int main(int argc,char **argv)
{
PetscInt i,n = 1000,*values;
PetscRandom rnd;
PetscScalar value,avg = 0.0;
PetscErrorCode ierr;
PetscMPIInt rank;
PetscInt view_rank=-1;
#if defined(PETSC_USE_LOG)
PetscLogEvent event;
#endif
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-view_randomvalues",&view_rank,NULL);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rnd);CHKERRQ(ierr);
/* force imaginary part of random number to always be zero; thus obtain reproducible results with real and complex numbers */
ierr = PetscRandomSetInterval(rnd,0.0,1.0);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rnd);CHKERRQ(ierr);
ierr = PetscMalloc1(n,&values);CHKERRQ(ierr);
for (i=0; i<n; i++) {
ierr = PetscRandomGetValue(rnd,&value);CHKERRQ(ierr);
avg += value;
if (view_rank == (PetscInt)rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] value[%D] = %6.4e\n",rank,i,(double)PetscRealPart(value));CHKERRQ(ierr);
}
values[i] = (PetscInt)(n*PetscRealPart(value) + 2.0);
}
avg = avg/((PetscReal)n);
if (view_rank == (PetscInt)rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"[%d] Average value %6.4e\n",rank,(double)PetscRealPart(avg));CHKERRQ(ierr);
}
ierr = PetscSortInt(n,values);CHKERRQ(ierr);
ierr = PetscLogEventRegister("Sort",0,&event);CHKERRQ(ierr);
ierr = PetscLogEventBegin(event,0,0,0,0);CHKERRQ(ierr);
ierr = PetscRandomSeed(rnd);CHKERRQ(ierr);
for (i=0; i<n; i++) {
ierr = PetscRandomGetValue(rnd,&value);CHKERRQ(ierr);
values[i] = (PetscInt)(n*PetscRealPart(value) + 2.0);
/* printf("value[%d] = %g\n",i,value); */
}
ierr = PetscSortInt(n,values);CHKERRQ(ierr);
ierr = PetscLogEventEnd(event,0,0,0,0);CHKERRQ(ierr);
for (i=1; i<n; i++) {
if (values[i] < values[i-1]) SETERRQ(PETSC_COMM_SELF,1,"Values not sorted");
}
ierr = PetscFree(values);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rnd);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
PetscLogDouble x,y;
double value;
void *arr[1000],*dummy;
int i,rand1[1000],rand2[1000];
PetscErrorCode ierr;
PetscRandom r;
PetscBool flg;
ierr = PetscInitialize(&argc,&argv,0,0);if (ierr) return ierr;
ierr = PetscRandomCreate(PETSC_COMM_SELF,&r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
for (i=0; i<1000; i++) {
ierr = PetscRandomGetValue(r,&value);CHKERRQ(ierr);
rand1[i] = (int)(value* 144327);
ierr = PetscRandomGetValue(r,&value);CHKERRQ(ierr);
rand2[i] = (int)(value* 144327);
}
/* Take care of paging effects */
ierr = PetscMalloc1(100,&dummy);CHKERRQ(ierr);
ierr = PetscFree(dummy);CHKERRQ(ierr);
ierr = PetscTime(&x);CHKERRQ(ierr);
/* Do all mallocs */
for (i=0; i< 1000; i++) {
ierr = PetscMalloc1(rand1[i],&arr[i]);CHKERRQ(ierr);
}
ierr = PetscTime(&x);CHKERRQ(ierr);
/* Do some frees */
for (i=0; i< 1000; i+=2) {
ierr = PetscFree(arr[i]);CHKERRQ(ierr);
}
/* Do some mallocs */
for (i=0; i< 1000; i+=2) {
ierr = PetscMalloc1(rand2[i],&arr[i]);CHKERRQ(ierr);
}
ierr = PetscTime(&y);CHKERRQ(ierr);
for (i=0; i< 1000; i++) {
ierr = PetscFree(arr[i]);CHKERRQ(ierr);
}
fprintf(stdout,"%-15s : %e sec, with options : ","PetscMalloc",(y-x)/500.0);
ierr = PetscOptionsHasName(NULL,"-malloc",&flg);CHKERRQ(ierr);
if (flg) fprintf(stdout,"-malloc ");
fprintf(stdout,"\n");
ierr = PetscRandomDestroy(&r);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
void stdNormalArray(double *eps, int size, PetscRandom ran)
{
int i;
double u1,u2,t;
PetscErrorCode ierr;
for (i=0;i<size;i+=2){
ierr = PetscRandomGetValue(ran,(PetscScalar*)&u1);CHKERRABORT(PETSC_COMM_WORLD,ierr);
ierr = PetscRandomGetValue(ran,(PetscScalar*)&u2);CHKERRABORT(PETSC_COMM_WORLD,ierr);
t = sqrt(-2*log(u1));
eps[i] = t * cos(2*PI*u2);
eps[i+1] = t * sin(2*PI*u2);
}
}
// http://mathworld.wolfram.com/SpherePointPicking.html
PetscErrorCode SphericalDistribution(PetscRandom rnd, PetscReal a, Coor *d)
{
PetscReal u,q;
PetscRandomGetValue(rnd,&u); // [0,1]
u = (1-a) * u + a; // [a,1]
PetscRandomGetValue(rnd,&q); // [0,1]
q = 2 * PETSC_PI * q; // [0, 2pi]
d->x = PetscSqrtScalar( 1 - u*u ) * cos(q);
d->y = PetscSqrtScalar( 1 - u*u ) * sin(q);
d->z = u;
return 0;
}
/*
Defines the ODE passed to the ODE solver
*/
static PetscErrorCode IFunction(TS ts,PetscReal t,Vec U,Vec Udot,Vec F,AppCtx *ctx)
{
PetscErrorCode ierr;
PetscScalar *u,*udot,*f,r;
static PetscScalar R = .4;
PetscFunctionBegin;
ierr = PetscRandomGetValue(ctx->rand,&r);
CHKERRQ(ierr);
if (r > .9) R = .5;
if (r < .1) R = .4;
R = .4;
/* The next three lines allow us to access the entries of the vectors directly */
ierr = VecGetArray(U,&u);
CHKERRQ(ierr);
ierr = VecGetArray(Udot,&udot);
CHKERRQ(ierr);
ierr = VecGetArray(F,&f);
CHKERRQ(ierr);
f[0] = 2.0*ctx->H*udot[0]/ctx->omega_s + ctx->E*ctx->V*PetscSinScalar(u[1])/ctx->X - R;
f[1] = udot[1] - u[0] + ctx->omega_s;
ierr = VecRestoreArray(U,&u);
CHKERRQ(ierr);
ierr = VecRestoreArray(Udot,&udot);
CHKERRQ(ierr);
ierr = VecRestoreArray(F,&f);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
PetscErrorCode ComputeRHSMatrix(PetscInt m,PetscInt nrhs,Mat* C)
{
PetscErrorCode ierr;
PetscRandom rand;
Mat RHS;
PetscScalar *array,rval;
PetscInt i,k;
PetscFunctionBegin;
ierr = MatCreate(PETSC_COMM_WORLD,&RHS);CHKERRQ(ierr);
ierr = MatSetSizes(RHS,m,PETSC_DECIDE,PETSC_DECIDE,nrhs);CHKERRQ(ierr);
ierr = MatSetType(RHS,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSetUp(RHS);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatDenseGetArray(RHS,&array);CHKERRQ(ierr);
for (i=0; i<m; i++){
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[i] = rval;
}
if (nrhs > 1){
for (k=1; k<nrhs; k++){
for (i=0; i<m; i++){
array[m*k+i] = array[i];
}
}
}
ierr = MatDenseRestoreArray(RHS,&array);CHKERRQ(ierr);
ierr = MatAssemblyBegin(RHS,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(RHS,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
*C = RHS;
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv) {
Mat A,B,As;
const PetscInt *ai,*aj;
PetscInt i,j,k,nz,n,asi[]={0,2,3,4,6,7};
PetscInt asj[]={0,4,1,2,3,4,4};
PetscScalar asa[7],*aa;
PetscRandom rctx;
PetscErrorCode ierr;
PetscMPIInt size;
PetscBool flg;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a uniprocessor example only!");
/* Create a aij matrix for checking */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,5,5,2,PETSC_NULL,&A);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
k = 0;
for (i=0; i<5; i++) {
nz = asi[i+1] - asi[i]; /* length of i_th row of A */
for (j=0; j<nz; j++){
ierr = PetscRandomGetValue(rctx,&asa[k]);CHKERRQ(ierr);
ierr = MatSetValues(A,1,&i,1,&asj[k],&asa[k],INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(A,1,&i,1,&asj[k],&asa[k],INSERT_VALUES);CHKERRQ(ierr);
if (i != asj[k]){ /* insert symmetric entry */
ierr = MatSetValues(A,1,&asj[k],1,&i,&asa[k],INSERT_VALUES);CHKERRQ(ierr);
}
k++;
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Create a baij matrix using MatCreateSeqBAIJWithArrays() */
ierr = MatGetRowIJ(A,0,PETSC_FALSE,PETSC_FALSE,&n,&ai,&aj,&flg);CHKERRQ(ierr);
ierr = MatSeqAIJGetArray(A,&aa);CHKERRQ(ierr);
/* WARNING: This sharing is dangerous if either A or B is later assembled */
ierr = MatCreateSeqBAIJWithArrays(PETSC_COMM_SELF,1,5,5,(PetscInt*)ai,(PetscInt*)aj,aa,&B);CHKERRQ(ierr);
ierr = MatSeqAIJRestoreArray(A,&aa);CHKERRQ(ierr);
ierr = MatRestoreRowIJ(A,0,PETSC_FALSE,PETSC_FALSE,&n,&ai,&aj,&flg);CHKERRQ(ierr);
ierr = MatMultEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"MatMult(A,B) are NOT equal");
/* Create a sbaij matrix using MatCreateSeqSBAIJWithArrays() */
ierr = MatCreateSeqSBAIJWithArrays(PETSC_COMM_SELF,1,5,5,asi,asj,asa,&As);CHKERRQ(ierr);
ierr = MatMultEqual(A,As,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_NOTSAMETYPE,"MatMult(A,As) are NOT equal");
/* Free spaces */
ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&As);CHKERRQ(ierr);
ierr = PetscFinalize();
return(0);
}
int main(int argc,char **argv)
{
PetscInt i,n = 1000,*values;
int event;
PetscRandom rand;
PetscScalar value;
PetscErrorCode ierr;
PetscBool values_view=PETSC_FALSE;
PetscMPIInt rank;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(0,"-values_view",&values_view,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = PetscMalloc(n*sizeof(PetscInt),&values);CHKERRQ(ierr);
for (i=0; i<n; i++) {
ierr = PetscRandomGetValue(rand,&value);CHKERRQ(ierr);
values[i] = (PetscInt)(n*PetscRealPart(value) + 2.0);
}
ierr = PetscSortInt(n,values);CHKERRQ(ierr);
ierr = PetscLogEventRegister("Sort",0,&event);CHKERRQ(ierr);
ierr = PetscLogEventBegin(event,0,0,0,0);CHKERRQ(ierr);
for (i=0; i<n; i++) {
ierr = PetscRandomGetValue(rand,&value);CHKERRQ(ierr);
values[i] = (PetscInt)(n*PetscRealPart(value) + 2.0);
}
ierr = PetscSortInt(n,values);CHKERRQ(ierr);
ierr = PetscLogEventEnd(event,0,0,0,0);CHKERRQ(ierr);
for (i=1; i<n; i++) {
if (values[i] < values[i-1]) SETERRQ(PETSC_COMM_SELF,1,"Values not sorted");
if (values_view && !rank){ierr = PetscPrintf(PETSC_COMM_SELF,"%d %d\n",i,values[i]);CHKERRQ(ierr);}
}
ierr = PetscFree(values);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode stdNormalArray(PetscReal *eps, PetscInt numdim, PetscRandom ran)
{
PetscInt i;
PetscScalar u1,u2;
PetscReal t;
PetscErrorCode ierr;
PetscFunctionBegin;
for (i=0; i<numdim; i+=2) {
ierr = PetscRandomGetValue(ran,&u1);CHKERRQ(ierr);
ierr = PetscRandomGetValue(ran,&u2);CHKERRQ(ierr);
t = PetscSqrtReal(-2*PetscLogReal(PetscRealPart(u1)));
eps[i] = t * PetscCosReal(2*PETSC_PI*PetscRealPart(u2));
eps[i+1] = t * PetscSinReal(2*PETSC_PI*PetscRealPart(u2));
}
PetscFunctionReturn(0);
}
PetscErrorCode VecSetRandom_Seq(Vec xin,PetscRandom r)
{
PetscErrorCode ierr;
PetscInt n = xin->map->n,i;
PetscScalar *xx;
PetscFunctionBegin;
ierr = VecGetArray(xin,&xx);CHKERRQ(ierr);
for (i=0; i<n; i++) {ierr = PetscRandomGetValue(r,&xx[i]);CHKERRQ(ierr);}
ierr = VecRestoreArray(xin,&xx);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
BVSetRandom - Set the columns of a BV to random numbers.
Logically Collective on BV
Input Parameters:
+ bv - basis vectors
- rctx - the random number context, formed by PetscRandomCreate(), or NULL and
it will create one internally.
Note:
All active columns (except the leading ones) are modified.
Level: advanced
.seealso: BVSetRandomColumn(), BVSetActiveColumns()
@*/
PetscErrorCode BVSetRandom(BV bv,PetscRandom rctx)
{
PetscErrorCode ierr;
PetscRandom rand=NULL;
PetscInt i,low,high,k;
PetscScalar *px,t;
Vec x;
PetscFunctionBegin;
PetscValidHeaderSpecific(bv,BV_CLASSID,1);
if (rctx) PetscValidHeaderSpecific(rctx,PETSC_RANDOM_CLASSID,2);
else {
ierr = PetscRandomCreate(PetscObjectComm((PetscObject)bv),&rand);CHKERRQ(ierr);
ierr = PetscRandomSetSeed(rand,0x12345678);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
rctx = rand;
}
PetscValidType(bv,1);
BVCheckSizes(bv,1);
ierr = PetscLogEventBegin(BV_SetRandom,bv,rctx,0,0);CHKERRQ(ierr);
for (k=bv->l;k<bv->k;k++) {
ierr = BVGetColumn(bv,k,&x);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(x,&low,&high);CHKERRQ(ierr);
ierr = VecGetArray(x,&px);CHKERRQ(ierr);
for (i=0;i<bv->N;i++) {
ierr = PetscRandomGetValue(rctx,&t);CHKERRQ(ierr);
if (i>=low && i<high) px[i-low] = t;
}
ierr = VecRestoreArray(x,&px);CHKERRQ(ierr);
ierr = BVRestoreColumn(bv,k,&x);CHKERRQ(ierr);
}
ierr = PetscLogEventEnd(BV_SetRandom,bv,rctx,0,0);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscObjectStateIncrease((PetscObject)bv);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
/*@
BVSetRandomColumn - Set one column of a BV to random numbers.
