ColPack
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00001 // An example of Column compression and recovery for Jacobian 00002 /* How to compile this driver manually: 00003 Please make sure that "baseDir" point to the directory (folder) containing the input matrix file, and 00004 s_InputFile should point to the input file that you want to use 00005 To compile the code, replace the Main.cpp file in Main directory with this file 00006 and run "make" in ColPack installation directory. Make will generate "ColPack.exe" executable 00007 Run "ColPack.exe" 00008 00009 Note: If you got "symbol lookup error ... undefined symbol " 00010 Please make sure that your LD_LIBRARY_PATH contains libColPack.so 00011 00012 Return by recovery routine: three vectors in "Storage Formats for the Direct Sparse Solvers" 00013 http://www.intel.com/software/products/mkl/docs/webhelp/appendices/mkl_appA_SMSF.html#mkl_appA_SMSF_1 00014 unsigned int** ip2_RowIndex 00015 unsigned int** ip2_ColumnIndex 00016 double** dp2_JacobianValue // corresponding non-zero values 00017 //*/ 00018 00019 #include "ColPackHeaders.h" 00020 00021 using namespace ColPack; 00022 using namespace std; 00023 00024 #ifndef TOP_DIR 00025 #define TOP_DIR "." 00026 #endif 00027 00028 // baseDir should point to the directory (folder) containing the input file 00029 string baseDir=TOP_DIR; 00030 00031 #include "extra.h" //This .h file contains functions that are used in the below examples: 00032 //ReadMM(), MatrixMultiplication...(), Times2Plus1point5(), displayMatrix() and displayCompressedRowMatrix() 00033 00034 int main() 00035 { 00036 // s_InputFile = baseDir + <name of the input file> 00037 string s_InputFile; //path of the input file 00038 s_InputFile = baseDir; 00039 s_InputFile += DIR_SEPARATOR; s_InputFile += "Graphs"; s_InputFile += DIR_SEPARATOR; s_InputFile += "column-compress.mtx"; 00040 00041 // Step 1: Determine sparsity structure of the Jacobian. 00042 // This step is done by an AD tool. For the purpose of illustration here, we read the structure from a file, 00043 // and store the structure in a Compressed Row Format. 00044 unsigned int *** uip3_SparsityPattern = new unsigned int **; //uip3_ means triple pointers of type unsigned int 00045 double*** dp3_Value = new double**; //dp3_ means triple pointers of type double. Other prefixes follow the same notation 00046 int rowCount, columnCount; 00047 ConvertMatrixMarketFormat2RowCompressedFormat(s_InputFile, uip3_SparsityPattern, dp3_Value,rowCount, columnCount); 00048 00049 cout<<"just for debugging purpose, display the 2 matrices: the matrix with SparsityPattern only and the matrix with Value"<<endl; 00050 cout<<fixed<<showpoint<<setprecision(2); //formatting output 00051 cout<<"(*uip3_SparsityPattern)"<<endl; 00052 displayCompressedRowMatrix((*uip3_SparsityPattern),rowCount); 00053 cout<<"(*dp3_Value)"<<endl; 00054 displayCompressedRowMatrix((*dp3_Value),rowCount); 00055 cout<<"Finish ConvertMatrixMarketFormat2RowCompressedFormat()"<<endl; 00056 Pause(); 00057 00058 //Step 2: Obtain the seed matrix via coloring. 