/*
Setup for the custom preconditioner
*/
PetscErrorCode MyPCSetUp(PC pc)
{
AppCtx *app;
PetscErrorCode ierr;
DA da;
PetscFunctionBegin;
ierr = PCShellGetContext(pc,(void**)&app);
CHKERRQ(ierr);
/* create the linear solver for the Neutron diffusion */
ierr = DMMGCreate(app->comm,1,0,&app->fdmmg);
CHKERRQ(ierr);
ierr = DMMGSetOptionsPrefix(app->fdmmg,"phi_");
CHKERRQ(ierr);
ierr = DMMGSetUser(app->fdmmg,0,app);
CHKERRQ(ierr);
ierr = DACreate2d(app->comm,DA_NONPERIODIC,DA_STENCIL_STAR,app->nxv,app->nyvf,PETSC_DETERMINE,1,1,1,0,0,&da);
CHKERRQ(ierr);
ierr = DMMGSetDM(app->fdmmg,(DM)da);
CHKERRQ(ierr);
ierr = DMMGSetKSP(app->fdmmg,PETSC_NULL,MyFormMatrix);
CHKERRQ(ierr);
app->dx = DMMGGetRHS(app->fdmmg);
app->dy = DMMGGetx(app->fdmmg);
ierr = VecDuplicate(app->dy,&app->c);
CHKERRQ(ierr);
ierr = DADestroy(da);
CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscInt dof = 2,M = 3,N = 3,m = PETSC_DECIDE,n = PETSC_DECIDE;
PetscErrorCode ierr;
DA da;
Vec global,local;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(0,"-dof",&dof,0);CHKERRQ(ierr);
/* Create distributed array and get vectors */
ierr = DACreate2d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_BOX,
M,N,m,n,dof,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
ierr = DACreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DACreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = doit(da,global);CHKERRQ(ierr);
ierr = VecView(global,0);CHKERRQ(ierr);
/* Free memory */
ierr = VecDestroy(local);CHKERRQ(ierr);
ierr = VecDestroy(global);CHKERRQ(ierr);
ierr = DADestroy(da);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
void createMG(LocalData* data) {
assert(data != NULL);
int nlevels = 1;
PetscOptionsGetInt(PETSC_NULL, "-nlevels", &nlevels, PETSC_NULL);
int coarseSize = 1 + (((data->N) - 1)>>(nlevels - 1));
int rank;
MPI_Comm_rank((data->commAll), &rank);
if(!rank) {
std::cout<<"nlevels = "<<nlevels<<std::endl;
std::cout<<"coarseSize = "<<coarseSize<<std::endl;
}
DMMGCreate(PETSC_COMM_SELF, -nlevels, PETSC_NULL, &(data->mgObj));
DMMGSetOptionsPrefix(data->mgObj, "loc_");
DA da;
DACreate2d(PETSC_COMM_SELF, DA_NONPERIODIC, DA_STENCIL_BOX, coarseSize, coarseSize,
PETSC_DECIDE, PETSC_DECIDE, (data->dofsPerNode), 1, PETSC_NULL, PETSC_NULL, &da);
DMMGSetDM((data->mgObj), (DM)da);
DADestroy(da);
DMMGSetKSP((data->mgObj), PETSC_NULL, &computeMGmatrix);
PetscObjectIncrementTabLevel((PetscObject)(DMMGGetKSP(data->mgObj)), PETSC_NULL, 2);
}
int main( int argc, char **args)
{
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &args, (char *) 0, ""); CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "Start\n"); CHKERRQ(ierr);
DA da;
ierr = DACreate2d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_STAR,
64,64,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0, &da); CHKERRQ(ierr);
int rank;
MPI_Comm_rank(PETSC_COMM_WORLD, &rank);
printf("[%d] rank\n", rank);
Vec p;
ierr = DACreateGlobalVector(da,&p); CHKERRQ(ierr);
ierr = VecSet( p, 1.);
char file[256] = "vec";
sprintf( file, "vec-%d", rank);
PetscViewer view;
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_WRITE,&view
); CHKERRQ(ierr);
ierr = VecView(p, view); CHKERRQ(ierr);
ierr = PetscViewerDestroy(view); CHKERRQ(ierr);
ierr = VecDestroy( p );
ierr = DADestroy( da );
ierr = PetscPrintf(PETSC_COMM_WORLD, "End\n"); CHKERRQ(ierr);
ierr = PetscFinalize(); CHKERRQ(ierr);
}
int main(int argc,char **argv)
{
Vec u,xy;
DA da;
PetscErrorCode ierr;
PetscInt m = 10, n = 10, dof = 2;
PF pf;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = DACreate2d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_BOX,m,n,PETSC_DECIDE,PETSC_DECIDE,dof,1,0,0,&da);CHKERRQ(ierr);
ierr = DASetUniformCoordinates(da,0.0,1.0,0.0,1.0,0.0,1.0);CHKERRQ(ierr);
ierr = DACreateGlobalVector(da,&u);CHKERRQ(ierr);
ierr = DAGetCoordinates(da,&xy);CHKERRQ(ierr);
ierr = DACreatePF(da,&pf);CHKERRQ(ierr);
ierr = PFSet(pf,myfunction,0,0,0,0);CHKERRQ(ierr);
ierr = PFSetFromOptions(pf);CHKERRQ(ierr);
ierr = PFApplyVec(pf,xy,u);CHKERRQ(ierr);
ierr = VecView(u,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
/*
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
*/
ierr = VecDestroy(xy);CHKERRQ(ierr);
ierr = PFDestroy(pf);CHKERRQ(ierr);
ierr = DADestroy(da);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscViewer viewer;
DA da;
Vec global,local,global2;
PetscMPIInt rank;
PetscTruth flg;
/*
Every PETSc routine should begin with the PetscInitialize() routine.
argc, argv - These command line arguments are taken to extract the options
supplied to PETSc and options supplied to MPI.
help - When PETSc executable is invoked with the option -help,
it prints the various options that can be applied at
runtime. The user can use the "help" variable place
additional help messages in this printout.
*/
ierr = PetscInitialize(&argc,&argv,(char *)0,help);CHKERRQ(ierr);
/* Create a DA and an associated vector */
ierr = DACreate2d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_BOX,100,90,PETSC_DECIDE,PETSC_DECIDE,2,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
ierr = DACreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DACreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = VecSet(global,-1.0);CHKERRQ(ierr);
ierr = DAGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DAGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = VecScale(local,rank+1);CHKERRQ(ierr);
ierr = DALocalToGlobal(da,local,ADD_VALUES,global);CHKERRQ(ierr);
/*
Write output file with PetscViewerHDF5 viewer.
*/
ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD,"hdf5output",FILE_MODE_WRITE,&viewer); CHKERRQ(ierr);
ierr = VecView(global,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
ierr = VecDuplicate(global,&global2);CHKERRQ(ierr);
ierr = VecCopy(global,global2);CHKERRQ(ierr);
ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD,"hdf5output",FILE_MODE_READ,&viewer); CHKERRQ(ierr);
ierr = VecLoadIntoVector(viewer,global);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
ierr = VecEqual(global,global2,&flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Vectors are equal\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD,"Vectors are not equal\n");CHKERRQ(ierr);
}
/* clean up and exit */
ierr = DADestroy(da);CHKERRQ(ierr);
ierr = VecDestroy(local);CHKERRQ(ierr);
ierr = VecDestroy(global);CHKERRQ(ierr);
ierr = VecDestroy(global2);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
DMMG *dmmg; /* multilevel grid structure */
AppCtx user; /* user-defined work context */
PetscInt mx,my,its;
PetscErrorCode ierr;
MPI_Comm comm;
SNES snes;
DA da2;
PetscInitialize(&argc,&argv,(char *)0,help);
comm = PETSC_COMM_WORLD;
/* Problem parameters (velocity of lid, prandtl, and grashof numbers) */
ierr = PetscOptionsGetReal(PETSC_NULL,"-lidvelocity",&user.lidvelocity,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(PETSC_NULL,"-prandtl",&user.prandtl,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(PETSC_NULL,"-grashof",&user.grashof,PETSC_NULL);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create user context, set problem data, create vector data structures.
