PetscErrorCode MatGetColumnVector_SMF(Mat mat,Vec Y, PetscInt col)
{
PetscErrorCode ierr;
MatSubMatFreeCtx ctx;
PetscFunctionBegin;
ierr = MatShellGetContext(mat,(void **)&ctx);CHKERRQ(ierr);
ierr = MatGetColumnVector(ctx->A,Y,col);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat C;
PetscInt i,j,m = 3,n = 2,Ii,J,col = 0;
PetscMPIInt size,rank;
PetscErrorCode ierr;
PetscScalar v;
Vec yy;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-col",&col,NULL);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
n = 2*size;
/* create the matrix for the five point stencil, YET AGAIN*/
ierr = MatCreateAIJ(PETSC_COMM_WORLD,PETSC_DECIDE,PETSC_DECIDE,
m*n,m*n,5,NULL,5,NULL,&C);CHKERRQ(ierr);
for (i=0; i<m; i++) {
for (j=2*rank; j<2*rank+2; j++) {
v = -1.0; Ii = j + n*i;
if (i>0) {J = Ii - n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (i<m-1) {J = Ii + n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j>0) {J = Ii - 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
if (j<n-1) {J = Ii + 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);}
v = 4.0; ierr = MatSetValues(C,1,&Ii,1,&Ii,&v,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&yy);CHKERRQ(ierr);
ierr = VecSetSizes(yy,PETSC_DECIDE,m*n);CHKERRQ(ierr);
ierr = VecSetFromOptions(yy);CHKERRQ(ierr);
ierr = MatGetColumnVector(C,yy,col);CHKERRQ(ierr);
ierr = VecView(yy,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecDestroy(&yy);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode BearQueryMat(PetscInt s, PetscScalar c, Mat invL1, Mat invU1, Mat invL2, Mat invU2, Mat H12, Mat H21, Vec order){
PetscErrorCode err;
PetscInt n1, n2, n, M, N;
PetscInt oseed;
PetscScalar val, one = 1.0;
PetscMPIInt size;
PetscLogDouble tic, toc;
Mat r = NULL;
Mat r1 = NULL, q1 = NULL, t1_1 = NULL, t1_2 = NULL, t1_3 = NULL, t1_4 = NULL, t1_5 = NULL; // dimension: n1
Mat r2 = NULL, q2 = NULL, q_tilda = NULL, t2_1 = NULL, t2_2 = NULL, t2_3 = NULL; // dimension: n2_idx
Vec vr=NULL, vr1=NULL, vr2=NULL;
PetscInt col = 0;
err = MPI_Comm_size(PETSC_COMM_WORLD, &size); CHKERRQ(err);
err = MatGetSize(H12, &n1, &n2); CHKERRQ(err);
n = n1 + n2;
err = PetscPrintf(PETSC_COMM_WORLD, "n1: %d, n2: %d\n", n1, n2); CHKERRQ(err);
err = MatCreateAIJ(PETSC_COMM_WORLD, PETSC_DECIDE, 1, n, size, 1, NULL, 1, NULL, &r); CHKERRQ(err);
err = MatCreateAIJ(PETSC_COMM_WORLD, PETSC_DECIDE, 1, n1, size, 1, NULL, 1, NULL, &q1); CHKERRQ(err);
err = MatCreateAIJ(PETSC_COMM_WORLD, PETSC_DECIDE, 1, n2, size, 1, NULL, 1, NULL, &q2); CHKERRQ(err);
// err = MatCreate(PETSC_COMM_WORLD, &q2); CHKERRQ(err);
// err = MatSetSizes(q2, PETSC_DECIDE, PETSC_DECIDE, n2, 1); CHKERRQ(err);
// err = MatSetType(q2, MATAIJ); CHKERRQ(err);
// err = MatSetUp(q2);
s = s - 1; // shift -1 for zero-based index
err = VecGetValues(order, 1, &s, &val); CHKERRQ(err);
oseed = (PetscInt) val;
// err = PetscPrintf(PETSC_COMM_WORLD, "Given seed: %d, Reorered seed: %d (0 ~ n-1)\n", s, oseed); CHKERRQ(err);
