int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt i,j,k,N=100,**counters,tsize;
PetscInitialize(&argc,&argv,(char *)0,help);
ierr = PetscThreadCommView(PETSC_COMM_WORLD,PETSC_VIEWER_STDOUT_WORLD);
CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-N",&N,PETSC_NULL);
CHKERRQ(ierr);
ierr = PetscThreadCommGetNThreads(PETSC_COMM_WORLD,&tsize);
CHKERRQ(ierr);
ierr = PetscMalloc(tsize*sizeof(*counters),&counters);
CHKERRQ(ierr);
ierr = PetscThreadCommRunKernel(PETSC_COMM_WORLD,(PetscThreadKernel)CounterInit_kernel,1,counters);
CHKERRQ(ierr);
for (i=0; i<10; i++) {
PetscReal t0,t1;
ierr = PetscThreadCommBarrier(PETSC_COMM_WORLD);
CHKERRQ(ierr);
ierr = PetscGetTime(&t0);
CHKERRQ(ierr);
for (j=0; j<N; j++) {
/* ierr = PetscThreadCommRunKernel(PETSC_COMM_WORLD,(PetscThreadKernel)CounterIncrement_kernel,1,counters);CHKERRQ(ierr); */
ierr = PetscThreadCommRunKernel1(PETSC_COMM_WORLD,(PetscThreadKernel)CounterIncrement_kernel,counters);
CHKERRQ(ierr);
}
ierr = PetscThreadCommBarrier(PETSC_COMM_WORLD);
CHKERRQ(ierr);
ierr = PetscGetTime(&t1);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Time per kernel: %g us\n",1e6*(t1-t0)/N);
CHKERRQ(ierr);
}
for (i=0; i<10; i++) {
PetscReal t0,t1;
ierr = PetscThreadCommBarrier(PETSC_COMM_WORLD);
CHKERRQ(ierr);
ierr = PetscGetTime(&t0);
CHKERRQ(ierr);
for (j=0; j<N; j++) {
#pragma omp parallel num_threads(tsize)
{
PetscInt trank = omp_get_thread_num();
CounterIncrement_kernel(trank,counters);
}
}
ierr = PetscThreadCommBarrier(PETSC_COMM_WORLD);
CHKERRQ(ierr);
ierr = PetscGetTime(&t1);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"OpenMP inline time per kernel: %g us\n",1e6*(t1-t0)/N);
CHKERRQ(ierr);
}
for (i=0; i<10; i++) {
PetscReal t0,t1;
ierr = PetscGetTime(&t0);
CHKERRQ(ierr);
for (j=0; j<N; j++) {
CounterIncrement_kernel(0,counters);
}
ierr = PetscGetTime(&t1);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Serial inline time per single kernel: %g us\n",1e6*(t1-t0)/N);
CHKERRQ(ierr);
}
for (i=0; i<10; i++) {
PetscReal t0,t1;
ierr = PetscGetTime(&t0);
CHKERRQ(ierr);
for (j=0; j<N; j++) {
for (k=0; k<tsize; k++) CounterIncrement_kernel(k,counters);
}
ierr = PetscGetTime(&t1);
CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Serial inline time per kernel: %g us\n",1e6*(t1-t0)/N);
CHKERRQ(ierr);
}
ierr = PetscThreadCommRunKernel(PETSC_COMM_WORLD,(PetscThreadKernel)CounterFree_kernel,1,counters);
CHKERRQ(ierr);
ierr = PetscThreadCommBarrier(PETSC_COMM_WORLD);
CHKERRQ(ierr);
ierr = PetscFree(counters);
CHKERRQ(ierr);
PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A,RHS,C,F,X;
Vec u,x,b;
PetscErrorCode ierr;
PetscMPIInt rank,nproc;
PetscInt i,m,n,nfact,nsolve,nrhs,ipack=0;
PetscScalar *array,rval;
PetscReal norm,tol=1.e-12;
IS perm,iperm;
MatFactorInfo info;
PetscRandom rand;
PetscBool flg,testMatSolve=PETSC_TRUE,testMatMatSolve=PETSC_TRUE;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
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);
/* Determine file from which we read the matrix A */
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/* Load matrix A */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
if (m != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "This example is not intended for rectangular matrices (%d, %d)", m, n);
/* Create dense matrix C and X; C holds true solution with identical colums */
nrhs = 2;
ierr = PetscOptionsGetInt(NULL,"-nrhs",&nrhs,NULL);CHKERRQ(ierr);
if (!rank) printf("ex125: nrhs %d\n",nrhs);
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,m,PETSC_DECIDE,PETSC_DECIDE,nrhs);CHKERRQ(ierr);
ierr = MatSetType(C,MATDENSE);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
ierr = MatSetRandom(C,rand);CHKERRQ(ierr);
ierr = MatDuplicate(C,MAT_DO_NOT_COPY_VALUES,&X);CHKERRQ(ierr);
/* Create vectors */
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecDuplicate(x,&u);CHKERRQ(ierr); /* save the true solution */
/* Test LU Factorization */
ierr = MatGetOrdering(A,MATORDERINGND,&perm,&iperm);CHKERRQ(ierr);
/*ierr = ISView(perm,PETSC_VIEWER_STDOUT_WORLD);*/
/*ierr = ISView(perm,PETSC_VIEWER_STDOUT_SELF);*/
ierr = PetscOptionsGetInt(NULL,"-mat_solver_package",&ipack,NULL);CHKERRQ(ierr);
switch (ipack) {
case 0:
#if defined(PETSC_HAVE_SUPERLU)
if (!rank) printf(" SUPERLU LU:\n");
ierr = MatGetFactor(A,MATSOLVERSUPERLU,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
break;
#endif
case 1:
#if defined(PETSC_HAVE_SUPERLU_DIST)
if (!rank) printf(" SUPERLU_DIST LU:\n");
ierr = MatGetFactor(A,MATSOLVERSUPERLU_DIST,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
break;
#endif
case 2:
#if defined(PETSC_HAVE_MUMPS)
if (!rank) printf(" MUMPS LU:\n");
ierr = MatGetFactor(A,MATSOLVERMUMPS,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
{
/* test mumps options */
PetscInt icntl_7 = 5;
ierr = MatMumpsSetIcntl(F,7,icntl_7);CHKERRQ(ierr);
}
break;
#endif
default:
if (!rank) printf(" PETSC LU:\n");
ierr = MatGetFactor(A,MATSOLVERPETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
}
info.fill = 5.0;
ierr = MatLUFactorSymbolic(F,A,perm,iperm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 2; nfact++) {
if (!rank) printf(" %d-the LU numfactorization \n",nfact);
ierr = MatLUFactorNumeric(F,A,&info);CHKERRQ(ierr);
/* Test MatMatSolve() */
/*
if ((ipack == 0 || ipack == 2) && testMatMatSolve) {
printf(" MatMatSolve() is not implemented for this package. Skip the testing.\n");
testMatMatSolve = PETSC_FALSE;
}
*/
if (testMatMatSolve) {
if (!nfact) {
ierr = MatMatMult(A,C,MAT_INITIAL_MATRIX,2.0,&RHS);CHKERRQ(ierr);
} else {
ierr = MatMatMult(A,C,MAT_REUSE_MATRIX,2.0,&RHS);CHKERRQ(ierr);
}
for (nsolve = 0; nsolve < 2; nsolve++) {
if (!rank) printf(" %d-the MatMatSolve \n",nsolve);
ierr = MatMatSolve(F,RHS,X);CHKERRQ(ierr);
/* Check the error */
ierr = MatAXPY(X,-1.0,C,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatNorm(X,NORM_FROBENIUS,&norm);CHKERRQ(ierr);
if (norm > tol) {
if (!rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"1st MatMatSolve: Norm of error %g, nsolve %d\n",norm,nsolve);CHKERRQ(ierr);
}
}
}
}
/* Test MatSolve() */
if (testMatSolve) {
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(A,x,b);CHKERRQ(ierr);
if (!rank) printf(" %d-the MatSolve \n",nsolve);
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) {
ierr = MatMult(A,x,u);CHKERRQ(ierr); /* u = A*x */
PetscReal resi;
ierr = VecAXPY(u,-1.0,b);CHKERRQ(ierr); /* u <- (-1.0)b + u */
ierr = VecNorm(u,NORM_2,&resi);CHKERRQ(ierr);
if (!rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"MatSolve: Norm of error %g, resi %g, LU numfact %d\n",norm,resi,nfact);CHKERRQ(ierr);
}
}
}
}
}
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
ierr = MatDestroy(&X);CHKERRQ(ierr);
if (testMatMatSolve) {
ierr = MatDestroy(&RHS);CHKERRQ(ierr);
}
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = ISDestroy(&iperm);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
Mat A,B,M,mat[2];
ST st;
Vec v,w;
STType type;
PetscScalar value[3],sigma,tau;
PetscInt n=10,i,Istart,Iend,col[3];
PetscBool FirstBlock=PETSC_FALSE,LastBlock=PETSC_FALSE;
PetscErrorCode ierr;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n1-D Laplacian plus diagonal, n=%D\n\n",n);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the operator matrix for the 1-D Laplacian
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
ierr = MatSetUp(B);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
if (Istart==0) FirstBlock=PETSC_TRUE;
if (Iend==n) LastBlock=PETSC_TRUE;
value[0]=-1.0; value[1]=2.0; value[2]=-1.0;
for (i=(FirstBlock? Istart+1: Istart); i<(LastBlock? Iend-1: Iend); i++) {
col[0]=i-1; col[1]=i; col[2]=i+1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValue(B,i,i,(PetscScalar)i,INSERT_VALUES);CHKERRQ(ierr);
}
if (LastBlock) {
i=n-1; col[0]=n-2; col[1]=n-1;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValue(B,i,i,(PetscScalar)i,INSERT_VALUES);CHKERRQ(ierr);
}
if (FirstBlock) {
i=0; col[0]=0; col[1]=1; value[0]=2.0; value[1]=-1.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValue(B,i,i,-1.0,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);
ierr = MatGetVecs(A,&v,&w);CHKERRQ(ierr);
ierr = VecSet(v,1.0);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the spectral transformation object
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = STCreate(PETSC_COMM_WORLD,&st);CHKERRQ(ierr);
mat[0] = A;
mat[1] = B;
ierr = STSetOperators(st,2,mat);CHKERRQ(ierr);
ierr = STSetFromOptions(st);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Apply the transformed operator for several ST's
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* shift, sigma=0.0 */
ierr = STSetUp(st);CHKERRQ(ierr);
ierr = STGetType(st,&type);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"ST type %s\n",type);CHKERRQ(ierr);
ierr = STApply(st,v,w);CHKERRQ(ierr);
ierr = VecView(w,NULL);CHKERRQ(ierr);
/* shift, sigma=0.1 */
sigma = 0.1;
ierr = STSetShift(st,sigma);CHKERRQ(ierr);
ierr = STGetShift(st,&sigma);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"With shift=%g\n",(double)PetscRealPart(sigma));CHKERRQ(ierr);
ierr = STApply(st,v,w);CHKERRQ(ierr);
ierr = VecView(w,NULL);CHKERRQ(ierr);
/* sinvert, sigma=0.1 */
ierr = STPostSolve(st);CHKERRQ(ierr); /* undo changes if inplace */
ierr = STSetType(st,STSINVERT);CHKERRQ(ierr);
ierr = STGetType(st,&type);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"ST type %s\n",type);CHKERRQ(ierr);
ierr = STGetShift(st,&sigma);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"With shift=%g\n",(double)PetscRealPart(sigma));CHKERRQ(ierr);
ierr = STApply(st,v,w);CHKERRQ(ierr);
ierr = VecView(w,NULL);CHKERRQ(ierr);
/* sinvert, sigma=-0.5 */
sigma = -0.5;
ierr = STSetShift(st,sigma);CHKERRQ(ierr);
ierr = STGetShift(st,&sigma);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"With shift=%g\n",(double)PetscRealPart(sigma));CHKERRQ(ierr);
ierr = STApply(st,v,w);CHKERRQ(ierr);
ierr = VecView(w,NULL);CHKERRQ(ierr);
/* cayley, sigma=-0.5, tau=-0.5 (equal to sigma by default) */
ierr = STPostSolve(st);CHKERRQ(ierr); /* undo changes if inplace */
ierr = STSetType(st,STCAYLEY);CHKERRQ(ierr);
ierr = STSetUp(st);CHKERRQ(ierr);
ierr = STGetType(st,&type);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"ST type %s\n",type);CHKERRQ(ierr);
ierr = STGetShift(st,&sigma);CHKERRQ(ierr);
ierr = STCayleyGetAntishift(st,&tau);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"With shift=%g, antishift=%g\n",(double)PetscRealPart(sigma),(double)PetscRealPart(tau));CHKERRQ(ierr);
ierr = STApply(st,v,w);CHKERRQ(ierr);
ierr = VecView(w,NULL);CHKERRQ(ierr);
/* cayley, sigma=1.1, tau=1.1 (still equal to sigma) */
sigma = 1.1;
ierr = STSetShift(st,sigma);CHKERRQ(ierr);
ierr = STGetShift(st,&sigma);CHKERRQ(ierr);
ierr = STCayleyGetAntishift(st,&tau);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"With shift=%g, antishift=%g\n",(double)PetscRealPart(sigma),(double)PetscRealPart(tau));CHKERRQ(ierr);
ierr = STApply(st,v,w);CHKERRQ(ierr);
ierr = VecView(w,NULL);CHKERRQ(ierr);
/* cayley, sigma=1.1, tau=-1.0 */
tau = -1.0;
ierr = STCayleySetAntishift(st,tau);CHKERRQ(ierr);
ierr = STGetShift(st,&sigma);CHKERRQ(ierr);
ierr = STCayleyGetAntishift(st,&tau);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"With shift=%g, antishift=%g\n",(double)PetscRealPart(sigma),(double)PetscRealPart(tau));CHKERRQ(ierr);
ierr = STApply(st,v,w);CHKERRQ(ierr);
ierr = VecView(w,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Check inner product matrix in Cayley
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = STGetBilinearForm(st,&M);CHKERRQ(ierr);
ierr = MatMult(M,v,w);CHKERRQ(ierr);
ierr = VecView(w,NULL);CHKERRQ(ierr);
ierr = STDestroy(&st);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&M);CHKERRQ(ierr);
ierr = VecDestroy(&v);CHKERRQ(ierr);
ierr = VecDestroy(&w);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
PetscErrorCode WashNetworkCreate(MPI_Comm comm,PetscInt pipesCase,Wash *wash_ptr,int **elist)
{
PetscErrorCode ierr;
PetscInt nnodes,npipes;
PetscMPIInt rank;
Wash wash;
PetscInt i,numVertices,numEdges;
int *edgelist;
Junction junctions=NULL;
Pipe pipes=NULL;
PetscFunctionBegin;
ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr);
ierr = PetscCalloc1(1,&wash);CHKERRQ(ierr);
wash->comm = comm;
*wash_ptr = wash;
wash->Q0 = 0.477432; /* copied from initial soluiton */
wash->H0 = 150.0;
wash->HL = 143.488; /* copied from initial soluiton */
wash->nnodes_loc = 0;
numVertices = 0;
numEdges = 0;
edgelist = NULL;
if (!rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Setup pipesCase %D\n",pipesCase);CHKERRQ(ierr);
}
nnodes = 6;
ierr = PetscOptionsGetInt(NULL,NULL, "-npipenodes", &nnodes, NULL);CHKERRQ(ierr);
/* Set global number of pipes, edges, and junctions */
/*-------------------------------------------------*/
switch (pipesCase) {
case 0:
/* pipeCase 0: */
/* =============================
v0 --E0--> v1--E1--> v2 --E2-->v3
================================ */
npipes = 3;
ierr = PetscOptionsGetInt(NULL,NULL, "-npipes", &npipes, NULL);CHKERRQ(ierr);
wash->nedge = npipes;
wash->nvertex = npipes + 1;
/* Set local edges and vertices -- proc[0] sets entire network, then distributes */
numVertices = 0;
numEdges = 0;
edgelist = NULL;
if (!rank) {
numVertices = wash->nvertex;
numEdges = wash->nedge;
ierr = PetscCalloc1(2*numEdges,&edgelist);CHKERRQ(ierr);
for (i=0; i<numEdges; i++) {
edgelist[2*i] = i; edgelist[2*i+1] = i+1;
}
/* Add network components */
/*------------------------*/
ierr = PetscCalloc2(numVertices,&junctions,numEdges,&pipes);CHKERRQ(ierr);
/* vertex */
for (i=0; i<numVertices; i++) {
junctions[i].id = i;
junctions[i].isEnd = 0;
junctions[i].nedges_in = 1; junctions[i].nedges_out = 1;
/* Set GPS data */
junctions[i].latitude = 0.0;
junctions[i].longitude = 0.0;
}
junctions[0].isEnd = -1;
junctions[0].nedges_in = 0;
junctions[numVertices-1].isEnd = 1;
junctions[numVertices-1].nedges_out = 0;
/* edge and pipe */
for (i=0; i<numEdges; i++) {
pipes[i].id = i;
pipes[i].nnodes = nnodes;
}
}
break;
case 1:
/* pipeCase 1: */
/* ==========================
v2
^
|
E2
|
v0 --E0--> v3--E1--> v1
============================= */
npipes = 3;
wash->nedge = npipes;
wash->nvertex = npipes + 1;
/* Set local edges and vertices -- proc[0] sets entire network, then distributes */
if (!rank) {
numVertices = wash->nvertex;
numEdges = wash->nedge;
ierr = PetscCalloc1(2*numEdges,&edgelist);CHKERRQ(ierr);
edgelist[0] = 0; edgelist[1] = 3; /* edge[0] */
edgelist[2] = 3; edgelist[3] = 1; /* edge[1] */
edgelist[4] = 3; edgelist[5] = 2; /* edge[2] */
/* Add network components */
/*------------------------*/
ierr = PetscCalloc2(numVertices,&junctions,numEdges,&pipes);CHKERRQ(ierr);
/* vertex */
for (i=0; i<numVertices; i++) {
junctions[i].id = i;
/* Set GPS data */
junctions[i].latitude = 0.0;
junctions[i].longitude = 0.0;
}
junctions[0].isEnd = -1; junctions[0].nedges_in = 0; junctions[0].nedges_out = 1;
junctions[1].isEnd = 1; junctions[1].nedges_in = 1; junctions[1].nedges_out = 0;
junctions[2].isEnd = 1; junctions[2].nedges_in = 1; junctions[2].nedges_out = 0;
junctions[3].isEnd = 0; junctions[3].nedges_in = 1; junctions[3].nedges_out = 2;
/* edge and pipe */
for (i=0; i<numEdges; i++) {
pipes[i].id = i;
pipes[i].nnodes = nnodes;
}
}
break;
case 2:
/* pipeCase 2: */
/* ==========================
v2--> E2
|
v0 --E0--> v3--E1--> v1
============================= */
/* Set application parameters -- to be used in function evalutions */
npipes = 3;
wash->nedge = npipes;
wash->nvertex = npipes + 1;
/* Set local edges and vertices -- proc[0] sets entire network, then distributes */
if (!rank) {
numVertices = wash->nvertex;
numEdges = wash->nedge;
ierr = PetscCalloc1(2*numEdges,&edgelist);CHKERRQ(ierr);
edgelist[0] = 0; edgelist[1] = 3; /* edge[0] */
edgelist[2] = 3; edgelist[3] = 1; /* edge[1] */
edgelist[4] = 2; edgelist[5] = 3; /* edge[2] */
/* Add network components */
/*------------------------*/
ierr = PetscCalloc2(numVertices,&junctions,numEdges,&pipes);CHKERRQ(ierr);
/* vertex */
for (i=0; i<numVertices; i++) {
junctions[i].id = i;
/* Set GPS data */
junctions[i].latitude = 0.0;
junctions[i].longitude = 0.0;
}
junctions[0].isEnd = -1; junctions[0].nedges_in = 0; junctions[0].nedges_out = 1;
junctions[1].isEnd = 1; junctions[1].nedges_in = 1; junctions[1].nedges_out = 0;
junctions[2].isEnd = -1; junctions[2].nedges_in = 0; junctions[2].nedges_out = 1;
junctions[3].isEnd = 0; junctions[3].nedges_in = 2; junctions[3].nedges_out = 1;
/* edge and pipe */
for (i=0; i<numEdges; i++) {
pipes[i].id = i;
pipes[i].nnodes = nnodes;
}
}
break;
default:
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"not done yet");
}
*wash_ptr = wash;
wash->nedge = numEdges;
wash->nvertex = numVertices;
*elist = edgelist;
wash->junction = junctions;
wash->pipe = pipes;
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
Mat A,F,B,X,C,Aher,G;
Vec b,x,c,d,e;
PetscErrorCode ierr;
PetscInt m = 5,n,p,i,j,nrows,ncols;
PetscScalar *v,*barray,rval;
PetscReal norm,tol=1.e-12;
PetscMPIInt size,rank;
PetscRandom rand;
const PetscInt *rows,*cols;
IS isrows,iscols;
PetscBool mats_view=PETSC_FALSE;
MatFactorInfo finfo;
PetscInitialize(&argc,&argv,(char*) 0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rand);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rand);CHKERRQ(ierr);
/* Get local dimensions of matrices */
ierr = PetscOptionsGetInt(NULL,"-m",&m,NULL);CHKERRQ(ierr);
n = m;
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
p = m/2;
ierr = PetscOptionsGetInt(NULL,"-p",&p,NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(NULL,"-mats_view",&mats_view);CHKERRQ(ierr);
/* Create matrix A */
ierr = PetscPrintf(PETSC_COMM_WORLD," Create Elemental matrix A\n");CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(A,MATELEMENTAL);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);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(rand,&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);
if (mats_view) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "A: nrows %d, m %d; ncols %d, n %d\n",nrows,m,ncols,n);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Create rhs matrix B */
ierr = PetscPrintf(PETSC_COMM_WORLD," Create rhs matrix B\n");CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,m,p,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(B,MATELEMENTAL);CHKERRQ(ierr);
ierr = MatSetFromOptions(B);CHKERRQ(ierr);
ierr = MatSetUp(B);CHKERRQ(ierr);
ierr = MatGetOwnershipIS(B,&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(rand,&rval);CHKERRQ(ierr);
v[i*ncols+j] = rval;
}
}
ierr = MatSetValues(B,nrows,rows,ncols,cols,v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(B,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);
if (mats_view) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "B: nrows %d, m %d; ncols %d, p %d\n",nrows,m,ncols,p);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Create rhs vector b and solution x (same size as b) */
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecSetSizes(b,m,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(b);CHKERRQ(ierr);
ierr = VecGetArray(b,&barray);CHKERRQ(ierr);
for (j=0; j<m; j++) {
ierr = PetscRandomGetValue(rand,&rval);CHKERRQ(ierr);
barray[j] = rval;
}
ierr = VecRestoreArray(b,&barray);CHKERRQ(ierr);
ierr = VecAssemblyBegin(b);CHKERRQ(ierr);