Logically Collective on BV
Input Parameters:
+ bv - basis vectors
. j - column number to be set
- rctx - the random number context, formed by PetscRandomCreate(), or NULL and
it will create one internally.
Note:
This operation is analogue to VecSetRandom - the difference is that the
generated random vector is the same irrespective of the size of the
communicator (if all processes pass a PetscRandom context initialized
with the same seed).
Level: advanced
.seealso: BVSetRandom(), BVSetActiveColumns()
@*/
PetscErrorCode BVSetRandomColumn(BV bv,PetscInt j,PetscRandom rctx)
{
PetscErrorCode ierr;
PetscRandom rand=NULL;
PetscInt i,low,high;
PetscScalar *px,t;
Vec x;
PetscFunctionBegin;
PetscValidHeaderSpecific(bv,BV_CLASSID,1);
PetscValidLogicalCollectiveInt(bv,j,2);
if (rctx) PetscValidHeaderSpecific(rctx,PETSC_RANDOM_CLASSID,3);
else {
ierr = PetscRandomCreate(PetscObjectComm((PetscObject)bv),&rand);CHKERRQ(ierr);
ierr = PetscRandomSetSeed(rand,0x12345678);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
rctx = rand;
}
PetscValidType(bv,1);
BVCheckSizes(bv,1);
if (j<0 || j>=bv->m) SETERRQ2(PetscObjectComm((PetscObject)bv),PETSC_ERR_ARG_OUTOFRANGE,"Argument j has wrong value %D, the number of columns is %D",j,bv->m);
ierr = PetscLogEventBegin(BV_SetRandom,bv,rctx,0,0);CHKERRQ(ierr);
ierr = BVGetColumn(bv,j,&x);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(x,&low,&high);CHKERRQ(ierr);
ierr = VecGetArray(x,&px);CHKERRQ(ierr);
for (i=0;i<bv->N;i++) {
ierr = PetscRandomGetValue(rctx,&t);CHKERRQ(ierr);
if (i>=low && i<high) px[i-low] = t;
}
ierr = VecRestoreArray(x,&px);CHKERRQ(ierr);
ierr = BVRestoreColumn(bv,j,&x);CHKERRQ(ierr);
ierr = PetscLogEventEnd(BV_SetRandom,bv,rctx,0,0);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscObjectStateIncrease((PetscObject)bv);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat A,B;
Vec xx,s1,s2,yy;
PetscErrorCode ierr;
PetscInt m=45,rows[2],cols[2],bs=1,i,row,col,*idx,M;
PetscScalar rval,vals1[4],vals2[4];
PetscRandom rdm;
IS is1,is2;
PetscReal s1norm,s2norm,rnorm,tol = 1.e-4;
PetscTruth flg;
MatFactorInfo info;
PetscInitialize(&argc,&args,(char *)0,help);
/* Test MatSetValues() and MatGetValues() */
ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_block_size",&bs,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_size",&m,PETSC_NULL);CHKERRQ(ierr);
M = m*bs;
ierr = MatCreateSeqBAIJ(PETSC_COMM_SELF,bs,M,M,1,PETSC_NULL,&A);CHKERRQ(ierr);
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,M,M,15,PETSC_NULL,&B);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rdm);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,M,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&yy);CHKERRQ(ierr);
/* For each row add atleast 15 elements */
for (row=0; row<M; row++) {
for (i=0; i<25*bs; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
col = (PetscInt)(PetscRealPart(rval)*M);
ierr = MatSetValues(A,1,&row,1,&col,&rval,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,1,&row,1,&col,&rval,INSERT_VALUES);CHKERRQ(ierr);
}
}
/* Now set blocks of values */
for (i=0; i<20*bs; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[0] = (PetscInt)(PetscRealPart(rval)*M);
vals1[0] = rval;
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[1] = (PetscInt)(PetscRealPart(rval)*M);
vals1[1] = rval;
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[0] = (PetscInt)(PetscRealPart(rval)*M);
vals1[2] = rval;
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[1] = (PetscInt)(PetscRealPart(rval)*M);
vals1[3] = rval;
ierr = MatSetValues(A,2,rows,2,cols,vals1,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,2,rows,2,cols,vals1,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Test MatNorm() */
ierr = MatNorm(A,NORM_FROBENIUS,&s1norm);CHKERRQ(ierr);
ierr = MatNorm(B,NORM_FROBENIUS,&s2norm);CHKERRQ(ierr);
rnorm = PetscAbsScalar(s2norm-s1norm)/s2norm;
if ( rnorm>tol ) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_FROBENIUS()- NormA=%16.14e NormB=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_INFINITY,&s1norm);CHKERRQ(ierr);
ierr = MatNorm(B,NORM_INFINITY,&s2norm);CHKERRQ(ierr);
rnorm = PetscAbsScalar(s2norm-s1norm)/s2norm;
if ( rnorm>tol ) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_INFINITY()- NormA=%16.14e NormB=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_1,&s1norm);CHKERRQ(ierr);
ierr = MatNorm(B,NORM_1,&s2norm);CHKERRQ(ierr);
rnorm = PetscAbsScalar(s2norm-s1norm)/s2norm;
if ( rnorm>tol ) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm_NORM_1()- NormA=%16.14e NormB=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
/* MatShift() */
rval = 10*s1norm;
ierr = MatShift(A,rval);CHKERRQ(ierr);
ierr = MatShift(B,rval);CHKERRQ(ierr);
/* Test MatTranspose() */
ierr = MatTranspose(A,MAT_REUSE_MATRIX,&A);CHKERRQ(ierr);
ierr = MatTranspose(B,MAT_REUSE_MATRIX,&B);CHKERRQ(ierr);
/* Now do MatGetValues() */
for (i=0; i<30; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[0] = (PetscInt)(PetscRealPart(rval)*M);
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[1] = (PetscInt)(PetscRealPart(rval)*M);
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[0] = (PetscInt)(PetscRealPart(rval)*M);
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[1] = (PetscInt)(PetscRealPart(rval)*M);
ierr = MatGetValues(A,2,rows,2,cols,vals1);CHKERRQ(ierr);
ierr = MatGetValues(B,2,rows,2,cols,vals2);CHKERRQ(ierr);
ierr = PetscMemcmp(vals1,vals2,4*sizeof(PetscScalar),&flg);CHKERRQ(ierr);
if (!flg) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetValues bs = %D\n",bs);CHKERRQ(ierr);
}
}
/* Test MatMult(), MatMultAdd() */
for (i=0; i<40; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = VecSet(s2,0.0);CHKERRQ(ierr);
ierr = MatMult(A,xx,s1);CHKERRQ(ierr);
ierr = MatMultAdd(A,xx,s2,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"MatMult not equal to MatMultAdd Norm1=%e Norm2=%e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatMult() */
ierr = MatMultEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMult()\n");CHKERRQ(ierr);
}
/* Test MatMultAdd() */
ierr = MatMultAddEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMultAdd()\n");CHKERRQ(ierr);
}
/* Test MatMultTranspose() */
ierr = MatMultTransposeEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMultTranspose()\n");CHKERRQ(ierr);
}
/* Test MatMultTransposeAdd() */
ierr = MatMultTransposeAddEqual(A,B,10,&flg);CHKERRQ(ierr);
if (!flg){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMultTransposeAdd()\n");CHKERRQ(ierr);
}
/* Do LUFactor() on both the matrices */
ierr = PetscMalloc(M*sizeof(PetscInt),&idx);CHKERRQ(ierr);
for (i=0; i<M; i++) idx[i] = i;
ierr = ISCreateGeneral(PETSC_COMM_SELF,M,idx,&is1);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,M,idx,&is2);CHKERRQ(ierr);
ierr = PetscFree(idx);CHKERRQ(ierr);
ierr = ISSetPermutation(is1);CHKERRQ(ierr);
ierr = ISSetPermutation(is2);CHKERRQ(ierr);
ierr = MatFactorInfoInitialize(&info);CHKERRQ(ierr);
info.fill = 2.0;
info.dtcol = 0.0;
info.zeropivot = 1.e-14;
info.pivotinblocks = 1.0;
ierr = MatLUFactor(B,is1,is2,&info);CHKERRQ(ierr);
ierr = MatLUFactor(A,is1,is2,&info);CHKERRQ(ierr);
/* Test MatSolveAdd() */
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = VecSetRandom(yy,rdm);CHKERRQ(ierr);
ierr = MatSolveAdd(B,xx,yy,s2);CHKERRQ(ierr);
ierr = MatSolveAdd(A,xx,yy,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolveAdd - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatSolveAdd() when x = A'b +x */
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = VecSetRandom(s1,rdm);CHKERRQ(ierr);
ierr = VecCopy(s2,s1);CHKERRQ(ierr);
ierr = MatSolveAdd(B,xx,s2,s2);CHKERRQ(ierr);
ierr = MatSolveAdd(A,xx,s1,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolveAdd(same) - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatSolve() */
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = MatSolve(B,xx,s2);CHKERRQ(ierr);
ierr = MatSolve(A,xx,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolve - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
/* Test MatSolveTranspose() */
if (bs < 8) {
for (i=0; i<10; i++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = MatSolveTranspose(B,xx,s2);CHKERRQ(ierr);
ierr = MatSolveTranspose(A,xx,s1);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatSolveTranspose - Norm1=%16.14e Norm2=%16.14e bs = %D\n",s1norm,s2norm,bs);CHKERRQ(ierr);
}
}
}
ierr = MatDestroy(A);CHKERRQ(ierr);
ierr = MatDestroy(B);CHKERRQ(ierr);
ierr = VecDestroy(xx);CHKERRQ(ierr);
ierr = VecDestroy(s1);CHKERRQ(ierr);
ierr = VecDestroy(s2);CHKERRQ(ierr);
ierr = VecDestroy(yy);CHKERRQ(ierr);
ierr = ISDestroy(is1);CHKERRQ(ierr);
ierr = ISDestroy(is2);CHKERRQ(ierr);
ierr = PetscRandomDestroy(rdm);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Mat C,F,Cpetsc,Csymm;
Vec u,x,b,bpla;
PetscErrorCode ierr;
PetscMPIInt rank,nproc;
PetscInt i,j,k,M = 10,m,nfact,nsolve,Istart,Iend,*im,*in,start,end;
PetscScalar *array,rval;
PetscReal norm,tol=1.e-12;
IS perm,iperm;
MatFactorInfo info;
PetscRandom rand;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &nproc);CHKERRQ(ierr);
/* Test non-symmetric operations */
/*-------------------------------*/
/* Create a Plapack dense matrix C */
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,M,M);CHKERRQ(ierr);
ierr = MatSetType(C,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
/* Create vectors */
ierr = MatGetOwnershipRange(C,&start,&end);CHKERRQ(ierr);
m = end - start;
/* printf("[%d] C - local size m: %d\n",rank,m); */
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,m,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecDuplicate(x,&bpla);CHKERRQ(ierr);
ierr = VecDuplicate(x,&u);CHKERRQ(ierr); /* save the true solution */
/* Create a petsc dense matrix Cpetsc */
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&Cpetsc);CHKERRQ(ierr);
ierr = MatSetSizes(Cpetsc,m,m,M,M);CHKERRQ(ierr);
ierr = MatSetType(Cpetsc,MATDENSE);CHKERRQ(ierr);
ierr = MatMPIDenseSetPreallocation(Cpetsc,PETSC_NULL);CHKERRQ(ierr);
ierr = MatSetFromOptions(Cpetsc);CHKERRQ(ierr);
ierr = MatSetUp(Cpetsc);CHKERRQ(ierr);
ierr = MatSetOption(Cpetsc,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatSetOption(C,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
/* Assembly */
/* PLAPACK doesn't support INSERT_VALUES mode, zero all entries before calling MatSetValues() */
ierr = MatZeroEntries(C);CHKERRQ(ierr);
ierr = MatZeroEntries(Cpetsc);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(C,&Istart,&Iend);CHKERRQ(ierr);
/* printf(" [%d] C m: %d, Istart/end: %d %d\n",rank,m,Istart,Iend); */
ierr = PetscMalloc((m*M+1)*sizeof(PetscScalar),&array);CHKERRQ(ierr);
ierr = PetscMalloc2(m,PetscInt,&im,M,PetscInt,&in);CHKERRQ(ierr);
k = 0;
for (j=0; j<M; j++){ /* column oriented! */
in[j] = j;
for (i=0; i<m; i++){
im[i] = i+Istart;
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[k++] = rval;
}
}
ierr = MatSetValues(Cpetsc,m,im,M,in,array,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,m,im,M,in,array,ADD_VALUES);CHKERRQ(ierr);
ierr = PetscFree(array);CHKERRQ(ierr);
ierr = PetscFree2(im,in);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/*
if (!rank) {printf("main, Cpetsc: \n");}
ierr = MatView(Cpetsc,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
*/
ierr = MatGetOrdering(C,MATORDERINGNATURAL,&perm,&iperm);CHKERRQ(ierr);
/* Test nonsymmetric MatMult() */
ierr = VecGetArray(x,&array);CHKERRQ(ierr);
for (i=0; i<m; i++){
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[i] = rval;
}
ierr = VecRestoreArray(x,&array);CHKERRQ(ierr);
ierr = MatMult(Cpetsc,x,b);CHKERRQ(ierr);
ierr = MatMult(C,x,bpla);CHKERRQ(ierr);
ierr = VecAXPY(bpla,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(bpla,NORM_2,&norm);CHKERRQ(ierr);
if (norm > 1.e-12 && !rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"Nonsymmetric MatMult_Plapack error: |b_pla - b|= %g\n",norm);CHKERRQ(ierr);
}
/* Test LU Factorization */
if (nproc == 1){
ierr = MatGetFactor(C,MATSOLVERPETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
} else {
ierr = MatGetFactor(C,MATSOLVERPLAPACK,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
}
ierr = MatLUFactorSymbolic(F,C,perm,iperm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 2; nfact++){
if (!rank) printf(" LU nfact %d\n",nfact);
if (nfact>0){ /* change matrix value for testing repeated MatLUFactorNumeric() */
if (!rank){
i = j = 0;
rval = nfact;
ierr = MatSetValues(Cpetsc,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
} else { /* PLAPACK seems requiring all processors call MatSetValues(), so we add 0.0 on processesses with rank>0! */
i = j = 0;
rval = 0.0;
ierr = MatSetValues(Cpetsc,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
}
ierr = MatLUFactorNumeric(F,C,&info);CHKERRQ(ierr);
/* Test MatSolve() */
for (nsolve = 0; nsolve < 2; nsolve++){
ierr = VecGetArray(x,&array);CHKERRQ(ierr);
for (i=0; i<m; i++){
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[i] = rval;
/* array[i] = rank + 1; */
}
ierr = VecRestoreArray(x,&array);CHKERRQ(ierr);
ierr = VecCopy(x,u);CHKERRQ(ierr);
ierr = MatMult(C,x,b);CHKERRQ(ierr);
ierr = MatSolve(F,b,x);CHKERRQ(ierr);
/* Check the error */
ierr = VecAXPY(u,-1.0,x);CHKERRQ(ierr); /* u <- (-1.0)x + u */
ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol){
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: Norm of error %g, LU nfact %d\n",norm,nfact);CHKERRQ(ierr);
}
}
}
}
ierr = MatDestroy(&F);CHKERRQ(ierr);
/* Test non-symmetric operations */
/*-------------------------------*/
/* Create a symmetric Plapack dense matrix Csymm */
ierr = MatCreate(PETSC_COMM_WORLD,&Csymm);CHKERRQ(ierr);
ierr = MatSetSizes(Csymm,PETSC_DECIDE,PETSC_DECIDE,M,M);CHKERRQ(ierr);
ierr = MatSetType(Csymm,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(Csymm);CHKERRQ(ierr);
ierr = MatSetUp(Csymm);CHKERRQ(ierr);
ierr = MatSetOption(Csymm,MAT_ROW_ORIENTED,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatSetOption(Csymm,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatSetOption(Csymm,MAT_SYMMETRY_ETERNAL,PETSC_TRUE);CHKERRQ(ierr);
ierr = MatZeroEntries(Csymm);CHKERRQ(ierr);
ierr = MatZeroEntries(Cpetsc);CHKERRQ(ierr);
for (i=Istart; i<Iend; i++){
for (j=0; j<=i; j++){
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
ierr = MatSetValues(Cpetsc,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(Csymm,1,&i,1,&j,&rval,ADD_VALUES);CHKERRQ(ierr);
if (j<i){
/* Although PLAPACK only requires lower triangular entries, we must add all the entries.
