3+i+(I+1)*PacketSize); }\
-                     pstore(C0+i+(I)*PacketSize, c0);            \
-                     pstore(C1+i+(I)*PacketSize, c1)
-        
-        // process rows of A' - C' with aggressive vectorization and peeling 
-        for(Index i=0; i<actual_b_end1; i+=PacketSize*8)
-        {
-          EIGEN_ASM_COMMENT("SPARSELU_GEMML_KERNEL1");
-                    prefetch((A0+i+(5)*PacketSize));
-                    prefetch((A1+i+(5)*PacketSize));
-          if(RK==4) prefetch((A2+i+(5)*PacketSize));
-          if(RK==4) prefetch((A3+i+(5)*PacketSize));
-
-          WORK(0);
-          WORK(1);
-          WORK(2);
-          WORK(3);
-          WORK(4);
-          WORK(5);
-          WORK(6);
-          WORK(7);
-        }
-        // process the remaining rows with vectorization only
-        for(Index i=actual_b_end1; i<actual_b_end2; i+=PacketSize)
-        {
-          WORK(0);
-        }
-#undef WORK
-        // process the remaining rows without vectorization
-        for(Index i=actual_b_end2; i<actual_b; ++i)
-        {
-          if(RK==4)
-          {
-            C0[i] += A0[i]*Bc0[0]+A1[i]*Bc0[1]+A2[i]*Bc0[2]+A3[i]*Bc0[3];
-            C1[i] += A0[i]*Bc1[0]+A1[i]*Bc1[1]+A2[i]*Bc1[2]+A3[i]*Bc1[3];
-          }
-          else
-          {
-            C0[i] += A0[i]*Bc0[0]+A1[i]*Bc0[1];
-            C1[i] += A0[i]*Bc1[0]+A1[i]*Bc1[1];
-          }
-        }
-        
-        Bc0 += RK;
-        Bc1 += RK;
-      } // peeled loop on k
-    } // peeled loop on the columns j
-    // process the last column (we now perform a matrix-vector product)
-    if((n-n_end)>0)
-    {
-      const Scalar* Bc0 = B+(n-1)*ldb;
-      
-      for(Index k=0; k<d_end; k+=RK)
-      {
-        
-        // load and expand a 1 x RK block of B
-        Packet b00, b10, b20, b30;
-                  b00 = pset1<Packet>(Bc0[0]);
-                  b10 = pset1<Packet>(Bc0[1]);
-        if(RK==4) b20 = pset1<Packet>(Bc0[2]);
-        if(RK==4) b30 = pset1<Packet>(Bc0[3]);
-        
-        Packet a0, a1, a2, a3, c0, t0/*, t1*/;
-        
-        const Scalar* A0 = A+ib+(k+0)*lda;
-        const Scalar* A1 = A+ib+(k+1)*lda;
-        const Scalar* A2 = A+ib+(k+2)*lda;
-        const Scalar* A3 = A+ib+(k+3)*lda;
-        
-        Scalar* C0 = C+ib+(n_end)*ldc;
-        
-                  a0 = pload<Packet>(A0);
-                  a1 = pload<Packet>(A1);
-        if(RK==4)
-        {
-          a2 = pload<Packet>(A2);
-          a3 = pload<Packet>(A3);
-        }
-        else
-        {
-          // workaround "may be used uninitialized in this function" warning
-          a2 = a3 = a0;
-        }
-        
-#define WORK(I) \
-                   c0 = pload<Packet>(C0+i+(I)*PacketSize);     \
-                   KMADD(c0, a0, b00, t0)                       \
-                   a0 = pload<Packet>(A0+i+(I+1)*PacketSize);   \
-                   KMADD(c0, a1, b10, t0)                       \
-                   a1 = pload<Packet>(A1+i+(I+1)*PacketSize);   \
-        if(RK==4){ KMADD(c0, a2, b20, t0)                      }\
-        if(RK==4){ a2 = pload<Packet>(A2+i+(I+1)*PacketSize);  }\