ierr = VecAssemblyEnd(b);CHKERRQ(ierr);
if (mats_view) {
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD, "[%d] b: m %d\n",rank,m);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD,PETSC_STDOUT);CHKERRQ(ierr);
ierr = VecView(b,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecDuplicate(b,&x);CHKERRQ(ierr);
/* Create matrix X - same size as B */
ierr = PetscPrintf(PETSC_COMM_WORLD," Create solution matrix X\n");CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&X);CHKERRQ(ierr);
ierr = MatSetSizes(X,m,p,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(X,MATELEMENTAL);CHKERRQ(ierr);
ierr = MatSetFromOptions(X);CHKERRQ(ierr);
ierr = MatSetUp(X);CHKERRQ(ierr);
ierr = MatAssemblyBegin(X,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(X,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* Cholesky factorization */
/*------------------------*/
ierr = PetscPrintf(PETSC_COMM_WORLD," Create Elemental matrix Aher\n");CHKERRQ(ierr);
ierr = MatHermitianTranspose(A,MAT_INITIAL_MATRIX,&Aher);CHKERRQ(ierr);
ierr = MatAXPY(Aher,1.0,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr); /* Aher = A + A^T */
if (!rank) { /* add 100.0 to diagonals of Aher to make it spd */
PetscInt M,N;
ierr = MatGetSize(Aher,&M,&N);CHKERRQ(ierr);
for (i=0; i<M; i++) {
rval = 100.0;
ierr = MatSetValues(Aher,1,&i,1,&i,&rval,ADD_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(Aher,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(Aher,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
if (mats_view) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Aher:\n");CHKERRQ(ierr);
ierr = MatView(Aher,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Cholesky factorization */
/*------------------------*/
ierr = PetscPrintf(PETSC_COMM_WORLD," Test Cholesky Solver \n");CHKERRQ(ierr);
/* In-place Cholesky */
/* Create matrix factor G, then copy Aher to G */
ierr = MatCreate(PETSC_COMM_WORLD,&G);CHKERRQ(ierr);
ierr = MatSetSizes(G,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(G,MATELEMENTAL);CHKERRQ(ierr);
ierr = MatSetFromOptions(G);CHKERRQ(ierr);
ierr = MatSetUp(G);CHKERRQ(ierr);
ierr = MatAssemblyBegin(G,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(G,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatCopy(Aher,G,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
/* Only G = U^T * U is implemented for now */
ierr = MatCholeskyFactor(G,0,0);CHKERRQ(ierr);
if (mats_view) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "Cholesky Factor G:\n");CHKERRQ(ierr);
ierr = MatView(G,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Solve U^T * U x = b and U^T * U X = B */
ierr = MatSolve(G,b,x);CHKERRQ(ierr);
ierr = MatMatSolve(G,B,X);CHKERRQ(ierr);
ierr = MatDestroy(&G);CHKERRQ(ierr);
/* Out-place Cholesky */
ierr = MatGetFactor(Aher,MATSOLVERELEMENTAL,MAT_FACTOR_CHOLESKY,&G);CHKERRQ(ierr);
ierr = MatCholeskyFactorSymbolic(G,Aher,0,&finfo);CHKERRQ(ierr);
ierr = MatCholeskyFactorNumeric(G,Aher,&finfo);CHKERRQ(ierr);
if (mats_view) {
ierr = MatView(G,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = MatSolve(G,b,x);CHKERRQ(ierr);
ierr = MatMatSolve(G,B,X);CHKERRQ(ierr);
ierr = MatDestroy(&G);CHKERRQ(ierr);
/* Check norm(Aher*x - b) */
ierr = VecCreate(PETSC_COMM_WORLD,&c);CHKERRQ(ierr);
ierr = VecSetSizes(c,m,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(c);CHKERRQ(ierr);
ierr = MatMult(Aher,x,c);CHKERRQ(ierr);
ierr = VecAXPY(c,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(c,NORM_1,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: |Aher*x - b| for Cholesky %G\n",norm);CHKERRQ(ierr);
}
/* Check norm(Aher*X - B) */
ierr = MatMatMult(Aher,X,MAT_INITIAL_MATRIX,PETSC_DEFAULT,&C);CHKERRQ(ierr);
ierr = MatAXPY(C,-1.0,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatNorm(C,NORM_1,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: |Aher*X - B| for Cholesky %G\n",norm);CHKERRQ(ierr);
}
/* LU factorization */
/*------------------*/
ierr = PetscPrintf(PETSC_COMM_WORLD," Test LU Solver \n");CHKERRQ(ierr);
/* In-place LU */
/* Create matrix factor F, then copy A to F */
ierr = MatCreate(PETSC_COMM_WORLD,&F);CHKERRQ(ierr);
ierr = MatSetSizes(F,m,n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetType(F,MATELEMENTAL);CHKERRQ(ierr);
ierr = MatSetFromOptions(F);CHKERRQ(ierr);
ierr = MatSetUp(F);CHKERRQ(ierr);
ierr = MatAssemblyBegin(F,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(F,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatCopy(A,F,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
/* Create vector d to test MatSolveAdd() */
ierr = VecDuplicate(x,&d);CHKERRQ(ierr);
ierr = VecCopy(x,d);CHKERRQ(ierr);
/* PF=LU or F=LU factorization - perms is ignored by Elemental;
set finfo.dtcol !0 or 0 to enable/disable partial pivoting */
finfo.dtcol = 0.1;
ierr = MatLUFactor(F,0,0,&finfo);CHKERRQ(ierr);
/* Solve LUX = PB or LUX = B */
ierr = MatSolveAdd(F,b,d,x);CHKERRQ(ierr);
ierr = MatMatSolve(F,B,X);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
/* Check norm(A*X - B) */
ierr = VecCreate(PETSC_COMM_WORLD,&e);CHKERRQ(ierr);
ierr = VecSetSizes(e,m,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(e);CHKERRQ(ierr);
ierr = MatMult(A,x,c);CHKERRQ(ierr);
ierr = MatMult(A,d,e);CHKERRQ(ierr);
ierr = VecAXPY(c,-1.0,e);CHKERRQ(ierr);
ierr = VecAXPY(c,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(c,NORM_1,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: |A*x - b| for LU %G\n",norm);CHKERRQ(ierr);
}
ierr = MatMatMult(A,X,MAT_REUSE_MATRIX,PETSC_DEFAULT,&C);CHKERRQ(ierr);
ierr = MatAXPY(C,-1.0,B,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = MatNorm(C,NORM_1,&norm);CHKERRQ(ierr);
if (norm > tol) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Warning: |A*X - B| for LU %G\n",norm);CHKERRQ(ierr);
}
/* Out-place LU */
ierr = MatGetFactor(A,MATSOLVERELEMENTAL,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
ierr = MatLUFactorSymbolic(F,A,0,0,&finfo);CHKERRQ(ierr);
ierr = MatLUFactorNumeric(F,A,&finfo);CHKERRQ(ierr);
if (mats_view) {
ierr = MatView(F,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = MatSolve(F,b,x);CHKERRQ(ierr);
ierr = MatMatSolve(F,B,X);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
/* Free space */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&Aher);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = MatDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&c);CHKERRQ(ierr);
ierr = VecDestroy(&d);CHKERRQ(ierr);
ierr = VecDestroy(&e);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rand);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
int time; /* amount of loops */
struct in put;
PetscScalar rh; /* relative humidity */
PetscScalar x; /* memory varialbe for relative humidity calculation */
PetscScalar deep_grnd_temp; /* temperature of ground under top soil surface layer */
PetscScalar emma; /* absorption-emission constant for air */
PetscScalar pressure1 = 101300; /* surface pressure */
PetscScalar mixratio; /* mixing ratio */
PetscScalar airtemp; /* temperature of air near boundary layer inversion */
PetscScalar dewtemp; /* dew point temperature */
PetscScalar sfctemp; /* temperature at surface */
PetscScalar pwat; /* total column precipitable water */
PetscScalar cloudTemp; /* temperature at base of cloud */
AppCtx user; /* user-defined work context */
MonitorCtx usermonitor; /* user-defined monitor context */
PetscMPIInt rank,size;
TS ts;
SNES snes;
DM da;
Vec T,rhs; /* solution vector */
Mat J; /* Jacobian matrix */
PetscReal ftime,dt;
PetscInt steps,dof = 5;
PetscBool use_coloring = PETSC_TRUE;
MatFDColoring matfdcoloring = 0;
PetscBool monitor_off = PETSC_FALSE;
ierr = PetscInitialize(&argc,&argv,(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);
/* Inputs */
readinput(&put);
sfctemp = put.Ts;
dewtemp = put.Td;
cloudTemp = put.Tc;
airtemp = put.Ta;
pwat = put.pwt;
if (!rank) PetscPrintf(PETSC_COMM_SELF,"Initial Temperature = %g\n",(double)sfctemp); /* input surface temperature */
deep_grnd_temp = sfctemp - 10; /* set underlying ground layer temperature */
emma = emission(pwat); /* accounts for radiative effects of water vapor */
/* Converts from Fahrenheit to Celsuis */
sfctemp = fahr_to_cel(sfctemp);
airtemp = fahr_to_cel(airtemp);
dewtemp = fahr_to_cel(dewtemp);
cloudTemp = fahr_to_cel(cloudTemp);
deep_grnd_temp = fahr_to_cel(deep_grnd_temp);
/* Converts from Celsius to Kelvin */
sfctemp += 273;
airtemp += 273;
dewtemp += 273;
cloudTemp += 273;
deep_grnd_temp += 273;
/* Calculates initial relative humidity */
x = calcmixingr(dewtemp,pressure1);
mixratio = calcmixingr(sfctemp,pressure1);
rh = (x/mixratio)*100;
if (!rank) printf("Initial RH = %.1f percent\n\n",(double)rh); /* prints initial relative humidity */
time = 3600*put.time; /* sets amount of timesteps to run model */
/* Configure PETSc TS solver */
/*------------------------------------------*/
/* Create grid */
ierr = DMDACreate2d(PETSC_COMM_WORLD,DM_BOUNDARY_PERIODIC,DM_BOUNDARY_PERIODIC,DMDA_STENCIL_STAR,-20,-20,
PETSC_DECIDE,PETSC_DECIDE,dof,1,NULL,NULL,&da);CHKERRQ(ierr);
ierr = DMDASetUniformCoordinates(da, 0.0, 1.0, 0.0, 1.0, 0.0, 1.0);CHKERRQ(ierr);
/* Define output window for each variable of interest */
ierr = DMDASetFieldName(da,0,"Ts");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,1,"Ta");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,2,"u");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,3,"v");CHKERRQ(ierr);
ierr = DMDASetFieldName(da,4,"p");CHKERRQ(ierr);
/* set values for appctx */
user.da = da;
user.Ts = sfctemp;
user.fract = put.fr; /* fraction of sky covered by clouds */
user.dewtemp = dewtemp; /* dew point temperature (mositure in air) */
user.csoil = 2000000; /* heat constant for layer */
user.dzlay = 0.08; /* thickness of top soil layer */
user.emma = emma; /* emission parameter */
user.wind = put.wnd; /* wind spped */
user.pressure1 = pressure1; /* sea level pressure */
user.airtemp = airtemp; /* temperature of air near boundar layer inversion */
user.Tc = cloudTemp; /* temperature at base of lowest cloud layer */
user.init = put.init; /* user chosen initiation scenario */
user.lat = 70*0.0174532; /* converts latitude degrees to latitude in radians */
user.deep_grnd_temp = deep_grnd_temp; /* temp in lowest ground layer */
/* set values for MonitorCtx */
usermonitor.drawcontours = PETSC_FALSE;
ierr = PetscOptionsHasName(NULL,NULL,"-drawcontours",&usermonitor.drawcontours);CHKERRQ(ierr);
if (usermonitor.drawcontours) {
PetscReal bounds[] = {1000.0,-1000., -1000.,-1000., 1000.,-1000., 1000.,-1000., 1000,-1000, 100700,100800};
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,0,0,0,300,300,&usermonitor.drawviewer);CHKERRQ(ierr);
ierr = PetscViewerDrawSetBounds(usermonitor.drawviewer,dof,bounds);CHKERRQ(ierr);
}
usermonitor.interval = 1;
ierr = PetscOptionsGetInt(NULL,NULL,"-monitor_interval",&usermonitor.interval,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Extract global vectors from DA;
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMCreateGlobalVector(da,&T);CHKERRQ(ierr);
ierr = VecDuplicate(T,&rhs);CHKERRQ(ierr); /* r: vector to put the computed right hand side */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr);
ierr = TSSetRHSFunction(ts,rhs,RhsFunc,&user);CHKERRQ(ierr);
/* Set Jacobian evaluation routine - use coloring to compute finite difference Jacobian efficiently */
ierr = DMSetMatType(da,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(da,&J);CHKERRQ(ierr);
ierr = TSGetSNES(ts,&snes);CHKERRQ(ierr);
if (use_coloring) {
ISColoring iscoloring;
ierr = DMCreateColoring(da,IS_COLORING_GLOBAL,&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringCreate(J,iscoloring,&matfdcoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetFromOptions(matfdcoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetUp(J,iscoloring,matfdcoloring);CHKERRQ(ierr);
ierr = ISColoringDestroy(&iscoloring);CHKERRQ(ierr);
ierr = MatFDColoringSetFunction(matfdcoloring,(PetscErrorCode (*)(void))SNESTSFormFunction,ts);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefaultColor,matfdcoloring);CHKERRQ(ierr);
} else {
ierr = SNESSetJacobian(snes,J,J,SNESComputeJacobianDefault,NULL);CHKERRQ(ierr);
}
/* Define what to print for ts_monitor option */
ierr = PetscOptionsHasName(NULL,NULL,"-monitor_off",&monitor_off);CHKERRQ(ierr);
if (!monitor_off) {
ierr = TSMonitorSet(ts,Monitor,&usermonitor,NULL);CHKERRQ(ierr);
}
ierr = FormInitialSolution(da,T,&user);CHKERRQ(ierr);
dt = TIMESTEP; /* initial time step */
ftime = TIMESTEP*time;
if (!rank) printf("time %d, ftime %g hour, TIMESTEP %g\n",time,(double)(ftime/3600),(double)dt);
ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
ierr = TSSetDuration(ts,time,ftime);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
ierr = TSSetSolution(ts,T);CHKERRQ(ierr);
ierr = TSSetDM(ts,da);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set runtime options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSolve(ts,T);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);
if (!rank) PetscPrintf(PETSC_COMM_WORLD,"Solution T after %g hours %d steps\n",(double)(ftime/3600),steps);
if (matfdcoloring) {ierr = MatFDColoringDestroy(&matfdcoloring);CHKERRQ(ierr);}
if (usermonitor.drawcontours) {
ierr = PetscViewerDestroy(&usermonitor.drawviewer);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&T);CHKERRQ(ierr);
ierr = VecDestroy(&rhs);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **args)
{
Vec x,y,b,s1,s2;
Mat A; /* linear system matrix */
Mat sA; /* symmetric part of the matrices */
PetscInt n,mbs=16,bs=1,nz=3,prob=2,i,j,col[3],row,Ii,J,n1;
const PetscInt *ip_ptr;
PetscScalar neg_one = -1.0,value[3],alpha=0.1;
PetscMPIInt size;
PetscErrorCode ierr;
IS ip, isrow, iscol;
PetscRandom rdm;
PetscBool reorder=PETSC_FALSE;
MatInfo minfo1,minfo2;
PetscReal norm1,norm2,tol=1.e-10;
PetscInitialize(&argc,&args,(char*)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,1,"This is a uniprocessor example only!");
ierr = PetscOptionsGetInt(NULL,NULL,"-bs",&bs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-mbs",&mbs,NULL);CHKERRQ(ierr);
n = mbs*bs;
ierr=MatCreateSeqBAIJ(PETSC_COMM_WORLD,bs,n,n,nz,NULL, &A);CHKERRQ(ierr);
ierr=MatCreateSeqSBAIJ(PETSC_COMM_WORLD,bs,n,n,nz,NULL, &sA);CHKERRQ(ierr);
/* Test MatGetOwnershipRange() */
ierr = MatGetOwnershipRange(A,&Ii,&J);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(sA,&i,&j);CHKERRQ(ierr);
if (i-Ii || j-J) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetOwnershipRange() in MatSBAIJ format\n");CHKERRQ(ierr);
}
/* Assemble matrix */
if (bs == 1) {
ierr = PetscOptionsGetInt(NULL,NULL,"-test_problem",&prob,NULL);CHKERRQ(ierr);
if (prob == 1) { /* tridiagonal matrix */
value[0] = -1.0; value[1] = 2.0; value[2] = -1.0;
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,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
i = n - 1; col[0]=0; col[1] = n - 2; col[2] = n - 1;
value[0]= 0.1; value[1]=-1; value[2]=2;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
i = 0; col[0] = 0; col[1] = 1; col[2]=n-1;
value[0] = 2.0; value[1] = -1.0; value[2]=0.1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
} else if (prob ==2) { /* matrix for the five point stencil */
n1 = (PetscInt) (PetscSqrtReal((PetscReal)n) + 0.001);
if (n1*n1 - n) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_ARG_WRONG,"sqrt(n) must be a positive interger!");
for (i=0; i<n1; i++) {
for (j=0; j<n1; j++) {
Ii = j + n1*i;
if (i>0) {
J = Ii - n1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
if (i<n1-1) {
J = Ii + n1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
if (j>0) {
J = Ii - 1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
if (j<n1-1) {
J = Ii + 1;
ierr = MatSetValues(A,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&Ii,1,&J,&neg_one,INSERT_VALUES);CHKERRQ(ierr);
}
/*
ierr = MatSetValues(A,1,&I,1,&I,&four,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&I,1,&I,&four,INSERT_VALUES);CHKERRQ(ierr);
*/
}
}
}
} else { /* bs > 1 */
#if defined(DIAGB)
for (block=0; block<n/bs; block++) {
/* diagonal blocks */
value[0] = -1.0; value[1] = 4.0; value[2] = -1.0;
for (i=1+block*bs; i<bs-1+block*bs; i++) {
col[0] = i-1; col[1] = i; col[2] = i+1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
i = bs - 1+block*bs; col[0] = bs - 2+block*bs; col[1] = bs - 1+block*bs;
value[0]=-1.0; value[1]=4.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
i = 0+block*bs; col[0] = 0+block*bs; col[1] = 1+block*bs;
value[0]=4.0; value[1] = -1.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
#endif
/* off-diagonal blocks */
value[0]=-1.0;
for (i=0; i<(n/bs-1)*bs; i++) {
col[0]=i+bs;
ierr = MatSetValues(A,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&i,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
col[0]=i; row=i+bs;
ierr = MatSetValues(A,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(sA,1,&row,1,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* PetscPrintf(PETSC_COMM_SELF,"\n The Matrix: \n");
MatView(A, VIEWER_DRAW_WORLD);
MatView(A, VIEWER_STDOUT_WORLD); */
ierr = MatAssemblyBegin(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(sA,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* PetscPrintf(PETSC_COMM_SELF,"\n Symmetric Part of Matrix: \n");
MatView(sA, VIEWER_DRAW_WORLD);
MatView(sA, VIEWER_STDOUT_WORLD);
*/
/* Test MatNorm() */
ierr = MatNorm(A,NORM_FROBENIUS,&norm1);CHKERRQ(ierr);
ierr = MatNorm(sA,NORM_FROBENIUS,&norm2);CHKERRQ(ierr);
norm1 -= norm2;
if (norm1<-tol || norm1>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm(), fnorm1-fnorm2=%16.14e\n",norm1);CHKERRQ(ierr);
}
ierr = MatNorm(A,NORM_INFINITY,&norm1);CHKERRQ(ierr);
ierr = MatNorm(sA,NORM_INFINITY,&norm2);CHKERRQ(ierr);
norm1 -= norm2;
if (norm1<-tol || norm1>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatNorm(), inf_norm1-inf_norm2=%16.14e\n",norm1);CHKERRQ(ierr);
}
/* Test MatGetInfo(), MatGetSize(), MatGetBlockSize() */
ierr = MatGetInfo(A,MAT_LOCAL,&minfo1);CHKERRQ(ierr);
ierr = MatGetInfo(sA,MAT_LOCAL,&minfo2);CHKERRQ(ierr);
/*
printf("matrix nonzeros (BAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo1.nz_used,(int)minfo1.nz_allocated);
printf("matrix nonzeros(SBAIJ format) = %d, allocated nonzeros= %d\n", (int)minfo2.nz_used,(int)minfo2.nz_allocated);
*/
i = (int) (minfo1.nz_used - minfo2.nz_used);
j = (int) (minfo1.nz_allocated - minfo2.nz_allocated);
if (i<0 || j<0) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetInfo()\n");CHKERRQ(ierr);
}
ierr = MatGetSize(A,&Ii,&J);CHKERRQ(ierr);
ierr = MatGetSize(sA,&i,&j);CHKERRQ(ierr);
if (i-Ii || j-J) {
PetscPrintf(PETSC_COMM_SELF,"Error: MatGetSize()\n");CHKERRQ(ierr);
}
ierr = MatGetBlockSize(A, &Ii);CHKERRQ(ierr);
ierr = MatGetBlockSize(sA, &i);CHKERRQ(ierr);
if (i-Ii) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatGetBlockSize()\n");CHKERRQ(ierr);
}
/* Test MatDiagonalScale(), MatGetDiagonal(), MatScale() */
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rdm);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,n,&x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&s1);CHKERRQ(ierr);
ierr = VecDuplicate(x,&s2);CHKERRQ(ierr);
ierr = VecDuplicate(x,&y);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecSetRandom(x,rdm);CHKERRQ(ierr);
ierr = MatDiagonalScale(A,x,x);CHKERRQ(ierr);