if(oseed < n1){
//err = MatSetValues(q1, 1, &oseed, 1, &col, &one, INSERT_VALUES); CHKERRQ(err);
err = MatSetValue(q1, oseed, col, one, INSERT_VALUES); CHKERRQ(err);
}else{
oseed = oseed - n1;
//err = MatSetValues(q2, 1, &oseed, 1, &col, &one, INSERT_VALUES); CHKERRQ(err);
err = MatSetValue(q2, oseed, col, one, INSERT_VALUES); CHKERRQ(err);
//err = printVecSum(q2);
}
err = MatAssemblyBegin(q1, MAT_FINAL_ASSEMBLY); CHKERRQ(err);
err = MatAssemblyEnd(q1, MAT_FINAL_ASSEMBLY); CHKERRQ(err);
err = MatAssemblyBegin(q2, MAT_FINAL_ASSEMBLY); CHKERRQ(err);
err = MatAssemblyEnd(q2, MAT_FINAL_ASSEMBLY); CHKERRQ(err);
err = printMatInfo("q1", q1);
err = printMatInfo("q2", q2);
//err = MatView(q1, PETSC_VIEWER_STDOUT_WORLD);
//err = MatView(q2, PETSC_VIEWER_STDOUT_WORLD);
err = MatDuplicate(q1, MAT_DO_NOT_COPY_VALUES, &r1); CHKERRQ(err);
err = MatDuplicate(q1, MAT_DO_NOT_COPY_VALUES, &t1_1); CHKERRQ(err);
err = MatDuplicate(q1, MAT_DO_NOT_COPY_VALUES, &t1_2); CHKERRQ(err);
err = MatDuplicate(q1, MAT_DO_NOT_COPY_VALUES, &t1_3); CHKERRQ(err);
err = MatDuplicate(q1, MAT_DO_NOT_COPY_VALUES, &t1_4); CHKERRQ(err);
err = MatDuplicate(q1, MAT_DO_NOT_COPY_VALUES, &t1_5); CHKERRQ(err);
err = MatDuplicate(q2, MAT_DO_NOT_COPY_VALUES, &r2); CHKERRQ(err);
err = MatDuplicate(q2, MAT_DO_NOT_COPY_VALUES, &q_tilda); CHKERRQ(err);
err = MatDuplicate(q2, MAT_DO_NOT_COPY_VALUES, &t2_1); CHKERRQ(err);
err = MatDuplicate(q2, MAT_DO_NOT_COPY_VALUES, &t2_2); CHKERRQ(err);
err = MatDuplicate(q2, MAT_DO_NOT_COPY_VALUES, &t2_3); CHKERRQ(err);
err = MatMatMult(invL1, q1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &t1_1); CHKERRQ(err);
err = MatMatMult(invU1, t1_1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &t1_2); CHKERRQ(err);
err = MatMatMult(H21, t1_2, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &t2_1); CHKERRQ(err);
err = MatScale(t2_1, -1.0); CHKERRQ(err);
err = MatAXPY(t2_1, 1.0, q2, DIFFERENT_NONZERO_PATTERN); CHKERRQ(err);
//MatView(t1_1, PETSC_VIEWER_STDOUT_WORLD);
err = PetscTime(&tic);
err = MatMatMult(invL2, t2_1, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &t2_2); CHKERRQ(err);
err = MatMatMult(invU2, t2_2, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &r2); CHKERRQ(err);
err = PetscTime(&toc);
err = PetscPrintf(PETSC_COMM_WORLD, "running time: %f sec\n", toc-tic); CHKERRQ(err);
err = MatMatMult(H12, r2, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &t1_3); CHKERRQ(err);
err = MatScale(t1_3, -1.0); CHKERRQ(err);
err = MatAXPY(t1_3, 1.0, q1, DIFFERENT_NONZERO_PATTERN); CHKERRQ(err);
err = MatMatMult(invL1, t1_3, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &t1_5); CHKERRQ(err);
err = MatMatMult(invU1, t1_5, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &r1); CHKERRQ(err);
//MatView(r1, PETSC_VIEWER_STDOUT_WORLD);
MatGetSize(r1, &M, &N);
PetscPrintf(PETSC_COMM_WORLD, "%d %d\n", M, N);
err = VecCreateMPI(PETSC_COMM_WORLD, PETSC_DECIDE, n1, &vr1);