MatSetValues_Plapack() will ignore the upper triangular entries AFTER an index map! */
ierr = MatSetValues(Cpetsc,1,&j,1,&i,&rval,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(Csymm,1,&j,1,&i,&rval,ADD_VALUES);CHKERRQ(ierr);
}
}
}
ierr = MatAssemblyBegin(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Cpetsc,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(Csymm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Csymm,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Test symmetric MatMult() */
ierr = VecGetArray(x,&array);CHKERRQ(ierr);
for (i=0; i<m; i++){
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[i] = rval;
}
ierr = VecRestoreArray(x,&array);CHKERRQ(ierr);
ierr = MatMult(Cpetsc,x,b);CHKERRQ(ierr);
ierr = MatMult(Csymm,x,bpla);CHKERRQ(ierr);
ierr = VecAXPY(bpla,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(bpla,NORM_2,&norm);CHKERRQ(ierr);
if (norm > 1.e-12 && !rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"Symmetric MatMult_Plapack error: |b_pla - b|= %g\n",norm);CHKERRQ(ierr);
}
/* Test Cholesky Factorization */
ierr = MatShift(Csymm,M);CHKERRQ(ierr); /* make Csymm positive definite */
if (nproc == 1){
ierr = MatGetFactor(Csymm,MATSOLVERPETSC,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr);
} else {
ierr = MatGetFactor(Csymm,MATSOLVERPLAPACK,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr);
}
ierr = MatCholeskyFactorSymbolic(F,Csymm,perm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 2; nfact++){
if (!rank) printf(" Cholesky nfact %d\n",nfact);
ierr = MatCholeskyFactorNumeric(F,Csymm,&info);CHKERRQ(ierr);
/* Test MatSolve() */
for (nsolve = 0; nsolve < 2; nsolve++){
ierr = VecGetArray(x,&array);CHKERRQ(ierr);
for (i=0; i<m; i++){
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
array[i] = rval;
}
ierr = VecRestoreArray(x,&array);CHKERRQ(ierr);
ierr = VecCopy(x,u);CHKERRQ(ierr);
ierr = MatMult(Csymm,x,b);CHKERRQ(ierr);
ierr = MatSolve(F,b,x);CHKERRQ(ierr);
/* Check the error */
ierr = VecAXPY(u,-1.0,x);CHKERRQ(ierr); /* u <- (-1.0)x + u */
ierr = VecNorm(u,NORM_2,&norm);CHKERRQ(ierr);
if (norm > tol){
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: Norm of error %g, Cholesky nfact %d\n",norm,nfact);CHKERRQ(ierr);
}
}
}
}
ierr = MatDestroy(&F);CHKERRQ(ierr);
/* Free data structures */
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = ISDestroy(&iperm);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&bpla);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = MatDestroy(&Cpetsc);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&Csymm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscInt main(PetscInt argc,char **args)
{
Mat A,As;
Vec x,y,ys;
PetscTruth flg,disp_mat=PETSC_FALSE,disp_vec=PETSC_FALSE;
PetscErrorCode ierr;
PetscMPIInt size,rank;
PetscInt m,i,j;
PetscScalar v,sigma2;
PetscRandom rctx;
PetscReal h2,sigma1=100.0,norm;
PetscInt dim,Ii,J,n = 3,use_random,rstart,rend;
PetscInitialize(&argc,&args,(char *)0,help);
#if !defined(PETSC_USE_COMPLEX)
SETERRQ(1,"This example requires complex numbers");
#endif
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL, "-display_mat", &disp_mat);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL, "-display_vec", &disp_vec);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(PETSC_NULL,"-sigma1",&sigma1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
dim = n*n;
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,dim,dim);CHKERRQ(ierr);
ierr = MatSetType(A,MATAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-norandom",&flg);CHKERRQ(ierr);
if (flg) use_random = 0;
else use_random = 1;
if (use_random) {
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(rctx,0.0,PETSC_i);CHKERRQ(ierr);
ierr = PetscRandomGetValue(rctx,&sigma2);CHKERRQ(ierr); /* RealPart(sigma2) == 0.0 */
} else {
sigma2 = 10.0*PETSC_i;
}
h2 = 1.0/((n+1)*(n+1));
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
for (Ii=rstart; Ii<rend; Ii++) {
v = -1.0; i = Ii/n; j = Ii - i*n;
if (i>0) {
J = Ii-n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (i<n-1) {
J = Ii+n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (j>0) {
J = Ii-1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (j<n-1) {
J = Ii+1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
v = 4.0 - sigma1*h2;
ierr = MatSetValues(A,1,&Ii,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Check whether A is symmetric */
ierr = PetscOptionsHasName(PETSC_NULL, "-check_symmetric", &flg);CHKERRQ(ierr);
if (flg) {
Mat Trans;
ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Trans);
ierr = MatEqual(A, Trans, &flg);
if (!flg) SETERRQ(PETSC_ERR_USER,"A is not symmetric");
ierr = MatDestroy(Trans);CHKERRQ(ierr);
}
ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
/* make A complex Hermitian */
Ii = 0; J = dim-1;
if (Ii >= rstart && Ii < rend){
v = sigma2*h2; /* RealPart(v) = 0.0 */
ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
v = -sigma2*h2;
ierr = MatSetValues(A,1,&J,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
Ii = dim-2; J = dim-1;
if (Ii >= rstart && Ii < rend){
v = sigma2*h2; /* RealPart(v) = 0.0 */
ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
v = -sigma2*h2;
ierr = MatSetValues(A,1,&J,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Check whether A is Hermitian */
ierr = PetscOptionsHasName(PETSC_NULL, "-check_Hermitian", &flg);CHKERRQ(ierr);
if (flg) {
Mat Hermit;
if (disp_mat){
if (!rank) printf(" A:\n");
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = MatHermitianTranspose(A,MAT_INITIAL_MATRIX, &Hermit);
if (disp_mat){
if (!rank) printf(" A_Hermitian:\n");
ierr = MatView(Hermit,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = MatEqual(A, Hermit, &flg);
if (!flg) SETERRQ(PETSC_ERR_USER,"A is not Hermitian");
ierr = MatDestroy(Hermit);CHKERRQ(ierr);
}
ierr = MatSetOption(A,MAT_HERMITIAN,PETSC_TRUE);CHKERRQ(ierr);
/* Create a Hermitian matrix As in sbaij format */
ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&As);CHKERRQ(ierr);
if (disp_mat){
if (!rank) {ierr = PetscPrintf(PETSC_COMM_SELF," As:\n");CHKERRQ(ierr);}
ierr = MatView(As,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
if (use_random){
ierr = VecSetRandom(x,rctx);CHKERRQ(ierr);
} else {
ierr = VecSet(x,1.0);CHKERRQ(ierr);
}
/* Create vectors */
ierr = VecCreate(PETSC_COMM_WORLD,&y);CHKERRQ(ierr);
ierr = VecSetSizes(y,m,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(y);CHKERRQ(ierr);
ierr = VecDuplicate(y,&ys);CHKERRQ(ierr);
/* Test MatMult */
ierr = MatMult(A,x,y);CHKERRQ(ierr);
ierr = MatMult(As,x,ys);CHKERRQ(ierr);
if (disp_vec){
printf("y = A*x:\n");
ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"ys = As*x:\n");
ierr = VecView(ys,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecAXPY(y,-1.0,ys);CHKERRQ(ierr);
ierr = VecNorm(y,NORM_INFINITY,&norm);CHKERRQ(ierr);
if (norm > 1.e-12 || disp_vec){
printf("|| A*x - As*x || = %G\n",norm);
}
/* Free spaces */
if (use_random) {ierr = PetscRandomDestroy(rctx);CHKERRQ(ierr);}
ierr = MatDestroy(A);CHKERRQ(ierr);
ierr = MatDestroy(As);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = VecDestroy(y);CHKERRQ(ierr);
ierr = VecDestroy(ys);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Mat A,Atrans,sA,*submatA,*submatsA;
PetscInt bs=1,m=43,ov=1,i,j,k,*rows,*cols,M,nd=5,*idx,mm,nn;
PetscErrorCode ierr;
PetscMPIInt size;
PetscScalar *vals,rval,one=1.0;
IS *is1,*is2;
PetscRandom rand;
Vec xx,s1,s2;
PetscReal s1norm,s2norm,rnorm,tol = 1.e-10;
PetscBool flg;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_block_size",&bs,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-mat_size",&m,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-ov",&ov,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-nd",&nd,PETSC_NULL);CHKERRQ(ierr);
/* create a SeqBAIJ matrix A */
M = m*bs;
ierr = MatCreateSeqBAIJ(PETSC_COMM_SELF,bs,M,M,1,PETSC_NULL,&A);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = PetscMalloc(bs*sizeof(PetscInt),&rows);CHKERRQ(ierr);
ierr = PetscMalloc(bs*sizeof(PetscInt),&cols);CHKERRQ(ierr);
ierr = PetscMalloc(bs*bs*sizeof(PetscScalar),&vals);CHKERRQ(ierr);
ierr = PetscMalloc(M*sizeof(PetscScalar),&idx);CHKERRQ(ierr);
/* Now set blocks of random values */
/* first, set diagonal blocks as zero */
for (j=0; j<bs*bs; j++) vals[j] = 0.0;
for (i=0; i<m; i++){
cols[0] = i*bs; rows[0] = i*bs;
for (j=1; j<bs; j++) {
rows[j] = rows[j-1]+1;
cols[j] = cols[j-1]+1;
}
ierr = MatSetValues(A,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
}
/* second, add random blocks */
for (i=0; i<20*bs; i++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
cols[0] = bs*(int)(PetscRealPart(rval)*m);
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
rows[0] = bs*(int)(PetscRealPart(rval)*m);
for (j=1; j<bs; j++) {
rows[j] = rows[j-1]+1;
cols[j] = cols[j-1]+1;
}
for (j=0; j<bs*bs; j++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
vals[j] = rval;
}
ierr = MatSetValues(A,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* make A a symmetric matrix: A <- A^T + A */
ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Atrans);CHKERRQ(ierr);
ierr = MatAXPY(A,one,Atrans,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatDestroy(&Atrans);CHKERRQ(ierr);
ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Atrans);
ierr = MatEqual(A, Atrans, &flg);
if (!flg) {
SETERRQ(PETSC_COMM_SELF,1,"A+A^T is non-symmetric");
}
ierr = MatDestroy(&Atrans);CHKERRQ(ierr);
/* create a SeqSBAIJ matrix sA (= A) */
ierr = MatConvert(A,MATSEQSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr);
/* Test sA==A through MatMult() */
for (i=0; i<nd; i++) {
ierr = MatGetSize(A,&mm,&nn);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,mm,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
for (j=0; j<3; j++) {
ierr = VecSetRandom(xx,rand);CHKERRQ(ierr);
ierr = MatMult(A,xx,s1);CHKERRQ(ierr);
ierr = MatMult(sA,xx,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMult - Norm1=%16.14e Norm2=%16.14e\n",s1norm,s2norm);CHKERRQ(ierr);
}
}
ierr = VecDestroy(&xx);CHKERRQ(ierr);
ierr = VecDestroy(&s1);CHKERRQ(ierr);
ierr = VecDestroy(&s2);CHKERRQ(ierr);
}
/* Test MatIncreaseOverlap() */
ierr = PetscMalloc(nd*sizeof(IS **),&is1);CHKERRQ(ierr);
ierr = PetscMalloc(nd*sizeof(IS **),&is2);CHKERRQ(ierr);
for (i=0; i<nd; i++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
size = (int)(PetscRealPart(rval)*m);
for (j=0; j<size; j++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
idx[j*bs] = bs*(int)(PetscRealPart(rval)*m);
for (k=1; k<bs; k++) idx[j*bs+k] = idx[j*bs]+k;
}
ierr = ISCreateGeneral(PETSC_COMM_SELF,size*bs,idx,PETSC_COPY_VALUES,is1+i);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,size*bs,idx,PETSC_COPY_VALUES,is2+i);CHKERRQ(ierr);
}
/* for debugging */
/*
ierr = MatView(A,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = MatView(sA,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
*/
ierr = MatIncreaseOverlap(A,nd,is1,ov);CHKERRQ(ierr);
ierr = MatIncreaseOverlap(sA,nd,is2,ov);CHKERRQ(ierr);
for (i=0; i<nd; ++i) {
ierr = ISSort(is1[i]);CHKERRQ(ierr);
ierr = ISSort(is2[i]);CHKERRQ(ierr);
}
for (i=0; i<nd; ++i) {
ierr = ISEqual(is1[i],is2[i],&flg);CHKERRQ(ierr);
if (!flg){
/* ISView(is1[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ISView(is2[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); */
SETERRQ1(PETSC_COMM_SELF,1,"i=%d, is1 != is2",i);
}
}
ierr = MatGetSubMatrices(A,nd,is1,is1,MAT_INITIAL_MATRIX,&submatA);CHKERRQ(ierr);
ierr = MatGetSubMatrices(sA,nd,is2,is2,MAT_INITIAL_MATRIX,&submatsA);CHKERRQ(ierr);
/* Test MatMult() */
for (i=0; i<nd; i++) {