ierr = MatDiagonalScale(sA,x,x);CHKERRQ(ierr);
ierr = MatGetDiagonal(A,s1);CHKERRQ(ierr);
ierr = MatGetDiagonal(sA,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr);
norm1 -= norm2;
if (norm1<-tol || norm1>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatGetDiagonal() \n");CHKERRQ(ierr);
}
ierr = MatScale(A,alpha);CHKERRQ(ierr);
ierr = MatScale(sA,alpha);CHKERRQ(ierr);
/* Test MatMult(), MatMultAdd() */
for (i=0; i<40; i++) {
ierr = VecSetRandom(x,rdm);CHKERRQ(ierr);
ierr = MatMult(A,x,s1);CHKERRQ(ierr);
ierr = MatMult(sA,x,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr);
norm1 -= norm2;
if (norm1<-tol || norm1>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error: MatMult(), MatDiagonalScale() or MatScale()\n");CHKERRQ(ierr);
}
}
for (i=0; i<40; i++) {
ierr = VecSetRandom(x,rdm);CHKERRQ(ierr);
ierr = VecSetRandom(y,rdm);CHKERRQ(ierr);
ierr = MatMultAdd(A,x,y,s1);CHKERRQ(ierr);
ierr = MatMultAdd(sA,x,y,s2);CHKERRQ(ierr);
ierr = VecNorm(s1,NORM_1,&norm1);CHKERRQ(ierr);
ierr = VecNorm(s2,NORM_1,&norm2);CHKERRQ(ierr);
norm1 -= norm2;
if (norm1<-tol || norm1>tol) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Error:MatMultAdd(), MatDiagonalScale() or MatScale() \n");CHKERRQ(ierr);
}
}
/* Test MatReordering() */
ierr = MatGetOrdering(A,MATORDERINGNATURAL,&isrow,&iscol);CHKERRQ(ierr);
ip = isrow;
if (reorder) {
IS nip;
PetscInt *nip_ptr;
ierr = PetscMalloc1(mbs,&nip_ptr);CHKERRQ(ierr);
ierr = ISGetIndices(ip,&ip_ptr);CHKERRQ(ierr);
ierr = PetscMemcpy(nip_ptr,ip_ptr,mbs*sizeof(PetscInt));CHKERRQ(ierr);
i = nip_ptr[1]; nip_ptr[1] = nip_ptr[mbs-2]; nip_ptr[mbs-2] = i;
i = nip_ptr[0]; nip_ptr[0] = nip_ptr[mbs-1]; nip_ptr[mbs-1] = i;
ierr = ISRestoreIndices(ip,&ip_ptr);CHKERRQ(ierr);
ierr = ISCreateGeneral(PETSC_COMM_SELF,mbs,nip_ptr,PETSC_COPY_VALUES,&nip);CHKERRQ(ierr);
ierr = PetscFree(nip_ptr);CHKERRQ(ierr);
ierr = MatReorderingSeqSBAIJ(sA, ip);CHKERRQ(ierr);
ierr = ISDestroy(&nip);CHKERRQ(ierr);
/* ierr = ISView(ip, VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = MatView(sA,VIEWER_DRAW_SELF);CHKERRQ(ierr); */
}
ierr = ISDestroy(&iscol);CHKERRQ(ierr);
/* ierr = ISDestroy(&isrow);CHKERRQ(ierr);*/
ierr = ISDestroy(&isrow);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&sA);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&s1);CHKERRQ(ierr);
ierr = VecDestroy(&s2);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Mat A,B,C;
PetscInt i,j,k,m = 3,n = 3,bs = 1;
PetscErrorCode ierr;
PetscMPIInt size;
ierr = PetscInitialize(&argc,&args,(char*)0,help);CHKERRQ(ierr);
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 = PetscOptionsGetInt(NULL,NULL,"-m",&m,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-bs",&bs,NULL);CHKERRQ(ierr);
/* adjust sizes by block size */
if (m%bs) m += bs-m%bs;
if (n%bs) n += bs-n%bs;
ierr = MatCreate(PETSC_COMM_SELF,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,m*n,m*n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetBlockSize(A,bs);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr);
ierr = MatSetSizes(B,m*n,m*n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetBlockSize(B,bs);CHKERRQ(ierr);
ierr = MatSetType(B,MATSEQBAIJ);CHKERRQ(ierr);
ierr = MatSetUp(B);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,m*n,m*n,PETSC_DECIDE,PETSC_DECIDE);CHKERRQ(ierr);
ierr = MatSetBlockSize(C,bs);CHKERRQ(ierr);
ierr = MatSetType(C,MATSEQSBAIJ);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
ierr = MatSetOption(C,MAT_IGNORE_LOWER_TRIANGULAR,PETSC_TRUE);CHKERRQ(ierr);
for (i=0; i<m; i++) {
for (j=0; j<n; j++) {
PetscScalar v = -1.0;
PetscInt Ii = j + n*i,J;
J = Ii - n;
if (J>=0) {
ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
}
J = Ii + n;
if (J<m*n) {
ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
}
J = Ii - 1;
if (J>=0) {
ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
}
J = Ii + 1;
if (J<m*n) {
ierr = MatSetValues(A,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,1,&Ii,1,&J,&v,INSERT_VALUES);CHKERRQ(ierr);
}
v = 4.0;
ierr = MatSetValues(A,1,&Ii,1,&Ii,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(B,1,&Ii,1,&Ii,&v,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatSetValues(C,1,&Ii,1,&Ii,&v,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);
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* test MatGetRowIJ for the three Mat types */
ierr = MatView(A,NULL);CHKERRQ(ierr);
ierr = MatView(B,NULL);CHKERRQ(ierr);
ierr = MatView(C,NULL);CHKERRQ(ierr);
for (i=0;i<2;i++) {
PetscInt shift = i;
for (j=0;j<2;j++) {
PetscBool symmetric = ((j>0) ? PETSC_FALSE : PETSC_TRUE);
for (k=0;k<2;k++) {
PetscBool compressed = ((k>0) ? PETSC_FALSE : PETSC_TRUE);
ierr = DumpCSR(A,shift,symmetric,compressed);CHKERRQ(ierr);
ierr = DumpCSR(B,shift,symmetric,compressed);CHKERRQ(ierr);
ierr = DumpCSR(C,shift,symmetric,compressed);CHKERRQ(ierr);
}
}
}
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
/*
Mm_ratio - ration of grid lines between fine and coarse grids.
*/
int main(int argc,char **argv)
{
PetscErrorCode ierr;
AppCtx user;
PetscMPIInt size,rank;
PetscInt m,n,M,N,i,nrows;
PetscScalar one = 1.0;
PetscReal fill=2.0;
Mat A,P,R,C,PtAP;
PetscScalar *array;
PetscRandom rdm;
PetscBool Test_3D=PETSC_FALSE,flg;
const PetscInt *ia,*ja;
ierr = PetscInitialize(&argc,&argv,NULL,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);
/* Get size of fine grids and coarse grids */
user.ratio = 2;
user.coarse.mx = 4; user.coarse.my = 4; user.coarse.mz = 4;
ierr = PetscOptionsGetInt(NULL,NULL,"-Mx",&user.coarse.mx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-My",&user.coarse.my,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-Mz",&user.coarse.mz,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-ratio",&user.ratio,NULL);CHKERRQ(ierr);
if (user.coarse.mz) Test_3D = PETSC_TRUE;
user.fine.mx = user.ratio*(user.coarse.mx-1)+1;
user.fine.my = user.ratio*(user.coarse.my-1)+1;
user.fine.mz = user.ratio*(user.coarse.mz-1)+1;
if (!rank) {
if (!Test_3D) {
ierr = PetscPrintf(PETSC_COMM_SELF,"coarse grids: %D %D; fine grids: %D %D\n",user.coarse.mx,user.coarse.my,user.fine.mx,user.fine.my);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_SELF,"coarse grids: %D %D %D; fine grids: %D %D %D\n",user.coarse.mx,user.coarse.my,user.coarse.mz,user.fine.mx,user.fine.my,user.fine.mz);CHKERRQ(ierr);
}
}
/* Set up distributed array for fine grid */
if (!Test_3D) {
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.fine.mx,user.fine.my,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.fine.da);CHKERRQ(ierr);
} else {
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.fine.mx,user.fine.my,user.fine.mz,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,
1,1,NULL,NULL,NULL,&user.fine.da);CHKERRQ(ierr);
}
ierr = DMSetFromOptions(user.fine.da);CHKERRQ(ierr);
ierr = DMSetUp(user.fine.da);CHKERRQ(ierr);
/* Create and set A at fine grids */
ierr = DMSetMatType(user.fine.da,MATAIJ);CHKERRQ(ierr);
ierr = DMCreateMatrix(user.fine.da,&A);CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
ierr = MatGetSize(A,&M,&N);CHKERRQ(ierr);
/* set val=one to A (replace with random values!) */
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rdm);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(rdm);CHKERRQ(ierr);
if (size == 1) {
ierr = MatGetRowIJ(A,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr);
if (flg) {
ierr = MatSeqAIJGetArray(A,&array);CHKERRQ(ierr);
for (i=0; i<ia[nrows]; i++) array[i] = one;
ierr = MatSeqAIJRestoreArray(A,&array);CHKERRQ(ierr);
}
ierr = MatRestoreRowIJ(A,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr);
} else {
Mat AA,AB;
ierr = MatMPIAIJGetSeqAIJ(A,&AA,&AB,NULL);CHKERRQ(ierr);
ierr = MatGetRowIJ(AA,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr);
if (flg) {
ierr = MatSeqAIJGetArray(AA,&array);CHKERRQ(ierr);
for (i=0; i<ia[nrows]; i++) array[i] = one;
ierr = MatSeqAIJRestoreArray(AA,&array);CHKERRQ(ierr);
}
ierr = MatRestoreRowIJ(AA,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr);
ierr = MatGetRowIJ(AB,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr);
if (flg) {
ierr = MatSeqAIJGetArray(AB,&array);CHKERRQ(ierr);
for (i=0; i<ia[nrows]; i++) array[i] = one;
ierr = MatSeqAIJRestoreArray(AB,&array);CHKERRQ(ierr);
}
ierr = MatRestoreRowIJ(AB,0,PETSC_FALSE,PETSC_FALSE,&nrows,&ia,&ja,&flg);CHKERRQ(ierr);
}
/* Set up distributed array for coarse grid */
if (!Test_3D) {
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.coarse.mx,user.coarse.my,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&user.coarse.da);CHKERRQ(ierr);
} else {
ierr = DMDACreate3d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,user.coarse.mx,user.coarse.my,user.coarse.mz,PETSC_DECIDE,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,NULL,&user.coarse.da);CHKERRQ(ierr);
}
ierr = DMSetFromOptions(user.coarse.da);CHKERRQ(ierr);
ierr = DMSetUp(user.coarse.da);CHKERRQ(ierr);
/* Create interpolation between the fine and coarse grids */
ierr = DMCreateInterpolation(user.coarse.da,user.fine.da,&P,NULL);CHKERRQ(ierr);
/* Get R = P^T */
ierr = MatTranspose(P,MAT_INITIAL_MATRIX,&R);CHKERRQ(ierr);
/* C = R*A*P */
ierr = MatMatMatMult(R,A,P,MAT_INITIAL_MATRIX,fill,&C);CHKERRQ(ierr);
ierr = MatMatMatMult(R,A,P,MAT_REUSE_MATRIX,fill,&C);CHKERRQ(ierr);
/* Test C == PtAP */
ierr = MatPtAP(A,P,MAT_INITIAL_MATRIX,fill,&PtAP);CHKERRQ(ierr);
ierr = MatPtAP(A,P,MAT_REUSE_MATRIX,fill,&PtAP);CHKERRQ(ierr);
ierr = MatEqual(C,PtAP,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"Matrices are not equal");
ierr = MatDestroy(&PtAP);CHKERRQ(ierr);
/* Clean up */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rdm);CHKERRQ(ierr);
ierr = DMDestroy(&user.fine.da);CHKERRQ(ierr);
ierr = DMDestroy(&user.coarse.da);CHKERRQ(ierr);
ierr = MatDestroy(&P);CHKERRQ(ierr);
ierr = MatDestroy(&R);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
Mat A; /* problem matrix */
EPS eps; /* eigenproblem solver context */
EPSType type;
PetscReal error,tol,re,im;
PetscScalar kr,ki,value[3];
Vec xr,xi;
PetscInt n=30,i,Istart,Iend,col[3],nev,maxit,its,nconv;
PetscBool FirstBlock=PETSC_FALSE,LastBlock=PETSC_FALSE;
PetscErrorCode ierr;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n1-D Laplacian Eigenproblem, n=%D\n\n",n);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the operator matrix that defines the eigensystem, Ax=kx
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
if (Istart==0) FirstBlock=PETSC_TRUE;
if (Iend==n) LastBlock=PETSC_TRUE;
value[0]=-1.0; value[1]=2.0; value[2]=-1.0;
for (i=(FirstBlock? Istart+1: Istart); i<(LastBlock? Iend-1: Iend); i++) {
col[0]=i-1; col[1]=i; col[2]=i+1;
ierr = MatSetValues(A,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (LastBlock) {
i=n-1; col[0]=n-2; col[1]=n-1;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (FirstBlock) {
i=0; col[0]=0; col[1]=1; value[0]=2.0; value[1]=-1.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetVecs(A,NULL,&xr);CHKERRQ(ierr);
ierr = MatGetVecs(A,NULL,&xi);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the eigensolver and set various options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create eigensolver context
*/
ierr = EPSCreate(PETSC_COMM_WORLD,&eps);CHKERRQ(ierr);
/*
Set operators. In this case, it is a standard eigenvalue problem
*/
ierr = EPSSetOperators(eps,A,NULL);CHKERRQ(ierr);
ierr = EPSSetProblemType(eps,EPS_HEP);CHKERRQ(ierr);
/*
Set solver parameters at runtime
*/
ierr = EPSSetFromOptions(eps);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the eigensystem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = EPSSolve(eps);CHKERRQ(ierr);
/*
Optional: Get some information from the solver and display it
*/
ierr = EPSGetIterationNumber(eps,&its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of iterations of the method: %D\n",its);CHKERRQ(ierr);
ierr = EPSGetType(eps,&type);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Solution method: %s\n\n",type);CHKERRQ(ierr);
ierr = EPSGetDimensions(eps,&nev,NULL,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of requested eigenvalues: %D\n",nev);CHKERRQ(ierr);
ierr = EPSGetTolerances(eps,&tol,&maxit);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Stopping condition: tol=%.4g, maxit=%D\n",(double)tol,maxit);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Display solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Get number of converged approximate eigenpairs
*/
ierr = EPSGetConverged(eps,&nconv);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of converged eigenpairs: %D\n\n",nconv);CHKERRQ(ierr);
if (nconv>0) {
/*
Display eigenvalues and relative errors
*/
ierr = PetscPrintf(PETSC_COMM_WORLD,
" k ||Ax-kx||/||kx||\n"
" ----------------- ------------------\n");CHKERRQ(ierr);
for (i=0;i<nconv;i++) {
/*
Get converged eigenpairs: i-th eigenvalue is stored in kr (real part) and
ki (imaginary part)
*/
ierr = EPSGetEigenpair(eps,i,&kr,&ki,xr,xi);CHKERRQ(ierr);
/*
Compute the relative error associated to each eigenpair
*/
ierr = EPSComputeRelativeError(eps,i,&error);CHKERRQ(ierr);
#if defined(PETSC_USE_COMPLEX)
re = PetscRealPart(kr);
im = PetscImaginaryPart(kr);
#else
re = kr;
im = ki;
#endif
if (im!=0.0) {
ierr = PetscPrintf(PETSC_COMM_WORLD," %9f%+9f j %12g\n",(double)re,(double)im,(double)error);CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD," %12f %12g\n",(double)re,(double)error);CHKERRQ(ierr);
}
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);
}
/*
Free work space
*/
ierr = EPSDestroy(&eps);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&xr);CHKERRQ(ierr);
ierr = VecDestroy(&xi);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
Example: mpiexec -n <np> ./ex130 -f <matrix binary file> -mat_solver_package 1 -mat_superlu_equil \n\n";
#include <petscmat.h>
#undef __FUNCT__
#define __FUNCT__ "main"
int main(int argc,char **args)
{
Mat A,F;
Vec u,x,b;
PetscErrorCode ierr;
PetscMPIInt rank,nproc;
PetscInt m,n,nfact,ipack=0;
PetscReal norm,tol=1.e-12,Anorm;
IS perm,iperm;
MatFactorInfo info;
PetscBool flg,testMatSolve=PETSC_TRUE;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
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);
/* Determine file from which we read the matrix A */
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f option");
/* Load matrix A */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecLoad(b,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&m,&n);CHKERRQ(ierr);
if (m != n) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ, "This example is not intended for rectangular matrices (%d, %d)", m, n);
ierr = MatNorm(A,NORM_INFINITY,&Anorm);CHKERRQ(ierr);
/* Create vectors */
ierr = VecDuplicate(b,&x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&u);CHKERRQ(ierr); /* save the true solution */
/* Test LU Factorization */
ierr = MatGetOrdering(A,MATORDERINGNATURAL,&perm,&iperm);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-mat_solver_package",&ipack,NULL);CHKERRQ(ierr);
switch (ipack) {
case 1:
#if defined(PETSC_HAVE_SUPERLU)
if (!rank) printf(" SUPERLU LU:\n");
ierr = MatGetFactor(A,MATSOLVERSUPERLU,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
break;
#endif
case 2:
#if defined(PETSC_HAVE_MUMPS)
if (!rank) printf(" MUMPS LU:\n");
ierr = MatGetFactor(A,MATSOLVERMUMPS,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
{
/* test mumps options */
PetscInt icntl_7 = 5;
ierr = MatMumpsSetIcntl(F,7,icntl_7);CHKERRQ(ierr);
}
break;
#endif
default:
if (!rank) printf(" PETSC LU:\n");
ierr = MatGetFactor(A,MATSOLVERPETSC,MAT_FACTOR_LU,&F);CHKERRQ(ierr);
}
info.fill = 5.0;
ierr = MatLUFactorSymbolic(F,A,perm,iperm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 1; nfact++) {
if (!rank) printf(" %d-the LU numfactorization \n",nfact);
ierr = MatLUFactorNumeric(F,A,&info);CHKERRQ(ierr);
/* Test MatSolve() */
if (testMatSolve) {
ierr = MatSolve(F,b,x);CHKERRQ(ierr);
/* Check the residual */
ierr = MatMult(A,x,u);CHKERRQ(ierr);
ierr = VecAXPY(u,-1.0,b);CHKERRQ(ierr);
ierr = VecNorm(u,NORM_INFINITY,&norm);CHKERRQ(ierr);
if (norm > tol) {
if (!rank) {
ierr = PetscPrintf(PETSC_COMM_SELF,"MatSolve: rel residual %g/%g = %g, LU numfact %d\n",norm,Anorm,norm/Anorm,nfact);CHKERRQ(ierr);
}
}
}
}
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = ISDestroy(&iperm);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
static PetscErrorCode InitializeDomainData(DomainData *dd)
{
PetscErrorCode ierr;
PetscMPIInt sizes,rank;
PetscInt factor;
PetscFunctionBeginUser;
dd->gcomm = PETSC_COMM_WORLD;
ierr = MPI_Comm_size(dd->gcomm,&sizes);CHKERRQ(ierr);
ierr = MPI_Comm_rank(dd->gcomm,&rank);CHKERRQ(ierr);
/* test data passed in */
if (sizes<2) SETERRQ(dd->gcomm,PETSC_ERR_USER,"This is not a uniprocessor test");
/* Get informations from command line */
/* Processors/subdomains per dimension */
/* Default is 1d problem */
dd->npx = sizes;
dd->npy = 0;
dd->npz = 0;
dd->dim = 1;
ierr = PetscOptionsGetInt(NULL,NULL,"-npx",&dd->npx,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-npy",&dd->npy,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-npz",&dd->npz,NULL);CHKERRQ(ierr);
if (dd->npy) dd->dim++;
if (dd->npz) dd->dim++;
/* Number of elements per dimension */
/* Default is one element per subdomain */
dd->nex = dd->npx;
dd->ney = dd->npy;
dd->nez = dd->npz;
ierr = PetscOptionsGetInt(NULL,NULL,"-nex",&dd->nex,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-ney",&dd->ney,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-nez",&dd->nez,NULL);CHKERRQ(ierr);
if (!dd->npy) {
dd->ney=0;
dd->nez=0;
}
if (!dd->npz) dd->nez=0;
/* Spectral degree */
dd->p = 3;
ierr = PetscOptionsGetInt(NULL,NULL,"-p",&dd->p,NULL);CHKERRQ(ierr);
/* pure neumann problem? */
dd->pure_neumann = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-pureneumann",&dd->pure_neumann,NULL);CHKERRQ(ierr);
/* How to enforce dirichlet boundary conditions (in case pureneumann has not been requested explicitly) */
dd->DBC_zerorows = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-usezerorows",&dd->DBC_zerorows,NULL);CHKERRQ(ierr);
if (dd->pure_neumann) dd->DBC_zerorows = PETSC_FALSE;
dd->scalingfactor = 1.0;
factor = 0.0;
ierr = PetscOptionsGetInt(NULL,NULL,"-jump",&factor,NULL);CHKERRQ(ierr);
/* checkerboard pattern */
dd->scalingfactor = PetscPowScalar(10.0,(PetscScalar)factor*PetscPowScalar(-1.0,(PetscScalar)rank));
/* test data passed in */
if (dd->dim==1) {
if (sizes!=dd->npx) SETERRQ(dd->gcomm,PETSC_ERR_USER,"Number of mpi procs in 1D must be equal to npx");
if (dd->nex<dd->npx) SETERRQ(dd->gcomm,PETSC_ERR_USER,"Number of elements per dim must be greater/equal than number of procs per dim");
} else if (dd->dim==2) {
if (sizes!=dd->npx*dd->npy) SETERRQ(dd->gcomm,PETSC_ERR_USER,"Number of mpi procs in 2D must be equal to npx*npy");
if (dd->nex<dd->npx || dd->ney<dd->npy) SETERRQ(dd->gcomm,PETSC_ERR_USER,"Number of elements per dim must be greater/equal than number of procs per dim");
} else {
if (sizes!=dd->npx*dd->npy*dd->npz) SETERRQ(dd->gcomm,PETSC_ERR_USER,"Number of mpi procs in 3D must be equal to npx*npy*npz");
if (dd->nex<dd->npx || dd->ney<dd->npy || dd->nez<dd->npz) SETERRQ(dd->gcomm,PETSC_ERR_USER,"Number of elements per dim must be greater/equal than number of procs per dim");
}
PetscFunctionReturn(0);
}
/*@C
PetscInitialize - Initializes the PETSc database and MPI.