Also, compute the initial guess.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Setup Physics 2:
- Lap(T) + PR*Div([U*T,V*T]) = 0
where U and V are given by the given x.u and x.v
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DACreate2d(comm,DA_NONPERIODIC,DA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0,&da2);CHKERRQ(ierr);
ierr = DASetFieldName(da2,0,"temperature");CHKERRQ(ierr);
/* Create the solver object and attach the grid/physics info */
ierr = DMMGCreate(comm,1,&user,&dmmg);CHKERRQ(ierr);
ierr = DMMGSetDM(dmmg,(DM)da2);CHKERRQ(ierr);
ierr = DMMGSetISColoringType(dmmg,IS_COLORING_GLOBAL);CHKERRQ(ierr);
ierr = DMMGSetInitialGuess(dmmg,FormInitialGuess);CHKERRQ(ierr);
ierr = DMMGSetSNES(dmmg,FormFunction,0);CHKERRQ(ierr);
ierr = DMMGSetFromOptions(dmmg);CHKERRQ(ierr);
ierr = DAGetInfo(da2,PETSC_NULL,&mx,&my,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
user.lidvelocity = 1.0/(mx*my);
user.prandtl = 1.0;
user.grashof = 1.0;
/* Solve the nonlinear system */
ierr = DMMGSolve(dmmg);CHKERRQ(ierr);
snes = DMMGGetSNES(dmmg);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Physics 2: Number of Newton iterations = %D\n\n", its);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free spaces
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DADestroy(da2);CHKERRQ(ierr);
ierr = DMMGDestroy(dmmg);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
void PETSC_STDCALL dacreate2d_(MPI_Comm *comm,DAPeriodicType *wrap,DAStencilType
*stencil_type,PetscInt *M,PetscInt *N,PetscInt *m,PetscInt *n,PetscInt *w,
PetscInt *s,PetscInt *lx,PetscInt *ly,DA *inra,PetscErrorCode *ierr)
{
CHKFORTRANNULLINTEGER(lx);
CHKFORTRANNULLINTEGER(ly);
*ierr = DACreate2d(MPI_Comm_f2c(*(MPI_Fint *)&*comm),*wrap,*stencil_type,*M,*N,*m,*n,*w,*s,lx,ly,inra);
}
PetscErrorCode testCreate2D()
{
int ga;
DA da;
DALocalInfo info;
Vec vec;
PetscErrorCode ierr;
PetscFunctionBegin;
int d1 = 1453, d2 = 1451;
ierr = DACreate2d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_STAR,
d1,d2,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0, &da); CHKERRQ(ierr);
ierr = DAGetLocalInfo(da,&info); CHKERRQ(ierr);
ierr = DACreateGlobalArray( da, &ga, &vec); CHKERRQ(ierr);
PetscReal **v;
ierr = DAVecGetArray(da,vec,&v); CHKERRQ(ierr);
int xe = info.xs+info.xm,
ye = info.ys+info.ym;
for (int j = info.ys; j < ye; ++j) {
for (int i = info.xs; i < xe; ++i) {
v[j][i] = 1.*i + d1 * j;
}
}
ierr = DAVecRestoreArray(da,vec,&v); CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD,"Updated local portion with DAVec\n");
PetscBarrier(0);
{
double *da_ptr;
VecGetArray(vec, &da_ptr);
double *ptr;
int low[2],hi[2],ld;
NGA_Distribution(ga,GA_Nodeid(),low,hi);
NGA_Access(ga,low,hi,&ptr,&ld);
printf("[%d] ga:%p\tda:%p\tdiff:%p\n", GA_Nodeid(), ptr, da_ptr, (ptr-da_ptr) );
NGA_Release_update(ga,low,hi);
}
int lo[2],ld;
double val;
for (int j = 0; j < d2; ++j) {
for (int i = 0; i < d1; ++i) {
lo[0] = j;
lo[1] = i;
NGA_Get(ga,lo,lo,&val,&ld);
if( PetscAbs( i + d1*j - val) > .1 )
printf(".");
// printf("[%d] (%3.0f,%3.0f)\n", GA_Nodeid(), 1.*i + d1*j, val);
}
}
GA_Print_stats();
ierr = VecDestroy(vec); CHKERRQ(ierr);
GA_Destroy(ga);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
DMMG *dmmg; /* multilevel grid structure */
PetscErrorCode ierr;
DA da;
AppCtx app;
PC pc;
KSP ksp;
PetscTruth isshell;
PetscViewer v1;
PetscInitialize(&argc,&argv,(char *)0,help);
PreLoadBegin(PETSC_TRUE,"SetUp");
app.comm = PETSC_COMM_WORLD;
app.nxv = 6;
app.nyvf = 3;
app.nyv = app.nyvf + 2;
ierr = PetscOptionsBegin(app.comm,PETSC_NULL,"Options for Grid Sizes",PETSC_NULL);
ierr = PetscOptionsInt("-nxv","Grid spacing in X direction",PETSC_NULL,app.nxv,&app.nxv,PETSC_NULL);
CHKERRQ(ierr);
ierr = PetscOptionsInt("-nyvf","Grid spacing in Y direction of Fuel",PETSC_NULL,app.nyvf,&app.nyvf,PETSC_NULL);
CHKERRQ(ierr);
ierr = PetscOptionsInt("-nyv","Total Grid spacing in Y direction of",PETSC_NULL,app.nyv,&app.nyv,PETSC_NULL);
CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = PetscViewerDrawOpen(app.comm,PETSC_NULL,"",-1,-1,-1,-1,&v1);
CHKERRQ(ierr);
/*
Create the DMComposite object to manage the three grids/physics.
We use a 1d decomposition along the y direction (since one of the grids is 1d).
