Actual source code: ex231.cxx
1: static char help[] = "A test for MatAssembly that heavily relies on PetscSortIntWithArrayPair\n";
3: /*
4: The characteristic of the array (about 4M in length) to sort in this test is that it has
5: many duplicated values that already clustered together (around 95 duplicates per unique integer).
7: It was gotten from a petsc performance bug report from the Moose project. One can use
8: it for future performance study.
10: Contributed-by: Fande Kong <fdkong.jd@gmail.com>, John Peterson <jwpeterson@gmail.com>
11: */
13: // PETSc includes
14: #include <petscmat.h>
16: // C++ includes
17: #include <iostream>
18: #include <fstream>
19: #include <sstream>
20: #include <algorithm>
21: #include <vector>
22: #include <string>
23: #include <set>
25: int main (int argc, char** argv)
26: {
28: PetscMPIInt size, rank;
29: char file[2][PETSC_MAX_PATH_LEN];
30: PetscBool flg;
31: const unsigned int n_dofs = 26559;
32: unsigned int first_local_index;
33: unsigned int last_local_index;
35: PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
36: MPI_Comm_size(PETSC_COMM_WORLD,&size);
37: MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
38: if (size > 2) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This example is for <=2 procs");
40: PetscOptionsGetString(NULL,NULL,"-f0",file[0],sizeof(file[0]),&flg);
41: if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Must indicate dof indices file for rank 0 with -f0 option");
42: if (size == 2) {
43: PetscOptionsGetString(NULL,NULL,"-f1",file[1],sizeof(file[1]),&flg);
44: if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"Must indicate dof indices file for rank 1 with -f1 option");
45: }
47: if (size == 1) {
48: first_local_index = 0;
49: last_local_index = 26559;
50: } else {
51: if (rank == 0) {
52: first_local_index = 0;
53: last_local_index = 13911;
54: } else {
55: first_local_index = 13911;
56: last_local_index = 26559;
57: }
58: }
60: // Read element dof indices from files
61: std::vector<std::vector<std::vector<PetscInt> > > elem_dof_indices(size);
62: for (PetscInt proc_id = 0; proc_id < size; ++proc_id) {
63: std::string line;
64: std::ifstream dof_file(file[proc_id]);
65: if (dof_file.good()) {
66: while (std::getline (dof_file,line)) {
67: std::vector<PetscInt> dof_indices;
68: std::stringstream sstream(line);
69: std::string token;
70: while (std::getline(sstream, token, ' ')) {dof_indices.push_back(std::atoi(token.c_str()));}
71: elem_dof_indices[proc_id].push_back(dof_indices);
72: }
73: } else SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_FILE_OPEN,"Could not open file %s",file[proc_id]);
74: }
76: // Debugging: Verify we read in elem_dof_indices correctly
77: // for (unsigned int i=0; i<elem_dof_indices.size(); ++i)
78: // {
79: // for (unsigned int j=0; j<elem_dof_indices[i].size(); ++j)
80: // {
81: // for (unsigned int k=0; k<elem_dof_indices[i][j].size(); ++k)
82: // std::cout << elem_dof_indices[i][j][k] << " ";
83: // std::cout << std::endl;
84: // }
85: // std::cout << std::endl;
86: // }
88: // Set up the (global) sparsity pattern
89: std::vector< std::set< unsigned int > > sparsity(n_dofs);
90: for (PetscInt proc_id = 0; proc_id < size; ++proc_id)
91: for (unsigned int k = 0; k < elem_dof_indices[proc_id].size(); k++) {
92: std::vector<PetscInt>& dof_indices = elem_dof_indices[proc_id][k];
93: for (unsigned int i = 0; i < dof_indices.size(); ++i)
94: for (unsigned int j = 0; j < dof_indices.size(); ++j)
95: sparsity[dof_indices[i]].insert(dof_indices[j]);
96: }
98: // Determine the local nonzeros on this processor
99: const unsigned int n_local_dofs = last_local_index - first_local_index;
100: std::vector<PetscInt> n_nz(n_local_dofs);
101: std::vector<PetscInt> n_oz(n_local_dofs);
103: for (unsigned int i = 0; i < n_local_dofs; ++i) {
104: for (std::set<unsigned int>::iterator iter = sparsity[i+first_local_index].begin(); iter != sparsity[i+first_local_index].end(); iter++) {
105: unsigned int dof = *iter;
106: if ((dof >= first_local_index) && (dof < last_local_index)) n_nz[i]++;
107: else n_oz[i]++;
108: }
109: }
111: // Debugging: print number of on/off diagonal nonzeros
112: // for (unsigned int i=0; i<n_nz.size(); ++i)
113: // std::cout << n_nz[i] << " ";
114: // std::cout << std::endl;
116: // for (unsigned int i=0; i<n_oz.size(); ++i)
117: // std::cout << n_oz[i] << " ";
118: // std::cout << std::endl;
120: // Compute and print max number of on- and off-diagonal nonzeros.
121: PetscInt n_nz_max = *std::max_element(n_nz.begin(), n_nz.end());
122: PetscInt n_oz_max = *std::max_element(n_oz.begin(), n_oz.end());
124: PetscSynchronizedPrintf(PETSC_COMM_WORLD, "Max on-diagonal non-zeros: = %d\n", n_nz_max);
125: PetscSynchronizedPrintf(PETSC_COMM_WORLD, "Max off-diagonal non-zeros: = %d\n", n_oz_max);
126: PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);
128: // Initialize the matrix similar to what we do in the PetscMatrix
129: // ctor and init() routines.
130: Mat mat;
131: MatCreate(PETSC_COMM_WORLD, &mat);
132: MatSetSizes(mat, n_local_dofs, n_local_dofs, n_dofs, n_dofs);
133: MatSetBlockSize(mat, 1);
134: MatSetType(mat, MATAIJ); // Automatically chooses seqaij or mpiaij
135: MatSeqAIJSetPreallocation(mat, 0, &n_nz[0]);
136: MatMPIAIJSetPreallocation(mat, 0, &n_nz[0], 0, &n_oz[0]);
137: MatSetOption(mat, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE);
139: // Local "element" loop
140: for (unsigned int k = 0; k < elem_dof_indices[rank].size(); k++) {
141: std::vector<PetscInt>& dof_indices = elem_dof_indices[rank][k];
142: // DenseMatrix< Number > zero_mat( dof_indices.size(), dof_indices.size());
143: // B.add_matrix( zero_mat, dof_indices);
144: std::vector<PetscScalar> ones(dof_indices.size() * dof_indices.size(), 1.);
145: MatSetValues(mat, dof_indices.size(), &dof_indices[0], dof_indices.size(), &dof_indices[0], &ones[0], ADD_VALUES);
146: }
148: // Matrix assembly
149: MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);
150: MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);
152: // Clean up
153: MatDestroy(&mat);
154: PetscFinalize();
155: return ierr;
156: }
157: /*TEST
158: build:
159: requires: !defined(PETSC_HAVE_SUN_CXX)
161: test:
162: nsize: 2
163: args: -f0 ${DATAFILESPATH}/meshes/moose_dof_indices_np_2_proc_0.txt -f1 ${DATAFILESPATH}/meshes/moose_dof_indices_np_2_proc_1.txt
164: # Skip the test for Sun C++ compiler because of its warnings/errors in petscmat.h
165: requires: datafilespath
167: TEST*/