err = MatGetColumnVector(r1, vr1, 0);
err = VecCreateMPI(PETSC_COMM_WORLD, PETSC_DECIDE, n2, &vr2);
err = MatGetColumnVector(r2, vr2, 0);
err = printMatInfo("r2", r2);
/*
// Start matrix-vec multiplications
err = MatMult(invU2, t2_2, r2); CHKERRQ(err);
err = MatMult(H12, r2, t1_3); CHKERRQ(err);
err = VecAXPBYPCZ(t1_4, 1.0, -1.0, 0.0, q1, t1_3); CHKERRQ(err);
err = MatMult(invL1, t1_4, t1_5); CHKERRQ(err);
err = MatMult(invU1, t1_5, r1); CHKERRQ(err);
//err = printVecSum(r1);
//err = VecView(r2, PETSC_VIEWER_STDOUT_WORLD);
// Concatenate r1 and r2
err = VecMerge(r1, r2, r); CHKERRQ(err);
err = VecScale(r, c); CHKERRQ(err);
//err = VecView(r, PETSC_VIEWER_STDOUT_WORLD);
//err = VecDuplicate(r, &or); CHKERRQ(err);
err = VecReorder(r, order, or); CHKERRQ(err);
//err = VecView(or, PETSC_VIEWER_STDOUT_WORLD);
*/
err = MatDestroy(&r); CHKERRQ(err);
err = MatDestroy(&r1); CHKERRQ(err);
err = MatDestroy(&q1); CHKERRQ(err);
err = MatDestroy(&t1_1); CHKERRQ(err);
err = MatDestroy(&t1_2); CHKERRQ(err);
err = MatDestroy(&t1_3); CHKERRQ(err);
err = MatDestroy(&t1_4); CHKERRQ(err);
err = MatDestroy(&t1_5); CHKERRQ(err);
err = MatDestroy(&r2); CHKERRQ(err);
err = MatDestroy(&q2); CHKERRQ(err);
err = MatDestroy(&q_tilda); CHKERRQ(err);
err = MatDestroy(&t2_1); CHKERRQ(err);
err = MatDestroy(&t2_2); CHKERRQ(err);
err = MatDestroy(&t2_3); CHKERRQ(err);
return err;
}
PetscErrorCode EPSSetUp_LAPACK(EPS eps)
{
PetscErrorCode ierr,ierra,ierrb;
PetscBool isshift,denseok=PETSC_FALSE;
Mat A,B,OP,Adense,Bdense;
PetscScalar shift,*Ap,*Bp;
PetscInt i,ld,nmat;
KSP ksp;
PC pc;
Vec v;
PetscFunctionBegin;
eps->ncv = eps->n;
if (eps->mpd) { ierr = PetscInfo(eps,"Warning: parameter mpd ignored\n");CHKERRQ(ierr); }
if (!eps->which) { ierr = EPSSetWhichEigenpairs_Default(eps);CHKERRQ(ierr); }
if (eps->balance!=EPS_BALANCE_NONE) { ierr = PetscInfo(eps,"Warning: balancing ignored\n");CHKERRQ(ierr); }
if (eps->extraction) { ierr = PetscInfo(eps,"Warning: extraction type ignored\n");CHKERRQ(ierr); }
ierr = EPSAllocateSolution(eps,0);CHKERRQ(ierr);
/* attempt to get dense representations of A and B separately */
ierr = PetscObjectTypeCompare((PetscObject)eps->st,STSHIFT,&isshift);CHKERRQ(ierr);
if (isshift) {
ierr = STGetNumMatrices(eps->st,&nmat);CHKERRQ(ierr);
ierr = STGetOperators(eps->st,0,&A);CHKERRQ(ierr);
if (nmat>1) { ierr = STGetOperators(eps->st,1,&B);CHKERRQ(ierr); }
PetscPushErrorHandler(PetscIgnoreErrorHandler,NULL);
ierra = SlepcMatConvertSeqDense(A,&Adense);CHKERRQ(ierr);
if (eps->isgeneralized) {
ierrb = SlepcMatConvertSeqDense(B,&Bdense);CHKERRQ(ierr);
} else {
ierrb = 0;
}
PetscPopErrorHandler();
denseok = (ierra == 0 && ierrb == 0)? PETSC_TRUE: PETSC_FALSE;
} else Adense = NULL;
/* setup DS */
if (denseok) {
if (eps->isgeneralized) {
if (eps->ishermitian) {
if (eps->ispositive) {
ierr = DSSetType(eps->ds,DSGHEP);CHKERRQ(ierr);
} else {