*/
ierr = DMCompositeCreate(app.comm,&app.pack);
CHKERRQ(ierr);
/* 6 fluid unknowns, 3 ghost points on each end for either periodicity or simply boundary conditions */
ierr = DACreate1d(app.comm,DA_XPERIODIC,app.nxv,6,3,0,&da);
CHKERRQ(ierr);
ierr = DASetFieldName(da,0,"prss");
CHKERRQ(ierr);
ierr = DASetFieldName(da,1,"ergg");
CHKERRQ(ierr);
ierr = DASetFieldName(da,2,"ergf");
CHKERRQ(ierr);
ierr = DASetFieldName(da,3,"alfg");
CHKERRQ(ierr);
ierr = DASetFieldName(da,4,"velg");
CHKERRQ(ierr);
ierr = DASetFieldName(da,5,"velf");
CHKERRQ(ierr);
ierr = DMCompositeAddDM(app.pack,(DM)da);
CHKERRQ(ierr);
ierr = DADestroy(da);
CHKERRQ(ierr);
ierr = DACreate2d(app.comm,DA_YPERIODIC,DA_STENCIL_STAR,app.nxv,app.nyv,PETSC_DETERMINE,1,1,1,0,0,&da);
CHKERRQ(ierr);
ierr = DASetFieldName(da,0,"Tempature");
CHKERRQ(ierr);
ierr = DMCompositeAddDM(app.pack,(DM)da);
CHKERRQ(ierr);
ierr = DADestroy(da);
CHKERRQ(ierr);
ierr = DACreate2d(app.comm,DA_XYPERIODIC,DA_STENCIL_STAR,app.nxv,app.nyvf,PETSC_DETERMINE,1,2,1,0,0,&da);
CHKERRQ(ierr);
ierr = DASetFieldName(da,0,"Phi");
CHKERRQ(ierr);
ierr = DASetFieldName(da,1,"Pre");
CHKERRQ(ierr);
ierr = DMCompositeAddDM(app.pack,(DM)da);
CHKERRQ(ierr);
ierr = DADestroy(da);
CHKERRQ(ierr);
app.pri = 1.0135e+5;
app.ugi = 2.5065e+6;
app.ufi = 4.1894e+5;
app.agi = 1.00e-1;
app.vgi = 1.0e-1 ;
app.vfi = 1.0e-1;
app.prin = 1.0135e+5;
app.ugin = 2.5065e+6;
app.ufin = 4.1894e+5;
app.agin = 1.00e-1;
app.vgin = 1.0e-1 ;
app.vfin = 1.0e-1;
app.prout = 1.0135e+5;
app.ugout = 2.5065e+6;
app.ufout = 4.1894e+5;
app.agout = 3.0e-1;
app.twi = 373.15e+0;
app.phii = 1.0e+0;
app.prei = 1.0e-5;
/*
Create the solver object and attach the grid/physics info
*/
ierr = DMMGCreate(app.comm,1,0,&dmmg);
CHKERRQ(ierr);
ierr = DMMGSetDM(dmmg,(DM)app.pack);
CHKERRQ(ierr);
ierr = DMMGSetUser(dmmg,0,&app);
CHKERRQ(ierr);
ierr = DMMGSetISColoringType(dmmg,IS_COLORING_GLOBAL);
CHKERRQ(ierr);
CHKMEMQ;
ierr = DMMGSetInitialGuess(dmmg,FormInitialGuess);
CHKERRQ(ierr);
ierr = DMMGSetSNES(dmmg,FormFunction,0);
CHKERRQ(ierr);
ierr = DMMGSetFromOptions(dmmg);
CHKERRQ(ierr);
/* Supply custom shell preconditioner if requested */
ierr = SNESGetKSP(DMMGGetSNES(dmmg),&ksp);
CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);
CHKERRQ(ierr);
ierr = PetscTypeCompare((PetscObject)pc,PCSHELL,&isshell);
CHKERRQ(ierr);
if (isshell) {
ierr = PCShellSetContext(pc,&app);
CHKERRQ(ierr);
ierr = PCShellSetSetUp(pc,MyPCSetUp);
CHKERRQ(ierr);
ierr = PCShellSetApply(pc,MyPCApply);
CHKERRQ(ierr);
ierr = PCShellSetDestroy(pc,MyPCDestroy);
CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve the nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
PreLoadStage("Solve");
ierr = DMMGSolve(dmmg);
CHKERRQ(ierr);
ierr = VecView(DMMGGetx(dmmg),v1);
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space. All PETSc objects should be destroyed when they
are no longer needed.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscViewerDestroy(v1);
CHKERRQ(ierr);
ierr = DMCompositeDestroy(app.pack);
CHKERRQ(ierr);
ierr = DMMGDestroy(dmmg);
CHKERRQ(ierr);
PreLoadEnd();
ierr = PetscFinalize();
CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
PetscInt rank,size,npt;
PetscScalar dx,dy,cx,cy;
PetscErrorCode ierr;
Vec x,x0,tempvec, *vinda,*vindb,*vindc;
PetscInt i,j,k,n,n2,pmax,puse,Istart,Iend,localsize,niter;
PetscScalar **x0array, **aarray,**barray;
PetscInt *cacheInt;
PetscScalar *cacheScalar;
DA myDA;
PetscScalar *Mixnorm;
PetscInt iter,*iterind,*nind;
FILE *fidoutput, *fidtimelog;
char fname[50],ftimelog[50];
PetscViewer socketviewer;
PetscInt withMatlab, doFFT, doSmoothing;
PetscTruth Matlabflag, FFTflag, Smoothingflag;
PetscInt timelogcount;
MPI_Status status;
PetscLogDouble v1,v2,elapsed_time;
timelogcount = 0;
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);
ierr = PetscOptionsGetInt(PETSC_NULL,"-withMatlab",&withMatlab,&Matlabflag);CHKERRQ(ierr);
if (Matlabflag == PETSC_FALSE){withMatlab = 0;}else{withMatlab = 1;}
ierr = PetscOptionsGetInt(PETSC_NULL,"-doFFT",&doFFT,&FFTflag);CHKERRQ(ierr);
if (FFTflag == PETSC_FALSE){doFFT = 0;}else{doFFT = 1;}
ierr = PetscOptionsGetInt(PETSC_NULL,"-doSmoothing",&doSmoothing,&Smoothingflag);CHKERRQ(ierr);
if (Smoothingflag == PETSC_FALSE){doSmoothing = 0;}else{doSmoothing = 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 n from Matlab
IntReceive(socketviewer, &nind);
n = *nind;
// Receive iter from Matlab
IntReceive(socketviewer, &iterind);
iter = *iterind;
}else{
ierr = PetscOptionsGetInt(PETSC_NULL,"-ngrid",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-niter",&iter,PETSC_NULL);CHKERRQ(ierr);
}
/////////////////////////////////////////////////////////////////////////////////////
ierr = PetscPrintf(PETSC_COMM_WORLD,"PETSC: number of grid is %d \n", n);
ierr = PetscPrintf(PETSC_COMM_WORLD,"PETSC: number of iteration is %d \n", iter);
Mixnorm = malloc(iter*sizeof(PetscScalar));
dx = 1.0/n;
dy = 1.0/n;
n2 = (PetscInt)(n*0.5);
npt = 5;
pmax = 5e5;
puse = pmax;
PetscInt logmax = 1000;
PetscScalar Timelog[logmax];
PetscLogDouble t1,t2;
ierr = PetscPrintf(PETSC_COMM_WORLD,"PETSC: estimated buffer size (per processer) %f Mbytes \n", pmax*1.0/1e6*8*17 );
ierr = PetscPrintf(PETSC_COMM_WORLD,"PETSC: estimated variable size %f Mbytes\n", 1.0*n*n/1e6*8*1);
/////////////////////////////////////////////////////////////////////////////////////
// ierr = VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE ,n,&tempvec);CHKERRQ(ierr);
// ierr = VecGetOwnershipRange(tempvec,&Istart,&Iend);CHKERRQ(ierr);
// localsize = Iend-Istart;
// ierr = VecDestroy(tempvec);CHKERRQ(ierr);
/////////////////////////////////////////////////////////////////////////////////////
if(doSmoothing==1){
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n\n\n\n\nPETSC: Now Do DACreate2d \n\n\n\n" );
ierr = PetscPrintf(PETSC_COMM_WORLD,"\n\n\n\n\nPETSC: %d %d %d\n\n\n\n",n2,n,size);
DACreate2d(MPI_COMM_WORLD,DA_XYPERIODIC,DA_STENCIL_BOX,n2,n,1,size,1,2,PETSC_NULL,PETSC_NULL,&myDA);
DACreateGlobalVector(myDA,&x0);
DAGetCorners(myDA,PETSC_NULL,&Istart,PETSC_NULL,PETSC_NULL,&localsize,PETSC_NULL);
Iend = Istart+localsize;
}else{
ierr = VecCreateMPI(PETSC_COMM_WORLD,PETSC_DECIDE ,n,&tempvec);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(tempvec,&Istart,&Iend);CHKERRQ(ierr);
localsize = Iend-Istart;
ierr = VecDestroy(tempvec);CHKERRQ(ierr);
VecCreateMPI(PETSC_COMM_WORLD,localsize*n2,PETSC_DETERMINE ,&x0);
}
//ierr = PetscPrintf(PETSC_COMM_WORLD,"\n\n\n\n\nPETSC: So far so good\n\n\n\n");
VecGetArray2d(x0,n2,localsize,0,0,&x0array);
// Create initial vector
for(j=0;j<localsize;j++){
for(i=0;i<n2;i++){
cx = (Istart+j+0.5)*dx;
x0array[i][j] = cos(2*M_PI*cx);
}
}
VecRestoreArray2d(x0,n2,localsize,0,0,&x0array);
ierr = VecDuplicate(x0,&x);CHKERRQ(ierr);
ierr = VecNorm(x0,NORM_2,Mixnorm); CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD,"PETSC: initial norm= %f \n",*(Mixnorm+0)/n );
vinda = &x0;
vindb = &x;
sprintf(fname, "mixnorm_%d_%d",n,iter);
ierr =PetscPrintf(PETSC_COMM_WORLD,"\n iter norm time unit time\n");CHKERRQ(ierr);
ierr =PetscFOpen(PETSC_COMM_WORLD,fname,"w",&fidoutput);CHKERRQ(ierr);
///////////////////////////////////////////////////////////////////////////////////////////////////
// Memory allocation for the iteration scheme
// cacheInt = malloc(1*pmax*sizeof(PetscInt));
// cacheScalar = malloc(2*pmax*sizeof(PetscScalar));
cacheInt = malloc(2*pmax*sizeof(PetscInt));
cacheScalar = malloc(2*pmax*sizeof(PetscScalar));
///////////////////////////////////////////////////////////////////////////////////////////////////
// Iteration here!
