Actual source code: ex72.c
1: static char help[] = "Read a non-complex sparse matrix from a Matrix Market (v. 2.0) file\n\
2: and write it to a file in petsc sparse binary format. If the matrix is symmetric, the binary file is in \n\
3: PETSc MATSBAIJ format, otherwise it is in MATAIJ format \n\
4: Usage: ./ex72 -fin <infile> -fout <outfile> \n\
5: (See https://math.nist.gov/MatrixMarket/ for details.)\n\
6: The option -permute <natural,rcm,nd,...> permutes the matrix using the ordering type.\n\
7: The option -aij_only allows to use MATAIJ for all cases.\n\\n";
9: /*
10: NOTES:
12: 1) Matrix Market files are always 1-based, i.e. the index of the first
13: element of a matrix is (1,1), not (0,0) as in C. ADJUST THESE
14: OFFSETS ACCORDINGLY offsets accordingly when reading and writing
15: to files.
17: 2) ANSI C requires one to use the "l" format modifier when reading
18: double precision floating point numbers in scanf() and
19: its variants. For example, use "%lf", "%lg", or "%le"
20: when reading doubles, otherwise errors will occur.
21: */
22: #include <petscmat.h>
23: #include "ex72mmio.h"
25: int main(int argc,char **argv)
26: {
27: MM_typecode matcode;
28: FILE *file;
29: PetscInt M, N, ninput;
30: PetscInt *ia, *ja;
31: Mat A;
32: char filein[PETSC_MAX_PATH_LEN],fileout[PETSC_MAX_PATH_LEN];
33: char ordering[256] = MATORDERINGRCM;
34: PetscInt i,j,nz,ierr,size,*rownz;
35: PetscScalar *val,zero = 0.0;
36: PetscViewer view;
37: PetscBool sametype,flag,symmetric = PETSC_FALSE,skew = PETSC_FALSE,real = PETSC_FALSE,pattern = PETSC_FALSE,aijonly = PETSC_FALSE, permute = PETSC_FALSE;
38: IS rowperm = NULL,colperm = NULL;
40: PetscInitialize(&argc,&argv,(char *)0,help);
41: MPI_Comm_size(PETSC_COMM_WORLD,&size);
44: PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Matrix Market example options","");
45: {
46: PetscOptionsString("-fin","Input Matrix Market file","",filein,filein,sizeof(filein),&flag);
48: PetscOptionsString("-fout","Output file in petsc sparse binary format","",fileout,fileout,sizeof(fileout),&flag);
50: PetscOptionsBool("-aij_only","Use MATAIJ for all cases","",aijonly,&aijonly,NULL);
51: PetscOptionsFList("-permute","Permute matrix and vector to solving in new ordering","",MatOrderingList,ordering,ordering,sizeof(ordering),&permute);
52: }
53: PetscOptionsEnd();
55: /* Read in matrix */
56: PetscFOpen(PETSC_COMM_SELF,filein,"r",&file);
60: /* This is how one can screen matrix types if their application */
61: /* only supports a subset of the Matrix Market data types. */
64: if (mm_is_symmetric(matcode)) symmetric = PETSC_TRUE;
65: if (mm_is_skew(matcode)) skew = PETSC_TRUE;
66: if (mm_is_real(matcode)) real = PETSC_TRUE;
67: if (mm_is_pattern(matcode)) pattern = PETSC_TRUE;
69: /* Find out size of sparse matrix .... */
72: mm_write_banner(stdout, matcode);
73: PetscPrintf(PETSC_COMM_SELF,"M: %d, N: %d, nnz: %d\n",M,N,nz);
75: /* Reseve memory for matrices */
76: PetscMalloc4(nz,&ia,nz,&ja,nz,&val,M,&rownz);
77: for (i=0; i<M; i++) rownz[i] = 1; /* Since we will add 0.0 to diagonal entries */
79: /* NOTE: when reading in doubles, ANSI C requires the use of the "l" */
80: /* specifier as in "%lg", "%lf", "%le", otherwise errors will occur */
81: /* (ANSI C X3.159-1989, Sec. 4.9.6.2, p. 136 lines 13-15) */
83: for (i=0; i<nz; i++) {
84: if (pattern) {
85: ninput = fscanf(file, "%d %d\n", &ia[i], &ja[i]);
87: val[i] = 1.0;
88: } else if (real) {