ierr = MatGetSize(submatA[i],&mm,&nn);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,mm,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
for (j=0; j<3; j++) {
ierr = VecSetRandom(xx,rand);CHKERRQ(ierr);
ierr = MatMult(submatA[i],xx,s1);CHKERRQ(ierr);
ierr = MatMult(submatsA[i],xx,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMult - Norm1=%16.14e Norm2=%16.14e\n",s1norm,s2norm);CHKERRQ(ierr);
}
}
ierr = VecDestroy(&xx);CHKERRQ(ierr);
ierr = VecDestroy(&s1);CHKERRQ(ierr);
ierr = VecDestroy(&s2);CHKERRQ(ierr);
}
/* Now test MatGetSubmatrices with MAT_REUSE_MATRIX option */
ierr = MatGetSubMatrices(A,nd,is1,is1,MAT_REUSE_MATRIX,&submatA);CHKERRQ(ierr);
ierr = MatGetSubMatrices(sA,nd,is2,is2,MAT_REUSE_MATRIX,&submatsA);CHKERRQ(ierr);
/* Test MatMult() */
for (i=0; i<nd; i++) {
ierr = MatGetSize(submatA[i],&mm,&nn);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,mm,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
for (j=0; j<3; j++) {
ierr = VecSetRandom(xx,rand);CHKERRQ(ierr);
ierr = MatMult(submatA[i],xx,s1);CHKERRQ(ierr);
ierr = MatMult(submatsA[i],xx,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMult - Norm1=%16.14e Norm2=%16.14e\n",s1norm,s2norm);CHKERRQ(ierr);
}
}
ierr = VecDestroy(&xx);CHKERRQ(ierr);
ierr = VecDestroy(&s1);CHKERRQ(ierr);
ierr = VecDestroy(&s2);CHKERRQ(ierr);
}
/* Free allocated memory */
for (i=0; i<nd; ++i) {
ierr = ISDestroy(&is1[i]);CHKERRQ(ierr);
ierr = ISDestroy(&is2[i]);CHKERRQ(ierr);
ierr = MatDestroy(&submatA[i]);CHKERRQ(ierr);
ierr = MatDestroy(&submatsA[i]);CHKERRQ(ierr);
}
ierr = PetscFree(submatA);CHKERRQ(ierr);
ierr = PetscFree(submatsA);CHKERRQ(ierr);
ierr = PetscFree(is1);CHKERRQ(ierr);
ierr = PetscFree(is2);CHKERRQ(ierr);
ierr = PetscFree(idx);CHKERRQ(ierr);
ierr = PetscFree(rows);CHKERRQ(ierr);
ierr = PetscFree(cols);CHKERRQ(ierr);
ierr = PetscFree(vals);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&sA);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
Mat A,B,C,D;
PetscInt i,M=10,N=5,j,nrows,ncols,am,an,rstart,rend;
PetscErrorCode ierr;
PetscRandom r;
PetscBool equal,iselemental;
PetscReal fill = 1.0;
IS isrows,iscols;
const PetscInt *rows,*cols;
PetscScalar *v,rval;
#if defined(PETSC_HAVE_ELEMENTAL)
PetscBool Test_MatMatMult=PETSC_TRUE;
#else
PetscBool Test_MatMatMult=PETSC_FALSE;
#endif
PetscMPIInt size;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,M,N);CHKERRQ(ierr);
ierr = MatSetType(A,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
/* Set local matrix entries */
ierr = MatGetOwnershipIS(A,&isrows,&iscols);CHKERRQ(ierr);
ierr = ISGetLocalSize(isrows,&nrows);CHKERRQ(ierr);
ierr = ISGetIndices(isrows,&rows);CHKERRQ(ierr);
ierr = ISGetLocalSize(iscols,&ncols);CHKERRQ(ierr);
ierr = ISGetIndices(iscols,&cols);CHKERRQ(ierr);
ierr = PetscMalloc1(nrows*ncols,&v);CHKERRQ(ierr);
for (i=0; i<nrows; i++) {
for (j=0; j<ncols; j++) {
ierr = PetscRandomGetValue(r,&rval);CHKERRQ(ierr);
v[i*ncols+j] = rval;
}
}
ierr = MatSetValues(A,nrows,rows,ncols,cols,v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = ISRestoreIndices(isrows,&rows);CHKERRQ(ierr);
ierr = ISRestoreIndices(iscols,&cols);CHKERRQ(ierr);
ierr = ISDestroy(&isrows);CHKERRQ(ierr);
ierr = ISDestroy(&iscols);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&r);CHKERRQ(ierr);
/* Test MatTranspose() */
ierr = MatCreateTranspose(A,&C);CHKERRQ(ierr);
ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); /* B = A^T */
ierr = MatMultEqual(C,B,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"A^T*x != (x^T*A)^T");
ierr = MatTranspose(A,MAT_REUSE_MATRIX,&B);CHKERRQ(ierr); /* B = A^T */
ierr = MatMultEqual(C,B,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"A^T*x != (x^T*A)^T");
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDuplicate(A,MAT_COPY_VALUES,&B);CHKERRQ(ierr);
ierr = MatTranspose(B,MAT_INPLACE_MATRIX,&B);CHKERRQ(ierr);
ierr = MatMultEqual(C,B,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"A^T*x != (x^T*A)^T");
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
/* Test MatMatMult() */
if (Test_MatMatMult) {
#if !defined(PETSC_HAVE_ELEMENTAL)
if (size > 1) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"This test requires ELEMENTAL");
#endif
ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); /* B = A^T */
ierr = MatMatMult(B,A,MAT_INITIAL_MATRIX,fill,&C);CHKERRQ(ierr); /* C = B*A = A^T*A */
ierr = MatMatMult(B,A,MAT_REUSE_MATRIX,fill,&C);CHKERRQ(ierr);
/* Test MatDuplicate for matrix product */
ierr = MatDuplicate(C,MAT_COPY_VALUES,&D);CHKERRQ(ierr);
ierr = MatDestroy(&D);CHKERRQ(ierr);
/* Test B*A*x = C*x for n random vector x */
ierr = MatMatMultEqual(B,A,C,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"B*A*x != C*x");
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatMatMultSymbolic(B,A,fill,&C);CHKERRQ(ierr);
for (i=0; i<2; i++) {
/* Repeat the numeric product to test reuse of the previous symbolic product */
ierr = MatMatMultNumeric(B,A,C);CHKERRQ(ierr);
ierr = MatMatMultEqual(B,A,C,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"B*A*x != C*x");
}
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
}
/* Test MatTransposeMatMult() */
ierr = PetscObjectTypeCompare((PetscObject)A,MATELEMENTAL,&iselemental);CHKERRQ(ierr);
if (!iselemental) {
ierr = MatTransposeMatMult(A,A,MAT_INITIAL_MATRIX,fill,&D);CHKERRQ(ierr); /* D = A^T*A */
ierr = MatTransposeMatMult(A,A,MAT_REUSE_MATRIX,fill,&D);CHKERRQ(ierr);
/* Test MatDuplicate for matrix product */
ierr = MatDuplicate(D,MAT_COPY_VALUES,&C);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
/* ierr = MatView(D,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
ierr = MatTransposeMatMultEqual(A,A,D,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"D*x != A^T*A*x");
ierr = MatDestroy(&D);CHKERRQ(ierr);
/* Test D*x = A^T*C*A*x, where C is in AIJ format */
ierr = MatGetLocalSize(A,&am,&an);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
if (size == 1) {
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,am,am);CHKERRQ(ierr);
} else {
ierr = MatSetSizes(C,am,am,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
}
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(C,&rstart,&rend);CHKERRQ(ierr);
v[0] = 1.0;
for (i=rstart; i<rend; i++) {
ierr = MatSetValues(C,1,&i,1,&i,v,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* B = C*A, D = A^T*B */
ierr = MatMatMult(C,A,MAT_INITIAL_MATRIX,1.0,&B);CHKERRQ(ierr);
ierr = MatTransposeMatMult(A,B,MAT_INITIAL_MATRIX,fill,&D);CHKERRQ(ierr);
ierr = MatTransposeMatMultEqual(A,B,D,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"D*x != A^T*B*x");
ierr = MatDestroy(&D);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFree(v);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int test2(void)
{
PetscLogDouble t1,t2;
double value;
int i,ierr,z[20000],zi[20000],intval,tmp;
PetscScalar x[20000],y[20000];
PetscRandom r;
ierr = PetscRandomCreate(PETSC_COMM_SELF,&r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
/* Take care of paging effects */
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
for (i=0; i<20000; i++) {
x[i] = i;
y[i] = i;
z[i] = i;
zi[i] = i;
}
/* Form the random set of integers */
for (i=0; i<20000; i++) {
ierr = PetscRandomGetValue(r,&value);CHKERRQ(ierr);
intval = (int)(value*20000.0);
tmp = z[i];
z[i] = z[intval];
z[intval] = tmp;
}
for (i=0; i<20000; i++) {
ierr = PetscRandomGetValue(r,&value);CHKERRQ(ierr);
intval = (int)(value*20000.0);
tmp = zi[i];
zi[i] = zi[intval];
zi[intval] = tmp;
}
/* fprintf(stdout,"Done setup\n"); */
/* ierr = BlastCache();CHKERRQ(ierr); */
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
for (i=0; i<2000; i++) { x[i] = y[i]; }
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
fprintf(stdout,"%-27s : %e sec\n","x[i] = y[i]",(t2-t1)/2000.0);
/* ierr = BlastCache();CHKERRQ(ierr); */
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
for (i=0; i<2000; i++) { y[i] = x[z[i]]; }
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
fprintf(stdout,"%-27s : %e sec\n","x[i] = y[idx[i]]",(t2-t1)/2000.0);
/* ierr = BlastCache();CHKERRQ(ierr); */
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
for (i=0; i<2000; i++) { x[z[i]] = y[i]; }
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
fprintf(stdout,"%-27s : %e sec\n","x[z[i]] = y[i]",(t2-t1)/2000.0);
/* ierr = BlastCache();CHKERRQ(ierr); */
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
for (i=0; i<2000; i++) { y[z[i]] = x[zi[i]]; }
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
fprintf(stdout,"%-27s : %e sec\n","x[z[i]] = y[zi[i]]",(t2-t1)/2000.0);
PetscRandomDestroy(r);
PetscFunctionReturn(0);
}
int main(int argc,char **argv) {
Mat A,B;
PetscInt i,j,column;
PetscInt *di,*dj,*oi,*oj;
PetscScalar *oa,*da,value;
PetscRandom rctx;
PetscErrorCode ierr;
PetscBool equal;
Mat_SeqAIJ *daij,*oaij;
Mat_MPIAIJ *Ampiaij;
PetscMPIInt size,rank;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size == 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"Must run with 2 or more processes");CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
/* Create a mpiaij matrix for checking */
ierr = MatCreateAIJ(PETSC_COMM_WORLD,5,5,PETSC_DECIDE,PETSC_DECIDE,0,PETSC_NULL,0,PETSC_NULL,&A);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
for (i=5*rank; i<5*rank+5; i++) {
for (j=0; j<5*size; j++){
ierr = PetscRandomGetValue(rctx,&value);CHKERRQ(ierr);
column = (PetscInt) (5*size*PetscRealPart(value));
ierr = PetscRandomGetValue(rctx,&value);CHKERRQ(ierr);
ierr = MatSetValues(A,1,&i,1,&column,&value,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
Ampiaij = (Mat_MPIAIJ*) A->data;
daij = (Mat_SeqAIJ*) Ampiaij->A->data;
oaij = (Mat_SeqAIJ*) Ampiaij->B->data;
di = daij->i;
dj = daij->j;
da = daij->a;
oi = oaij->i;
oa = oaij->a;
ierr = PetscMalloc(oi[5]*sizeof(PetscInt),&oj);CHKERRQ(ierr);
ierr = PetscMemcpy(oj,oaij->j,oi[5]*sizeof(PetscInt));CHKERRQ(ierr);
/* modify the column entries in the non-diagonal portion back to global numbering */
for (i=0; i<oi[5]; i++) {
oj[i] = Ampiaij->garray[oj[i]];
}
ierr = MatCreateMPIAIJWithSplitArrays(PETSC_COMM_WORLD,5,5,PETSC_DETERMINE,PETSC_DETERMINE,di,dj,da,oi,oj,oa,&B);CHKERRQ(ierr);
ierr = MatSetUp(B);CHKERRQ(ierr);
ierr = MatEqual(A,B,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Likely a bug in MatCreateMPIAIJWithSplitArrays()");
/* Free spaces */
ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscFree(oj);CHKERRQ(ierr);
ierr = PetscFinalize();
return(0);
}
int main(int argc,char **args)
{
Vec x,b,u; /* approx solution, RHS, exact solution */
Mat A; /* linear system matrix */
KSP ksp; /* linear solver context */
PetscReal norm; /* norm of solution error */
PetscInt dim,i,j,Ii,J,Istart,Iend,n = 6,its,use_random;
PetscErrorCode ierr;
PetscScalar v,none = -1.0,sigma2,pfive = 0.5,*xa;
PetscRandom rctx;
PetscReal h2,sigma1 = 100.0;
PetscBool flg = PETSC_FALSE;
PetscScalar a = 1.0+PETSC_i;
PetscInitialize(&argc,&args,(char*)0,help);
#if !defined(PETSC_USE_COMPLEX)
SETERRQ(PETSC_COMM_WORLD,1,"This example requires complex numbers");
#endif
a=1.0+PETSC_i;
printf("%g+%gi\n",(double)PetscRealPart(a),(double)PetscImaginaryPart(a));
ierr = PetscOptionsGetReal(NULL,"-sigma1",&sigma1,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
dim = n*n;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the matrix and right-hand-side vector that define
the linear system, Ax = b.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create parallel matrix, specifying only its global dimensions.
When using MatCreate(), the matrix format can be specified at
runtime. Also, the parallel partitioning of the matrix is
determined by PETSc at runtime.