for(niter=0;niter<iter;niter++){
ierr = PetscGetTime(&v1);CHKERRQ(ierr);
// BackwardAverage(vinda, vindb, cacheInt, cacheScalar, n, npt, pmax, Istart,Iend);
// BackwardAverageR(vinda, vindb, cacheInt, cacheScalar, n, npt, pmax, Istart,Iend);
BackwardAverageRL(vinda, vindb, cacheInt, cacheScalar, n, npt, pmax, Istart,Iend);
vindc = vindb;
vindb = vinda;
vinda = vindc;
// if(doSmoothing==1){Smoothing(vinda, vindb,n, myDA, Istart,Iend);}
ierr = PetscGetTime(&v2);CHKERRQ(ierr);
//vindc = vindb;
//vindb = vinda;
//vinda = vindc;
ierr = VecNorm(*vinda,NORM_2,Mixnorm+niter); CHKERRQ(ierr);
*(Mixnorm+niter) = *(Mixnorm+niter)/n;
elapsed_time = v2 - v1;
PetscPrintf(PETSC_COMM_WORLD," %d %f %f %f \n",niter,*(Mixnorm+niter),elapsed_time,elapsed_time/n/n*1e6 );
PetscFPrintf(PETSC_COMM_WORLD,fidoutput," %d %f %f %f\n"
,niter,*(Mixnorm+niter),elapsed_time,elapsed_time/n/n*1e6 );
}
////////////////////////////////////////////////////////////////////////////////////////////////////
//Change oremtation of vector
VecGetArray2d(*vinda,n2,localsize,0,0,&aarray);
VecGetArray2d(*vindb,localsize,n2,0,0,&barray);
for(j=0;j<localsize;j++){
for(i=0;i<n2;i++){
barray[j][i] = aarray[i][j];
}
}
VecRestoreArray2d(*vinda,n2,localsize,0,0,&aarray);
VecRestoreArray2d(*vindb,localsize,n2,0,0,&barray);
vindc = vindb;
vindb = vinda;
vinda = vindc;
////////////////////////////////////////////////////////////////////////////////////////////////////
// FFT part
if(doFFT==1){FFT2D(*vinda,*vindb, localsize, n, Istart,Iend, iter,doSmoothing);}
////////////////////////////////////////////////////////////////////////////////////////////////////
/*
if(rank==0){
sprintf(ftimelog, "timelog_%d_%d",n,iter);
fidtimelog = fopen(ftimelog,"w");
for(i=0;i<timelogcount;i++){ fprintf(fidtimelog,"%f ",Timelog[i]); }
fprintf(fidtimelog,"\n ");
for(j = 1;j<size;j++){
MPI_Recv(Timelog,timelogcount,MPI_DOUBLE,j,j,PETSC_COMM_WORLD,&status);
for(i=0;i<timelogcount;i++){ fprintf(fidtimelog,"%f ",Timelog[i]); }
fprintf(fidtimelog,"\n ");
}
fclose(fidtimelog);
}else{
MPI_Send(Timelog ,timelogcount,MPI_DOUBLE,0,rank,PETSC_COMM_WORLD);
}
PetscFClose(PETSC_COMM_WORLD,fidoutput);
*/
///////////////////////////////////////////////////////////////////////////
if(withMatlab==1){
VecView(*vinda,socketviewer);
PetscScalarView(iter,Mixnorm,socketviewer);
}
// free(x0array);
free(Mixnorm);
free(cacheInt);
free(cacheScalar);
ierr = VecDestroy(x0);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD,"Done!");
//////////////////////////////////////////////////////////////////////////////////////
ierr = PetscFinalize();CHKERRQ(ierr);
int main(int argc,char **argv)
{
DMMG *dmmg_comp; /* multilevel grid structure */
AppCtx user; /* user-defined work context */
PetscInt mx,my,its,max_its,i;
PetscErrorCode ierr;
MPI_Comm comm;
SNES snes;
DA da1,da2;
DMComposite pack;
DMMG *dmmg1,*dmmg2;
PetscTruth SolveSubPhysics=PETSC_FALSE,GaussSeidel=PETSC_TRUE,Jacobi=PETSC_FALSE;
Vec X1,X1_local,X2,X2_local;
PetscViewer viewer;
PetscInitialize(&argc,&argv,(char *)0,help);
comm = PETSC_COMM_WORLD;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create user context, set problem data, create vector data structures.