ierr = DSSetType(eps->ds,DSGNHEP);CHKERRQ(ierr); /* TODO: should be DSGHIEP */
}
} else {
ierr = DSSetType(eps->ds,DSGNHEP);CHKERRQ(ierr);
}
} else {
if (eps->ishermitian) {
ierr = DSSetType(eps->ds,DSHEP);CHKERRQ(ierr);
} else {
ierr = DSSetType(eps->ds,DSNHEP);CHKERRQ(ierr);
}
}
} else {
ierr = DSSetType(eps->ds,DSNHEP);CHKERRQ(ierr);
}
ierr = DSAllocate(eps->ds,eps->ncv);CHKERRQ(ierr);
ierr = DSGetLeadingDimension(eps->ds,&ld);CHKERRQ(ierr);
ierr = DSSetDimensions(eps->ds,eps->ncv,0,0,0);CHKERRQ(ierr);
if (denseok) {
ierr = STGetShift(eps->st,&shift);CHKERRQ(ierr);
if (shift != 0.0) {
ierr = MatShift(Adense,shift);CHKERRQ(ierr);
}
/* use dummy pc and ksp to avoid problems when B is not positive definite */
ierr = STGetKSP(eps->st,&ksp);CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPPREONLY);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCNONE);CHKERRQ(ierr);
} else {
ierr = PetscInfo(eps,"Using slow explicit operator\n");CHKERRQ(ierr);
ierr = STComputeExplicitOperator(eps->st,&OP);CHKERRQ(ierr);
ierr = MatDestroy(&Adense);CHKERRQ(ierr);
ierr = SlepcMatConvertSeqDense(OP,&Adense);CHKERRQ(ierr);
}
/* fill DS matrices */
ierr = VecCreateSeqWithArray(PETSC_COMM_SELF,1,ld,NULL,&v);CHKERRQ(ierr);
ierr = DSGetArray(eps->ds,DS_MAT_A,&Ap);CHKERRQ(ierr);
for (i=0;i<ld;i++) {
ierr = VecPlaceArray(v,Ap+i*ld);CHKERRQ(ierr);
ierr = MatGetColumnVector(Adense,v,i);CHKERRQ(ierr);
ierr = VecResetArray(v);CHKERRQ(ierr);
}
ierr = DSRestoreArray(eps->ds,DS_MAT_A,&Ap);CHKERRQ(ierr);
if (denseok && eps->isgeneralized) {
ierr = DSGetArray(eps->ds,DS_MAT_B,&Bp);CHKERRQ(ierr);
for (i=0;i<ld;i++) {
ierr = VecPlaceArray(v,Bp+i*ld);CHKERRQ(ierr);
ierr = MatGetColumnVector(Bdense,v,i);CHKERRQ(ierr);
ierr = VecResetArray(v);CHKERRQ(ierr);
}
ierr = DSRestoreArray(eps->ds,DS_MAT_B,&Bp);CHKERRQ(ierr);
}
ierr = VecDestroy(&v);CHKERRQ(ierr);
ierr = MatDestroy(&Adense);CHKERRQ(ierr);
if (!denseok) { ierr = MatDestroy(&OP);CHKERRQ(ierr); }
if (denseok && eps->isgeneralized) { ierr = MatDestroy(&Bdense);CHKERRQ(ierr); }
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat A,B,Y; /*input : the three imput matrix */
Mat P; /* P=QR factorization*/
PetscViewer fd1,fd2;
char file[4][PETSC_MAX_PATH_LEN];
//Mat C; /*C=B*Y*/
PetscInt m,n; /*size of matrix C;*/
Mat E,X; /*lhs and rhs of the linear equations;*/
Vec b,x; /*column vector of rhs;*/
KSP ksp; /* linear solver context */
PetscErrorCode ierr;
PetscInt i,its; /*iteration numbers of KSP*/
PetscBool flg;
m=10;
n=4;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = PetscOptionsGetString(NULL,"-fa",file[0],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if(!flg){SETERRQ(PETSC_COMM_WORLD,1,"Please provide matrix A!\n");}
ierr = PetscOptionsGetString(NULL,"-fb",file[1],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if(!flg){SETERRQ(PETSC_COMM_WORLD,1,"Please provide matrix B!\n");}
ierr = PetscOptionsGetString(NULL,"-fy",file[2],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if(!flg){SETERRQ(PETSC_COMM_WORLD,1,"Please provide matrix Y!\n");}