*/
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,dim,dim);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
/*
Currently, all PETSc parallel matrix formats are partitioned by
contiguous chunks of rows across the processors. Determine which
rows of the matrix are locally owned.
*/
ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
/*
Set matrix elements in parallel.
- Each processor needs to insert only elements that it owns
locally (but any non-local elements will be sent to the
appropriate processor during matrix assembly).
- Always specify global rows and columns of matrix entries.
*/
ierr = PetscOptionsGetBool(NULL,"-norandom",&flg,NULL);CHKERRQ(ierr);
if (flg) use_random = 0;
else use_random = 1;
if (use_random) {
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(rctx,0.0,PETSC_i);CHKERRQ(ierr);
} else {
sigma2 = 10.0*PETSC_i;
}
h2 = 1.0/((n+1)*(n+1));
for (Ii=Istart; Ii<Iend; Ii++) {
v = -1.0; i = Ii/n; j = Ii - i*n;
if (i>0) {
J = Ii-n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
}
if (i<n-1) {
J = Ii+n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
}
if (j>0) {
J = Ii-1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
}
if (j<n-1) {
J = Ii+1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
}
if (use_random) {ierr = PetscRandomGetValue(rctx,&sigma2);CHKERRQ(ierr);}
v = 4.0 - sigma1*h2 + sigma2*h2;
ierr = MatSetValues(A,1,&Ii,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
if (use_random) {ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);}
/*
Assemble matrix, using the 2-step process:
MatAssemblyBegin(), MatAssemblyEnd()
Computations can be done while messages are in transition
by placing code between these two statements.
*/
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/*
Create parallel vectors.
- When using VecCreate(), VecSetSizes() and VecSetFromOptions(),
we specify only the vector's global
dimension; the parallel partitioning is determined at runtime.
- Note: We form 1 vector from scratch and then duplicate as needed.
*/
ierr = VecCreate(PETSC_COMM_WORLD,&u);CHKERRQ(ierr);
ierr = VecSetSizes(u,PETSC_DECIDE,dim);CHKERRQ(ierr);
ierr = VecSetFromOptions(u);CHKERRQ(ierr);
ierr = VecDuplicate(u,&b);CHKERRQ(ierr);
ierr = VecDuplicate(b,&x);CHKERRQ(ierr);
/*
Set exact solution; then compute right-hand-side vector.
*/
if (use_random) {
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
ierr = VecSetRandom(u,rctx);CHKERRQ(ierr);
} else {
ierr = VecSet(u,pfive);CHKERRQ(ierr);
}
ierr = MatMult(A,u,b);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the linear solver and set various options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create linear solver context
*/
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
/*
Set operators. Here the matrix that defines the linear system
also serves as the preconditioning matrix.
*/
ierr = KSPSetOperators(ksp,A,A);CHKERRQ(ierr);
/*
Set runtime options, e.g.,
-ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
*/
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the linear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Check solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Print the first 3 entries of x; this demonstrates extraction of the
real and imaginary components of the complex vector, x.
*/
flg = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,"-print_x3",&flg,NULL);CHKERRQ(ierr);
if (flg) {
ierr = VecGetArray(x,&xa);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"The first three entries of x are:\n");CHKERRQ(ierr);
for (i=0; i<3; i++) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"x[%D] = %g + %g i\n",i,(double)PetscRealPart(xa[i]),(double)PetscImaginaryPart(xa[i]));CHKERRQ(ierr);
}
ierr = VecRestoreArray(x,&xa);CHKERRQ(ierr);
}
/*
Check the error
*/
ierr = VecAXPY(x,none,u);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of error %g iterations %D\n",(double)norm,its);CHKERRQ(ierr);
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
if (use_random) {ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);}
ierr = VecDestroy(&u);CHKERRQ(ierr); ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscInt main(PetscInt argc,char **args)
{
Mat A,As;
PetscBool flg,disp_mat=PETSC_FALSE;
PetscErrorCode ierr;
PetscMPIInt size,rank;
PetscInt i,j;
PetscScalar v,sigma2;
PetscRandom rctx;
PetscReal h2,sigma1=100.0;
PetscInt dim,Ii,J,n = 3,use_random,rstart,rend;
KSP ksp;
PC pc;
Mat F;
PetscInt nneg, nzero, npos;
PetscInitialize(&argc,&args,(char *)0,help);
#if !defined(PETSC_USE_COMPLEX)
SETERRQ(PETSC_COMM_WORLD,1,"This example requires complex numbers");
#endif
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL, "-display_mat", &disp_mat);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(PETSC_NULL,"-sigma1",&sigma1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
dim = n*n;
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,dim,dim);CHKERRQ(ierr);
ierr = MatSetType(A,MATAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-norandom",&flg);CHKERRQ(ierr);
if (flg) use_random = 0;
else use_random = 1;
if (use_random) {
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(rctx,0.0,PETSC_i);CHKERRQ(ierr);
ierr = PetscRandomGetValue(rctx,&sigma2);CHKERRQ(ierr); /* RealPart(sigma2) == 0.0 */
} else {
sigma2 = 10.0*PETSC_i;
}
h2 = 1.0/((n+1)*(n+1));
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
for (Ii=rstart; Ii<rend; Ii++) {
v = -1.0; i = Ii/n; j = Ii - i*n;
if (i>0) {
J = Ii-n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (i<n-1) {
J = Ii+n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (j>0) {
J = Ii-1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (j<n-1) {
J = Ii+1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
v = 4.0 - sigma1*h2;
ierr = MatSetValues(A,1,&Ii,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Check whether A is symmetric */
ierr = PetscOptionsHasName(PETSC_NULL, "-check_symmetric", &flg);CHKERRQ(ierr);
if (flg) {
Mat Trans;
ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Trans);
ierr = MatEqual(A, Trans, &flg);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"A is not symmetric");
ierr = MatDestroy(&Trans);CHKERRQ(ierr);
}
ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
/* make A complex Hermitian */
Ii = 0; J = dim-1;
if (Ii >= rstart && Ii < rend){
v = sigma2*h2; /* RealPart(v) = 0.0 */
ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
v = -sigma2*h2;
ierr = MatSetValues(A,1,&J,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
Ii = dim-2; J = dim-1;
if (Ii >= rstart && Ii < rend){
v = sigma2*h2; /* RealPart(v) = 0.0 */
ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
v = -sigma2*h2;
ierr = MatSetValues(A,1,&J,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Check whether A is Hermitian */
ierr = PetscOptionsHasName(PETSC_NULL, "-check_Hermitian", &flg);CHKERRQ(ierr);
if (flg) {
Mat Hermit;
if (disp_mat){
if (!rank) printf(" A:\n");
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = MatHermitianTranspose(A,MAT_INITIAL_MATRIX, &Hermit);
if (disp_mat){
if (!rank) printf(" A_Hermitian:\n");
ierr = MatView(Hermit,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = MatEqual(A, Hermit, &flg);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_USER,"A is not Hermitian");
ierr = MatDestroy(&Hermit);CHKERRQ(ierr);
}
ierr = MatSetOption(A,MAT_HERMITIAN,PETSC_TRUE);CHKERRQ(ierr);
/* Create a Hermitian matrix As in sbaij format */
ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&As);CHKERRQ(ierr);
if (disp_mat){
if (!rank) {ierr = PetscPrintf(PETSC_COMM_SELF," As:\n");CHKERRQ(ierr);}
ierr = MatView(As,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Test MatGetInertia() */
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPPREONLY);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,As,As,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCCHOLESKY);CHKERRQ(ierr);
ierr = PCSetFromOptions(pc);CHKERRQ(ierr);
ierr = PCSetUp(pc);CHKERRQ(ierr);
ierr = PCFactorGetMatrix(pc,&F);CHKERRQ(ierr);
ierr = MatGetInertia(F,&nneg,&nzero,&npos);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF," MatInertia: nneg: %D, nzero: %D, npos: %D\n",nneg,nzero,npos);CHKERRQ(ierr);
}
/* Free spaces */
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
if (use_random) {ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&As);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscInt main(PetscInt argc,char **args)
{
Mat A,A_dense,B;
Vec *evecs;
PetscBool flg,TestZHEEV=PETSC_TRUE,TestZHEEVX=PETSC_FALSE,TestZHEGV=PETSC_FALSE,TestZHEGVX=PETSC_FALSE;
PetscErrorCode ierr;
PetscBool isSymmetric;
PetscScalar sigma,*arrayA,*arrayB,*evecs_array=NULL,*work;
PetscReal *evals,*rwork;
PetscMPIInt size;
PetscInt m,i,j,nevs,il,iu,cklvl=2;
PetscReal vl,vu,abstol=1.e-8;
PetscBLASInt *iwork,*ifail,lwork,lierr,bn;
PetscReal tols[2];
PetscInt nzeros[2],nz;
PetscReal ratio;
PetscScalar v,none = -1.0,sigma2,pfive = 0.5,*xa;
PetscRandom rctx;
PetscReal h2,sigma1 = 100.0;
PetscInt dim,Ii,J,Istart,Iend,n = 6,its,use_random,one=1;
PetscInitialize(&argc,&args,(char*)0,help);
#if !defined(PETSC_USE_COMPLEX)
SETERRQ(PETSC_COMM_WORLD,1,"This example requires complex numbers");
#endif
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_SUP,"This is a uniprocessor example only!");
ierr = PetscOptionsHasName(NULL, "-test_zheevx", &flg);CHKERRQ(ierr);
if (flg) {
TestZHEEV = PETSC_FALSE;
TestZHEEVX = PETSC_TRUE;
}
ierr = PetscOptionsHasName(NULL, "-test_zhegv", &flg);CHKERRQ(ierr);
if (flg) {
TestZHEEV = PETSC_FALSE;
TestZHEGV = PETSC_TRUE;
}
ierr = PetscOptionsHasName(NULL, "-test_zhegvx", &flg);CHKERRQ(ierr);
if (flg) {
TestZHEEV = PETSC_FALSE;
TestZHEGVX = PETSC_TRUE;
}
ierr = PetscOptionsGetReal(NULL,"-sigma1",&sigma1,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
dim = n*n;
ierr = MatCreate(PETSC_COMM_SELF,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,dim,dim);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-norandom",&flg);CHKERRQ(ierr);
if (flg) use_random = 0;
else use_random = 1;
if (use_random) {
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(rctx,0.0,PETSC_i);CHKERRQ(ierr);
} else {
sigma2 = 10.0*PETSC_i;
}
h2 = 1.0/((n+1)*(n+1));
for (Ii=0; Ii<dim; Ii++) {
v = -1.0; i = Ii/n; j = Ii - i*n;
if (i>0) {
J = Ii-n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
}
if (i<n-1) {
J = Ii+n; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
}
if (j>0) {
J = Ii-1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
}
if (j<n-1) {
J = Ii+1; ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
}
if (use_random) {ierr = PetscRandomGetValue(rctx,&sigma2);CHKERRQ(ierr);}
v = 4.0 - sigma1*h2;
ierr = MatSetValues(A,1,&Ii,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
/* make A complex Hermitian */
v = sigma2*h2;
Ii = 0; J = 1;
ierr = MatSetValues(A,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);
v = -sigma2*h2;
ierr = MatSetValues(A,1,&J,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
if (use_random) {ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
m = n = dim;
/* Check whether A is symmetric */
ierr = PetscOptionsHasName(NULL, "-check_symmetry", &flg);CHKERRQ(ierr);
if (flg) {
Mat Trans;
ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Trans);
ierr = MatEqual(A, Trans, &isSymmetric);
if (!isSymmetric) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_USER,"A must be symmetric");
ierr = MatDestroy(&Trans);CHKERRQ(ierr);
}
/* Convert aij matrix to MatSeqDense for LAPACK */
ierr = PetscObjectTypeCompare((PetscObject)A,MATSEQDENSE,&flg);CHKERRQ(ierr);