Also, compute the initial guess.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Setup Physics 1:
- Lap(U) - Grad_y(Omega) = 0
- Lap(V) + Grad_x(Omega) = 0
- Lap(Omega) + Div([U*Omega,V*Omega]) - GR*Grad_x(T) = 0
where T is given by the given x.temp
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DACreate2d(comm,DA_NONPERIODIC,DA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,3,1,0,0,&da1);CHKERRQ(ierr);
ierr = DASetFieldName(da1,0,"x-velocity");CHKERRQ(ierr);
ierr = DASetFieldName(da1,1,"y-velocity");CHKERRQ(ierr);
ierr = DASetFieldName(da1,2,"Omega");CHKERRQ(ierr);
/* Create the solver object and attach the grid/physics info */
ierr = DMMGCreate(comm,1,&user,&dmmg1);CHKERRQ(ierr);
ierr = DMMGSetDM(dmmg1,(DM)da1);CHKERRQ(ierr);
ierr = DMMGSetISColoringType(dmmg1,IS_COLORING_GLOBAL);CHKERRQ(ierr);
ierr = DMMGSetInitialGuess(dmmg1,FormInitialGuess1);CHKERRQ(ierr);
ierr = DMMGSetSNES(dmmg1,FormFunction1,0);CHKERRQ(ierr);
ierr = DMMGSetFromOptions(dmmg1);CHKERRQ(ierr);
/* Set problem parameters (velocity of lid, prandtl, and grashof numbers) */
ierr = DAGetInfo(da1,PETSC_NULL,&mx,&my,0,0,0,0,0,0,0,0);CHKERRQ(ierr);
user.lidvelocity = 1.0/(mx*my);
user.prandtl = 1.0;
user.grashof = 1000.0;
ierr = PetscOptionsGetReal(PETSC_NULL,"-lidvelocity",&user.lidvelocity,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(PETSC_NULL,"-prandtl",&user.prandtl,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetReal(PETSC_NULL,"-grashof",&user.grashof,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-solvesubphysics",&SolveSubPhysics);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-Jacobi",&Jacobi);CHKERRQ(ierr);
if (Jacobi) GaussSeidel=PETSC_FALSE;
ierr = PetscPrintf(comm,"grashof: %g, ",user.grashof);CHKERRQ(ierr);
if (GaussSeidel){
ierr = PetscPrintf(comm,"use Block Gauss-Seidel\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(comm,"use Block Jacobi\n");CHKERRQ(ierr);
}
ierr = PetscPrintf(comm,"===========================================\n");CHKERRQ(ierr);
/* Solve the nonlinear system 1 */
if (SolveSubPhysics){
ierr = DMMGSolve(dmmg1);CHKERRQ(ierr);
snes = DMMGGetSNES(dmmg1);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Physics 1: Number of Newton iterations = %D\n\n", its);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Setup Physics 2:
- Lap(T) + PR*Div([U*T,V*T]) = 0
where U and V are given by the given x.u and x.v
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DACreate2d(comm,DA_NONPERIODIC,DA_STENCIL_STAR,-4,-4,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0,&da2);CHKERRQ(ierr);
ierr = DASetFieldName(da2,0,"temperature");CHKERRQ(ierr);
/* Create the solver object and attach the grid/physics info */
ierr = DMMGCreate(comm,1,&user,&dmmg2);CHKERRQ(ierr);
ierr = DMMGSetDM(dmmg2,(DM)da2);CHKERRQ(ierr);
ierr = DMMGSetISColoringType(dmmg2,IS_COLORING_GLOBAL);CHKERRQ(ierr);
ierr = DMMGSetInitialGuess(dmmg2,FormInitialGuess2);CHKERRQ(ierr);
ierr = DMMGSetSNES(dmmg2,FormFunction2,0);CHKERRQ(ierr);
ierr = DMMGSetFromOptions(dmmg2);CHKERRQ(ierr);
/* Solve the nonlinear system 2 */
if (SolveSubPhysics){
ierr = DMMGSolve(dmmg2);CHKERRQ(ierr);
snes = DMMGGetSNES(dmmg2);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Physics 2: Number of Newton iterations = %D\n\n", its);CHKERRQ(ierr);
}
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Solve system 1 and 2 iteratively
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DACreateLocalVector(da1,&X1_local);CHKERRQ(ierr);
ierr = DACreateLocalVector(da2,&X2_local);CHKERRQ(ierr);
/* Only 1 snes iteration is allowed for each subphysics */
/*
snes = DMMGGetSNES(dmmg1);
ierr = SNESSetTolerances(snes,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1,PETSC_DEFAULT);CHKERRQ(ierr);
snes = DMMGGetSNES(dmmg2);
ierr = SNESSetTolerances(snes,PETSC_DEFAULT,PETSC_DEFAULT,PETSC_DEFAULT,1,PETSC_DEFAULT);CHKERRQ(ierr);
*/
max_its = 5;
ierr = PetscOptionsGetInt(PETSC_NULL,"-mp_max_it",&max_its,PETSC_NULL);CHKERRQ(ierr);
user.nsolve = 0;
for (i=0; i<max_its; i++){
ierr = PetscPrintf(comm,"\nIterative nsolve %D ...\n", user.nsolve);CHKERRQ(ierr);
if (!GaussSeidel){
/* get the ghosted X1_local for Physics 2 */
X1 = DMMGGetx(dmmg1); //Jacobian
if (i){ierr = DAVecRestoreArray(da1,X1_local,(Field1 **)&user.x1);CHKERRQ(ierr);}
ierr = DAGlobalToLocalBegin(da1,X1,INSERT_VALUES,X1_local);CHKERRQ(ierr);
ierr = DAGlobalToLocalEnd(da1,X1,INSERT_VALUES,X1_local);CHKERRQ(ierr);
ierr = DAVecGetArray(da1,X1_local,(Field1 **)&user.x1);CHKERRQ(ierr);
}
ierr = DMMGSolve(dmmg1);CHKERRQ(ierr);
snes = DMMGGetSNES(dmmg1);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
if (GaussSeidel){
/* get the ghosted X1_local for Physics 2 */
X1 = DMMGGetx(dmmg1);
if (i){ierr = DAVecRestoreArray(da1,X1_local,(Field1 **)&user.x1);CHKERRQ(ierr);}
ierr = DAGlobalToLocalBegin(da1,X1,INSERT_VALUES,X1_local);CHKERRQ(ierr);
ierr = DAGlobalToLocalEnd(da1,X1,INSERT_VALUES,X1_local);CHKERRQ(ierr);
ierr = DAVecGetArray(da1,X1_local,(Field1 **)&user.x1);CHKERRQ(ierr);
}
ierr = PetscPrintf(comm," Iterative physics 1: Number of Newton iterations = %D\n", its);CHKERRQ(ierr);
user.nsolve++;
ierr = DMMGSolve(dmmg2);CHKERRQ(ierr);
snes = DMMGGetSNES(dmmg2);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
/* get the ghosted X2_local for Physics 1 */
X2 = DMMGGetx(dmmg2);
if (i){ierr = DAVecRestoreArray(da2,X2_local,(Field2 **)&user.x2);CHKERRQ(ierr);}
ierr = DAGlobalToLocalBegin(da2,X2,INSERT_VALUES,X2_local);CHKERRQ(ierr);
ierr = DAGlobalToLocalEnd(da2,X2,INSERT_VALUES,X2_local);CHKERRQ(ierr);
ierr = DAVecGetArray(da2,X2_local,(Field2 **)&user.x2);CHKERRQ(ierr);
ierr = PetscPrintf(comm," Iterative physics 2: Number of Newton iterations = %D\n", its);CHKERRQ(ierr);
//user.nsolve++;
}
ierr = DAVecRestoreArray(da1,X1_local,(Field1 **)&user.x1);CHKERRQ(ierr);
ierr = DAVecRestoreArray(da2,X2_local,(Field2 **)&user.x2);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create the DMComposite object to manage the two grids/physics.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscPrintf(comm," \n\n DMComposite iteration......\n");CHKERRQ(ierr);
ierr = DMCompositeCreate(comm,&pack);CHKERRQ(ierr);