-        if(RK==4){ KMADD(c0, a3, b30, t0)                      }\
-        if(RK==4){ a3 = pload<Packet>(A3+i+(I+1)*PacketSize);  }\
-                   pstore(C0+i+(I)*PacketSize, c0);
-        
-        // aggressive vectorization and peeling
-        for(Index i=0; i<actual_b_end1; i+=PacketSize*8)
-        {
-          EIGEN_ASM_COMMENT("SPARSELU_GEMML_KERNEL2");
-          WORK(0);
-          WORK(1);
-          WORK(2);
-          WORK(3);
-          WORK(4);
-          WORK(5);
-          WORK(6);
-          WORK(7);
-        }
-        // vectorization only
-        for(Index i=actual_b_end1; i<actual_b_end2; i+=PacketSize)
-        {
-          WORK(0);
-        }
-        // remaining scalars
-        for(Index i=actual_b_end2; i<actual_b; ++i)
-        {
-          if(RK==4) 
-            C0[i] += A0[i]*Bc0[0]+A1[i]*Bc0[1]+A2[i]*Bc0[2]+A3[i]*Bc0[3];
-          else
-            C0[i] += A0[i]*Bc0[0]+A1[i]*Bc0[1];
-        }
-        
-        Bc0 += RK;
-#undef WORK
-      }
-    }
-    
-    // process the last columns of A, corresponding to the last rows of B
-    Index rd = d-d_end;
-    if(rd>0)
-    {
-      for(Index j=0; j<n; ++j)
-      {
-        enum {
-          Alignment = PacketSize>1 ? Aligned : 0
-        };
-        typedef Map<Matrix<Scalar,Dynamic,1>, Alignment > MapVector;
-        typedef Map<const Matrix<Scalar,Dynamic,1>, Alignment > ConstMapVector;
-        if(rd==1)       MapVector(C+j*ldc+ib,actual_b) += B[0+d_end+j*ldb] * ConstMapVector(A+(d_end+0)*lda+ib, actual_b);
-        
-        else if(rd==2)  MapVector(C+j*ldc+ib,actual_b) += B[0+d_end+j*ldb] * ConstMapVector(A+(d_end+0)*lda+ib, actual_b)
-                                                        + B[1+d_end+j*ldb] * ConstMapVector(A+(d_end+1)*lda+ib, actual_b);
-        
-        else            MapVector(C+j*ldc+ib,actual_b) += B[0+d_end+j*ldb] * ConstMapVector(A+(d_end+0)*lda+ib, actual_b)
-                                                        + B[1+d_end+j*ldb] * ConstMapVector(A+(d_end+1)*lda+ib, actual_b)
-                                                        + B[2+d_end+j*ldb] * ConstMapVector(A+(d_end+2)*lda+ib, actual_b);
-      }
-    }
-  
-  } // blocking on the rows of A and C
-}
-#undef KMADD
-
-} // namespace internal
-
-} // namespace Eigen
-
-#endif // EIGEN_SPARSELU_GEMM_KERNEL_H

sequenzo/dissimilarity_measures/src/eigen/Eigen/src/SparseLU/SparseLU_heap_relax_snode.h

@@ -1,126 +0,0 @@
-// This file is part of Eigen, a lightweight C++ template library
-// for linear algebra.
-//
-// Copyright (C) 2012 Désiré Nuentsa-Wakam <desire.nuentsa_wakam@inria.fr>
-//
-// This Source Code Form is subject to the terms of the Mozilla
-// Public License v. 2.0. If a copy of the MPL was not distributed
-// with this file, You can obtain one at http://mozilla.org/MPL/2.0/.
-
-/* This file is a modified version of heap_relax_snode.c file in SuperLU
- * -- SuperLU routine (version 3.0) --
- * Univ. of California Berkeley, Xerox Palo Alto Research Center,
- * and Lawrence Berkeley National Lab.
- * October 15, 2003
- *
- * Copyright (c) 1994 by Xerox Corporation.  All rights reserved.