PetscInitialize() calls MPI_Init() if that has yet to be called,
so this routine should always be called near the beginning of
your program -- usually the very first line!
Collective on MPI_COMM_WORLD or PETSC_COMM_WORLD if it has been set
Input Parameters:
+ argc - count of number of command line arguments
. args - the command line arguments
. file - [optional] PETSc database file, also checks ~username/.petscrc and .petscrc use NULL to not check for
code specific file. Use -skip_petscrc in the code specific file to skip the .petscrc files
- help - [optional] Help message to print, use NULL for no message
If you wish PETSc code to run ONLY on a subcommunicator of MPI_COMM_WORLD, create that
communicator first and assign it to PETSC_COMM_WORLD BEFORE calling PetscInitialize(). Thus if you are running a
four process job and two processes will run PETSc and have PetscInitialize() and PetscFinalize() and two process will not,
then do this. If ALL processes in the job are using PetscInitialize() and PetscFinalize() then you don't need to do this, even
if different subcommunicators of the job are doing different things with PETSc.
Options Database Keys:
+ -start_in_debugger [noxterm,dbx,xdb,gdb,...] - Starts program in debugger
. -on_error_attach_debugger [noxterm,dbx,xdb,gdb,...] - Starts debugger when error detected
. -on_error_emacs <machinename> causes emacsclient to jump to error file
. -on_error_abort calls abort() when error detected (no traceback)
. -on_error_mpiabort calls MPI_abort() when error detected
. -error_output_stderr prints error messages to stderr instead of the default stdout
. -error_output_none does not print the error messages (but handles errors in the same way as if this was not called)
. -debugger_nodes [node1,node2,...] - Indicates nodes to start in debugger
. -debugger_pause [sleeptime] (in seconds) - Pauses debugger
. -stop_for_debugger - Print message on how to attach debugger manually to
process and wait (-debugger_pause) seconds for attachment
. -malloc - Indicates use of PETSc error-checking malloc (on by default for debug version of libraries)
. -malloc no - Indicates not to use error-checking malloc
. -malloc_debug - check for memory corruption at EVERY malloc or free
. -malloc_test - like -malloc_dump -malloc_debug, but only active for debugging builds
. -fp_trap - Stops on floating point exceptions (Note that on the
IBM RS6000 this slows code by at least a factor of 10.)
. -no_signal_handler - Indicates not to trap error signals
. -shared_tmp - indicates /tmp directory is shared by all processors
. -not_shared_tmp - each processor has own /tmp
. -tmp - alternative name of /tmp directory
. -get_total_flops - returns total flops done by all processors
. -memory_info - Print memory usage at end of run
- -server <port> - start PETSc webserver (default port is 8080)
Options Database Keys for Profiling:
See the <a href="../../docs/manual.pdf#nameddest=ch_profiling">profiling chapter of the users manual</a> for details.
+ -info <optional filename> - Prints verbose information to the screen
. -info_exclude <null,vec,mat,pc,ksp,snes,ts> - Excludes some of the verbose messages
. -log_sync - Log the synchronization in scatters, inner products and norms
. -log_trace [filename] - Print traces of all PETSc calls to the screen (useful to determine where a program
hangs without running in the debugger). See PetscLogTraceBegin().
. -log_summary [filename] - Prints summary of flop and timing information to screen. If the filename is specified the
summary is written to the file. See PetscLogView().
. -log_summary_python [filename] - Prints data on of flop and timing usage to a file or screen. See PetscLogPrintSViewPython().
. -log_all [filename] - Logs extensive profiling information See PetscLogDump().
. -log [filename] - Logs basic profiline information See PetscLogDump().
- -log_mpe [filename] - Creates a logfile viewable by the utility Jumpshot (in MPICH distribution)
Only one of -log_trace, -log_summary, -log_all, -log, or -log_mpe may be used at a time
Environmental Variables:
+ PETSC_TMP - alternative tmp directory
. PETSC_SHARED_TMP - tmp is shared by all processes
. PETSC_NOT_SHARED_TMP - each process has its own private tmp
. PETSC_VIEWER_SOCKET_PORT - socket number to use for socket viewer
- PETSC_VIEWER_SOCKET_MACHINE - machine to use for socket viewer to connect to
Level: beginner
Notes:
If for some reason you must call MPI_Init() separately, call
it before PetscInitialize().
Fortran Version:
In Fortran this routine has the format
$ call PetscInitialize(file,ierr)
+ ierr - error return code
- file - [optional] PETSc database file, also checks ~username/.petscrc and .petscrc use NULL_CHARACTER to not check for
code specific file. Use -skip_petscrc in the code specific file to skip the .petscrc files
Important Fortran Note:
In Fortran, you MUST use NULL_CHARACTER to indicate a
null character string; you CANNOT just use NULL as
in the C version. See the <a href="../../docs/manual.pdf">users manual</a> for details.
If your main program is C but you call Fortran code that also uses PETSc you need to call PetscInitializeFortran() soon after
calling PetscInitialize().
Concepts: initializing PETSc
.seealso: PetscFinalize(), PetscInitializeFortran(), PetscGetArgs(), PetscInitializeNoArguments()
@*/
PetscErrorCode PetscInitialize(int *argc,char ***args,const char file[],const char help[])
{
PetscErrorCode ierr;
PetscMPIInt flag, size;
PetscInt nodesize;
PetscBool flg;
char hostname[256];
PetscFunctionBegin;
if (PetscInitializeCalled) PetscFunctionReturn(0);
/* these must be initialized in a routine, not as a constant declaration*/
PETSC_STDOUT = stdout;
PETSC_STDERR = stderr;
ierr = PetscOptionsCreate();CHKERRQ(ierr);
/*
We initialize the program name here (before MPI_Init()) because MPICH has a bug in
it that it sets args[0] on all processors to be args[0] on the first processor.
*/
if (argc && *argc) {
ierr = PetscSetProgramName(**args);CHKERRQ(ierr);
} else {
ierr = PetscSetProgramName("Unknown Name");CHKERRQ(ierr);
}
ierr = MPI_Initialized(&flag);CHKERRQ(ierr);
if (!flag) {
if (PETSC_COMM_WORLD != MPI_COMM_NULL) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"You cannot set PETSC_COMM_WORLD if you have not initialized MPI first");
#if defined(PETSC_HAVE_MPI_INIT_THREAD)
{
PetscMPIInt provided;
ierr = MPI_Init_thread(argc,args,MPI_THREAD_FUNNELED,&provided);CHKERRQ(ierr);
}
#else
ierr = MPI_Init(argc,args);CHKERRQ(ierr);
#endif
PetscBeganMPI = PETSC_TRUE;
}
if (argc && args) {
PetscGlobalArgc = *argc;
PetscGlobalArgs = *args;
}
PetscFinalizeCalled = PETSC_FALSE;
if (PETSC_COMM_WORLD == MPI_COMM_NULL) PETSC_COMM_WORLD = MPI_COMM_WORLD;
ierr = MPI_Comm_set_errhandler(PETSC_COMM_WORLD,MPI_ERRORS_RETURN);CHKERRQ(ierr);
/* Done after init due to a bug in MPICH-GM? */
ierr = PetscErrorPrintfInitialize();CHKERRQ(ierr);
ierr = MPI_Comm_rank(MPI_COMM_WORLD,&PetscGlobalRank);CHKERRQ(ierr);
ierr = MPI_Comm_size(MPI_COMM_WORLD,&PetscGlobalSize);CHKERRQ(ierr);
MPIU_BOOL = MPI_INT;
MPIU_ENUM = MPI_INT;
/*
Initialized the global complex variable; this is because with
shared libraries the constructors for global variables
are not called; at least on IRIX.
*/
#if defined(PETSC_HAVE_COMPLEX)
{
#if defined(PETSC_CLANGUAGE_CXX)
PetscComplex ic(0.0,1.0);
PETSC_i = ic;
#elif defined(PETSC_CLANGUAGE_C)
PETSC_i = _Complex_I;
#endif
}
#if !defined(PETSC_HAVE_MPI_C_DOUBLE_COMPLEX)
ierr = MPI_Type_contiguous(2,MPI_DOUBLE,&MPIU_C_DOUBLE_COMPLEX);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU_C_DOUBLE_COMPLEX);CHKERRQ(ierr);
ierr = MPI_Type_contiguous(2,MPI_FLOAT,&MPIU_C_COMPLEX);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU_C_COMPLEX);CHKERRQ(ierr);
#endif
#endif /* PETSC_HAVE_COMPLEX */
/*
Create the PETSc MPI reduction operator that sums of the first
half of the entries and maxes the second half.
*/
ierr = MPI_Op_create(PetscMaxSum_Local,1,&PetscMaxSum_Op);CHKERRQ(ierr);
#if defined(PETSC_USE_REAL___FLOAT128)
ierr = MPI_Type_contiguous(2,MPI_DOUBLE,&MPIU___FLOAT128);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU___FLOAT128);CHKERRQ(ierr);
#if defined(PETSC_HAVE_COMPLEX)
ierr = MPI_Type_contiguous(4,MPI_DOUBLE,&MPIU___COMPLEX128);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU___COMPLEX128);CHKERRQ(ierr);
#endif
ierr = MPI_Op_create(PetscMax_Local,1,&MPIU_MAX);CHKERRQ(ierr);
ierr = MPI_Op_create(PetscMin_Local,1,&MPIU_MIN);CHKERRQ(ierr);
#endif
#if (defined(PETSC_HAVE_COMPLEX) && !defined(PETSC_HAVE_MPI_C_DOUBLE_COMPLEX)) || defined(PETSC_USE_REAL___FLOAT128)
ierr = MPI_Op_create(PetscSum_Local,1,&MPIU_SUM);CHKERRQ(ierr);
#endif
ierr = MPI_Type_contiguous(2,MPIU_SCALAR,&MPIU_2SCALAR);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU_2SCALAR);CHKERRQ(ierr);
ierr = MPI_Op_create(PetscADMax_Local,1,&PetscADMax_Op);CHKERRQ(ierr);
ierr = MPI_Op_create(PetscADMin_Local,1,&PetscADMin_Op);CHKERRQ(ierr);
#if defined(PETSC_USE_64BIT_INDICES) || !defined(MPI_2INT)
ierr = MPI_Type_contiguous(2,MPIU_INT,&MPIU_2INT);CHKERRQ(ierr);
ierr = MPI_Type_commit(&MPIU_2INT);CHKERRQ(ierr);
#endif
/*
Attributes to be set on PETSc communicators
*/
ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelCounter,&Petsc_Counter_keyval,(void*)0);CHKERRQ(ierr);
ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelComm,&Petsc_InnerComm_keyval,(void*)0);CHKERRQ(ierr);
ierr = MPI_Keyval_create(MPI_NULL_COPY_FN,Petsc_DelComm,&Petsc_OuterComm_keyval,(void*)0);CHKERRQ(ierr);
/*
Build the options database
*/
ierr = PetscOptionsInsert(argc,args,file);CHKERRQ(ierr);
/*
Print main application help message
*/
ierr = PetscOptionsHasName(NULL,"-help",&flg);CHKERRQ(ierr);
if (help && flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD,help);CHKERRQ(ierr);
}
ierr = PetscOptionsCheckInitial_Private();CHKERRQ(ierr);
/* SHOULD PUT IN GUARDS: Make sure logging is initialized, even if we do not print it out */
#if defined(PETSC_USE_LOG)
ierr = PetscLogBegin_Private();CHKERRQ(ierr);
#endif
/*
Load the dynamic libraries (on machines that support them), this registers all
the solvers etc. (On non-dynamic machines this initializes the PetscDraw and PetscViewer classes)
*/
ierr = PetscInitialize_DynamicLibraries();CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = PetscInfo1(0,"PETSc successfully started: number of processors = %d\n",size);CHKERRQ(ierr);
ierr = PetscGetHostName(hostname,256);CHKERRQ(ierr);
ierr = PetscInfo1(0,"Running on machine: %s\n",hostname);CHKERRQ(ierr);
ierr = PetscOptionsCheckInitial_Components();CHKERRQ(ierr);
/* Check the options database for options related to the options database itself */
ierr = PetscOptionsSetFromOptions();CHKERRQ(ierr);
#if defined(PETSC_USE_PETSC_MPI_EXTERNAL32)
/*
Tell MPI about our own data representation converter, this would/should be used if extern32 is not supported by the MPI
Currently not used because it is not supported by MPICH.