ierr = PetscOptionsGetString(NULL,"-fp",file[3],PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if(!flg){SETERRQ(PETSC_COMM_WORLD,1,"Please provide matrix P!\n");}
/*Load the matrices*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[0],FILE_MODE_READ,&fd1);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file[1],FILE_MODE_READ,&fd2);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
ierr = MatLoad(A,fd1);CHKERRQ(ierr);
ierr = MatLoad(B,fd2);CHKERRQ(ierr);
readmm(file[2], &Y);
readmm(file[3], &P);
ierr = PetscPrintf(PETSC_COMM_SELF,"Read file completes.\n");CHKERRQ(ierr);
#if(cxDEBUG==1)
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
#endif
Mat Q1;
ierr = MatCreate(PETSC_COMM_WORLD, &Q1); CHKERRQ(ierr);
ierr = MatSetFromOptions(Q1); CHKERRQ(ierr);
ierr = MatMatMult(B,Y,MAT_INITIAL_MATRIX,PETSC_DEFAULT, &Q1);CHKERRQ(ierr);
#if(cxDEBUG==1)
ierr = PetscPrintf(PETSC_COMM_SELF,"Cao this is BY.\n");CHKERRQ(ierr);
ierr = MatView(Q1,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
#endif
getQ1(&Q1);
#if(cxDEBUG==1)
ierr = PetscPrintf(PETSC_COMM_SELF,"\nTHIS IS Q1.\n");CHKERRQ(ierr);
ierr = MatView(Q1,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
#endif
Mat SBP;
ierr = MatMatTransposeMult(Q1,Q1,MAT_INITIAL_MATRIX, PETSC_DEFAULT ,&SBP);
ierr = MatAssemblyBegin(SBP,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(SBP,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatShift(SBP,-1);
ierr = MatScale(SBP,-1);
#if(cxDEBUG==1)
ierr = PetscPrintf(PETSC_COMM_SELF,"\nTHIS IS SBP = Q1*Q1'.\n");CHKERRQ(ierr);
ierr = MatView(SBP,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"\nBelows is act_P.\n");CHKERRQ(ierr);
ierr = MatView(P ,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
#endif
ierr = MatMatMult(A,Y,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&E);CHKERRQ(ierr);
ierr = MatMatMult(SBP,E,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&E);CHKERRQ(ierr);
#if(cxDEBUG==1)
ierr = PetscPrintf(PETSC_COMM_SELF,"\nBelows is PAY.\n");CHKERRQ(ierr);
ierr = MatView(E,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
#endif
ierr = MatAssemblyBegin(E,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(E,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
//ierr = MatGetSize(E,&m,&n);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&X);CHKERRQ(ierr);
ierr = MatSetSizes(X,PETSC_DECIDE,PETSC_DECIDE,m,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(X);CHKERRQ(ierr);
ierr = MatSetUp(X); CHKERRQ(ierr);
ierr = MatZeroEntries(X);CHKERRQ(ierr);
ierr = MatAssemblyBegin(X,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(X,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
// PetscInt ix[m];
// for(i=0;i<m;i++){
// ix[i] = i;
// }
VecCreate(PETSC_COMM_WORLD,&b);
VecSetSizes(b,PETSC_DECIDE,m);
VecSetFromOptions(b);
VecCreate(PETSC_COMM_WORLD,&x);