00059 double*** dp3_Seed = new double**; 00060 int *ip1_SeedRowCount = new int; 00061 int *ip1_SeedColumnCount = new int; 00062 int *ip1_ColorCount = new int; //The number of distinct colors used to color the graph 00063 00064 //Step 2.1: Read the sparsity pattern of the given Jacobian matrix (compressed sparse rows format) 00065 //and create the corresponding bipartite graph 00066 BipartiteGraphPartialColoringInterface *g = new BipartiteGraphPartialColoringInterface(SRC_MEM_ADOLC, *uip3_SparsityPattern, rowCount, columnCount); 00067 00068 //Step 2.2: Do Partial-Distance-Two-Coloring the bipartite graph with the specified ordering 00069 g->PartialDistanceTwoColoring( "SMALLEST_LAST", "COLUMN_PARTIAL_DISTANCE_TWO"); 00070 00071 //Step 2.3 (Option 1): From the coloring information, create and return the seed matrix 00072 (*dp3_Seed) = g->GetSeedMatrix(ip1_SeedRowCount, ip1_SeedColumnCount); 00073 /* Notes: 00074 Step 2.3 (Option 2): From the coloring information, you can also get the vector of colorIDs of left or right vertices (depend on the s_ColoringVariant that you choose) 00075 vector<int> vi_VertexPartialColors; 00076 g->GetVertexPartialColors(vi_VertexPartialColors); 00077 */ 00078 cout<<"Finish GenerateSeed()"<<endl; 00079 *ip1_ColorCount = *ip1_SeedColumnCount; 00080 00081 //Display results of step 2 00082 printf(" dp3_Seed %d x %d \n", *ip1_SeedRowCount, *ip1_SeedColumnCount); 00083 displayMatrix(*dp3_Seed, *ip1_SeedRowCount, *ip1_SeedColumnCount); 00084 Pause(); 00085 00086 // Step 3: Obtain the Jacobian-seed matrix product. 00087 // This step will also be done by an AD tool. For the purpose of illustration here, the orginial matrix V 00088 // (for Values) is multiplied with the seed matrix S. The resulting matrix is stored in dp3_CompressedMatrix. 00089 double*** dp3_CompressedMatrix = new double**; 00090 cout<<"Start MatrixMultiplication()"<<endl; 00091 MatrixMultiplication_VxS(*uip3_SparsityPattern, *dp3_Value, rowCount, columnCount, *dp3_Seed, *ip1_ColorCount, dp3_CompressedMatrix); 00092 cout<<"Finish MatrixMultiplication()"<<endl; 00093 00094 displayMatrix(*dp3_CompressedMatrix,rowCount,*ip1_ColorCount); 00095 Pause(); 00096 00097 //Step 4: Recover the numerical values of the original matrix from the compressed representation. 00098 // The new values are store in "dp2_JacobianValue" 00099 unsigned int** ip2_RowIndex = new unsigned int*; 00100 unsigned int** ip2_ColumnIndex = new unsigned int*; 00101 double** dp2_JacobianValue = new double*; 00102 JacobianRecovery1D* jr1d = new JacobianRecovery1D; 00103 jr1d->RecoverD2Cln_SparseSolversFormat(g, *dp3_CompressedMatrix, *uip3_SparsityPattern, ip2_RowIndex, ip2_ColumnIndex, dp2_JacobianValue); 00104 cout<<"Finish Recover()"<<endl; 00105 00106 cout<<endl<<"Display result, the structure and values should be similar to the original one"<<endl; 00107 cout<<"Display *ip2_RowIndex"<<endl; 00108 displayVector(*ip2_RowIndex,g->GetRowVertexCount()+1); 00109 cout<<"Display *ip2_ColumnIndex"<<endl; 00110 displayVector(*ip2_ColumnIndex, (*ip2_RowIndex)[g->GetRowVertexCount()]-1); 00111 cout<<"Display *dp2_JacobianValue"<<endl; 00112 displayVector(*dp2_JacobianValue, (*ip2_RowIndex)[g->GetRowVertexCount()]-1); 00113 Pause(); 00114 00115 //Deallocate memory using functions in Utilities/MatrixDeallocation.h 00116 00117 free_2DMatrix(uip3_SparsityPattern, rowCount); 00118 uip3_SparsityPattern=NULL; 00119 00120 free_2DMatrix(dp3_Value, rowCount); 00121 dp3_Value=NULL; 00122 00123 delete dp3_Seed; 00124 dp3_Seed = NULL; 00125 00126 delete ip1_SeedRowCount; 00127 ip1_SeedRowCount=NULL; 00128 00129 delete ip1_SeedColumnCount; 00130 ip1_SeedColumnCount = NULL; 00131 00132 free_2DMatrix(dp3_CompressedMatrix, rowCount); 00133 dp3_CompressedMatrix = NULL; 00134 00135 delete ip1_ColorCount; 00136 ip1_ColorCount = NULL; 00137 00138 delete jr1d; 00139 jr1d = NULL; 00140 00141 delete ip2_RowIndex; 00142 delete ip2_ColumnIndex; 00143 delete dp2_JacobianValue; 00144 ip2_RowIndex=NULL; 00145 ip2_ColumnIndex=NULL; 00146 dp2_JacobianValue=NULL; 00147 00148 delete g; 00149 g=NULL; 00150 00151 return 0; 00152 }