ierr = DMCompositeAddDM(pack,(DM)da1);CHKERRQ(ierr);
ierr = DMCompositeAddDM(pack,(DM)da2);CHKERRQ(ierr);
/* Create the solver object and attach the grid/physics info */
ierr = DMMGCreate(comm,1,&user,&dmmg_comp);CHKERRQ(ierr);
ierr = DMMGSetDM(dmmg_comp,(DM)pack);CHKERRQ(ierr);
ierr = DMMGSetISColoringType(dmmg_comp,IS_COLORING_GLOBAL);CHKERRQ(ierr);
ierr = DMMGSetInitialGuess(dmmg_comp,FormInitialGuessComp);CHKERRQ(ierr);
ierr = DMMGSetSNES(dmmg_comp,FormFunctionComp,0);CHKERRQ(ierr);
ierr = DMMGSetFromOptions(dmmg_comp);CHKERRQ(ierr);
/* Solve the nonlinear system */
/* ierr = DMMGSolve(dmmg_comp);CHKERRQ(ierr);
snes = DMMGGetSNES(dmmg_comp);
ierr = SNESGetIterationNumber(snes,&its);CHKERRQ(ierr);
ierr = PetscPrintf(comm,"Composite Physics: Number of Newton iterations = %D\n\n", its);CHKERRQ(ierr);*/
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free spaces
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMCompositeDestroy(pack);CHKERRQ(ierr);
ierr = DADestroy(da1);CHKERRQ(ierr);
ierr = DADestroy(da2);CHKERRQ(ierr);
ierr = DMMGDestroy(dmmg_comp);CHKERRQ(ierr);
ierr = PetscViewerASCIIOpen(comm,"log.py",&viewer);CHKERRQ(ierr);
/* -log_summary */
ierr = PetscLogPrintSummaryToPy(comm,viewer);CHKERRQ(ierr);
/* -snes_view */
//snes = DMMGGetSNES(dmmg1);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
ierr = DMMGDestroy(dmmg1);CHKERRQ(ierr);
ierr = DMMGDestroy(dmmg2);CHKERRQ(ierr);
ierr = VecDestroy(X1_local);CHKERRQ(ierr);
ierr = VecDestroy(X2_local);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
PetscMPIInt size,rank;
PetscInt M=8,dof=1,stencil_width=1,i,start,end,P=5,N = 6,m=PETSC_DECIDE,n=PETSC_DECIDE,p=PETSC_DECIDE,pt = 0,st = 0;
PetscErrorCode ierr;
PetscTruth flg2,flg3,flg;
DAPeriodicType periodic = DA_NONPERIODIC;
DAStencilType stencil_type = DA_STENCIL_STAR;
DA da;
SDA sda;
Vec local,global,local_copy;
PetscScalar value,*in,*out;
PetscReal norm,work;
PetscViewer viewer;
char filename[PETSC_MAX_PATH_LEN];
FILE *file;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-N",&N,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-P",&P,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-dof",&dof,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-stencil_width",&stencil_width,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-periodic",&pt,PETSC_NULL);CHKERRQ(ierr);
periodic = (DAPeriodicType) pt;
ierr = PetscOptionsGetInt(PETSC_NULL,"-stencil_type",&st,PETSC_NULL);CHKERRQ(ierr);
stencil_type = (DAStencilType) st;
ierr = PetscOptionsHasName(PETSC_NULL,"-1d",&flg2);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-2d",&flg2);CHKERRQ(ierr);
ierr = PetscOptionsHasName(PETSC_NULL,"-3d",&flg3);CHKERRQ(ierr);
if (flg2) {
ierr = DACreate2d(PETSC_COMM_WORLD,periodic,stencil_type,M,N,m,n,dof,stencil_width,0,0,&da);CHKERRQ(ierr);
ierr = SDACreate2d(PETSC_COMM_WORLD,periodic,stencil_type,M,N,m,n,dof,stencil_width,0,0,&sda);CHKERRQ(ierr);
} else if (flg3) {
ierr = DACreate3d(PETSC_COMM_WORLD,periodic,stencil_type,M,N,P,m,n,p,dof,stencil_width,0,0,0,&da);CHKERRQ(ierr);
ierr = SDACreate3d(PETSC_COMM_WORLD,periodic,stencil_type,M,N,P,m,n,p,dof,stencil_width,0,0,0,&sda);CHKERRQ(ierr);
}
else {
ierr = DACreate1d(PETSC_COMM_WORLD,periodic,M,dof,stencil_width,PETSC_NULL,&da);CHKERRQ(ierr);
ierr = SDACreate1d(PETSC_COMM_WORLD,periodic,M,dof,stencil_width,PETSC_NULL,&sda);CHKERRQ(ierr);
}
ierr = DACreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DACreateLocalVector(da,&local);CHKERRQ(ierr);
ierr = VecDuplicate(local,&local_copy);CHKERRQ(ierr);
/* zero out vectors so that ghostpoints are zero */
value = 0;
ierr = VecSet(local,value);CHKERRQ(ierr);
ierr = VecSet(local_copy,value);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(global,&start,&end);CHKERRQ(ierr);
for (i=start; i<end; i++) {
value = i + 1;
ierr = VecSetValues(global,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecAssemblyBegin(global);CHKERRQ(ierr);
ierr = VecAssemblyEnd(global);CHKERRQ(ierr);
ierr = DAGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DAGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
flg = PETSC_FALSE;
ierr = PetscOptionsGetTruth(PETSC_NULL,"-same_array",&flg,PETSC_NULL);CHKERRQ(ierr);
if (flg) {
/* test the case where the input and output array is the same */
ierr = VecCopy(local,local_copy);CHKERRQ(ierr);
ierr = VecGetArray(local_copy,&in);CHKERRQ(ierr);
ierr = VecRestoreArray(local_copy,PETSC_NULL);CHKERRQ(ierr);
ierr = SDALocalToLocalBegin(sda,in,INSERT_VALUES,in);CHKERRQ(ierr);
ierr = SDALocalToLocalEnd(sda,in,INSERT_VALUES,in);CHKERRQ(ierr);
} else {
ierr = VecGetArray(local,&out);CHKERRQ(ierr);
ierr = VecRestoreArray(local,PETSC_NULL);CHKERRQ(ierr);
ierr = VecGetArray(local_copy,&in);CHKERRQ(ierr);
ierr = VecRestoreArray(local_copy,PETSC_NULL);CHKERRQ(ierr);
ierr = SDALocalToLocalBegin(sda,out,INSERT_VALUES,in);CHKERRQ(ierr);
ierr = SDALocalToLocalEnd(sda,out,INSERT_VALUES,in);CHKERRQ(ierr);
}
flg = PETSC_FALSE;
ierr = PetscOptionsGetTruth(PETSC_NULL,"-save",&flg,PETSC_NULL);CHKERRQ(ierr);
if (flg) {
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
sprintf(filename,"local.%d",rank);
ierr = PetscViewerASCIIOpen(PETSC_COMM_SELF,filename,&viewer);CHKERRQ(ierr);
ierr = PetscViewerASCIIGetPointer(viewer,&file);CHKERRQ(ierr);
ierr = VecView(local,viewer);CHKERRQ(ierr);
fprintf(file,"Vector with correct ghost points\n");
ierr = VecView(local_copy,viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
}
ierr = VecAXPY(local_copy,-1.0,local);CHKERRQ(ierr);
ierr = VecNorm(local_copy,NORM_MAX,&work);CHKERRQ(ierr);
ierr = MPI_Allreduce(&work,&norm,1,MPIU_REAL,MPI_MAX,PETSC_COMM_WORLD);CHKERRQ(ierr);
if (norm != 0.0) {
ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Norm of difference %G should be zero\n",norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," Number of processors %d\n",size);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," M,N,P,dof %D %D %D %D\n",M,N,P,dof);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," stencil_width %D stencil_type %d periodic %d\n",stencil_width,(int)stencil_type,(int)periodic);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD," dimension %d\n",1 + (int) flg2 + (int) flg3);CHKERRQ(ierr);