if (flg) {
ierr = MatDuplicate(A,MAT_COPY_VALUES,&A_dense);CHKERRQ(ierr);
} else {
ierr = MatConvert(A,MATSEQDENSE,MAT_INITIAL_MATRIX,&A_dense);CHKERRQ(ierr);
}
ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,PETSC_DECIDE,PETSC_DECIDE,dim,dim);CHKERRQ(ierr);
ierr = MatSetType(B,MATSEQDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
v = 1.0;
for (Ii=0; Ii<dim; Ii++) {
ierr = MatSetValues(B,1,&Ii,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
/* Solve standard eigenvalue problem: A*x = lambda*x */
/*===================================================*/
ierr = PetscBLASIntCast(2*n,&lwork);CHKERRQ(ierr);
ierr = PetscBLASIntCast(n,&bn);CHKERRQ(ierr);
ierr = PetscMalloc(n*sizeof(PetscReal),&evals);CHKERRQ(ierr);
ierr = PetscMalloc(lwork*sizeof(PetscScalar),&work);CHKERRQ(ierr);
ierr = MatDenseGetArray(A_dense,&arrayA);CHKERRQ(ierr);
if (TestZHEEV) { /* test zheev() */
printf(" LAPACKsyev: compute all %d eigensolutions...\n",m);
ierr = PetscMalloc((3*n-2)*sizeof(PetscReal),&rwork);CHKERRQ(ierr);
LAPACKsyev_("V","U",&bn,arrayA,&bn,evals,work,&lwork,rwork,&lierr);
ierr = PetscFree(rwork);CHKERRQ(ierr);
evecs_array = arrayA;
nevs = m;
il =1; iu=m;
}
if (TestZHEEVX) {
il = 1;
ierr = PetscBLASIntCast((0.2*m),&iu);CHKERRQ(ierr);
printf(" LAPACKsyevx: compute %d to %d-th eigensolutions...\n",il,iu);
ierr = PetscMalloc((m*n+1)*sizeof(PetscScalar),&evecs_array);CHKERRQ(ierr);
ierr = PetscMalloc((7*n+1)*sizeof(PetscReal),&rwork);CHKERRQ(ierr);
ierr = PetscMalloc((5*n+1)*sizeof(PetscBLASInt),&iwork);CHKERRQ(ierr);
ierr = PetscMalloc((n+1)*sizeof(PetscBLASInt),&ifail);CHKERRQ(ierr);
/* in the case "I", vl and vu are not referenced */
vl = 0.0; vu = 8.0;
LAPACKsyevx_("V","I","U",&bn,arrayA,&bn,&vl,&vu,&il,&iu,&abstol,&nevs,evals,evecs_array,&n,work,&lwork,rwork,iwork,ifail,&lierr);
ierr = PetscFree(iwork);CHKERRQ(ierr);
ierr = PetscFree(ifail);CHKERRQ(ierr);
ierr = PetscFree(rwork);CHKERRQ(ierr);
}
if (TestZHEGV) {
printf(" LAPACKsygv: compute all %d eigensolutions...\n",m);
ierr = PetscMalloc((3*n+1)*sizeof(PetscReal),&rwork);CHKERRQ(ierr);
ierr = MatDenseGetArray(B,&arrayB);CHKERRQ(ierr);
LAPACKsygv_(&one,"V","U",&bn,arrayA,&bn,arrayB,&bn,evals,work,&lwork,rwork,&lierr);
evecs_array = arrayA;
nevs = m;
il = 1; iu=m;
ierr = MatDenseRestoreArray(B,&arrayB);CHKERRQ(ierr);
ierr = PetscFree(rwork);CHKERRQ(ierr);
}
if (TestZHEGVX) {
il = 1;
ierr = PetscBLASIntCast((0.2*m),&iu);CHKERRQ(ierr);
printf(" LAPACKsygv: compute %d to %d-th eigensolutions...\n",il,iu);
ierr = PetscMalloc((m*n+1)*sizeof(PetscScalar),&evecs_array);CHKERRQ(ierr);
ierr = PetscMalloc((6*n+1)*sizeof(PetscBLASInt),&iwork);CHKERRQ(ierr);
ifail = iwork + 5*n;
ierr = PetscMalloc((7*n+1)*sizeof(PetscReal),&rwork);CHKERRQ(ierr);
ierr = MatDenseGetArray(B,&arrayB);CHKERRQ(ierr);
vl = 0.0; vu = 8.0;
LAPACKsygvx_(&one,"V","I","U",&bn,arrayA,&bn,arrayB,&bn,&vl,&vu,&il,&iu,&abstol,&nevs,evals,evecs_array,&n,work,&lwork,rwork,iwork,ifail,&lierr);
ierr = MatDenseRestoreArray(B,&arrayB);CHKERRQ(ierr);
ierr = PetscFree(iwork);CHKERRQ(ierr);
ierr = PetscFree(rwork);CHKERRQ(ierr);
}
ierr = MatDenseRestoreArray(A_dense,&arrayA);CHKERRQ(ierr);
if (nevs <= 0) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_CONV_FAILED, "nev=%d, no eigensolution has found", nevs);
/* View evals */
ierr = PetscOptionsHasName(NULL, "-eig_view", &flg);CHKERRQ(ierr);
if (flg) {
printf(" %d evals: \n",nevs);
for (i=0; i<nevs; i++) printf("%d %G\n",i+il,evals[i]);
}
/* Check residuals and orthogonality */
ierr = PetscMalloc((nevs+1)*sizeof(Vec),&evecs);CHKERRQ(ierr);
for (i=0; i<nevs; i++) {
ierr = VecCreate(PETSC_COMM_SELF,&evecs[i]);CHKERRQ(ierr);
ierr = VecSetSizes(evecs[i],PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(evecs[i]);CHKERRQ(ierr);
ierr = VecPlaceArray(evecs[i],evecs_array+i*n);CHKERRQ(ierr);
}
tols[0] = 1.e-8; tols[1] = 1.e-8;
ierr = CkEigenSolutions(cklvl,A,il-1,iu-1,evals,evecs,tols);CHKERRQ(ierr);
for (i=0; i<nevs; i++) { ierr = VecDestroy(&evecs[i]);CHKERRQ(ierr);}
ierr = PetscFree(evecs);CHKERRQ(ierr);
/* Free work space. */
if (TestZHEEVX || TestZHEGVX) {
ierr = PetscFree(evecs_array);CHKERRQ(ierr);
}
ierr = PetscFree(evals);CHKERRQ(ierr);
ierr = PetscFree(work);CHKERRQ(ierr);
ierr = MatDestroy(&A_dense);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode FiberFieldInitLocalFiber( FiberField fibers, int numVerticies, PetscReal l0,
FiberTypeID vertexType, FiberTypeID edgeType, FiberTypeID bendingEdgeType )
{
int i;
int flen = numVerticies;
Array fiber = fibers->fiber;
Vertex v0;
Vertex v1;
Vertex v2;
PetscRandom rnd = fibers->rnd;
PetscBool hitBoundary;
Coor rndSphere;
Coor n;
Coor r;
Coor s;
Coor d;
Coor lmin = fibers->localBounds.min;
Coor lmax = fibers->localBounds.max;
PetscReal NORTH_HEMISPHERE = 0.65;
const PetscReal WHOLE_SPHERE = 0.0;
const PetscReal DELTA = PETSC_SMALL;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = ArraySetSize(fiber, 0); CHKERRQ(ierr);
ierr = ArraySetMaxSize( fibers->verts, flen + ArrayLength(fibers->verts) ); CHKERRQ(ierr);
// add small delta
lmin.x += DELTA;
lmin.y += DELTA;
lmin.z += DELTA;
lmax.x -= DELTA;
lmax.y -= DELTA;
lmax.z -= DELTA;
ierr = PetscOptionsGetReal(0,"-fiber_bend",&NORTH_HEMISPHERE,0); CHKERRQ(ierr);
// Initialize v0 anywhere in the local bbox
ierr = FiberFieldAddVertex( fibers, vertexType, &v0); CHKERRQ(ierr);
ierr = ArrayAppendPtr( fiber, v0); CHKERRQ(ierr);
PetscRandomGetValue(rnd,&v0->X.x); // [0,1]
PetscRandomGetValue(rnd,&v0->X.y); // [0,1]
PetscRandomGetValue(rnd,&v0->X.z); // [0,1]
// map [0, 1] to local bbox [lmin, lmax]
v0->X.x = (1-v0->X.x) * lmin.x + v0->X.x * lmax.x;
v0->X.y = (1-v0->X.y) * lmin.y + v0->X.y * lmax.y;
v0->X.z = (1-v0->X.z) * lmin.z + v0->X.z * lmax.z;
// Initialize v1 anywhere spherically from v0
ierr = FiberFieldAddVertex( fibers, vertexType, &v1); CHKERRQ(ierr);
ierr = ArrayAppendPtr( fiber, v1); CHKERRQ(ierr);
SphericalDistribution(rnd, WHOLE_SPHERE, &d);
v1->X.x = v0->X.x + l0*d.x;
v1->X.y = v0->X.y + l0*d.y;
v1->X.z = v0->X.z + l0*d.z;
BoundaryCheck( lmin, lmax, &v1->X, &hitBoundary );
if (hitBoundary) {
ierr = FiberFieldAddEdge( fibers, v0, v1, edgeType, l0 ); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
for (i = 1; i < flen-1; i++ ) {
ierr = FiberFieldAddVertex( fibers, vertexType, &v2); CHKERRQ(ierr);
ierr = ArrayAppendPtr( fiber, v2); CHKERRQ(ierr);
SphericalDistribution(rnd, NORTH_HEMISPHERE, &rndSphere);
Rotation(v0->X,v1->X,&n,&r,&s);
MatVec(&n,&r,&s,&rndSphere, &d);
v2->X.x = v1->X.x + l0*d.x;
v2->X.y = v1->X.y + l0*d.y;
v2->X.z = v1->X.z + l0*d.z;
BoundaryCheck( lmin, lmax, &v2->X, &hitBoundary );
if (hitBoundary) {
break;
}
v0 = v1;
v1 = v2;
}
flen = ArrayLength( fiber );
Vertex *v = ArrayGetData( fiber );
// Link fiber edges: v_i -- v_i+1
for (i = 0; i < flen-1; i++) {
ierr = FiberFieldAddEdge( fibers, v[i], v[i+1], edgeType, l0 ); CHKERRQ(ierr);
}
// Link bending edges: v_i-1 -- v_i+1
for (i = 1; i < flen-1; i++) {
ierr = FiberFieldAddEdge( fibers, v[i-1], v[i+1], bendingEdgeType, 2*l0 ); CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat A,Atrans,sA,*submatA,*submatsA;
PetscErrorCode ierr;
PetscMPIInt size,rank;
PetscInt bs=1,mbs=10,ov=1,i,j,k,*rows,*cols,nd=2,*idx,rstart,rend,sz,M,N,Mbs;
PetscScalar *vals,rval,one=1.0;
IS *is1,*is2;
PetscRandom rand;
PetscBool flg,TestOverlap,TestSubMat,TestAllcols,test_sorted=PETSC_FALSE;
PetscInt vid = -1;
#if defined(PETSC_USE_LOG)
PetscLogStage stages[2];
#endif
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-mat_block_size",&bs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-mat_mbs",&mbs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-ov",&ov,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-nd",&nd,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-view_id",&vid,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL, "-test_overlap", &TestOverlap);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL, "-test_submat", &TestSubMat);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,NULL, "-test_allcols", &TestAllcols);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_sorted",&test_sorted,NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,mbs*bs,mbs*bs,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(A,MATBAIJ);CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation(A,bs,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
ierr = MatMPIBAIJSetPreallocation(A,bs,PETSC_DEFAULT,NULL,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr);
Mbs = M/bs;
ierr = PetscMalloc1(bs,&rows);CHKERRQ(ierr);
ierr = PetscMalloc1(bs,&cols);CHKERRQ(ierr);
ierr = PetscMalloc1(bs*bs,&vals);CHKERRQ(ierr);
ierr = PetscMalloc1(M,&idx);CHKERRQ(ierr);
/* Now set blocks of values */
for (j=0; j<bs*bs; j++) vals[j] = 0.0;
for (i=0; i<Mbs; i++) {
cols[0] = i*bs; rows[0] = i*bs;
for (j=1; j<bs; j++) {
rows[j] = rows[j-1]+1;
cols[j] = cols[j-1]+1;
}
ierr = MatSetValues(A,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
}
/* second, add random blocks */
for (i=0; i<20*bs; i++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
cols[0] = bs*(PetscInt)(PetscRealPart(rval)*Mbs);
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
rows[0] = rstart + bs*(PetscInt)(PetscRealPart(rval)*mbs);
for (j=1; j<bs; j++) {
rows[j] = rows[j-1]+1;
cols[j] = cols[j-1]+1;
}
for (j=0; j<bs*bs; j++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
vals[j] = rval;
}
ierr = MatSetValues(A,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* make A a symmetric matrix: A <- A^T + A */
ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Atrans);CHKERRQ(ierr);
ierr = MatAXPY(A,one,Atrans,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatDestroy(&Atrans);CHKERRQ(ierr);
ierr = MatTranspose(A,MAT_INITIAL_MATRIX, &Atrans);CHKERRQ(ierr);
ierr = MatEqual(A, Atrans, &flg);CHKERRQ(ierr);
if (flg) {
ierr = MatSetOption(A,MAT_SYMMETRIC,PETSC_TRUE);CHKERRQ(ierr);
} else SETERRQ(PETSC_COMM_SELF,1,"A+A^T is non-symmetric");
ierr = MatDestroy(&Atrans);CHKERRQ(ierr);
/* create a SeqSBAIJ matrix sA (= A) */
ierr = MatConvert(A,MATSBAIJ,MAT_INITIAL_MATRIX,&sA);CHKERRQ(ierr);
if (vid >= 0 && vid < size) {
if (!rank) printf("A: \n");
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
if (!rank) printf("sA: \n");
ierr = MatView(sA,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Test sA==A through MatMult() */
ierr = MatMultEqual(A,sA,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"Error in MatConvert(): A != sA");
/* Test MatIncreaseOverlap() */
ierr = PetscMalloc1(nd,&is1);CHKERRQ(ierr);
ierr = PetscMalloc1(nd,&is2);CHKERRQ(ierr);
for (i=0; i<nd; i++) {
if (!TestAllcols) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
sz = (PetscInt)((0.5+0.2*PetscRealPart(rval))*mbs); /* 0.5*mbs < sz < 0.7*mbs */
for (j=0; j<sz; j++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
idx[j*bs] = bs*(PetscInt)(PetscRealPart(rval)*Mbs);
for (k=1; k<bs; k++) idx[j*bs+k] = idx[j*bs]+k;
}
ierr = ISCreateGeneral(PETSC_COMM_SELF,sz*bs,idx,PETSC_COPY_VALUES,is1+i);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,sz*bs,idx,PETSC_COPY_VALUES,is2+i);CHKERRQ(ierr);
if (rank == vid) {
ierr = PetscPrintf(PETSC_COMM_SELF," [%d] IS sz[%d]: %d\n",rank,i,sz);CHKERRQ(ierr);
ierr = ISView(is2[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
}
} else { /* Test all rows and colums */
sz = M;
ierr = ISCreateStride(PETSC_COMM_SELF,sz,0,1,is1+i);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,sz,0,1,is2+i);CHKERRQ(ierr);
if (rank == vid) {
PetscBool colflag;
