diff src/PETSc_factory.cc @ 256:8fe68d94ab76

Add parallel assembly of matrices and vectors
author Eugenio Gianniti <eugenio.gianniti@mail.polimi.it>
date Wed, 30 Jul 2014 20:59:37 +0200
parents b1dc98050634
children 61830a4f9ab9
line wrap: on
line diff
--- a/src/PETSc_factory.cc	Wed Jul 30 18:09:13 2014 +0200
+++ b/src/PETSc_factory.cc	Wed Jul 30 20:59:37 2014 +0200
@@ -16,6 +16,10 @@
 */
 
 #include "PETSc_factory.h"
+#ifdef LATEST_DOLFIN
+#include <boost/mpi.hpp>
+#include <boost/serialization/vector.hpp>
+#endif
 
 femfenics_base_factory const&
 PETSc_factory::instance (void)
@@ -29,25 +33,17 @@
   {
     octave_value retval;
 
-    std::size_t nr = A.size (0), nc = A.size (1);
-
-    dim_vector dims (0, 1);
-    Array <octave_idx_type> 
-      ridx (dims, 0), 
-      cidx (dims, 0);
-    Array<double> data (dims, 0);
+    unsigned const size =
+#ifdef LATEST_DOLFIN
+      dolfin::MPI::size (MPI_COMM_WORLD);
+#else
+      dolfin::MPI::num_processes ();
+#endif
 
-    for (std::size_t i = 0; i < nr; ++i)
-      {
-        std::vector <double> data_tmp;
-        std::vector <std::size_t> cidx_tmp;
-        A.getrow (i, cidx_tmp, data_tmp);
-        std::vector <std::size_t> ridx_tmp (cidx_tmp.size (), i);
-        add_to_arrays (ridx, cidx, data, ridx_tmp, cidx_tmp, data_tmp);
-      }
-
-    SparseMatrix sm (data, ridx, cidx, nr, nc);
-    retval = sm;
+    if (size > 1)
+      retval = do_matrix_parallel (A);
+    else
+      retval = do_matrix_serial (A);
 
     return retval;
   }
@@ -57,16 +53,17 @@
   {
     octave_value retval;
 
-    dim_vector dims;
-    dims.resize (2);
-    dims(0) = b.size ();
-    dims(1) = 1;
-    Array <double> myb (dims);
+    unsigned const size =
+#ifdef LATEST_DOLFIN
+      dolfin::MPI::size (MPI_COMM_WORLD);
+#else
+      dolfin::MPI::num_processes ();
+#endif
 
-    for (std::size_t i = 0; i < b.size (); ++i)
-      myb.xelem (i) = b[i];
-
-    retval = myb;
+    if (size > 1)
+      retval = do_vector_parallel (b);
+    else
+      retval = do_vector_serial (b);
 