}
ierr = DADestroy(da);CHKERRQ(ierr);
ierr = SDADestroy(sda);CHKERRQ(ierr);
ierr = VecDestroy(local_copy);CHKERRQ(ierr);
ierr = VecDestroy(local);CHKERRQ(ierr);
ierr = VecDestroy(global);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
/*-----------------------------------------------------------------------*/
{
DMMG *dmmg; /* multilevel grid structure */
AppCtx *user; /* user-defined work context */
Parameter *param;
GridInfo grid;
int ierr,result;
MPI_Comm comm;
DA da;
PetscInitialize(&argc,&argv,(char *)0,help);
comm = PETSC_COMM_WORLD;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Set up the problem parameters.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = PetscMalloc(sizeof(AppCtx),&user);
CHKERRQ(ierr);
ierr = PetscBagCreate(comm,sizeof(Parameter),&(user->bag));
CHKERRQ(ierr);
user->grid = &grid;
ierr = SetParams(user);
CHKERRQ(ierr);
ierr = ReportParams(user);
CHKERRQ(ierr);
ierr = PetscBagGetData(user->bag,(void**)¶m);
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create distributed array multigrid object (DMMG) to manage parallel grid and vectors
for principal unknowns (x) and governing residuals (f)
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DMMGCreate(comm,grid.mglevels,user,&dmmg);
CHKERRQ(ierr);
ierr = DACreate2d(comm,grid.periodic,grid.stencil,grid.ni,grid.nj,PETSC_DECIDE,PETSC_DECIDE,grid.dof,grid.stencil_width,0,0,&da);
CHKERRQ(ierr);
ierr = DMMGSetDM(dmmg,(DM)da);
CHKERRQ(ierr);
ierr = DADestroy(da);
CHKERRQ(ierr);
ierr = DAGetInfo(da,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,&(param->pi),&(param->pj),PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL,PETSC_NULL);
CHKERRQ(ierr);
REG_INTG(user->bag,¶m->pi,param->pi ,"procs_x","<DO NOT SET> Processors in the x-direction");
REG_INTG(user->bag,¶m->pj,param->pj ,"procs_y","<DO NOT SET> Processors in the y-direction");
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create user context, set problem data, create vector data structures.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DAGetGlobalVector(da, &(user->Xold));
CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Initialize and solve the nonlinear system
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = Initialize(dmmg);
CHKERRQ(ierr);
ierr = DoSolve(dmmg);
CHKERRQ(ierr);
if (param->verify) result = param->verify_result;
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Free work space.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = DARestoreGlobalVector(da, &(user->Xold));
CHKERRQ(ierr);
ierr = PetscBagDestroy(user->bag);
CHKERRQ(ierr);
ierr = PetscFree(user);
CHKERRQ(ierr);
ierr = DMMGDestroy(dmmg);
CHKERRQ(ierr);
ierr = PetscFinalize();
CHKERRQ(ierr);
return result;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt its,n,Nx=PETSC_DECIDE,Ny=PETSC_DECIDE,nlocal,i;
PetscMPIInt size;
PC pc;
PetscInt mx,my;
Mat A;
GridCtx fine_ctx;
KSP ksp;
PetscTruth flg;
PetscInitialize(&argc,&argv,PETSC_NULL,help);
/* set up discretization matrix for fine grid */
/* ML requires input of fine-grid matrix. It determines nlevels. */
fine_ctx.mx = 9; fine_ctx.my = 9;
ierr = PetscOptionsGetInt(PETSC_NULL,"-mx",&mx,&flg);CHKERRQ(ierr);
if (flg) fine_ctx.mx = mx;
ierr = PetscOptionsGetInt(PETSC_NULL,"-my",&my,&flg);CHKERRQ(ierr);
if (flg) fine_ctx.my = my;
ierr = PetscPrintf(PETSC_COMM_WORLD,"Fine grid size %D by %D\n",fine_ctx.mx,fine_ctx.my);CHKERRQ(ierr);
n = fine_ctx.mx*fine_ctx.my;
MPI_Comm_size(PETSC_COMM_WORLD,&size);
ierr = PetscOptionsGetInt(PETSC_NULL,"-Nx",&Nx,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-Ny",&Ny,PETSC_NULL);CHKERRQ(ierr);
ierr = DACreate2d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_STAR,fine_ctx.mx,
fine_ctx.my,Nx,Ny,1,1,PETSC_NULL,PETSC_NULL,&fine_ctx.da);CHKERRQ(ierr);
ierr = DACreateGlobalVector(fine_ctx.da,&fine_ctx.x);CHKERRQ(ierr);
ierr = VecDuplicate(fine_ctx.x,&fine_ctx.b);CHKERRQ(ierr);
ierr = VecGetLocalSize(fine_ctx.x,&nlocal);CHKERRQ(ierr);
ierr = DACreateLocalVector(fine_ctx.da,&fine_ctx.localX);CHKERRQ(ierr);
ierr = VecDuplicate(fine_ctx.localX,&fine_ctx.localF);CHKERRQ(ierr);
ierr = MatCreateMPIAIJ(PETSC_COMM_WORLD,nlocal,nlocal,n,n,5,PETSC_NULL,3,PETSC_NULL,&A);CHKERRQ(ierr);
ierr = FormJacobian_Grid(&fine_ctx,&A);CHKERRQ(ierr);
/* create linear solver */
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPGetPC(ksp,&pc);CHKERRQ(ierr);
ierr = PCSetType(pc,PCML);CHKERRQ(ierr);
/* set options, then solve system */
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr); /* calls PCSetFromOptions_MG/ML */
for (i=0; i<3; i++){
if (i<2){ /* test DIFFERENT_NONZERO_PATTERN */
/* set values for rhs vector */
ierr = VecSet(fine_ctx.b,i+1.0);CHKERRQ(ierr);
/* modify A */
ierr = MatShift(A,1.0);CHKERRQ(ierr);
ierr = MatScale(A,2.0);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
} else { /* test SAME_NONZERO_PATTERN */
ierr = KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
}
ierr = KSPSolve(ksp,fine_ctx.b,fine_ctx.x);CHKERRQ(ierr);
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Number of iterations = %D\n",its);CHKERRQ(ierr);
}
/* free data structures */
ierr = VecDestroy(fine_ctx.x);CHKERRQ(ierr);
ierr = VecDestroy(fine_ctx.b);CHKERRQ(ierr);
ierr = DADestroy(fine_ctx.da);CHKERRQ(ierr);
ierr = VecDestroy(fine_ctx.localX);CHKERRQ(ierr);
ierr = VecDestroy(fine_ctx.localF);CHKERRQ(ierr);
ierr = MatDestroy(A);CHKERRQ(ierr);
ierr = KSPDestroy(ksp);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
PetscMPIInt rank;
PetscInt M = -10,N = -8;
PetscErrorCode ierr;
PetscTruth flg = PETSC_FALSE;
DA da;
PetscViewer viewer;
Vec local,global;
PetscScalar value;
DAPeriodicType ptype = DA_NONPERIODIC;
DAStencilType stype = DA_STENCIL_BOX;
#if defined(PETSC_HAVE_MATLAB_ENGINE)
PetscViewer mviewer;
#endif
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",300,0,300,300,&viewer);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MATLAB_ENGINE)
ierr = PetscViewerMatlabOpen(PETSC_COMM_WORLD,"tmp.mat",FILE_MODE_WRITE,&mviewer);CHKERRQ(ierr);
#endif
ierr = PetscOptionsGetTruth(PETSC_NULL,"-star_stencil",&flg,PETSC_NULL);CHKERRQ(ierr);
if (flg) stype = DA_STENCIL_STAR;