*/
#if !defined(PETSC_WORDS_BIGENDIAN)
ierr = MPI_Register_datarep((char*)"petsc",PetscDataRep_read_conv_fn,PetscDataRep_write_conv_fn,PetscDataRep_extent_fn,NULL);CHKERRQ(ierr);
#endif
#endif
ierr = PetscOptionsGetInt(NULL,"-hmpi_spawn_size",&nodesize,&flg);CHKERRQ(ierr);
if (flg) {
#if defined(PETSC_HAVE_MPI_COMM_SPAWN)
ierr = PetscHMPISpawn((PetscMPIInt) nodesize);CHKERRQ(ierr); /* worker nodes never return from here; they go directly to PetscEnd() */
#else
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"PETSc built without MPI 2 (MPI_Comm_spawn) support, use -hmpi_merge_size instead");
#endif
} else {
ierr = PetscOptionsGetInt(NULL,"-hmpi_merge_size",&nodesize,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscHMPIMerge((PetscMPIInt) nodesize,NULL,NULL);CHKERRQ(ierr);
if (PetscHMPIWorker) { /* if worker then never enter user code */
PetscInitializeCalled = PETSC_TRUE;
PetscEnd();
}
}
}
#if defined(PETSC_HAVE_CUDA)
{
PetscMPIInt p;
for (p = 0; p < PetscGlobalSize; ++p) {
if (p == PetscGlobalRank) cublasInit();
ierr = MPI_Barrier(PETSC_COMM_WORLD);CHKERRQ(ierr);
}
}
#endif
ierr = PetscOptionsHasName(NULL,"-python",&flg);CHKERRQ(ierr);
if (flg) {
PetscInitializeCalled = PETSC_TRUE;
ierr = PetscPythonInitialize(NULL,NULL);CHKERRQ(ierr);
}
ierr = PetscThreadCommInitializePackage();CHKERRQ(ierr);
/*
Setup building of stack frames for all function calls
*/
#if defined(PETSC_USE_DEBUG)
PetscThreadLocalRegister((PetscThreadKey*)&petscstack); /* Creates petscstack_key if needed */
ierr = PetscStackCreate();CHKERRQ(ierr);
#endif
#if defined(PETSC_SERIALIZE_FUNCTIONS)
ierr = PetscFPTCreate(10000);CHKERRQ(ierr);
#endif
/*
Once we are completedly initialized then we can set this variables
*/
PetscInitializeCalled = PETSC_TRUE;
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Mat C;
PetscScalar v,none = -1.0;
PetscInt i,j,Ii,J,Istart,Iend,N,m = 4,n = 4,its,k;
PetscErrorCode ierr;
PetscMPIInt size,rank;
PetscReal err_norm,res_norm,err_tol=1.e-7,res_tol=1.e-6;
Vec x,b,u,u_tmp;
PetscRandom r;
PC pc;
KSP ksp;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
N = m*n;
/* Generate matrix */
ierr = MatCreate(PETSC_COMM_WORLD,&C);CHKERRQ(ierr);
ierr = MatSetSizes(C,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);
ierr = MatSetFromOptions(C);CHKERRQ(ierr);
ierr = MatSetUp(C);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(C,&Istart,&Iend);CHKERRQ(ierr);
for (Ii=Istart; Ii<Iend; Ii++) {
v = -1.0; i = Ii/n; j = Ii - i*n;
if (i>0) {J = Ii - n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (i<m-1) {J = Ii + n; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (j>0) {J = Ii - 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
if (j<n-1) {J = Ii + 1; ierr = MatSetValues(C,1,&Ii,1,&J,&v,ADD_VALUES);CHKERRQ(ierr);}
v = 4.0; ierr = MatSetValues(C,1,&Ii,1,&Ii,&v,ADD_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(C,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* a shift can make C indefinite. Preconditioners LU, ILU (for BAIJ format) and ICC may fail */
/* ierr = MatShift(C,alpha);CHKERRQ(ierr); */
/* ierr = MatView(C,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
/* Setup and solve for system */
/* Create vectors. */
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,N);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecDuplicate(x,&u);CHKERRQ(ierr);
ierr = VecDuplicate(x,&u_tmp);CHKERRQ(ierr);
/* Set exact solution u; then compute right-hand-side vector b. */
ierr = PetscRandomCreate(PETSC_COMM_SELF,&r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
ierr = VecSetRandom(u,r);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&r);CHKERRQ(ierr);
ierr = MatMult(C,u,b);CHKERRQ(ierr);
for (k=0; k<3; k++){
if (k == 0){ /* CG */
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,C,C,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n CG: \n");CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPCG);CHKERRQ(ierr);
} else if (k == 1){ /* MINRES */
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,C,C,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n MINRES: \n");CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPMINRES);CHKERRQ(ierr);
} else { /* SYMMLQ */
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,C,C,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n SYMMLQ: \n");CHKERRQ(ierr);
ierr = KSPSetType(ksp,KSPSYMMLQ);CHKERRQ(ierr);
}
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
/* ierr = PCSetType(pc,PCICC);CHKERRQ(ierr); */
ierr = PCSetType(pc,PCJACOBI);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp,1.e-7,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRQ(ierr);
/*
Set runtime options, e.g.,
-ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
These options will override those specified above as long as
KSPSetFromOptions() is called _after_ any other customization
routines.
*/
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
/* Solve linear system; */
ierr = KSPSetUp(ksp);CHKERRQ(ierr);
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
/* Check error */
ierr = VecCopy(u,u_tmp);CHKERRQ(ierr);
ierr = VecAXPY(u_tmp,none,x);CHKERRQ(ierr);
ierr = VecNorm(u_tmp,NORM_2,&err_norm);CHKERRQ(ierr);
ierr = MatMult(C,x,u_tmp);CHKERRQ(ierr);
ierr = VecAXPY(u_tmp,none,b);CHKERRQ(ierr);
ierr = VecNorm(u_tmp,NORM_2,&res_norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Number of iterations = %3D\n",its);CHKERRQ(ierr);
if (res_norm > res_tol){
ierr = PetscPrintf(PETSC_COMM_WORLD,"Residual norm %G;",res_norm);CHKERRQ(ierr);
}
if (err_norm > err_tol){
ierr = PetscPrintf(PETSC_COMM_WORLD," Error norm %G.\n",err_norm);CHKERRQ(ierr);
}
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
}
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&u_tmp);CHKERRQ(ierr);
ierr = MatDestroy(&C);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Vec sol,x0,y0,z0;
PetscInt rank,size,Istart,Iend,Lsize;
Mat Dy,Dz,MarkovA,dAdy,dAdz;
PetscErrorCode ierr;
PetscViewer socketviewer;
CoordInfo *cdinfo;
// for streamline calculation
PetscScalar *xarray, *yarray,*zarray;
PetscScalar *x,*y,*z;
PetscInt n, withMatlab;
PetscTruth Matlabflag,flg;
PetscInt ny,nz;
PetscInt solmaxp;
PetscScalar solmax;
n = 5500;
withMatlab = 0;
ny = 2;
nz = 2;
PetscInitialize(&argc,&args,(char *)0,help);
MPI_Comm_size(PETSC_COMM_WORLD,&size);
MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nPETSC: Petsc Initializes successfully! \n");
ierr = PetscPrintf(PETSC_COMM_WORLD,"PETSC: comm_size is %d \n", size);
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
// Use Matlab as output
ierr = PetscOptionsGetInt(PETSC_NULL,"-withMatlab",&withMatlab,&Matlabflag);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-ngridy",&ny,&flg);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-ngridz",&nz,&flg);CHKERRQ(ierr);
if (Matlabflag == PETSC_FALSE){withMatlab = 0;}else{withMatlab = 1;}
if(withMatlab==1){
// Rank 0 connects to socket, use default socket
PetscViewerSocketOpen(PETSC_COMM_WORLD,0,PETSC_DEFAULT,&socketviewer);
ierr = PetscPrintf(PETSC_COMM_WORLD,"PETSC: socket opened! \n");CHKERRQ(ierr);
// receive cdinfo from Matlab
ierr = CdinfoReceive(socketviewer, &cdinfo);
// receive the velocity field from matlab.
ierr = VecReceive(socketviewer,VECSEQ,&sol);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"PETSC: sol is received from Matlab \n");CHKERRQ(ierr);
//test
ierr = VecLoadfromFile(PETSC_COMM_WORLD,"sol",VECSEQ,&sol);CHKERRQ(ierr);
ierr = CdinfoLoad(PETSC_COMM_WORLD,"cdinfofiled", &cdinfo);CHKERRQ(ierr);
ierr = VecReceive(socketviewer,VECMPI,&x0);CHKERRQ(ierr);
ierr = VecReceive(socketviewer,VECMPI,&y0);CHKERRQ(ierr);
ierr = VecReceive(socketviewer,VECMPI,&z0);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"PETSC: x0,y0 and z0 are received from Matlab \n");CHKERRQ(ierr);
}else{
// Load cdinfo
ierr = CdinfoLoad(PETSC_COMM_WORLD,"cdinfofiled", &cdinfo);CHKERRQ(ierr);
ierr = VecLoadfromFile(PETSC_COMM_WORLD,"sol",VECSEQ,&sol);CHKERRQ(ierr);
// Load x0, y0, z0 as initial points for streamlines
ierr = VecLoadfromFile(PETSC_COMM_WORLD,"x0filed",VECMPI,&x0);CHKERRQ(ierr);
ierr = VecLoadfromFile(PETSC_COMM_WORLD,"y0filed",VECMPI,&y0);CHKERRQ(ierr);
ierr = VecLoadfromFile(PETSC_COMM_WORLD,"z0filed",VECMPI,&z0);CHKERRQ(ierr);
}
ierr = VecMax(sol,&solmaxp,&solmax);CHKERRQ(ierr);
StreamlineMap(x0, y0, z0, sol, cdinfo, &Dy, &Dz,0.01/solmax, n ,10,&x,&y,&z);
MarkovMap2d(sol, ny, nz, cdinfo,&MarkovA,&dAdy,&dAdz);
ierr = VecGetOwnershipRange(x0,&Istart,&Iend);CHKERRQ(ierr);
Lsize = Iend - Istart;
if(withMatlab==1){
VecView(x0,socketviewer);
VecView(y0,socketviewer);
VecView(z0,socketviewer);
VecSave(x0,"xefilew");
VecSave(y0,"yefilew");
VecSave(z0,"zefilew");
PetscScalarView(Lsize*n,x,socketviewer);
PetscScalarView(Lsize*n,y,socketviewer);
PetscScalarView(Lsize*n,z,socketviewer);
SparseView(Dy,socketviewer);
SparseView(Dz,socketviewer);
}else{
SparseSave(MarkovA,"A");
VecSave(x0,"xefilew");
VecSave(y0,"yefilew");
VecSave(z0,"zefilew");
Vec vx,vy,vz;
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,Lsize*n,PETSC_DECIDE,x,&vx);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,Lsize*n,PETSC_DECIDE,y,&vy);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,Lsize*n,PETSC_DECIDE,z,&vz);CHKERRQ(ierr);
VecSave(vx,"xeallfilew");
VecSave(vy,"yeallfilew");
VecSave(vz,"zeallfilew");
ierr = VecDestroy(vx);CHKERRQ(ierr);
ierr = VecDestroy(vy);CHKERRQ(ierr);
ierr = VecDestroy(vz);CHKERRQ(ierr);
}
ierr = VecRestoreArray(x0,&xarray);CHKERRQ(ierr);
ierr = VecRestoreArray(y0,&yarray);CHKERRQ(ierr);
ierr = VecRestoreArray(z0,&zarray);CHKERRQ(ierr);
ierr = VecDestroy(x0);CHKERRQ(ierr);
ierr = VecDestroy(y0);CHKERRQ(ierr);
ierr = VecDestroy(z0);CHKERRQ(ierr);
ierr = MatDestroy(Dy);CHKERRQ(ierr);
ierr = MatDestroy(Dz);CHKERRQ(ierr);
ierr = MatDestroy(dAdy);CHKERRQ(ierr);
ierr = MatDestroy(dAdz);CHKERRQ(ierr);
ierr = MatDestroy(MarkovA);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc, char *argv[])
{
PetscErrorCode ierr;
DM dau,dak,pack;
const PetscInt *lxu;
PetscInt *lxk,m,sizes;
User user;
SNES snes;
Vec X,F,Xu,Xk,Fu,Fk;
Mat B;
IS *isg;
PetscBool view_draw,pass_dm;
PetscInitialize(&argc,&argv,0,help);
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,-10,1,1,NULL,&dau);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(dau,"u_");CHKERRQ(ierr);
ierr = DMSetFromOptions(dau);CHKERRQ(ierr);
ierr = DMDAGetOwnershipRanges(dau,&lxu,0,0);CHKERRQ(ierr);
ierr = DMDAGetInfo(dau,0, &m,0,0, &sizes,0,0, 0,0,0,0,0,0);CHKERRQ(ierr);
ierr = PetscMalloc1(sizes,&lxk);CHKERRQ(ierr);
ierr = PetscMemcpy(lxk,lxu,sizes*sizeof(*lxk));CHKERRQ(ierr);
lxk[0]--;
ierr = DMDACreate1d(PETSC_COMM_WORLD,DM_BOUNDARY_NONE,m-1,1,1,lxk,&dak);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(dak,"k_");CHKERRQ(ierr);
ierr = DMSetFromOptions(dak);CHKERRQ(ierr);
ierr = PetscFree(lxk);CHKERRQ(ierr);
ierr = DMCompositeCreate(PETSC_COMM_WORLD,&pack);CHKERRQ(ierr);
ierr = DMSetOptionsPrefix(pack,"pack_");CHKERRQ(ierr);
ierr = DMCompositeAddDM(pack,dau);CHKERRQ(ierr);
ierr = DMCompositeAddDM(pack,dak);CHKERRQ(ierr);
ierr = DMDASetFieldName(dau,0,"u");CHKERRQ(ierr);
ierr = DMDASetFieldName(dak,0,"k");CHKERRQ(ierr);
ierr = DMSetFromOptions(pack);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(pack,&X);CHKERRQ(ierr);
ierr = VecDuplicate(X,&F);CHKERRQ(ierr);
ierr = PetscNew(&user);CHKERRQ(ierr);
user->pack = pack;
ierr = DMCompositeGetGlobalISs(pack,&isg);CHKERRQ(ierr);
ierr = DMCompositeGetLocalVectors(pack,&user->Uloc,&user->Kloc);CHKERRQ(ierr);
ierr = DMCompositeScatter(pack,X,user->Uloc,user->Kloc);CHKERRQ(ierr);
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,NULL,"Coupled problem options","SNES");CHKERRQ(ierr);
{
user->ptype = 0; view_draw = PETSC_FALSE; pass_dm = PETSC_TRUE;
ierr = PetscOptionsInt("-problem_type","0: solve for u only, 1: solve for k only, 2: solve for both",0,user->ptype,&user->ptype,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-view_draw","Draw the final coupled solution regardless of whether only one physics was solved",0,view_draw,&view_draw,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-pass_dm","Pass the packed DM to SNES to use when determining splits and forward into splits",0,pass_dm,&pass_dm,NULL);CHKERRQ(ierr);
}
ierr = PetscOptionsEnd();CHKERRQ(ierr);
ierr = FormInitial_Coupled(user,X);CHKERRQ(ierr);
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
switch (user->ptype) {
case 0:
ierr = DMCompositeGetAccess(pack,X,&Xu,0);CHKERRQ(ierr);
ierr = DMCompositeGetAccess(pack,F,&Fu,0);CHKERRQ(ierr);
ierr = DMCreateMatrix(dau,&B);CHKERRQ(ierr);
ierr = SNESSetFunction(snes,Fu,FormFunction_All,user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,B,B,FormJacobian_All,user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes,dau);CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,Xu);CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(pack,X,&Xu,0);CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(pack,F,&Fu,0);CHKERRQ(ierr);
break;
case 1:
ierr = DMCompositeGetAccess(pack,X,0,&Xk);CHKERRQ(ierr);
ierr = DMCompositeGetAccess(pack,F,0,&Fk);CHKERRQ(ierr);
ierr = DMCreateMatrix(dak,&B);CHKERRQ(ierr);
ierr = SNESSetFunction(snes,Fk,FormFunction_All,user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,B,B,FormJacobian_All,user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = SNESSetDM(snes,dak);CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,Xk);CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(pack,X,0,&Xk);CHKERRQ(ierr);
ierr = DMCompositeRestoreAccess(pack,F,0,&Fk);CHKERRQ(ierr);
break;
case 2:
ierr = DMCreateMatrix(pack,&B);CHKERRQ(ierr);
/* This example does not correctly allocate off-diagonal blocks. These options allows new nonzeros (slow). */
ierr = MatSetOption(B,MAT_NEW_NONZERO_LOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = MatSetOption(B,MAT_NEW_NONZERO_ALLOCATION_ERR,PETSC_FALSE);CHKERRQ(ierr);
ierr = SNESSetFunction(snes,F,FormFunction_All,user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,B,B,FormJacobian_All,user);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
if (!pass_dm) { /* Manually provide index sets and names for the splits */
KSP ksp;
PC pc;
ierr = SNESGetKSP(snes,&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCFieldSplitSetIS(pc,"u",isg[0]);CHKERRQ(ierr);
ierr = PCFieldSplitSetIS(pc,"k",isg[1]);CHKERRQ(ierr);
} else {
/* The same names come from the options prefix for dau and dak. This option can support geometric multigrid inside
* of splits, but it requires using a DM (perhaps your own implementation). */
ierr = SNESSetDM(snes,pack);CHKERRQ(ierr);
}
ierr = SNESSolve(snes,NULL,X);CHKERRQ(ierr);
break;
}
if (view_draw) {ierr = VecView(X,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);}
if (0) {
PetscInt col = 0;
PetscBool mult_dup = PETSC_FALSE,view_dup = PETSC_FALSE;
Mat D;
Vec Y;
ierr = PetscOptionsGetInt(0,"-col",&col,0);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(0,"-mult_dup",&mult_dup,0);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(0,"-view_dup",&view_dup,0);CHKERRQ(ierr);
ierr = VecDuplicate(X,&Y);CHKERRQ(ierr);
/* ierr = MatAssemblyBegin(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); */
/* ierr = MatAssemblyEnd(B,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); */
ierr = MatConvert(B,MATAIJ,MAT_INITIAL_MATRIX,&D);CHKERRQ(ierr);
ierr = VecZeroEntries(X);CHKERRQ(ierr);
ierr = VecSetValue(X,col,1.0,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecAssemblyBegin(X);CHKERRQ(ierr);
ierr = VecAssemblyEnd(X);CHKERRQ(ierr);
ierr = MatMult(mult_dup ? D : B,X,Y);CHKERRQ(ierr);
ierr = MatView(view_dup ? D : B,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* ierr = VecView(X,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
ierr = VecView(Y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = MatDestroy(&D);CHKERRQ(ierr);
ierr = VecDestroy(&Y);CHKERRQ(ierr);
}
ierr = DMCompositeRestoreLocalVectors(pack,&user->Uloc,&user->Kloc);CHKERRQ(ierr);
ierr = PetscFree(user);CHKERRQ(ierr);
ierr = ISDestroy(&isg[0]);CHKERRQ(ierr);
ierr = ISDestroy(&isg[1]);CHKERRQ(ierr);
ierr = PetscFree(isg);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&F);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = DMDestroy(&dau);CHKERRQ(ierr);
ierr = DMDestroy(&dak);CHKERRQ(ierr);
ierr = DMDestroy(&pack);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt i,n = 5;
PetscInt getpetsc[] = {0,3,4},getapp[] = {2,1,9,7};
PetscInt getpetsc1[] = {0,3,4},getapp1[] = {2,1,9,7};
PetscInt getpetsc2[] = {0,3,4},getapp2[] = {2,1,9,7};
PetscInt getpetsc3[] = {0,3,4},getapp3[] = {2,1,9,7};
PetscInt getpetsc4[] = {0,3,4},getapp4[] = {2,1,9,7};
PetscMPIInt rank,size;
IS ispetsc,isapp;
AO ao;
const PetscInt *app;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
/* create the index sets */
ierr = ISCreateStride(PETSC_COMM_WORLD,n,rank,size,&isapp);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_WORLD,n,n*rank,1,&ispetsc);CHKERRQ(ierr); /* natural numbering */
/* create the application ordering */
ierr = AOCreateBasicIS(isapp,ispetsc,&ao);CHKERRQ(ierr);
ierr = AOView(ao,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = AOPetscToApplication(ao,4,getapp);CHKERRQ(ierr);
ierr = AOApplicationToPetsc(ao,3,getpetsc);CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d] 2,1,9,7 PetscToApplication %D %D %D %D\n",
rank,getapp[0],getapp[1],getapp[2],getapp[3]);CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d] 0,3,4 ApplicationToPetsc %D %D %D\n",
rank,getpetsc[0],getpetsc[1],getpetsc[2]);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD);CHKERRQ(ierr);
ierr = AODestroy(&ao);CHKERRQ(ierr);
/* test MemoryScalable ao */
/*-------------------------*/
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"\nTest AOCreateMemoryScalable: \n");
}
ierr = AOCreateMemoryScalableIS(isapp,ispetsc,&ao);CHKERRQ(ierr);CHKERRQ(ierr);
ierr = AOView(ao,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = AOPetscToApplication(ao,4,getapp1);CHKERRQ(ierr);
ierr = AOApplicationToPetsc(ao,3,getpetsc1);CHKERRQ(ierr);
/* Check accuracy */;
for (i=0; i<4;i++)
if (getapp1[i] != getapp[i]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"getapp1 %d != getapp %d",getapp1[i],getapp[i]);
for (i=0; i<3;i++)
if (getpetsc1[i] != getpetsc[i]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"getpetsc1 %d != getpetsc %d",getpetsc1[i],getpetsc[i]);
ierr = AODestroy(&ao);CHKERRQ(ierr);
/* test MemoryScalable ao: ispetsc = PETSC_NULL */
/*-----------------------------------------------*/
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"\nTest AOCreateMemoryScalable with ispetsc=PETSC_NULL:\n");
}
ierr = AOCreateMemoryScalableIS(isapp,PETSC_NULL,&ao);CHKERRQ(ierr);CHKERRQ(ierr);
ierr = AOView(ao,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = AOPetscToApplication(ao,4,getapp2);CHKERRQ(ierr);
ierr = AOApplicationToPetsc(ao,3,getpetsc2);CHKERRQ(ierr);
/* Check accuracy */;
for (i=0; i<4;i++)
if (getapp2[i] != getapp[i]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"getapp2 %d != getapp %d",getapp2[i],getapp[i]);
for (i=0; i<3;i++)
if (getpetsc2[i] != getpetsc[i]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"getpetsc2 %d != getpetsc %d",getpetsc2[i],getpetsc[i]);
ierr = AODestroy(&ao);CHKERRQ(ierr);
/* test AOCreateMemoryScalable() ao: */
ierr = ISGetIndices(isapp,&app);CHKERRQ(ierr);
ierr = AOCreateMemoryScalable(PETSC_COMM_WORLD,n,app,PETSC_NULL,&ao);CHKERRQ(ierr);
ierr = ISRestoreIndices(isapp,&app);CHKERRQ(ierr);
ierr = AOPetscToApplication(ao,4,getapp4);CHKERRQ(ierr);
ierr = AOApplicationToPetsc(ao,3,getpetsc4);CHKERRQ(ierr);
/* Check accuracy */;
for (i=0; i<4;i++)
if (getapp4[i] != getapp[i]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"getapp4 %d != getapp %d",getapp4[i],getapp[i]);
for (i=0; i<3;i++)
if (getpetsc4[i] != getpetsc[i]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"getpetsc4 %d != getpetsc %d",getpetsc4[i],getpetsc[i]);
ierr = AODestroy(&ao);CHKERRQ(ierr);
/* test general API */
/*------------------*/
if (!rank){
ierr = PetscPrintf(PETSC_COMM_SELF,"\nTest general API: \n");
}
ierr = AOCreate(PETSC_COMM_WORLD,&ao);CHKERRQ(ierr);
ierr = AOSetIS(ao,isapp,ispetsc);CHKERRQ(ierr);
ierr = AOSetType(ao,AOMEMORYSCALABLE);CHKERRQ(ierr);
ierr = AOSetFromOptions(ao);CHKERRQ(ierr);
/* ispetsc and isapp are nolonger used. */
ierr = ISDestroy(&ispetsc);CHKERRQ(ierr);
ierr = ISDestroy(&isapp);CHKERRQ(ierr);
ierr = AOPetscToApplication(ao,4,getapp3);CHKERRQ(ierr);
ierr = AOApplicationToPetsc(ao,3,getpetsc3);CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d] 2,1,9,7 PetscToApplication %D %D %D %D\n",
rank,getapp3[0],getapp3[1],getapp3[2],getapp3[3]);CHKERRQ(ierr);
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d] 0,3,4 ApplicationToPetsc %D %D %D\n",
rank,getpetsc3[0],getpetsc3[1],getpetsc3[2]);CHKERRQ(ierr);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD);CHKERRQ(ierr);
/* Check accuracy */;
for (i=0; i<4;i++)
if (getapp3[i] != getapp[i]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"getapp3 %d != getapp %d",getapp3[i],getapp[i]);
for (i=0; i<3;i++)
if (getpetsc3[i] != getpetsc[i]) SETERRQ2(PETSC_COMM_SELF,PETSC_ERR_USER,"getpetsc3 %d != getpetsc %d",getpetsc3[i],getpetsc[i]);
ierr = AODestroy(&ao);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
Mat A; /* operator matrix */
Vec u,v; /* left and right singular vectors */
SVD svd; /* singular value problem solver context */
SVDType type;
PetscReal error,tol,sigma,mu=PETSC_SQRT_MACHINE_EPSILON;
PetscInt n=100,i,j,Istart,Iend,nsv,maxit,its,nconv;
PetscErrorCode ierr;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(NULL,"-mu",&mu,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nLauchli singular value decomposition, (%D x %D) mu=%g\n\n",n+1,n,(double)mu);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Build the Lauchli matrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,n+1,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
for (i=Istart;i<Iend;i++) {
if (i == 0) {
for (j=0;j<n;j++) {
ierr = MatSetValue(A,0,j,1.0,INSERT_VALUES);CHKERRQ(ierr);
}
} else {
ierr = MatSetValue(A,i,i-1,mu,INSERT_VALUES);CHKERRQ(ierr);
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetVecs(A,&v,&u);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the singular value solver and set various options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create singular value solver context
*/
ierr = SVDCreate(PETSC_COMM_WORLD,&svd);CHKERRQ(ierr);
/*
Set operator
*/
ierr = SVDSetOperator(svd,A);CHKERRQ(ierr);
/*
Use thick-restart Lanczos as default solver
*/
ierr = SVDSetType(svd,SVDTRLANCZOS);CHKERRQ(ierr);
/*
Set solver parameters at runtime
*/
ierr = SVDSetFromOptions(svd);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the singular value system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SVDSolve(svd);CHKERRQ(ierr);
ierr = SVDGetIterationNumber(svd,&its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of iterations of the method: %D\n",its);CHKERRQ(ierr);
/*
Optional: Get some information from the solver and display it
*/
ierr = SVDGetType(svd,&type);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Solution method: %s\n\n",type);CHKERRQ(ierr);
ierr = SVDGetDimensions(svd,&nsv,NULL,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of requested singular values: %D\n",nsv);CHKERRQ(ierr);
ierr = SVDGetTolerances(svd,&tol,&maxit);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Stopping condition: tol=%.4g, maxit=%D\n",(double)tol,maxit);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Display solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Get number of converged singular triplets
*/
ierr = SVDGetConverged(svd,&nconv);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of converged approximate singular triplets: %D\n\n",nconv);CHKERRQ(ierr);
if (nconv>0) {
/*
Display singular values and relative errors
*/
ierr = PetscPrintf(PETSC_COMM_WORLD,
" sigma relative error\n"
" --------------------- ------------------\n");CHKERRQ(ierr);
for (i=0;i<nconv;i++) {
/*
Get converged singular triplets: i-th singular value is stored in sigma
*/
ierr = SVDGetSingularTriplet(svd,i,&sigma,u,v);CHKERRQ(ierr);
/*
Compute the error associated to each singular triplet
*/
ierr = SVDComputeRelativeError(svd,i,&error);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," % 6f ",(double)sigma);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," % 12g\n",(double)error);CHKERRQ(ierr);
}
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n");CHKERRQ(ierr);
}
/*
Free work space
*/
ierr = SVDDestroy(&svd);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&v);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
int main(int argc, char **argv) {
PetscInitialize(&argc, &argv, "cmame.opt", help);
int rank;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
// The global domain size
double gSize[3];
gSize[0] = 1.; gSize[1] = 1.; gSize[2] = 1.;
// Parameters for the balancing algorithm.