- *
- * THIS MATERIAL IS PROVIDED AS IS, WITH ABSOLUTELY NO WARRANTY
- * EXPRESSED OR IMPLIED.  ANY USE IS AT YOUR OWN RISK.
- *
- * Permission is hereby granted to use or copy this program for any
- * purpose, provided the above notices are retained on all copies.
- * Permission to modify the code and to distribute modified code is
- * granted, provided the above notices are retained, and a notice that
- * the code was modified is included with the above copyright notice.
- */
-
-#ifndef SPARSELU_HEAP_RELAX_SNODE_H
-#define SPARSELU_HEAP_RELAX_SNODE_H
-
-namespace Eigen {
-namespace internal {
-
-/** 
- * \brief Identify the initial relaxed supernodes
- * 
- * This routine applied to a symmetric elimination tree. 
- * It assumes that the matrix has been reordered according to the postorder of the etree
- * \param n The number of columns
- * \param et elimination tree 
- * \param relax_columns Maximum number of columns allowed in a relaxed snode 
- * \param descendants Number of descendants of each node in the etree
- * \param relax_end last column in a supernode
- */
-template <typename Scalar, typename StorageIndex>
-void SparseLUImpl<Scalar,StorageIndex>::heap_relax_snode (const Index n, IndexVector& et, const Index relax_columns, IndexVector& descendants, IndexVector& relax_end)
-{
-  
-  // The etree may not be postordered, but its heap ordered  
-  IndexVector post;
-  internal::treePostorder(StorageIndex(n), et, post); // Post order etree
-  IndexVector inv_post(n+1); 
-  for (StorageIndex i = 0; i < n+1; ++i) inv_post(post(i)) = i; // inv_post = post.inverse()???
-  
-  // Renumber etree in postorder 
-  IndexVector iwork(n);
-  IndexVector et_save(n+1);
-  for (Index i = 0; i < n; ++i)
-  {
-    iwork(post(i)) = post(et(i));
-  }
-  et_save = et; // Save the original etree
-  et = iwork; 
-  
-  // compute the number of descendants of each node in the etree
-  relax_end.setConstant(emptyIdxLU);
-  Index j, parent; 
-  descendants.setZero();
-  for (j = 0; j < n; j++) 
-  {
-    parent = et(j);
-    if (parent != n) // not the dummy root
-      descendants(parent) += descendants(j) + 1;
-  }
-  // Identify the relaxed supernodes by postorder traversal of the etree
-  Index snode_start; // beginning of a snode 
-  StorageIndex k;
-  Index nsuper_et_post = 0; // Number of relaxed snodes in postordered etree 
-  Index nsuper_et = 0; // Number of relaxed snodes in the original etree 
-  StorageIndex l; 
-  for (j = 0; j < n; )
-  {
-    parent = et(j);
-    snode_start = j; 
-    while ( parent != n && descendants(parent) < relax_columns ) 
-    {
-      j = parent; 
-      parent = et(j);
-    }
-    // Found a supernode in postordered etree, j is the last column 
-    ++nsuper_et_post;
-    k = StorageIndex(n);
-    for (Index i = snode_start; i <= j; ++i)
-      k = (std::min)(k, inv_post(i));
-    l = inv_post(j);
-    if ( (l - k) == (j - snode_start) )  // Same number of columns in the snode
-    {
-      // This is also a supernode in the original etree
-      relax_end(k) = l; // Record last column 
-      ++nsuper_et; 
-    }
-    else 
-    {
-      for (Index i = snode_start; i <= j; ++i) 
-      {
-        l = inv_post(i);
-        if (descendants(i) == 0) 
-        {
-          relax_end(l) = l;
-          ++nsuper_et;
-        }
-      }
-    }
-    j++;
-    // Search for a new leaf
-    while (descendants(j) != 0 && j < n) j++;
-  } // End postorder traversal of the etree
-  
-  // Recover the original etree
-  et = et_save; 
-}
-
-} // end namespace internal
-
-} // end namespace Eigen
-#endif // SPARSELU_HEAP_RELAX_SNODE_H