     return retval;
   }
@@ -107,4 +104,157 @@
       }
 
     return;
-  }
\ No newline at end of file
+  }
+
+octave_value
+PETSc_factory::do_matrix_serial (dolfin::Matrix const& A) const
+  {
+    octave_value retval;
+
+    std::size_t nr = A.size (0), nc = A.size (1);
+
+    dim_vector dims (0, 1);
+    Array <octave_idx_type> 
+      ridx (dims, 0), 
+      cidx (dims, 0);
+    Array<double> data (dims, 0);
+
+    for (std::size_t i = 0; i < nr; ++i)
+      {
+        std::vector <double> data_tmp;
+        std::vector <std::size_t> cidx_tmp;
+        A.getrow (i, cidx_tmp, data_tmp);
+        std::vector <std::size_t> ridx_tmp (cidx_tmp.size (), i);
+        add_to_arrays (ridx, cidx, data, ridx_tmp, cidx_tmp, data_tmp);
+      }
+
+    SparseMatrix sm (data, ridx, cidx, nr, nc);
+    retval = sm;
+
+    return retval;
+  }
+
+octave_value
+PETSc_factory::do_matrix_parallel (dolfin::Matrix const& A) const
+  {
+    octave_value retval;
+
+    std::vector <std::size_t> rows, cols;
+    std::vector <double> vals;
+    std::size_t const nrows = A.size (0), ncols = A.size (1);
+
+    std::pair <std::size_t, std::size_t> const range = A.local_range (0);
+    for (std::size_t i = range.first; i < range.second; ++i)
+      {
+        std::vector <std::size_t> cols_tmp;
+        std::vector <double> vals_tmp;
+        A.getrow (i, cols_tmp, vals_tmp);
+        cols.insert (cols.end (), cols_tmp.begin (), cols_tmp.end ());
+        vals.insert (vals.end (), vals_tmp.begin (), vals_tmp.end ());
+        for (std::size_t j = 0; j < cols_tmp.size (); ++j)
+          rows.push_back (i);
+      }
+
+    boost::mpi::communicator world;
+
+    unsigned const size = world.size ();
+    unsigned const rank = world.rank ();
+
+    for (unsigned p = 1; p < size; ++p)
+      {
+        if (rank == p)
+          {
+            unsigned const tag = 3*(p-1);
+            world.send (0, tag, rows);
+            world.send (0, tag+1, cols);
+            world.send (0, tag+2, vals);
+          }
+      }
+
+    if (rank == 0)
+      {
+        dim_vector dims (0, 1);
+        Array <octave_idx_type> ridx (dims, 0), cidx (dims, 0);
+        Array <double> data (dims, 0);
+        add_to_arrays (ridx, cidx, data, rows, cols, vals);
+
+        for (unsigned p = 1; p < size; ++p)
+          {
+            std::vector <double> new_vals;
+            std::vector <std::size_t> new_rows, new_cols;
+            unsigned const tag = 3*(p-1);
+
+            world.recv (p, tag, new_rows);
+            world.recv (p, tag+1, new_cols);
+            world.recv (p, tag+2, new_vals);
+
+            add_to_arrays (ridx, cidx, data, new_rows, new_cols, new_vals);
+          }
+
+        SparseMatrix sm (data, ridx, cidx, nrows, ncols);
+        retval = sm;
+      }
+    else
+      // Return an identity matrix just to avoid warnings or errors
+      {
+        dim_vector dims (nrows, 1);
+        Array <octave_idx_type> ridx (dims), cidx (dims);
+        Array <double> data (dims, 1);
+
+        for (std::size_t i = 0; i < nrows; ++i)
+          {
+            ridx.xelem (i) = i;
+            cidx.xelem (i) = i;
+          }
+
+        SparseMatrix sm (data, ridx, cidx, nrows, ncols);
+        retval = sm;
+      }
+
+    return retval;
+  }
+
+octave_value
+PETSc_factory::do_vector_serial (dolfin::Vector const& b) const
+  {
+    octave_value retval;
+
+    dim_vector dims;
+    dims.resize (2);
+    dims(0) = b.size ();
+    dims(1) = 1;
+    Array <double> myb (dims);
+
+    for (std::size_t i = 0; i < b.size (); ++i)
+      myb.xelem (i) = b[i];
+
+    retval = myb;
+
+    return retval;
+  }
+
+octave_value
+PETSc_factory::do_vector_parallel (dolfin::Vector const& b) const
+  {
+    octave_value retval;
+
+    std::size_t const length = b.size ();
+    dim_vector dims (length, 1);
+    Array <double> vec (dims, 0);
+
+    std::vector <double> entries;
+    b.gather_on_zero (entries);
+
+#ifdef LATEST_DOLFIN
+    if (dolfin::MPI::rank (MPI_COMM_WORLD) == 0)
+#else
+    if (dolfin::MPI::process_number () == 0)
+#endif
+      for (std::size_t i = 0; i < length; ++i)
+        vec.xelem (i) = entries[i];
+
+    // On nodes other than zero, return an all zero vector of the right length
+    retval = vec;
+
+    return retval;
+  }