// Refer to manual for details ...
bool incCorner = 1; // balance across corners = true
unsigned int maxNumPts= 1; // maximum number of points per octant
unsigned int dim=3; // spatial dimensions
// unsigned int maxDepth=8; // maximum depth of the octree, has to be <= 30
int maxDepth=8; // maximum depth of the octree, has to be <= 30
int Ns = 32;
unsigned int dof = 3;
char problemName[PETSC_MAX_PATH_LEN];
char filename[PETSC_MAX_PATH_LEN];
double t0 = 0.0;
double dt = 0.1;
double t1 = 1.0;
double beta = 0.000001;
Vec rho; // density - elemental scalar
Vec lambda; // Lame parameter - lambda - elemental scalar
Vec mu; // Lame parameter - mu - elemental scalar
Vec fibers; // Fiber orientations - nodal vector (3-dof)
std::vector<Vec> tau; // the scalar activation - nodal scalar
std::vector<ot::TreeNode> linOct, balOct, newLinOct;
std::vector<double> pts;
// Initial conditions
Vec initialDisplacement;
Vec initialVelocity;
double nu, E;
nu = 0.45;
E = 1000;
timeInfo ti;
PetscTruth mf = PETSC_FALSE;
bool mfree = false;
PetscOptionsGetTruth(0, "-mfree", &mf, 0);
if (mf == PETSC_TRUE) {
mfree = true;
} else
mfree = false;
double ctrst = 1.0;
// get Ns
CHKERRQ ( PetscOptionsGetInt(0,"-Ns",&Ns,0) );
CHKERRQ ( PetscOptionsGetInt(0,"-mdepth",&maxDepth,0) );
CHKERRQ ( PetscOptionsGetScalar(0,"-ctrst",&ctrst,0) );
CHKERRQ ( PetscOptionsGetScalar(0,"-t0",&t0,0) );
CHKERRQ ( PetscOptionsGetScalar(0,"-nu",&nu,0) );
CHKERRQ ( PetscOptionsGetScalar(0,"-Youngs",&E,0) );
CHKERRQ ( PetscOptionsGetScalar(0,"-t1",&t1,0) );
CHKERRQ ( PetscOptionsGetScalar(0,"-dt",&dt,0) );
CHKERRQ ( PetscOptionsGetScalar(0,"-beta",&beta,0) );
CHKERRQ ( PetscOptionsGetString(PETSC_NULL,"-pn",problemName,PETSC_MAX_PATH_LEN-1,PETSC_NULL));
// Time info for timestepping
ti.start = t0;
ti.stop = t1;
ti.step = dt;
if (!rank) {
std::cout << "Grid size is " << Ns+1 << " and NT is " << (int)ceil(1.0/dt) << std::endl;
std::cout << "MaxDepth is " << maxDepth << std::endl;
}
/*
for (int i=0; i<3*Ns*Ns*Ns; i++) {
double val = gaussian(); //randgauss(0., 1., 2.0, 0.);
// std::cout << val << std::endl;
pts.push_back(val);
}
MPI_Barrier(MPI_COMM_WORLD);
*/
/*********************************************************************** */
// CONSTRUCT: Construct the linear octree from the points ...
/*********************************************************************** */
// ot::points2Octree(pts, gSize, linOct, dim, maxDepth, maxNumPts, MPI_COMM_WORLD);
// The points are not needed anymore, and can be cleared to free memory.
// pts.clear();
if (!rank) {
ot::readNodesFromFile("test.256.oct", newLinOct);
std::cout << "Finished reading" << std::endl;
}
// std::sort(linOct.begin(), linOct.end());
std::cout << rank << " Original octree size is " << newLinOct.size() << std::endl;
/*
par::Partition<ot::TreeNode>(linoct, newLinOct, MPI_COMM_WORLD);
linOct.clear();
*/
par::sampleSort<ot::TreeNode>(newLinOct, linOct, MPI_COMM_WORLD);
newLinOct.clear();
std::cout << rank << ": after Part octree size is " << linOct.size() << std::endl;
/*********************************************************************** */
// BALANCE: Balance the linear octree to enforce the 2:1 balance conditions.
/*********************************************************************** */
ot::balanceOctree (linOct, balOct, dim, maxDepth, incCorner, MPI_COMM_WORLD);
std::cout << "Balanced octree size is " << balOct.size() << std::endl;
// The linear octree (unbalanced) can be cleared to free memory.
linOct.clear();
// If desired the octree can be written to a file using the supplied routine ...
ot::writeNodesToFile("filename.oct", balOct);
/*********************************************************************** */
// MESH : Construct the octree-based Distruted Array.
/*********************************************************************** */
ot::DA da(balOct,MPI_COMM_WORLD);
balOct.clear();
MPI_Barrier(MPI_COMM_WORLD);
if (!rank)
std::cout <<"Finshed Meshing" << std::endl;
PetscFinalize();
return 0;
// create Matrices and Vectors
elasMass *Mass = new elasMass(feMat::OCT); // Mass Matrix
elasStiffness *Stiffness = new elasStiffness(feMat::OCT); // Stiffness matrix
raleighDamping *Damping = new raleighDamping(feMat::OCT); // Damping Matrix
cardiacForce *Force = new cardiacForce(feVec::OCT); // Force Vector
// create vectors
da.createVector(rho, false, false, 1);
da.createVector(mu, false, false, 1);
da.createVector(lambda, false, false, 1);
da.createVector(initialDisplacement, false, false, dof);
da.createVector(initialVelocity, false, false, dof);
// Set initial conditions
CHKERRQ( VecSet ( initialDisplacement, 0.0) );
CHKERRQ( VecSet ( initialVelocity, 0.0) );
int parFac = 2;
int numParams = 120;
CHKERRQ ( PetscOptionsGetInt(0,"-pFac", &parFac,0) );
numParams = parFac*parFac*parFac*5*3;
if (!rank)
std::cout << "Total number of unknowns is " << numParams << std::endl;
// Generate the basis ...
std::vector < radialBasis > spatialBasis;
bSplineBasis temporalBasis(3, 5); // this creates and sets up the basis ...
// temporalBasis.knot();
double fac = 1.0/parFac;
double ssq = fac*fac/5.5452; // 8log(2) = 5.5452
PetscPrintf(0, "SSQ is %f\n", ssq);
// Now to set up the radial bases ...
for (int k=0; k<parFac; k++) {
for (int j=0; j<parFac; j++) {
for (int i=0; i<parFac; i++) {
// std::cout << "Adding radial basis at: " << fac/2+i*fac << ", " << fac/2+j*fac << ", " << fac/2+k*fac << std::endl;
radialBasis tmp(Point( fac/2+i*fac,fac/2+j*fac,fac/2+k*fac), Point(ssq,ssq,ssq));
spatialBasis.push_back(tmp);
}
}
}
/*
// Homogeneous material properties ...
CHKERRQ( VecSet ( rho, 1.0) );
nu = 0.45; E = 1000;
double mmu = E/(2*(1+nu));
double llam = E*nu/((1+nu)*(1-2*nu));
CHKERRQ( VecSet ( mu, mmu) );
CHKERRQ( VecSet ( lambda, llam) );
*/
PetscScalar *muArray, *lamArray, *rhoArray;
// Read in material properties from file ...
unsigned int elemSize = Ns*Ns*Ns;
unsigned char *tmp_mat = new unsigned char[elemSize];
double *tmp_tau = new double[elemSize];
double *tmp_fib = new double[dof*elemSize];
// generate filenames & read in the raw arrays first ...
std::ifstream fin;
sprintf(filename, "%s.%d.img", problemName, Ns);
fin.open(filename, std::ios::binary); fin.read((char *)tmp_mat, elemSize); fin.close();
nu = 0.35; E = 1000;
double mmu = E/(2*(1+nu));
double llam = E*nu/((1+nu)*(1-2*nu));
nu = 0.45; E = 1000*ctrst;
double mmu2 = E/(2*(1+nu));
double llam2 = E*nu/((1+nu)*(1-2*nu));
da.vecGetBuffer(mu, muArray,true,true,false,1);
da.vecGetBuffer(lambda, lamArray,true,true,false,1);
da.vecGetBuffer(rho, rhoArray,true,true,false,1);
for ( da.init<ot::DA::ALL>(), da.init<ot::DA::WRITABLE>(); da.curr() < da.end<ot::DA::ALL>(); da.next<ot::DA::ALL>()) {
unsigned int i = da.curr();
Point pt;
pt = da.getCurrentOffset();
int indx = pt.z()*Ns*Ns + pt.y()*Ns + pt.x();
if ( tmp_mat[indx] ) {
muArray[i] = mmu2;
lamArray[i] = llam2;
rhoArray[i] = 1.0;
} else {
muArray[i] = mmu;
lamArray[i] = llam;
rhoArray[i] = 1.0;
}
}
da.vecRestoreBuffer(mu, muArray,true,true,false,1);
da.vecRestoreBuffer(lambda, lamArray,true,true,false,1);
da.vecRestoreBuffer(rho, rhoArray,true,true,false,1);
delete [] tmp_mat;
// Now set the activation ...
unsigned int numSteps = (unsigned int)(ceil(( ti.stop - ti.start)/ti.step));
Vec tauVec, tmpTau;
// Create elemental vector ...
da.createVector(tmpTau, true, true, 1);
da.createVector(fibers, true, true, 3);
PetscScalar *tauArray;
// load the fibers ...
da.vecGetBuffer(fibers, tauArray, true, true, 3);
sprintf(filename, "%s.%d.fibers", problemName, Ns);
std::ifstream fin3(filename, std::ios::binary); fin3.read((char *)tmp_fib, dof*elemSize*sizeof(double)); fin3.close();
for ( da.init<ot::DA::ALL>(), da.init<ot::DA::WRITABLE>(); da.curr() < da.end<ot::DA::ALL>(); da.next<ot::DA::ALL>()) {
unsigned int i = da.curr();
Point pt;
pt = da.getCurrentOffset();
int indx = pt.z()*Ns*Ns + pt.y()*Ns + pt.x();
for (int d=0; d<dof; d++) {
tauArray[dof*i+d] = tmp_tau[dof*indx+d];
}
}
da.vecRestoreBuffer(fibers, tauArray, true, true, 3);
delete [] tmp_fib;
// loop through time steps
for (unsigned int t=0; t<numSteps+1; t++) {
// a. Create new nodal vector ...
da.createVector(tauVec, false, true, 1);
VecSet( tmpTau, 0.0 );
da.vecGetBuffer(tmpTau, tauArray, true, true, 1);
// b. read in the activation
// std::cout << "Setting force vectors" << std::endl;
sprintf(filename, "%s.%d.%.3d.fld", problemName, Ns, t);
// std::cout << "Reading force file " << filename << std::endl;
fin.open(filename); fin.read((char *)tmp_tau, elemSize*sizeof(double)); fin.close();
// c. set the values ...
for ( da.init<ot::DA::ALL>(), da.init<ot::DA::WRITABLE>(); da.curr() < da.end<ot::DA::ALL>(); da.next<ot::DA::ALL>()) {
unsigned int i = da.curr();
Point pt;
pt = da.getCurrentOffset();
int indx = pt.z()*Ns*Ns + pt.y()*Ns + pt.x();
tauArray[i] = tmp_tau[indx];
}
// restore
da.vecRestoreBuffer(tmpTau, tauArray, true, true, 1);
// d. element2node
elementToNode(da, tmpTau, tauVec, 1);
// store in vector
tau.push_back(tauVec);
}
// Setup Matrices and Force Vector ...
Mass->setProblemDimensions(1.0, 1.0, 1.0);
Mass->setDA(&da);
Mass->setDof(dof);
Mass->setDensity(rho);
Stiffness->setProblemDimensions(1.0, 1.0, 1.0);
Stiffness->setDA(&da);
Stiffness->setDof(dof);
Stiffness->setLame(lambda, mu);
Damping->setAlpha(0.0);
Damping->setBeta(0.00075);
Damping->setMassMatrix(Mass);
Damping->setStiffnessMatrix(Stiffness);
Damping->setDA(&da);
Damping->setDof(dof);
// Force Vector
Force->setProblemDimensions(1.0,1.0,1.0);
Force->setDA(&da);
// Force->setFDynamic(tau);
Force->setActivationVec(tau);
Force->setFiberOrientations(fibers);
Force->setTimeInfo(&ti);
// Newmark time stepper ...
newmark *ts = new newmark;
ts->setMassMatrix(Mass);
ts->setDampingMatrix(Damping);
ts->setStiffnessMatrix(Stiffness);
ts->damp(false);
ts->setTimeFrames(1);
ts->storeVec(true);
ts->setForceVector(Force);
ts->setInitialDisplacement(initialDisplacement);
ts->setInitialVelocity(initialVelocity);
ts->setTimeInfo(&ti);
ts->setAdjoint(false); // set if adjoint or forward
ts->useMatrixFree(mfree);
//if (!rank)
// std::cout << RED"Initializing Newmark"NRM << std::endl;
double itime = MPI_Wtime();
ts->init(); // initialize IMPORTANT
//if (!rank)
// std::cout << RED"Starting Newmark Solve"NRM << std::endl;
double stime = MPI_Wtime();
ts->solve();// solve
double etime = MPI_Wtime();
// PetscFinalize();
Vec alpha, outvec;
PetscScalar *avec;
VecCreateSeq(PETSC_COMM_SELF, numParams, &alpha);
VecGetArray(alpha, &avec);
for (int j=0; j<numParams; j++)
avec[j] = 0.0;
avec[1] = 1.0;
VecRestoreArray(alpha, &avec);
VecDuplicate(alpha, &outvec);
// Inverse solver set up
parametricActivationInverse *hyperInv = new parametricActivationInverse;
hyperInv->setBasis(spatialBasis, temporalBasis);
hyperInv->setForwardInitialConditions(initialDisplacement, initialVelocity);
hyperInv->setTimeStepper(ts); // set the timestepper
hyperInv->setInitialGuess(alpha);// set the initial guess
hyperInv->setRegularizationParameter(beta); // set the regularization paramter
// hyperInv->setObservations(solvec); // set the data for the problem
hyperInv->init(); // initialize the inverse solver
hyperInv->solve();
Vec FinalSolution;
hyperInv->getCurrentControl(FinalSolution);
char fname[256];
sprintf(fname, "%s.soln.%d.%d.raw",problemName, Ns, parFac );
std::ofstream sol;
if (!rank) {
sol.open(fname, std::ios::binary);
VecGetArray(FinalSolution, &avec);
sol.write((char *)avec, numParams*sizeof(PetscScalar));
VecRestoreArray(outvec, &avec);
sol.close();
}
PetscFinalize();
}
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,NULL, "-test_zheevx", &flg);CHKERRQ(ierr);
if (flg) {
TestZHEEV = PETSC_FALSE;
TestZHEEVX = PETSC_TRUE;
}
ierr = PetscOptionsHasName(NULL,NULL, "-test_zhegv", &flg);CHKERRQ(ierr);
if (flg) {
TestZHEEV = PETSC_FALSE;
TestZHEGV = PETSC_TRUE;
}
ierr = PetscOptionsHasName(NULL,NULL, "-test_zhegvx", &flg);CHKERRQ(ierr);
if (flg) {
TestZHEEV = PETSC_FALSE;
TestZHEGVX = PETSC_TRUE;
}
ierr = PetscOptionsGetReal(NULL,NULL,"-sigma1",&sigma1,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,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,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,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 = PetscMalloc1(n,&evals);CHKERRQ(ierr);
ierr = PetscMalloc1(lwork,&work);CHKERRQ(ierr);
ierr = MatDenseGetArray(A_dense,&arrayA);CHKERRQ(ierr);
if (TestZHEEV) { /* test zheev() */
printf(" LAPACKsyev: compute all %d eigensolutions...\n",m);
ierr = PetscMalloc1(3*n-2,&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 = PetscMalloc1(m*n+1,&evecs_array);CHKERRQ(ierr);
ierr = PetscMalloc1(7*n+1,&rwork);CHKERRQ(ierr);
ierr = PetscMalloc1(5*n+1,&iwork);CHKERRQ(ierr);
ierr = PetscMalloc1(n+1,&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 = PetscMalloc1(3*n+1,&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 = PetscMalloc1(m*n+1,&evecs_array);CHKERRQ(ierr);
ierr = PetscMalloc1(6*n+1,&iwork);CHKERRQ(ierr);
ifail = iwork + 5*n;
ierr = PetscMalloc1(7*n+1,&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,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,(double)evals[i]);
}
/* Check residuals and orthogonality */
ierr = PetscMalloc1(nevs+1,&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;
}
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 */
PC pc; /* preconditioner context */
PetscReal norm,tol=1.e-14; /* norm of solution error */
PetscErrorCode ierr;
PetscInt i,n = 10,col[3],its;
PetscMPIInt size;
PetscScalar neg_one = -1.0,one = 1.0,value[3];
PetscBool nonzeroguess = PETSC_FALSE;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
if (size != 1) SETERRQ(PETSC_COMM_WORLD,1,"This is a uniprocessor example only!");
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(PETSC_NULL,"-nonzero_guess",&nonzeroguess,PETSC_NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Compute the matrix and right-hand-side vector that define
the linear system, Ax = b.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create vectors. Note that we form 1 vector from scratch and
then duplicate as needed.