89: ninput = fscanf(file, "%d %d %lg\n", &ia[i], &ja[i], &val[i]);
91: }
92: ia[i]--; ja[i]--; /* adjust from 1-based to 0-based */
93: if (ia[i] != ja[i]) { /* already counted the diagonals above */
94: if ((symmetric && aijonly) || skew) { /* transpose */
95: rownz[ia[i]]++;
96: rownz[ja[i]]++;
97: } else rownz[ia[i]]++;
98: }
99: }
100: PetscFClose(PETSC_COMM_SELF,file);
101: PetscPrintf(PETSC_COMM_SELF,"Reading matrix completes.\n");
103: /* Create, preallocate, and then assemble the matrix */
104: MatCreate(PETSC_COMM_SELF,&A);
105: MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,M,N);
107: if (symmetric && !aijonly) {
108: MatSetType(A,MATSEQSBAIJ);
109: MatSetFromOptions(A);
110: MatSetUp(A);
111: MatSeqSBAIJSetPreallocation(A,1,0,rownz);
112: PetscObjectTypeCompare((PetscObject)A,MATSEQSBAIJ,&sametype);
114: } else {
115: MatSetType(A,MATSEQAIJ);
116: MatSetFromOptions(A);
117: MatSetUp(A);
118: MatSeqAIJSetPreallocation(A,0,rownz);
119: PetscObjectTypeCompare((PetscObject)A,MATSEQAIJ,&sametype);
121: }
123: /* Add zero to diagonals, in case the matrix missing diagonals */
124: for (j=0; j<M; j++) MatSetValues(A,1,&j,1,&j,&zero,INSERT_VALUES);
125: /* Add values to the matrix, these correspond to lower triangular part for symmetric or skew matrices */
126: for (j=0; j<nz; j++) MatSetValues(A,1,&ia[j],1,&ja[j],&val[j],INSERT_VALUES);
128: /* Add values to upper triangular part for some cases */
129: if (symmetric && aijonly) {
130: /* MatrixMarket matrix stores symm matrix in lower triangular part. Take its transpose */
131: for (j=0; j<nz; j++) MatSetValues(A,1,&ja[j],1,&ia[j],&val[j],INSERT_VALUES);
132: }
133: if (skew) {
134: for (j=0; j<nz; j++) {
135: val[j] = -val[j];
136: MatSetValues(A,1,&ja[j],1,&ia[j],&val[j],INSERT_VALUES);
137: }
138: }
140: MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);
141: MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);
143: if (permute) {
144: Mat Aperm;
145: MatGetOrdering(A,ordering,&rowperm,&colperm);
146: MatPermute(A,rowperm,colperm,&Aperm);
147: MatDestroy(&A);
148: A = Aperm; /* Replace original operator with permuted version */
149: }
151: /* Write out matrix */
152: PetscPrintf(PETSC_COMM_SELF,"Writing matrix to binary file %s using PETSc %s format ...\n",fileout,(symmetric && !aijonly)?"SBAIJ":"AIJ");
153: PetscViewerBinaryOpen(PETSC_COMM_SELF,fileout,FILE_MODE_WRITE,&view);
154: MatView(A,view);
155: PetscViewerDestroy(&view);
156: PetscPrintf(PETSC_COMM_SELF,"Writing matrix completes.\n");
158: PetscFree4(ia,ja,val,rownz);
159: MatDestroy(&A);
160: ISDestroy(&rowperm);
161: ISDestroy(&colperm);
162: PetscFinalize();
163: return 0;
164: }
166: /*TEST
168: build:
169: requires: !complex double !defined(PETSC_USE_64BIT_INDICES)
170: depends: ex72mmio.c
172: test:
173: suffix: 1
174: args: -fin ${wPETSC_DIR}/share/petsc/datafiles/matrices/amesos2_test_mat0.mtx -fout petscmat.aij
175: output_file: output/ex72_1.out
177: test:
178: suffix: 2
179: args: -fin ${wPETSC_DIR}/share/petsc/datafiles/matrices/LFAT5.mtx -fout petscmat.sbaij
180: output_file: output/ex72_2.out
182: test:
183: suffix: 3
184: args: -fin ${wPETSC_DIR}/share/petsc/datafiles/matrices/m_05_05_crk.mtx -fout petscmat2.aij
185: output_file: output/ex72_3.out
187: test:
188: suffix: 4
189: args: -fin ${wPETSC_DIR}/share/petsc/datafiles/matrices/amesos2_test_mat0.mtx -fout petscmat.aij -permute rcm
190: output_file: output/ex72_4.out
191: TEST*/