VecSetSizes(x,PETSC_DECIDE,m);
VecSetFromOptions(x);
//#if(cxDEBUG==1)
ierr = PetscPrintf(PETSC_COMM_SELF,"\nBEFORE CG Check A\n");CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"\nBEFORE CG Check SBP\n");CHKERRQ(ierr);
ierr = MatView(SBP,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"\nBEFORE CG Check E\n");CHKERRQ(ierr);
ierr = MatView(E,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
//#endif
for(i=0;i<n;i++){
MatGetColumnVector(E,b,i);
PetscPrintf(PETSC_COMM_WORLD,"the rhs\n");
VecView(b,PETSC_VIEWER_STDOUT_WORLD);
KSPCreate(PETSC_COMM_WORLD,&ksp);
KSPSetOperators(ksp,A,SBP);
KSPSetNormType(ksp,KSP_NORM_UNPRECONDITIONED);
KSPSetCheckNormIteration(ksp,-1);
KSPSetTolerances(ksp,1.0e-06,PETSC_DEFAULT,PETSC_DEFAULT,400);
KSPSetInitialGuessNonzero(ksp,PETSC_FALSE);
KSPSetFromOptions(ksp);
KSPSolve(ksp,b,x);
KSPGetIterationNumber(ksp,&its);
PetscPrintf(PETSC_COMM_WORLD,"%d-th equation,iteration=%D\n",i,its);
VecView(x,PETSC_VIEWER_STDOUT_WORLD);
}
return 0;
}
int
SparseGp_logLikeGrad (SparseGp *gp, HyperParam hp, int lengthInd, double *logLikeGrad)
{
PetscErrorCode ierr;
(void) ierr;
/* compute t' inv(K) (dKdt inv(K) t) */
/* 1. solve inv(K) t */
PetscInt N = gp->trainLabels->size;
Vec invKt;
ierr = petsc_util_createVec (&invKt, gp->nlocal, N);
SparseGp_solve (gp, gp->_trainLabels, &invKt);
/* 2. multiply dKdt by invKt */
Vec dKdtInvKt;
ierr = petsc_util_createVec (&dKdtInvKt, gp->nlocal, N);
SparseGp_KGradient (gp, hp, lengthInd);
MatMult (gp->_KGradient, invKt, dKdtInvKt);
/* 3. solve invK (vector from step 2.) */
Vec invKDkdtInvKt;
ierr = petsc_util_createVec (&invKDkdtInvKt, gp->nlocal, N);
SparseGp_solve (gp, dKdtInvKt, &invKDkdtInvKt);
/* 4. compute inner product */
double dotProd;
VecDot (gp->_trainLabels, invKDkdtInvKt, &dotProd);
/* compute trace (invK dKdt) */
/* 1. for each column in dKdt, solve */
double myTrace = 0;
Vec col, solution;
petsc_util_createVec (&col, gp->nlocal, N);
petsc_util_createVec (&solution, gp->nlocal, N);
for (int i=0; i<N; i++) {
/* IOU_ROOT_PRINT ("%d --- %d\n", i, N); */
int row = i;
ierr = MatGetColumnVector (gp->_KGradient, col, row);
/* IOU_ROOT_PRINT ("solving...\n"); */
SparseGp_solve (gp, col, &solution);
/* IOU_ROOT_PRINT ("solved\n"); */
if (row < gp->rend && row >= gp->rstart) {
double ii;
VecGetValues (solution, 1, &row, &ii);
myTrace += ii;
}
}
/* gather all trace terms */
int numProcs;
MPI_Comm_size (PETSC_COMM_WORLD, &numProcs);
double diag[numProcs];
int ret = MPI_Allgather (&myTrace, 1, MPI_DOUBLE, diag, 1, MPI_DOUBLE, PETSC_COMM_WORLD);
(void) ret;
double trace = 0;
for (int i=0; i<numProcs; i++)
trace += diag[i];
/* IOU_ROOT_PRINT ("Cleaning up...\n"); */
/* clean up */
VecDestroy (&invKt);
VecDestroy (&dKdtInvKt);
VecDestroy (&invKDkdtInvKt);
VecDestroy (&col);
VecDestroy (&solution);
/* IOU_ROOT_PRINT ("Done cleaning up...\n"); */
*logLikeGrad = 0.5*dotProd + 0.5*trace;
return EXIT_SUCCESS;
}