*/
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) x, "Solution");CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecDuplicate(x,&u);CHKERRQ(ierr);
/*
Create matrix. When using MatCreate(), the matrix format can
be specified at runtime.
Performance tuning note: For problems of substantial size,
preallocation of matrix memory is crucial for attaining good
performance. See the matrix chapter of the users manual for details.
*/
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
/*
Assemble matrix
*/
value[0] = -1.0; value[1] = 2.0; value[2] = -1.0;
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,value,INSERT_VALUES);CHKERRQ(ierr);
}
i = n - 1; col[0] = n - 2; col[1] = n - 1;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
i = 0; col[0] = 0; col[1] = 1; value[0] = 2.0; value[1] = -1.0;
ierr = MatSetValues(A,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/*
Set exact solution; then compute right-hand-side vector.
*/
ierr = VecSet(u,one);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,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
/*
Set linear solver defaults for this problem (optional).
- By extracting the KSP and PC contexts from the KSP context,
we can then directly call any KSP and PC routines to set
various options.
- The following four statements are optional; all of these
parameters could alternatively be specified at runtime via
KSPSetFromOptions();
*/
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCJACOBI);CHKERRQ(ierr);
ierr = KSPSetTolerances(ksp,1.e-5,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT);CHKERRQ(ierr);
/*
Set runtime options, e.g.,
-ksp_type <type> -pc_type <type> -ksp_monitor -ksp_rtol <rtol>
These options will override those specified above as long as
KSPSetFromOptions() is called _after_ any other customization
routines.
*/
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
if (nonzeroguess) {
PetscScalar p = .5;
ierr = VecSet(x,p);CHKERRQ(ierr);
ierr = KSPSetInitialGuessNonzero(ksp,PETSC_TRUE);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the linear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Solve linear system
*/
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
/*
View solver info; we could instead use the option -ksp_view to
print this info to the screen at the conclusion of KSPSolve().
*/
ierr = KSPView(ksp,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Check solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Check the error
*/
ierr = VecAXPY(x,neg_one,u);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
if (norm > tol){
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of error %G, Iterations %D\n",
norm,its);CHKERRQ(ierr);
}
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr); ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
/*
Always call PetscFinalize() before exiting a program. This routine
- finalizes the PETSc libraries as well as MPI
- provides summary and diagnostic information if certain runtime
options are chosen (e.g., -log_summary).
*/
ierr = PetscFinalize();
return 0;
}
int main(int argc, char *argv[])
{
double r,dt;
int n;
unsigned long i,myNumSim,totalNumSim,numdim;
/* double payoff; */
double *vol, *St0, x, totalx;
int np,myid;
time_t start,stop;
double *eps;
himaInfo hinfo;
PetscRandom ran;
PetscErrorCode ierr;
PetscBool flg;
PetscInitialize(&argc,&argv,(char *)0,help);
#if defined(PETSC_USE_COMPLEX)
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_SUP,"This example does not work for scalar type complex\n");
#endif
time(&start);
ierr = PetscRandomCreate(PETSC_COMM_WORLD,&ran);
CHKERRQ(ierr);
#if defined(PETSC_HAVE_SPRNG)
ierr = PetscRandomSetType(ran,PETSCSPRNG);
CHKERRQ(ierr);
#elif defined(PETSC_HAVE_RAND)
ierr = PetscRandomSetType(ran,PETSCRAND);
CHKERRQ(ierr);
#endif
ierr = PetscRandomSetFromOptions(ran);
CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD, &np);
CHKERRQ(ierr); /* number of nodes */
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &myid);
CHKERRQ(ierr); /* my ranking */
ierr = PetscOptionsHasName(PETSC_NULL, "-check_generators", &flg);
CHKERRQ(ierr);
if (flg) {
ierr = PetscRandomGetValue(ran,(PetscScalar *)&r);
ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d] rval: %g\n",myid,r);
ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD);
}
hinfo.n = 31;
hinfo.r = 0.04;
hinfo.dt = 1.0/12; /* a month as a period */
hinfo.totalNumSim = 1000;
ierr = PetscOptionsGetInt(PETSC_NULL,"-num_of_stocks",&(hinfo.n),PETSC_NULL);
CHKERRQ(ierr);
if (hinfo.n <1 || hinfo.n > 31) SETERRQ1(PETSC_COMM_SELF,PETSC_ERR_SUP,"Only 31 stocks listed in stock.txt. num_of_stocks %D must between 1 and 31",hinfo.n);
ierr = PetscOptionsGetReal(PETSC_NULL,"-interest_rate",&(hinfo.r),PETSC_NULL);
CHKERRQ(ierr);
ierr = PetscOptionsGetReal(PETSC_NULL,"-time_interval",&(hinfo.dt),PETSC_NULL);
CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-num_of_simulations",&(hinfo.totalNumSim),PETSC_NULL);
CHKERRQ(ierr);
n = hinfo.n;
r = hinfo.r;
dt = hinfo.dt;
totalNumSim = hinfo.totalNumSim;
vol = hinfo.vol = (double *)malloc(sizeof(double)*(2*n+1));
St0 = hinfo.St0 = hinfo.vol + n;
ierr = readData(PETSC_COMM_WORLD,&hinfo);
CHKERRQ(ierr);
numdim = n*(n+1)/2;
if (numdim%2 == 1) {
numdim++;
}
eps = (double *)malloc(sizeof(double)*numdim);
myNumSim = divWork(myid,totalNumSim,np);
x = 0;
for (i=0; i<myNumSim; i++) {
stdNormalArray(eps,numdim,ran);
x += basketPayoff(vol,St0,n,r,dt,eps);
}
ierr = MPI_Reduce(&x, &totalx, 1, MPI_DOUBLE, MPI_SUM,0,PETSC_COMM_WORLD);
CHKERRQ(ierr);
time(&stop);
/* payoff = exp(-r*dt*n)*(totalx/totalNumSim);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Option price = $%.3f using %ds of %s computation with %d %s for %d stocks, %d trading period per year, %.2f%% interest rate\n",
payoff,(int)(stop - start),"parallel",np,"processors",n,(int)(1/dt),r);CHKERRQ(ierr); */
free(vol);
free(eps);
ierr = PetscRandomDestroy(&ran);
CHKERRQ(ierr);
PetscFinalize();
return 0;
}
/* ------------------------------------------------------- */
int main(int argc,char ** argv)
{
PetscErrorCode ierr;
Wash wash;
Junction junctions,junction;
Pipe pipe,pipes;
PetscInt numEdges,numVertices,KeyPipe,KeyJunction;
int *edgelist = NULL;
PetscInt i,e,v,eStart,eEnd,vStart,vEnd,pipeOffset,key,frombType,tobType;
PetscInt vfrom,vto,vkey,fromOffset,toOffset,type,varoffset,pipeoffset;
PetscInt from_nedge_in,from_nedge_out,to_nedge_in;
const PetscInt *cone;
DM networkdm;
PetscMPIInt size,rank;
PetscReal ftime = 2500.0;
Vec X;
TS ts;
PetscInt maxsteps=-1,steps;
TSConvergedReason reason;
PetscBool viewpipes;
PetscInt pipesCase;
DMNetworkMonitor monitor;
DMNetworkComponentGenericDataType *nwarr;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
/* Create and setup network */
/*--------------------------*/
ierr = DMNetworkCreate(PETSC_COMM_WORLD,&networkdm);CHKERRQ(ierr);
if (size == 1) {
ierr = DMNetworkMonitorCreate(networkdm,&monitor);CHKERRQ(ierr);
}
/* Register the components in the network */
ierr = DMNetworkRegisterComponent(networkdm,"junctionstruct",sizeof(struct _p_Junction),&KeyJunction);CHKERRQ(ierr);
ierr = DMNetworkRegisterComponent(networkdm,"pipestruct",sizeof(struct _p_Pipe),&KeyPipe);CHKERRQ(ierr);
/* Set global number of pipes, edges, and vertices */
pipesCase = 2;
ierr = PetscOptionsGetInt(NULL,NULL, "-case", &pipesCase, NULL);CHKERRQ(ierr);
ierr = WashNetworkCreate(PETSC_COMM_WORLD,pipesCase,&wash,&edgelist);CHKERRQ(ierr);
numEdges = wash->nedge;
numVertices = wash->nvertex;
junctions = wash->junction;
pipes = wash->pipe;
/* Set number of vertices and edges */
ierr = DMNetworkSetSizes(networkdm,numVertices,numEdges,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
/* Add edge connectivity */
ierr = DMNetworkSetEdgeList(networkdm,edgelist);CHKERRQ(ierr);
/* Set up the network layout */
ierr = DMNetworkLayoutSetUp(networkdm);CHKERRQ(ierr);
/* Add EDGEDATA component to all edges -- currently networkdm is a sequential network */
ierr = DMNetworkGetEdgeRange(networkdm,&eStart,&eEnd);CHKERRQ(ierr);
ierr = DMNetworkGetVertexRange(networkdm,&vStart,&vEnd);CHKERRQ(ierr);
for (e = eStart; e < eEnd; e++) {
/* Add Pipe component to all edges -- create pipe here */
ierr = DMNetworkAddComponent(networkdm,e,KeyPipe,&pipes[e-eStart]);CHKERRQ(ierr);
/* Add number of variables to each edge */
ierr = DMNetworkAddNumVariables(networkdm,e,2*pipes[e-eStart].nnodes);CHKERRQ(ierr);
if (size == 1) { /* Add monitor -- show Q_{pipes[e-eStart].id}? */
ierr = DMNetworkMonitorAdd(monitor, "Pipe Q", e, pipes[e-eStart].nnodes, 0, 2, -0.8, 0.8, PETSC_TRUE);CHKERRQ(ierr);
ierr = DMNetworkMonitorAdd(monitor, "Pipe H", e, pipes[e-eStart].nnodes, 1, 2, -400.0, 800.0, PETSC_TRUE);CHKERRQ(ierr);
}
}
/* Add Junction component to all vertices */
for (v = vStart; v < vEnd; v++) {
ierr = DMNetworkAddComponent(networkdm,v,KeyJunction,&junctions[v-vStart]);CHKERRQ(ierr);
/* Add number of variables to vertex */
ierr = DMNetworkAddNumVariables(networkdm,v,2);CHKERRQ(ierr);
}
/* Set up DM for use */
ierr = DMSetUp(networkdm);CHKERRQ(ierr);
ierr = WashNetworkCleanUp(wash,edgelist);CHKERRQ(ierr);
/* Network partitioning and distribution of data */
if (size > 1) {
DM distnetworkdm;
ierr = DMNetworkDistribute(networkdm,0,&distnetworkdm);CHKERRQ(ierr);
ierr = DMDestroy(&networkdm);CHKERRQ(ierr);
networkdm = distnetworkdm;
}
/* PipeSetUp -- each process only sets its own pipes */
/*---------------------------------------------------*/
ierr = DMNetworkGetComponentDataArray(networkdm,&nwarr);CHKERRQ(ierr);
ierr = DMNetworkGetEdgeRange(networkdm,&eStart,&eEnd);CHKERRQ(ierr);
for (e=eStart; e<eEnd; e++) { /* each edge has only one component, pipe */
ierr = DMNetworkGetComponentTypeOffset(networkdm,e,0,&type,&pipeoffset);CHKERRQ(ierr);
ierr = DMNetworkGetVariableOffset(networkdm,e,&varoffset);CHKERRQ(ierr);
pipe = (Pipe)(nwarr + pipeoffset);
/* Setup conntected vertices */
ierr = DMNetworkGetConnectedNodes(networkdm,e,&cone);CHKERRQ(ierr);
vfrom = cone[0]; /* local ordering */
vto = cone[1];
/* vfrom */
ierr = DMNetworkGetComponentTypeOffset(networkdm,vfrom,0,&vkey,&fromOffset);CHKERRQ(ierr);
junction = (Junction)(nwarr+fromOffset);
from_nedge_in = junction->nedges_in;
from_nedge_out = junction->nedges_out;
/* vto */
ierr = DMNetworkGetComponentTypeOffset(networkdm,vto,0,&vkey,&toOffset);CHKERRQ(ierr);
junction = (Junction)(nwarr+toOffset);
to_nedge_in = junction->nedges_in;
pipe->comm = PETSC_COMM_SELF; /* must be set here, otherwise crashes in my mac??? */
wash->nnodes_loc += pipe->nnodes; /* local total num of nodes, will be used by PipesView() */
ierr = PipeSetParameters(pipe,
600.0, /* length */
pipe->nnodes, /* nnodes -- rm from PipeSetParameters */
0.5, /* diameter */
1200.0, /* a */
0.018);CHKERRQ(ierr); /* friction */
/* set boundary conditions for this pipe */
if (from_nedge_in <= 1 && from_nedge_out > 0) {
frombType = 0;
} else {
frombType = 1;
}
if (to_nedge_in == 1) {
tobType = 0;
} else {
tobType = 1;
}
if (frombType == 0) {
pipe->boundary.Q0 = PIPE_CHARACTERISTIC; /* will be obtained from characteristic */
pipe->boundary.H0 = wash->H0;
} else {
pipe->boundary.Q0 = wash->Q0;
pipe->boundary.H0 = PIPE_CHARACTERISTIC; /* will be obtained from characteristic */
}
if (tobType == 0) {
pipe->boundary.QL = wash->QL;
pipe->boundary.HL = PIPE_CHARACTERISTIC; /* will be obtained from characteristic */
} else {
pipe->boundary.QL = PIPE_CHARACTERISTIC; /* will be obtained from characteristic */
pipe->boundary.HL = wash->HL;
}
ierr = PipeSetUp(pipe);CHKERRQ(ierr);
}
/* create vectors */
ierr = DMCreateGlobalVector(networkdm,&X);CHKERRQ(ierr);
ierr = DMCreateLocalVector(networkdm,&wash->localX);CHKERRQ(ierr);
ierr = DMCreateLocalVector(networkdm,&wash->localXdot);CHKERRQ(ierr);
/* Setup solver */
/*--------------------------------------------------------*/
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetDM(ts,(DM)networkdm);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,WASHIFunction,wash);CHKERRQ(ierr);
ierr = TSSetDuration(ts,maxsteps,ftime);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,0.1);CHKERRQ(ierr);
ierr = TSSetType(ts,TSBEULER);CHKERRQ(ierr);
if (size == 1) {
ierr = TSMonitorSet(ts, TSDMNetworkMonitor, monitor, NULL);CHKERRQ(ierr);
}
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
ierr = WASHSetInitialSolution(networkdm,X,wash);CHKERRQ(ierr);
ierr = TSSolve(ts,X);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);
ierr = TSGetConvergedReason(ts,&reason);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"%s at time %g after %D steps\n",TSConvergedReasons[reason],(double)ftime,steps);CHKERRQ(ierr);
/* ierr = VecView(X,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); */
/* View solution q and h */
/* --------------------- */
viewpipes = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL, "-pipe_view", &viewpipes,NULL);CHKERRQ(ierr);
if (viewpipes) {
ierr = PipesView(X,networkdm,wash);CHKERRQ(ierr);
}
/* Free spaces */
/* ----------- */
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = VecDestroy(&wash->localX);CHKERRQ(ierr);
ierr = VecDestroy(&wash->localXdot);CHKERRQ(ierr);
/* Destroy objects from each pipe that are created in PipeSetUp() */
ierr = DMNetworkGetEdgeRange(networkdm,&eStart, &eEnd);CHKERRQ(ierr);
for (i = eStart; i < eEnd; i++) {
ierr = DMNetworkGetComponentTypeOffset(networkdm,i,0,&key,&pipeOffset);CHKERRQ(ierr);
pipe = (Pipe)(nwarr+pipeOffset);
ierr = DMDestroy(&(pipe->da));CHKERRQ(ierr);
ierr = VecDestroy(&pipe->x);CHKERRQ(ierr);
}
if (size == 1) {
ierr = DMNetworkMonitorDestroy(&monitor);CHKERRQ(ierr);
}
ierr = DMDestroy(&networkdm);CHKERRQ(ierr);
ierr = PetscFree(wash);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
int main(int argc,char **argv)
{
TS ts; /* time integration context */
Vec X; /* solution, residual vectors */
Mat J; /* Jacobian matrix */
PetscErrorCode ierr;
PetscScalar *x;
PetscReal ftime;
PetscInt i,steps,nits,lits;
PetscBool view_final;
Ctx ctx;
PetscInitialize(&argc,&argv,(char*)0,help);
ctx.n = 3;
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&ctx.n,NULL);CHKERRQ(ierr);
if (ctx.n < 2) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_ARG_OUTOFRANGE,"The dimension specified with -n must be at least 2");
view_final = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-view_final",&view_final,NULL);CHKERRQ(ierr);
ctx.monitor_short = PETSC_FALSE;
ierr = PetscOptionsGetBool(NULL,NULL,"-monitor_short",&ctx.monitor_short,NULL);CHKERRQ(ierr);
/*
Create Jacobian matrix data structure and state vector
*/
ierr = MatCreate(PETSC_COMM_WORLD,&J);CHKERRQ(ierr);
ierr = MatSetSizes(J,PETSC_DECIDE,PETSC_DECIDE,ctx.n,ctx.n);CHKERRQ(ierr);
ierr = MatSetFromOptions(J);CHKERRQ(ierr);
ierr = MatSetUp(J);CHKERRQ(ierr);
ierr = MatCreateVecs(J,&X,NULL);CHKERRQ(ierr);
/* Create time integration context */
ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
ierr = TSSetType(ts,TSPSEUDO);CHKERRQ(ierr);
ierr = TSSetIFunction(ts,NULL,FormIFunction,&ctx);CHKERRQ(ierr);
ierr = TSSetIJacobian(ts,J,J,FormIJacobian,&ctx);CHKERRQ(ierr);
ierr = TSSetDuration(ts,1000,1e14);CHKERRQ(ierr);
ierr = TSSetExactFinalTime(ts,TS_EXACTFINALTIME_STEPOVER);CHKERRQ(ierr);
ierr = TSSetInitialTimeStep(ts,0.0,1e-3);CHKERRQ(ierr);
ierr = TSMonitorSet(ts,MonitorObjective,&ctx,NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Customize time integrator; set runtime options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = TSSetFromOptions(ts);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Evaluate initial guess; then solve nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecSet(X,0.0);CHKERRQ(ierr);
ierr = VecGetArray(X,&x);CHKERRQ(ierr);
#if 1
x[0] = 5.;
x[1] = -5.;
for (i=2; i<ctx.n; i++) x[i] = 5.;
#else
x[0] = 1.0;
x[1] = 15.0;
for (i=2; i<ctx.n; i++) x[i] = 10.0;
#endif
ierr = VecRestoreArray(X,&x);CHKERRQ(ierr);
ierr = TSSolve(ts,X);CHKERRQ(ierr);
ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);
ierr = TSGetSNESIterations(ts,&nits);CHKERRQ(ierr);
ierr = TSGetKSPIterations(ts,&lits);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Time integrator took (%D,%D,%D) iterations to reach final time %g\n",steps,nits,lits,(double)ftime);CHKERRQ(ierr);
if (view_final) {
ierr = VecView(X,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecDestroy(&X);CHKERRQ(ierr);
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = TSDestroy(&ts);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
-ov <overlap> : >=0 amount of overlap between domains\n\n";
#include <petscksp.h>
#undef __FUNCT__
#define __FUNCT__ "main"
int main(int argc,char **args)
{
PetscErrorCode ierr;
PetscInt nd = 2,ov=1,i,start,m,n,end,lsize;
PetscMPIInt rank;
PetscBool flg;
Mat A,B;
char file[PETSC_MAX_PATH_LEN];
PetscViewer fd;
IS *is1,*is2;
PetscRandom r;
PetscScalar rand;
PetscInitialize(&argc,&args,(char*)0,help);
#if defined(PETSC_USE_COMPLEX)
SETERRQ(PETSC_COMM_WORLD,1,"This example does not work with complex numbers");
#else
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL,"-f",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must use -f filename to indicate a file containing a PETSc binary matrix");
ierr = PetscOptionsGetInt(NULL,"-nd",&nd,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,"-ov",&ov,NULL);CHKERRQ(ierr);