ierr = ISIdentity(is2[i],&colflag);CHKERRQ(ierr);
printf("[%d] is2[%d], colflag %d\n",rank,(int)i,(int)colflag);
ierr = ISView(is2[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
}
}
}
ierr = PetscLogStageRegister("MatOv_SBAIJ",&stages[0]);CHKERRQ(ierr);
ierr = PetscLogStageRegister("MatOv_BAIJ",&stages[1]);CHKERRQ(ierr);
/* Test MatIncreaseOverlap */
if (TestOverlap) {
ierr = PetscLogStagePush(stages[0]);CHKERRQ(ierr);
ierr = MatIncreaseOverlap(sA,nd,is2,ov);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
ierr = PetscLogStagePush(stages[1]);CHKERRQ(ierr);
ierr = MatIncreaseOverlap(A,nd,is1,ov);CHKERRQ(ierr);
ierr = PetscLogStagePop();CHKERRQ(ierr);
if (rank == vid) {
printf("\n[%d] IS from BAIJ:\n",rank);
ierr = ISView(is1[0],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
printf("\n[%d] IS from SBAIJ:\n",rank);
ierr = ISView(is2[0],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
}
for (i=0; i<nd; ++i) {
ierr = ISEqual(is1[i],is2[i],&flg);CHKERRQ(ierr);
if (!flg) {
if (!rank) {
ierr = ISSort(is1[i]);CHKERRQ(ierr);
/* ISView(is1[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); */
ierr = ISSort(is2[i]);CHKERRQ(ierr);
/* ISView(is2[i],PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr); */
}
SETERRQ1(PETSC_COMM_SELF,1,"i=%D, is1 != is2",i);
}
}
}
/* Test MatCreateSubmatrices */
if (TestSubMat) {
if (test_sorted) {
for (i = 0; i < nd; ++i) {
ierr = ISSort(is1[i]);CHKERRQ(ierr);
}
}
ierr = MatCreateSubMatrices(A,nd,is1,is1,MAT_INITIAL_MATRIX,&submatA);CHKERRQ(ierr);
ierr = MatCreateSubMatrices(sA,nd,is1,is1,MAT_INITIAL_MATRIX,&submatsA);CHKERRQ(ierr);
ierr = MatMultEqual(A,sA,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"A != sA");
/* Now test MatCreateSubmatrices with MAT_REUSE_MATRIX option */
ierr = MatCreateSubMatrices(A,nd,is1,is1,MAT_REUSE_MATRIX,&submatA);CHKERRQ(ierr);
ierr = MatCreateSubMatrices(sA,nd,is1,is1,MAT_REUSE_MATRIX,&submatsA);CHKERRQ(ierr);
ierr = MatMultEqual(A,sA,10,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"MatCreateSubmatrices(): A != sA");
ierr = MatDestroySubMatrices(nd,&submatA);CHKERRQ(ierr);
ierr = MatDestroySubMatrices(nd,&submatsA);CHKERRQ(ierr);
}
/* Free allocated memory */
for (i=0; i<nd; ++i) {
ierr = ISDestroy(&is1[i]);CHKERRQ(ierr);
ierr = ISDestroy(&is2[i]);CHKERRQ(ierr);
}
ierr = PetscFree(is1);CHKERRQ(ierr);
ierr = PetscFree(is2);CHKERRQ(ierr);
ierr = PetscFree(idx);CHKERRQ(ierr);
ierr = PetscFree(rows);CHKERRQ(ierr);
ierr = PetscFree(cols);CHKERRQ(ierr);
ierr = PetscFree(vals);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&sA);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int test1(void)
{
PetscLogDouble t1,t2;
double value;
int i,ierr,*z,*zi,intval;
PetscScalar *x,*y;
PetscRandom r;
ierr = PetscRandomCreate(PETSC_COMM_SELF,&r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
ierr = PetscMalloc(20000*sizeof(PetscScalar),&x);CHKERRQ(ierr);
ierr = PetscMalloc(20000*sizeof(PetscScalar),&y);CHKERRQ(ierr);
ierr = PetscMalloc(2000*sizeof(int),&z);CHKERRQ(ierr);
ierr = PetscMalloc(2000*sizeof(int),&zi);CHKERRQ(ierr);
/* Take care of paging effects */
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
/* Form the random set of integers */
for (i=0; i<2000; i++) {
ierr = PetscRandomGetValue(r,&value);CHKERRQ(ierr);
intval = (int)(value*20000.0);
z[i] = intval;
}
for (i=0; i<2000; i++) {
ierr = PetscRandomGetValue(r,&value);CHKERRQ(ierr);
intval = (int)(value*20000.0);
zi[i] = intval;
}
/* fprintf(stdout,"Done setup\n"); */
ierr = BlastCache();CHKERRQ(ierr);
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
for (i=0; i<2000; i++) { x[i] = y[i]; }
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
fprintf(stdout,"%-27s : %e sec\n","x[i] = y[i]",(t2-t1)/2000.0);
ierr = BlastCache();CHKERRQ(ierr);
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
for (i=0; i<500; i+=4) {
x[i] = y[z[i]];
x[1+i] = y[z[1+i]];
x[2+i] = y[z[2+i]];
x[3+i] = y[z[3+i]];
}
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
fprintf(stdout,"%-27s : %e sec\n","x[i] = y[idx[i]] - unroll 4",(t2-t1)/2000.0);
ierr = BlastCache();CHKERRQ(ierr);
ierr = PetscGetTime(&t1);CHKERRQ(ierr)
for (i=0; i<2000; i++) { x[i] = y[z[i]]; }
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
fprintf(stdout,"%-27s : %e sec\n","x[i] = y[idx[i]]",(t2-t1)/2000.0);
ierr = BlastCache();CHKERRQ(ierr);
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
for (i=0; i<1000; i+=2) { x[i] = y[z[i]]; x[1+i] = y[z[1+i]]; }
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
fprintf(stdout,"%-27s : %e sec\n","x[i] = y[idx[i]] - unroll 2",(t2-t1)/2000.0);
ierr = BlastCache();CHKERRQ(ierr);
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
for (i=0; i<2000; i++) { x[z[i]] = y[i]; }
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
fprintf(stdout,"%-27s : %e sec\n","x[z[i]] = y[i]",(t2-t1)/2000.0);
ierr = BlastCache();CHKERRQ(ierr);
ierr = PetscGetTime(&t1);CHKERRQ(ierr);
for (i=0; i<2000; i++) { x[z[i]] = y[zi[i]]; }
ierr = PetscGetTime(&t2);CHKERRQ(ierr);
fprintf(stdout,"%-27s : %e sec\n","x[z[i]] = y[zi[i]]",(t2-t1)/2000.0);
ierr = PetscMemcpy(x,y,10);CHKERRQ(ierr);
ierr = PetscMemcpy(z,zi,10);CHKERRQ(ierr);
ierr = PetscFree(z);CHKERRQ(ierr);
ierr = PetscFree(zi);CHKERRQ(ierr);
ierr = PetscFree(x);CHKERRQ(ierr);
ierr = PetscFree(y);CHKERRQ(ierr);
PetscRandomDestroy(r);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
Mat A,B,C,D;
PetscInt i,M=10,N=5,j,nrows,ncols;
PetscErrorCode ierr;
PetscRandom r;
PetscBool equal,iselemental;
PetscReal fill = 1.0;
IS isrows,iscols;
const PetscInt *rows,*cols;
PetscScalar *v,rval;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,M,N);CHKERRQ(ierr);
ierr = MatSetType(A,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
/* Set local matrix entries */
ierr = MatGetOwnershipIS(A,&isrows,&iscols);CHKERRQ(ierr);
ierr = ISGetLocalSize(isrows,&nrows);CHKERRQ(ierr);
ierr = ISGetIndices(isrows,&rows);CHKERRQ(ierr);
ierr = ISGetLocalSize(iscols,&ncols);CHKERRQ(ierr);
ierr = ISGetIndices(iscols,&cols);CHKERRQ(ierr);
ierr = PetscMalloc(nrows*ncols*sizeof(*v),&v);CHKERRQ(ierr);
for (i=0; i<nrows; i++) {
for (j=0; j<ncols; j++) {
ierr = PetscRandomGetValue(r,&rval);CHKERRQ(ierr);
v[i*ncols+j] = rval;
}
}
ierr = MatSetValues(A,nrows,rows,ncols,cols,v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = ISRestoreIndices(isrows,&rows);CHKERRQ(ierr);
ierr = ISRestoreIndices(iscols,&cols);CHKERRQ(ierr);
ierr = ISDestroy(&isrows);CHKERRQ(ierr);
ierr = ISDestroy(&iscols);CHKERRQ(ierr);
ierr = PetscFree(v);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&r);CHKERRQ(ierr);
/* Test MatMatMult() */
ierr = MatTranspose(A,MAT_INITIAL_MATRIX,&B);CHKERRQ(ierr); /* B = A^T */
ierr = MatMatMult(B,A,MAT_INITIAL_MATRIX,fill,&C);CHKERRQ(ierr); /* C = B*A = A^T*A */
ierr = MatMatMultSymbolic(B,A,fill,&D);CHKERRQ(ierr); /* D = B*A = A^T*A */
for (i=0; i<2; i++) {
/* Repeat the numeric product to test reuse of the previous symbolic product */
ierr = MatMatMultNumeric(B,A,D);CHKERRQ(ierr);
}
ierr = MatMultEqual(C,D,10,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"C != D");
ierr = MatDestroy(&D);CHKERRQ(ierr);
/* Test MatTransposeMatMult() */
ierr = PetscObjectTypeCompare((PetscObject)A,MATELEMENTAL,&iselemental);CHKERRQ(ierr);
if (!iselemental) {
ierr = MatTransposeMatMult(A,A,MAT_INITIAL_MATRIX,fill,&D);CHKERRQ(ierr); /* D = A^T*A */
ierr = MatEqual(C,D,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONGSTATE,"C != D");
ierr = MatDestroy(&D);CHKERRQ(ierr);
}
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&B);
ierr = MatDestroy(&A);
PetscFinalize();
return(0);
}
int main(int argc,char **argv)
{
Mat A,B,C,D;
PetscInt i,j,k,M=10,N=5;
PetscScalar *array,*a;
PetscErrorCode ierr;
PetscRandom r;
PetscTruth equal=PETSC_FALSE;
PetscReal fill = 1.0;
PetscInt rstart,rend,nza,col,am,an,bm,bn;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-N",&N,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(PETSC_NULL,"-fill",&fill,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
/* create a aij matrix A */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,N,M);CHKERRQ(ierr);
ierr = MatSetType(A,MATAIJ);CHKERRQ(ierr);
nza = (PetscInt)(.3*M); /* num of nozeros in each row of A */
ierr = MatSeqAIJSetPreallocation(A,nza,PETSC_NULL);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(A,nza,PETSC_NULL,nza,PETSC_NULL);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
ierr = PetscMalloc((nza+1)*sizeof(PetscScalar),&a);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
for (j=0; j<nza; j++) {
ierr = PetscRandomGetValue(r,&a[j]);CHKERRQ(ierr);
col = (PetscInt)(M*PetscRealPart(a[j]));
ierr = MatSetValues(A,1,&i,1,&col,&a[j],ADD_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* create a dense matrix B */
ierr = MatGetLocalSize(A,&am,&an);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,PETSC_DECIDE,am,N,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(B,MATDENSE);CHKERRQ(ierr);
ierr = MatSeqDenseSetPreallocation(B,PETSC_NULL);CHKERRQ(ierr);
ierr = MatMPIDenseSetPreallocation(B,PETSC_NULL);CHKERRQ(ierr);
ierr = MatGetLocalSize(B,&bm,&bn);CHKERRQ(ierr);
ierr = MatGetArray(B,&array);CHKERRQ(ierr);
k = 0;
for (j=0; j<N; j++){ /* local column-wise entries */
for (i=0; i<bm; i++){
ierr = PetscRandomGetValue(r,&array[k++]);CHKERRQ(ierr);
}
}
ierr = MatRestoreArray(B,&array);CHKERRQ(ierr);
ierr = PetscRandomDestroy(r);CHKERRQ(ierr);
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Test MatMatMult() */
ierr = MatMatMult(B,A,MAT_INITIAL_MATRIX,fill,&C);CHKERRQ(ierr);
/*
ierr = PetscViewerSetFormat(PETSC_VIEWER_STDOUT_WORLD,PETSC_VIEWER_ASCII_MATLAB);
ierr = MatView(C,0);CHKERRQ(ierr);
ierr = MatView(B,0);CHKERRQ(ierr);
ierr = MatView(A,0);CHKERRQ(ierr);
*/
ierr = MatMatMultSymbolic(B,A,fill,&D);CHKERRQ(ierr);
for (i=0; i<2; i++){
ierr = MatMatMultNumeric(B,A,D);CHKERRQ(ierr);
}
ierr = MatEqual(C,D,&equal);CHKERRQ(ierr);
if (!equal) SETERRQ(PETSC_ERR_ARG_WRONGSTATE,"C != D");
ierr = MatDestroy(D);CHKERRQ(ierr);
ierr = MatDestroy(C);CHKERRQ(ierr);
ierr = MatDestroy(B);CHKERRQ(ierr);
ierr = MatDestroy(A);CHKERRQ(ierr);
ierr = PetscFree(a);CHKERRQ(ierr);
PetscFinalize();
return(0);
}
int main(int argc,char **args)
{
Mat A,B,*submatA,*submatB;
PetscInt bs=1,m=11,ov=1,i,j,k,*rows,*cols,nd=5,*idx,rstart,rend,sz,mm,nn,M,N,Mbs;
PetscErrorCode ierr;
PetscMPIInt size,rank;
PetscScalar *vals,rval;
IS *is1,*is2;
PetscRandom rdm;
Vec xx,s1,s2;
PetscReal s1norm,s2norm,rnorm,tol = 100*PETSC_SMALL;
PetscBool flg,test_nd0=PETSC_FALSE;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-mat_block_size",&bs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-mat_size",&m,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-ov",&ov,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-nd",&nd,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-test_nd0",&test_nd0,NULL);CHKERRQ(ierr);
/* Create a AIJ matrix A */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,m*bs,m*bs,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(A,MATAIJ);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(A,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(A,PETSC_DEFAULT,NULL,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetOption(A,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
/* Create a BAIJ matrix B */
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,m*bs,m*bs,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(B,MATBAIJ);CHKERRQ(ierr);
ierr = MatSeqBAIJSetPreallocation(B,bs,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