/* Read matrix and RHS */
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATMPIAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/* Read the matrix again as a sequential matrix */
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&B);CHKERRQ(ierr);
ierr = MatSetType(B,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatLoad(B,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/* Create the IS corresponding to subdomains */
ierr = PetscMalloc(nd*sizeof(IS **),&is1);CHKERRQ(ierr);
ierr = PetscMalloc(nd*sizeof(IS **),&is2);CHKERRQ(ierr);
/* Create the random Index Sets */
ierr = MatGetSize(A,&m,&n);CHKERRQ(ierr);
ierr = PetscRandomCreate(PETSC_COMM_SELF,&r);CHKERRQ(ierr);
ierr = PetscRandomSetFromOptions(r);CHKERRQ(ierr);
for (i=0; i<nd; i++) {
ierr = PetscRandomGetValue(r,&rand);CHKERRQ(ierr);
start = (PetscInt)(rand*m);
ierr = PetscRandomGetValue(r,&rand);CHKERRQ(ierr);
end = (PetscInt)(rand*m);
lsize = end - start;
if (start > end) { start = end; lsize = -lsize;}
ierr = ISCreateStride(PETSC_COMM_SELF,lsize,start,1,is1+i);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_SELF,lsize,start,1,is2+i);CHKERRQ(ierr);
}
ierr = MatIncreaseOverlap(A,nd,is1,ov);CHKERRQ(ierr);
ierr = MatIncreaseOverlap(B,nd,is2,ov);CHKERRQ(ierr);
/* Now see if the serial and parallel case have the same answers */
for (i=0; i<nd; ++i) {
ierr = ISEqual(is1[i],is2[i],&flg);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"proc:[%d], i=%D, flg =%d\n",rank,i,(int)flg);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 = PetscRandomDestroy(&r);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = PetscFinalize();
#endif
return 0;
}
int main(int argc,char **args)
{
Vec x,b;
Mat A,U,V,LR;
PetscInt i,j,Ii,J,Istart,Iend,m = 8,n = 7,rstart,rend;
PetscErrorCode ierr;
PetscBool flg;
PetscScalar *u,a;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the sparse matrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,m*n,m*n);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
for (Ii=Istart; Ii<Iend; Ii++) {
a = -1.0; i = Ii/n; j = Ii - i*n;
if (i>0) {J = Ii - n; ierr = MatSetValues(A,1,&Ii,1,&J,&a,INSERT_VALUES);CHKERRQ(ierr);}
if (i<m-1) {J = Ii + n; ierr = MatSetValues(A,1,&Ii,1,&J,&a,INSERT_VALUES);CHKERRQ(ierr);}
if (j>0) {J = Ii - 1; ierr = MatSetValues(A,1,&Ii,1,&J,&a,INSERT_VALUES);CHKERRQ(ierr);}
if (j<n-1) {J = Ii + 1; ierr = MatSetValues(A,1,&Ii,1,&J,&a,INSERT_VALUES);CHKERRQ(ierr);}
a = 4.0; ierr = MatSetValues(A,1,&Ii,1,&Ii,&a,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the dense matrices
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreate(PETSC_COMM_WORLD,&U);CHKERRQ(ierr);
ierr = MatSetSizes(U,PETSC_DECIDE,PETSC_DECIDE,m*n,3);CHKERRQ(ierr);
ierr = MatSetType(U,MATDENSE);CHKERRQ(ierr);
ierr = MatSetUp(U);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(U,&rstart,&rend);CHKERRQ(ierr);
ierr = MatDenseGetArray(U,&u);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
u[i-rstart] = (PetscReal)i;
u[i+rend-2*rstart] = (PetscReal)1000*i;
u[i+2*rend-3*rstart] = (PetscReal)100000*i;
}
ierr = MatDenseRestoreArray(U,&u);CHKERRQ(ierr);
ierr = MatAssemblyBegin(U,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(U,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&V);CHKERRQ(ierr);
ierr = MatSetSizes(V,PETSC_DECIDE,PETSC_DECIDE,m*n,3);CHKERRQ(ierr);
ierr = MatSetType(V,MATDENSE);CHKERRQ(ierr);
ierr = MatSetUp(V);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(U,&rstart,&rend);CHKERRQ(ierr);
ierr = MatDenseGetArray(V,&u);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) {
u[i-rstart] = (PetscReal)i;
u[i+rend-2*rstart] = (PetscReal)1.2*i;
u[i+2*rend-3*rstart] = (PetscReal)1.67*i+2;
}
ierr = MatDenseRestoreArray(V,&u);CHKERRQ(ierr);
ierr = MatAssemblyBegin(V,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(V,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create low rank created matrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreateLRC(A,U,V,&LR);CHKERRQ(ierr);
ierr = MatSetUp(LR);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create test vectors
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,m*n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(x,&rstart,&rend);CHKERRQ(ierr);
ierr = VecGetArray(x,&u);CHKERRQ(ierr);
for (i=rstart; i<rend; i++) u[i-rstart] = (PetscScalar)i;
ierr = VecRestoreArray(x,&u);CHKERRQ(ierr);
ierr = MatMult(LR,x,b);CHKERRQ(ierr);
/*
View the product if desired
*/
ierr = PetscOptionsHasName(PETSC_NULL,"-view_product",&flg);CHKERRQ(ierr);
if (flg) {ierr = VecView(b,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);}
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
/* you can destroy the matrices in any order you like */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&U);CHKERRQ(ierr);
ierr = MatDestroy(&V);CHKERRQ(ierr);
ierr = MatDestroy(&LR);CHKERRQ(ierr);
/*
Always call PetscFinalize() before exiting a program. This routine
- finalizes the PETSc libraries as well as MPI
- provides summary and diagnostic information if certain runtime
options are chosen (e.g., -log_summary).
*/
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
Mat A; /* eigenvalue problem matrix */
EPS eps; /* eigenproblem solver context */
EPSType type;
PetscScalar delta1,delta2,L,h,value[3];
PetscInt N=30,n,i,col[3],Istart,Iend,nev;
PetscBool FirstBlock=PETSC_FALSE,LastBlock=PETSC_FALSE;
CTX_BRUSSEL *ctx;
PetscErrorCode ierr;
SlepcInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,"-n",&N,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"\nBrusselator wave model, n=%D\n\n",N);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Generate the matrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create shell matrix context and set default parameters
*/
ierr = PetscNew(&ctx);CHKERRQ(ierr);
ctx->alpha = 2.0;
ctx->beta = 5.45;
delta1 = 0.008;
delta2 = 0.004;
L = 0.51302;
/*
Look the command line for user-provided parameters
*/
ierr = PetscOptionsGetScalar(NULL,"-L",&L,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-alpha",&ctx->alpha,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-beta",&ctx->beta,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-delta1",&delta1,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetScalar(NULL,"-delta2",&delta2,NULL);CHKERRQ(ierr);
/*
Create matrix T
*/
ierr = MatCreate(PETSC_COMM_WORLD,&ctx->T);CHKERRQ(ierr);
ierr = MatSetSizes(ctx->T,PETSC_DECIDE,PETSC_DECIDE,N,N);CHKERRQ(ierr);
ierr = MatSetFromOptions(ctx->T);CHKERRQ(ierr);
ierr = MatSetUp(ctx->T);CHKERRQ(ierr);
ierr = MatGetOwnershipRange(ctx->T,&Istart,&Iend);CHKERRQ(ierr);
if (Istart==0) FirstBlock=PETSC_TRUE;
if (Iend==N) LastBlock=PETSC_TRUE;
value[0]=1.0; value[1]=-2.0; value[2]=1.0;
for (i=(FirstBlock? Istart+1: Istart); i<(LastBlock? Iend-1: Iend); i++) {
col[0]=i-1; col[1]=i; col[2]=i+1;
ierr = MatSetValues(ctx->T,1,&i,3,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (LastBlock) {
i=N-1; col[0]=N-2; col[1]=N-1;
ierr = MatSetValues(ctx->T,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
if (FirstBlock) {
i=0; col[0]=0; col[1]=1; value[0]=-2.0; value[1]=1.0;
ierr = MatSetValues(ctx->T,1,&i,2,col,value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(ctx->T,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(ctx->T,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatGetLocalSize(ctx->T,&n,NULL);CHKERRQ(ierr);
/*
Fill the remaining information in the shell matrix context
and create auxiliary vectors
*/
h = 1.0 / (PetscReal)(N+1);
ctx->tau1 = delta1 / ((h*L)*(h*L));
ctx->tau2 = delta2 / ((h*L)*(h*L));
ctx->sigma = 0.0;
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,PETSC_DECIDE,NULL,&ctx->x1);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,PETSC_DECIDE,NULL,&ctx->x2);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,PETSC_DECIDE,NULL,&ctx->y1);CHKERRQ(ierr);
ierr = VecCreateMPIWithArray(PETSC_COMM_WORLD,1,n,PETSC_DECIDE,NULL,&ctx->y2);CHKERRQ(ierr);
/*
Create the shell matrix
*/
ierr = MatCreateShell(PETSC_COMM_WORLD,2*n,2*n,2*N,2*N,(void*)ctx,&A);CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_MULT,(void(*)())MatMult_Brussel);CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_SHIFT,(void(*)())MatShift_Brussel);CHKERRQ(ierr);
ierr = MatShellSetOperation(A,MATOP_GET_DIAGONAL,(void(*)())MatGetDiagonal_Brussel);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the eigensolver and set various options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Create eigensolver context
*/
ierr = EPSCreate(PETSC_COMM_WORLD,&eps);CHKERRQ(ierr);
/*
Set operators. In this case, it is a standard eigenvalue problem
*/
ierr = EPSSetOperators(eps,A,NULL);CHKERRQ(ierr);
ierr = EPSSetProblemType(eps,EPS_NHEP);CHKERRQ(ierr);
/*
Ask for the rightmost eigenvalues
*/
ierr = EPSSetWhichEigenpairs(eps,EPS_LARGEST_REAL);CHKERRQ(ierr);
/*
Set other solver options at runtime
*/
ierr = EPSSetFromOptions(eps);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the eigensystem
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = EPSSolve(eps);CHKERRQ(ierr);
/*
Optional: Get some information from the solver and display it
*/
ierr = EPSGetType(eps,&type);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Solution method: %s\n\n",type);CHKERRQ(ierr);
ierr = EPSGetDimensions(eps,&nev,NULL,NULL);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of requested eigenvalues: %D\n",nev);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Display solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = EPSPrintSolution(eps,NULL);CHKERRQ(ierr);
ierr = EPSDestroy(&eps);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&ctx->T);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->x1);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->x2);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->y1);CHKERRQ(ierr);
ierr = VecDestroy(&ctx->y2);CHKERRQ(ierr);
ierr = PetscFree(ctx);CHKERRQ(ierr);
ierr = SlepcFinalize();
return 0;
}
int main(int argc,char **argv)
{
SNES snes; /* SNES context */
Vec x,r,F; /* vectors */
Mat J; /* Jacobian */
PetscErrorCode ierr;
PetscInt it,n = 11,i;
PetscReal h,xp = 0.0;
PetscScalar v;
const PetscScalar a = X0DOT;
const PetscScalar b = X1;
const PetscScalar k = KPOW;
PetscScalar v2;
PetscScalar *xx;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetBool(NULL,NULL,"-second_order",&second_order,NULL);CHKERRQ(ierr);
h = 1.0/(n-1);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create nonlinear solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create vector data structures; set function evaluation routine
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecCreate(PETSC_COMM_SELF,&x);CHKERRQ(ierr);
ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecDuplicate(x,&r);CHKERRQ(ierr);
ierr = VecDuplicate(x,&F);CHKERRQ(ierr);
ierr = SNESSetFunction(snes,r,FormFunction,(void*)F);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create matrix data structures; set Jacobian evaluation routine
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = MatCreateSeqAIJ(PETSC_COMM_SELF,n,n,3,NULL,&J);CHKERRQ(ierr);
/*
Note that in this case we create separate matrices for the Jacobian
and preconditioner matrix. Both of these are computed in the
routine FormJacobian()
*/
/* ierr = SNESSetJacobian(snes,NULL,JPrec,FormJacobian,0);CHKERRQ(ierr); */
ierr = SNESSetJacobian(snes,J,J,FormJacobian,0);CHKERRQ(ierr);
/* ierr = SNESSetJacobian(snes,J,JPrec,FormJacobian,0);CHKERRQ(ierr); */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Customize nonlinear solver; set runtime options
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize application:
Store right-hand-side of PDE and exact solution
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* set right hand side and initial guess to be exact solution of continuim problem */
#define SQR(x) ((x)*(x))
xp = 0.0;
for (i=0; i<n; i++)
{
v = k*(k-1.)*(b-a)*PetscPowScalar(xp,k-2.) + SQR(a*xp) + SQR(b-a)*PetscPowScalar(xp,2.*k) + 2.*a*(b-a)*PetscPowScalar(xp,k+1.);
ierr = VecSetValues(F,1,&i,&v,INSERT_VALUES);CHKERRQ(ierr);
v2 = a*xp + (b-a)*PetscPowScalar(xp,k);
ierr = VecSetValues(x,1,&i,&v2,INSERT_VALUES);CHKERRQ(ierr);
xp += h;
}
/* perturb initial guess */
ierr = VecGetArray(x,&xx);
for (i=0; i<n; i++) {
v2 = xx[i]*sperturb;
ierr = VecSetValues(x,1,&i,&v2,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecRestoreArray(x,&xx);CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,x);CHKERRQ(ierr);
ierr = SNESGetIterationNumber(snes,&it);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_SELF,"SNES iterations = %D\n\n",it);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = VecDestroy(&x);CHKERRQ(ierr); ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = VecDestroy(&F);CHKERRQ(ierr); ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Vec x,b,u;
Mat A; /* linear system matrix */
KSP ksp; /* linear solver context */
PetscRandom rctx; /* random number generator context */
PetscReal norm; /* norm of solution error */
PetscInt i,j,k,l,n = 27,its,bs = 2,Ii,J;
PetscErrorCode ierr;
PetscScalar v;
ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-bs",&bs,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetSizes(A,n*bs,n*bs,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
ierr = MatSetBlockSize(A,bs);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQBAIJ);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSetUp(A);CHKERRQ(ierr);
/*
Don't bother to preallocate matrix
*/
ierr = PetscRandomCreate(PETSC_COMM_SELF,&rctx);CHKERRQ(ierr);
for (i=0; i<n; i++) {
for (j=0; j<n; j++) {
ierr = PetscRandomGetValue(rctx,&v);CHKERRQ(ierr);
if (PetscRealPart(v) < .25 || i == j) {
for (k=0; k<bs; k++) {
for (l=0; l<bs; l++) {
ierr = PetscRandomGetValue(rctx,&v);CHKERRQ(ierr);
Ii = i*bs + k;
J = j*bs + l;
if (Ii == J) v += 10.;
ierr = MatSetValue(A,Ii,J,v,INSERT_VALUES);CHKERRQ(ierr);
}
}
}
}
}
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&u);CHKERRQ(ierr);
ierr = VecSetSizes(u,PETSC_DECIDE,n*bs);CHKERRQ(ierr);
ierr = VecSetFromOptions(u);CHKERRQ(ierr);
ierr = VecDuplicate(u,&b);CHKERRQ(ierr);
ierr = VecDuplicate(b,&x);CHKERRQ(ierr);
ierr = VecSet(u,1.0);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);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the linear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Check solution and clean up
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/*
Check the error
*/
ierr = VecAXPY(x,-1.0,u);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&norm);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
/*
Print convergence information. PetscPrintf() produces a single
print statement from all processes that share a communicator.
An alternative is PetscFPrintf(), which prints to a file.
*/
if (norm > .1) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of residual %g iterations %D bs %D\n",(double)norm,its,bs);CHKERRQ(ierr);
}
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);
/*
Always call PetscFinalize() before exiting a program. This routine
- finalizes the PETSc libraries as well as MPI
- provides summary and diagnostic information if certain runtime
options are chosen (e.g., -log_summary).
*/
ierr = PetscFinalize();
return ierr;
}
int main(int argc, char **argv)
{
MPI_Comm comm;
SNES snes; /* nonlinear solver */
Vec u,r,b; /* solution, residual, and rhs vectors */
Mat A,J; /* Jacobian matrix */
PetscInt problem = 1, N = 10;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, PETSC_NULL, help);CHKERRQ(ierr);
comm = PETSC_COMM_WORLD;
ierr = PetscOptionsGetInt(PETSC_NULL, "-problem", &problem, PETSC_NULL);CHKERRQ(ierr);
ierr = VecCreate(comm, &u);CHKERRQ(ierr);
ierr = VecSetSizes(u, PETSC_DETERMINE, N);CHKERRQ(ierr);
ierr = VecSetFromOptions(u);CHKERRQ(ierr);
ierr = VecDuplicate(u, &r);CHKERRQ(ierr);
ierr = VecDuplicate(u, &b);CHKERRQ(ierr);
ierr = MatCreate(comm, &A);CHKERRQ(ierr);
ierr = MatSetSizes(A, PETSC_DETERMINE, PETSC_DETERMINE, N, N);CHKERRQ(ierr);
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(A, 5, PETSC_NULL);CHKERRQ(ierr);
J = A;
switch(problem) {
case 1:
ierr = ConstructProblem1(A, b);CHKERRQ(ierr);
break;
case 2:
ierr = ConstructProblem2(A, b);CHKERRQ(ierr);
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid problem number %d", problem);
}
ierr = SNESCreate(PETSC_COMM_WORLD, &snes);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes, A, J, ComputeJacobianLinear, PETSC_NULL);CHKERRQ(ierr);
ierr = SNESSetFunction(snes, r, ComputeFunctionLinear, A);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = SNESSolve(snes, b, u);CHKERRQ(ierr);
ierr = VecView(u, PETSC_NULL);CHKERRQ(ierr);
switch(problem) {
case 1:
ierr = CheckProblem1(A, b, u);CHKERRQ(ierr);
break;
case 2:
ierr = CheckProblem2(A, b, u);CHKERRQ(ierr);
break;
default:
SETERRQ1(comm, PETSC_ERR_ARG_OUTOFRANGE, "Invalid problem number %d", problem);
}
if (A != J) {
ierr = MatDestroy(&A);CHKERRQ(ierr);
}
ierr = MatDestroy(&J);CHKERRQ(ierr);
ierr = VecDestroy(&u);CHKERRQ(ierr);
ierr = VecDestroy(&r);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = SNESDestroy(&snes);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}