ierr = MatMPIBAIJSetPreallocation(B,bs,PETSC_DEFAULT,NULL,PETSC_DEFAULT,NULL);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rdm);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&rstart,&rend);CHKERRQ(ierr);
ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr);
Mbs = M/bs;
ierr = PetscMalloc1(bs,&rows);CHKERRQ(ierr);
ierr = PetscMalloc1(bs,&cols);CHKERRQ(ierr);
ierr = PetscMalloc1(bs*bs,&vals);CHKERRQ(ierr);
ierr = PetscMalloc1(M,&idx);CHKERRQ(ierr);
/* Now set blocks of values */
for (i=0; i<40*bs; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
cols[0] = bs*(int)(PetscRealPart(rval)*Mbs);
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
rows[0] = rstart + bs*(int)(PetscRealPart(rval)*m);
for (j=1; j<bs; j++) {
rows[j] = rows[j-1]+1;
cols[j] = cols[j-1]+1;
}
for (j=0; j<bs*bs; j++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
vals[j] = rval;
}
ierr = MatSetValues(A,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,bs,rows,bs,cols,vals,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Test MatIncreaseOverlap() */
ierr = PetscMalloc1(nd,&is1);CHKERRQ(ierr);
ierr = PetscMalloc1(nd,&is2);CHKERRQ(ierr);
if (!rank && test_nd0) nd = 0; /* test case */
for (i=0; i<nd; i++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
sz = (int)(PetscRealPart(rval)*m);
for (j=0; j<sz; j++) {
ierr = PetscRandomGetValue(rdm,&rval);CHKERRQ(ierr);
idx[j*bs] = bs*(int)(PetscRealPart(rval)*Mbs);
for (k=1; k<bs; k++) idx[j*bs+k] = idx[j*bs]+k;
}
ierr = ISCreateGeneral(PETSC_COMM_SELF,sz*bs,idx,PETSC_COPY_VALUES,is1+i);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,sz*bs,idx,PETSC_COPY_VALUES,is2+i);CHKERRQ(ierr);
}
ierr = MatIncreaseOverlap(A,nd,is1,ov);CHKERRQ(ierr);
ierr = MatIncreaseOverlap(B,nd,is2,ov);CHKERRQ(ierr);
for (i=0; i<nd; ++i) {
ierr = ISEqual(is1[i],is2[i],&flg);CHKERRQ(ierr);
if (!flg) {
ierr = PetscPrintf(PETSC_COMM_SELF,"i=%D, flg=%d :bs=%D m=%D ov=%D nd=%D np=%D\n",i,flg,bs,m,ov,nd,size);CHKERRQ(ierr);
}
}
for (i=0; i<nd; ++i) {
ierr = ISSort(is1[i]);CHKERRQ(ierr);
ierr = ISSort(is2[i]);CHKERRQ(ierr);
}
ierr = MatCreateSubMatrices(B,nd,is2,is2,MAT_INITIAL_MATRIX,&submatB);CHKERRQ(ierr);
ierr = MatCreateSubMatrices(A,nd,is1,is1,MAT_INITIAL_MATRIX,&submatA);CHKERRQ(ierr);
/* Test MatMult() */
for (i=0; i<nd; i++) {
ierr = MatGetSize(submatA[i],&mm,&nn);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,mm,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
for (j=0; j<3; j++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = MatMult(submatA[i],xx,s1);CHKERRQ(ierr);
ierr = MatMult(submatB[i],xx,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"[%d]Error:MatMult - Norm1=%16.14e Norm2=%16.14e\n",rank,s1norm,s2norm);CHKERRQ(ierr);
}
}
ierr = VecDestroy(&xx);CHKERRQ(ierr);
ierr = VecDestroy(&s1);CHKERRQ(ierr);
ierr = VecDestroy(&s2);CHKERRQ(ierr);
}
/* Now test MatCreateSubmatrices with MAT_REUSE_MATRIX option */
ierr = MatCreateSubMatrices(A,nd,is1,is1,MAT_REUSE_MATRIX,&submatA);CHKERRQ(ierr);
ierr = MatCreateSubMatrices(B,nd,is2,is2,MAT_REUSE_MATRIX,&submatB);CHKERRQ(ierr);
/* Test MatMult() */
for (i=0; i<nd; i++) {
ierr = MatGetSize(submatA[i],&mm,&nn);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,mm,&xx);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s1);CHKERRQ(ierr);
ierr = VecDuplicate(xx,&s2);CHKERRQ(ierr);
for (j=0; j<3; j++) {
ierr = VecSetRandom(xx,rdm);CHKERRQ(ierr);
ierr = MatMult(submatA[i],xx,s1);CHKERRQ(ierr);
ierr = MatMult(submatB[i],xx,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_2,&s1norm);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_2,&s2norm);CHKERRQ(ierr);
rnorm = s2norm-s1norm;
if (rnorm<-tol || rnorm>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"[%d]Error:MatMult - Norm1=%16.14e Norm2=%16.14e\n",rank,s1norm,s2norm);CHKERRQ(ierr);
}
}
ierr = VecDestroy(&xx);CHKERRQ(ierr);
ierr = VecDestroy(&s1);CHKERRQ(ierr);
ierr = VecDestroy(&s2);CHKERRQ(ierr);
}
/* Free allocated memory */
for (i=0; i<nd; ++i) {
ierr = ISDestroy(&is1[i]);CHKERRQ(ierr);
ierr = ISDestroy(&is2[i]);CHKERRQ(ierr);
}
ierr = MatDestroySubMatrices(nd,&submatA);CHKERRQ(ierr);
ierr = MatDestroySubMatrices(nd,&submatB);CHKERRQ(ierr);
ierr = PetscFree(is1);CHKERRQ(ierr);
ierr = PetscFree(is2);CHKERRQ(ierr);
ierr = PetscFree(idx);CHKERRQ(ierr);
ierr = PetscFree(rows);CHKERRQ(ierr);
ierr = PetscFree(cols);CHKERRQ(ierr);
ierr = PetscFree(vals);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode FormTestMatrix(Mat A,PetscInt n,TestType type)
{
#if !defined(PETSC_USE_COMPLEX)
SETERRQ(((PetscObject)A)->comm,1,"FormTestMatrix: These problems require complex numbers.");
#else
PetscScalar val[5];
PetscErrorCode ierr;
PetscInt i,j,Ii,J,col[5],Istart,Iend;
ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
if (type == TEST_1) {
val[0] = 1.0; val[1] = 4.0; val[2] = -2.0;
for (i=1; i<n-1; i++) {
col[0] = i-1; col[1] = i; col[2] = i+1;
ierr = MatSetValues(A,1,&i,3,col,val,INSERT_VALUES);CHKERRQ(ierr);
}
i = n-1; col[0] = n-2; col[1] = n-1;
ierr = MatSetValues(A,1,&i,2,col,val,INSERT_VALUES);CHKERRQ(ierr);
i = 0; col[0] = 0; col[1] = 1; val[0] = 4.0; val[1] = -2.0;
ierr = MatSetValues(A,1,&i,2,col,val,INSERT_VALUES);CHKERRQ(ierr);
}
else if (type == TEST_2) {
val[0] = 1.0; val[1] = 0.0; val[2] = 2.0; val[3] = 1.0;
for (i=2; i<n-1; i++) {
col[0] = i-2; col[1] = i-1; col[2] = i; col[3] = i+1;
ierr = MatSetValues(A,1,&i,4,col,val,INSERT_VALUES);CHKERRQ(ierr);
}
i = n-1; col[0] = n-3; col[1] = n-2; col[2] = n-1;
ierr = MatSetValues(A,1,&i,3,col,val,INSERT_VALUES);CHKERRQ(ierr);
i = 1; col[0] = 0; col[1] = 1; col[2] = 2;
ierr = MatSetValues(A,1,&i,3,col,&val[1],INSERT_VALUES);CHKERRQ(ierr);
i = 0;
ierr = MatSetValues(A,1,&i,2,col,&val[2],INSERT_VALUES);CHKERRQ(ierr);
}
else if (type == TEST_3) {
val[0] = PETSC_i * 2.0;
val[1] = 4.0; val[2] = 0.0; val[3] = 1.0; val[4] = 0.7;
for (i=1; i<n-3; i++) {
col[0] = i-1; col[1] = i; col[2] = i+1; col[3] = i+2; col[4] = i+3;
ierr = MatSetValues(A,1,&i,5,col,val,INSERT_VALUES);CHKERRQ(ierr);
}
i = n-3; col[0] = n-4; col[1] = n-3; col[2] = n-2; col[3] = n-1;
ierr = MatSetValues(A,1,&i,4,col,val,INSERT_VALUES);CHKERRQ(ierr);
i = n-2; col[0] = n-3; col[1] = n-2; col[2] = n-1;
ierr = MatSetValues(A,1,&i,3,col,val,INSERT_VALUES);CHKERRQ(ierr);
i = n-1; col[0] = n-2; col[1] = n-1;
ierr = MatSetValues(A,1,&i,2,col,val,INSERT_VALUES);CHKERRQ(ierr);
i = 0; col[0] = 0; col[1] = 1; col[2] = 2; col[3] = 3;
ierr = MatSetValues(A,1,&i,4,col,&val[1],INSERT_VALUES);CHKERRQ(ierr);
}
else if (type == HELMHOLTZ_1) {
/* Problem domain: unit square: (0,1) x (0,1)
Solve Helmholtz equation:
-delta u - sigma1*u + i*sigma2*u = f,
where delta = Laplace operator
Dirichlet b.c.'s on all sides
*/
PetscRandom rctx;
PetscReal h2,sigma1 = 5.0;
PetscScalar sigma2;
ierr = PetscOptionsGetReal(PETSC_NULL,"-sigma1",&sigma1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(rctx,0.0,PETSC_i);CHKERRQ(ierr);
h2 = 1.0/((n+1)*(n+1));
for (Ii=Istart; Ii<Iend; Ii++) {
*val = -1.0; i = Ii/n; j = Ii - i*n;
if (i>0) {
J = Ii-n; ierr = MatSetValues(A,1,&Ii,1,&J,val,ADD_VALUES);CHKERRQ(ierr);}
if (i<n-1) {
J = Ii+n; ierr = MatSetValues(A,1,&Ii,1,&J,val,ADD_VALUES);CHKERRQ(ierr);}
if (j>0) {
J = Ii-1; ierr = MatSetValues(A,1,&Ii,1,&J,val,ADD_VALUES);CHKERRQ(ierr);}
if (j<n-1) {
J = Ii+1; ierr = MatSetValues(A,1,&Ii,1,&J,val,ADD_VALUES);CHKERRQ(ierr);}
ierr = PetscRandomGetValue(rctx,&sigma2);CHKERRQ(ierr);
*val = 4.0 - sigma1*h2 + sigma2*h2;
ierr = MatSetValues(A,1,&Ii,1,&Ii,val,ADD_VALUES);CHKERRQ(ierr);
}
ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);
}
else if (type == HELMHOLTZ_2) {
/* Problem domain: unit square: (0,1) x (0,1)
Solve Helmholtz equation:
-delta u - sigma1*u = f,
where delta = Laplace operator
Dirichlet b.c.'s on 3 sides
du/dn = i*alpha*u on (1,y), 0<y<1
*/
PetscReal h2,sigma1 = 200.0;
PetscScalar alpha_h;
ierr = PetscOptionsGetReal(PETSC_NULL,"-sigma1",&sigma1,PETSC_NULL);CHKERRQ(ierr);
h2 = 1.0/((n+1)*(n+1));
alpha_h = (PETSC_i * 10.0) / (PetscReal)(n+1); /* alpha_h = alpha * h */
for (Ii=Istart; Ii<Iend; Ii++) {
*val = -1.0; i = Ii/n; j = Ii - i*n;
if (i>0) {
J = Ii-n; ierr = MatSetValues(A,1,&Ii,1,&J,val,ADD_VALUES);CHKERRQ(ierr);}
if (i<n-1) {
J = Ii+n; ierr = MatSetValues(A,1,&Ii,1,&J,val,ADD_VALUES);CHKERRQ(ierr);}
if (j>0) {
J = Ii-1; ierr = MatSetValues(A,1,&Ii,1,&J,val,ADD_VALUES);CHKERRQ(ierr);}
if (j<n-1) {
J = Ii+1; ierr = MatSetValues(A,1,&Ii,1,&J,val,ADD_VALUES);CHKERRQ(ierr);}
*val = 4.0 - sigma1*h2;
if (!((Ii+1)%n)) *val += alpha_h;
ierr = MatSetValues(A,1,&Ii,1,&Ii,val,ADD_VALUES);CHKERRQ(ierr);
}
}
else SETERRQ(((PetscObject)A)->comm,1,"FormTestMatrix: unknown test matrix type");
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
#endif
return 0;
}
PetscErrorCode ComputeMatrix(DM da,Mat B)
{
PetscErrorCode ierr;
PetscInt i,j,k,mx,my,mz,xm,ym,zm,xs,ys,zs,dof,k1,k2,k3;
PetscScalar *v,*v_neighbor,Hx,Hy,Hz,HxHydHz,HyHzdHx,HxHzdHy,r1,r2;
MatStencil row,col;
PetscRandom rand;
PetscFunctionBegin;
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetType(rand,PETSCRAND);CHKERRQ(ierr);
ierr = PetscRandomSetSeed(rand,1);CHKERRQ(ierr);
ierr = PetscRandomSetInterval(rand,-.001,.001);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = DMDAGetInfo(da,0,&mx,&my,&mz,0,0,0,&dof,0,0,0,0,0);CHKERRQ(ierr);
/* For simplicity, this example only works on mx=my=mz */
if ( mx != my || mx != mz) SETERRQ3(PETSC_COMM_SELF,1,"This example only works with mx %d = my %d = mz %d\n",mx,my,mz);
Hx = 1.0 / (PetscReal)(mx-1); Hy = 1.0 / (PetscReal)(my-1); Hz = 1.0 / (PetscReal)(mz-1);
HxHydHz = Hx*Hy/Hz; HxHzdHy = Hx*Hz/Hy; HyHzdHx = Hy*Hz/Hx;
ierr = PetscMalloc((2*dof*dof+1)*sizeof(PetscScalar),&v);CHKERRQ(ierr);
v_neighbor = v + dof*dof;
ierr = PetscMemzero(v,(2*dof*dof+1)*sizeof(PetscScalar));CHKERRQ(ierr);
k3 = 0;
for (k1=0; k1<dof; k1++){
for (k2=0; k2<dof; k2++){
if (k1 == k2){
v[k3] = 2.0*(HxHydHz + HxHzdHy + HyHzdHx);
v_neighbor[k3] = -HxHydHz;
} else {
ierr = PetscRandomGetValue(rand,&r1);CHKERRQ(ierr);
ierr = PetscRandomGetValue(rand,&r2);CHKERRQ(ierr);
v[k3] = r1;
v_neighbor[k3] = r2;
}
k3++;
}
}
ierr = DMDAGetCorners(da,&xs,&ys,&zs,&xm,&ym,&zm);CHKERRQ(ierr);
for (k=zs; k<zs+zm; k++){
for (j=ys; j<ys+ym; j++){
for (i=xs; i<xs+xm; i++){
row.i = i; row.j = j; row.k = k;
if (i==0 || j==0 || k==0 || i==mx-1 || j==my-1 || k==mz-1){ /* boudary points */
ierr = MatSetValuesBlockedStencil(B,1,&row,1,&row,v,INSERT_VALUES);CHKERRQ(ierr);
} else { /* interior points */
/* center */
col.i = i; col.j = j; col.k = k;
ierr = MatSetValuesBlockedStencil(B,1,&row,1,&col,v,INSERT_VALUES);CHKERRQ(ierr);
/* x neighbors */
col.i = i-1; col.j = j; col.k = k;
ierr = MatSetValuesBlockedStencil(B,1,&row,1,&col,v_neighbor,INSERT_VALUES);CHKERRQ(ierr);
col.i = i+1; col.j = j; col.k = k;
ierr = MatSetValuesBlockedStencil(B,1,&row,1,&col,v_neighbor,INSERT_VALUES);CHKERRQ(ierr);
/* y neighbors */
col.i = i; col.j = j-1; col.k = k;
ierr = MatSetValuesBlockedStencil(B,1,&row,1,&col,v_neighbor,INSERT_VALUES);CHKERRQ(ierr);
col.i = i; col.j = j+1; col.k = k;
ierr = MatSetValuesBlockedStencil(B,1,&row,1,&col,v_neighbor,INSERT_VALUES);CHKERRQ(ierr);
/* z neighbors */
col.i = i; col.j = j; col.k = k-1;
ierr = MatSetValuesBlockedStencil(B,1,&row,1,&col,v_neighbor,INSERT_VALUES);CHKERRQ(ierr);
col.i = i; col.j = j; col.k = k+1;
ierr = MatSetValuesBlockedStencil(B,1,&row,1,&col,v_neighbor,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
}
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = PetscFree(v);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