/* Create distributed array and get vectors */
ierr = DACreate2d(PETSC_COMM_WORLD,ptype,stype,M,N,PETSC_DECIDE,PETSC_DECIDE,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
ierr = DACreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = DACreateLocalVector(da,&local);CHKERRQ(ierr);
value = -3.0;
ierr = VecSet(global,value);CHKERRQ(ierr);
ierr = DAGlobalToLocalBegin(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = DAGlobalToLocalEnd(da,global,INSERT_VALUES,local);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
value = rank+1;
ierr = VecScale(local,value);CHKERRQ(ierr);
ierr = DALocalToGlobal(da,local,ADD_VALUES,global);CHKERRQ(ierr);
flg = PETSC_FALSE;
ierr = PetscOptionsGetTruth(PETSC_NULL, "-view_global", &flg,PETSC_NULL);CHKERRQ(ierr);
if (flg) { /* view global vector in natural ordering */
ierr = VecView(global,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = DAView(da,viewer);CHKERRQ(ierr);
ierr = VecView(global,viewer);CHKERRQ(ierr);
#if defined(PETSC_HAVE_MATLAB_ENGINE)
ierr = DAView(da,mviewer);CHKERRQ(ierr);
ierr = VecView(global,mviewer);CHKERRQ(ierr);
#endif
/* Free memory */
#if defined(PETSC_HAVE_MATLAB_ENGINE)
ierr = PetscViewerDestroy(mviewer);CHKERRQ(ierr);
#endif
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
ierr = VecDestroy(local);CHKERRQ(ierr);
ierr = VecDestroy(global);CHKERRQ(ierr);
ierr = DADestroy(da);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **argv)
{
PetscInt i,j,M = 10,N = 8,m = PETSC_DECIDE,n = PETSC_DECIDE;
PetscMPIInt rank;
PetscErrorCode ierr;
PetscTruth flg = PETSC_FALSE;
DA da;
PetscViewer viewer;
Vec localall,global;
PetscScalar value,*vlocal;
DAPeriodicType ptype = DA_NONPERIODIC;
DAStencilType stype = DA_STENCIL_BOX;
VecScatter tolocalall,fromlocalall;
PetscInt start,end;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
ierr = PetscViewerDrawOpen(PETSC_COMM_WORLD,0,"",300,0,300,300,&viewer);CHKERRQ(ierr);
/* Read options */
ierr = PetscOptionsGetInt(PETSC_NULL,"-M",&M,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-N",&N,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetTruth(PETSC_NULL,"-star_stencil",&flg,PETSC_NULL);CHKERRQ(ierr);
if (flg) stype = DA_STENCIL_STAR;
/* Create distributed array and get vectors */
ierr = DACreate2d(PETSC_COMM_WORLD,ptype,stype,
M,N,m,n,1,1,PETSC_NULL,PETSC_NULL,&da);CHKERRQ(ierr);
ierr = DACreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = VecCreateSeq(PETSC_COMM_SELF,M*N,&localall);CHKERRQ(ierr);
ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);
ierr = VecGetOwnershipRange(global,&start,&end);CHKERRQ(ierr);
for (i=start; i<end; i++) {
value = 5.0*rank;
ierr = VecSetValues(global,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = VecView(global,viewer);CHKERRQ(ierr);
/*
Create Scatter from global DA parallel vector to local vector that
contains all entries
*/
ierr = DAGlobalToNaturalAllCreate(da,&tolocalall);CHKERRQ(ierr);
ierr = DANaturalAllToGlobalCreate(da,&fromlocalall);CHKERRQ(ierr);
ierr = VecScatterBegin(tolocalall,global,localall,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(tolocalall,global,localall,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecGetArray(localall,&vlocal);CHKERRQ(ierr);
for (j=0; j<N; j++) {
for (i=0; i<M; i++) {
*vlocal++ += i + j*M;
}
}
ierr = VecRestoreArray(localall,&vlocal);CHKERRQ(ierr);
/* scatter back to global vector */
ierr = VecScatterBegin(fromlocalall,localall,global,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecScatterEnd(fromlocalall,localall,global,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
ierr = VecView(global,viewer);CHKERRQ(ierr);
/* Free memory */
ierr = VecScatterDestroy(tolocalall);CHKERRQ(ierr);
ierr = VecScatterDestroy(fromlocalall);CHKERRQ(ierr);
ierr = PetscViewerDestroy(viewer);CHKERRQ(ierr);
ierr = VecDestroy(localall);CHKERRQ(ierr);
ierr = VecDestroy(global);CHKERRQ(ierr);
ierr = DADestroy(da);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
PetscErrorCode vizGA2DA()
{
PetscErrorCode ierr;
int rank;
MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
int d1 = 40, d2 = 50;
DA da;
Vec vec;
const PetscInt *lx, *ly, *lz;
PetscInt m,n,p;
DALocalInfo info;
ierr = DACreate2d(PETSC_COMM_WORLD,DA_NONPERIODIC,DA_STENCIL_STAR,
d1,d2,PETSC_DECIDE,PETSC_DECIDE,1,1,0,0, &da); CHKERRQ(ierr);
ierr = DACreateGlobalVector(da, &vec); CHKERRQ(ierr);
ierr = DAGetOwnershipRanges(da, &lx, &ly, &lz); CHKERRQ(ierr);
ierr = DAGetLocalInfo(da,&info); CHKERRQ(ierr);
ierr = DAGetInfo(da,0,0,0,0,&m,&n,&p,0,0,0,0); CHKERRQ(ierr);
/**/
ierr = DAView(da, PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);
for (int i = 0; i < m; ++i) {
PetscPrintf(PETSC_COMM_WORLD,"%d\tlx: %d\n",i,lx[i]);
}
for (int i = 0; i < n; ++i) {
PetscPrintf(PETSC_COMM_WORLD,"%d\tly: %d\n",i,ly[i]);
}
/**/
int ga = GA_Create_handle();
int ndim = 2;
int dims[2] = {d2,d1};
GA_Set_data(ga,2,dims,MT_DBL);
int *map;
PetscMalloc( sizeof(int)*(m+n), &map);
map[0] = 0;
for( int i = 1; i < n; i++ )
{
map[i] = ly[i-1] + map[i-1];
}
map[n] = 0;
for( int i = n+1; i < m+n; i++ )
{
map[i] = lx[i-n-1] + map[i-1];
}
/* correct ordering, but nodeid's dont line up with mpi rank for petsc's da
* DA: +---+---+ GA: +---+---+
* +-2-+-3-+ +-1-+-3-+
* +---+---+ +---+---+
* +-0-+-1-+ +-0-+-2-+
* +---+---+ +---+---+
int *map;
PetscMalloc( sizeof(int)*(m+n), &map);
map[0] = 0;
for( int i = 1; i < m; i++ )
{
map[i] = lx[i] + map[i-1];
}
map[m] = 0;
for( int i = m+1; i < m+n; i++ )
{
map[i] = ly[i-m] + map[i-1];
}
*/
int block[2] = {n,m};
GA_Set_irreg_distr(ga,map,block);
ierr = GA_Allocate( ga );
if( !ierr ) GA_Error("\n\n\nga allocaltion failed\n\n",ierr);
if( !ga ) GA_Error("\n\n\n ga null \n\n",ierr);
if( rank != GA_Nodeid() ) GA_Error("MPI rank does not match GA_Nodeid()",1);
GA_Print_distribution(ga);
int lo[2], hi[2];
NGA_Distribution(ga,rank,lo,hi);
if( lo[1] != info.xs || hi[1] != info.xs+info.xm-1 ||
lo[0] != info.ys || hi[0] != info.ys+info.ym-1 )
{
PetscSynchronizedPrintf(PETSC_COMM_SELF,"[%d] lo:(%2d,%2d) hi:(%2d,%2d) \t DA: (%2d,%2d), (%2d, %2d)\n",
rank, lo[1], lo[0], hi[1], hi[0], info.xs, info.ys, info.xs+info.xm-1, info.ys+info.ym-1);
}
PetscBarrier(0);
PetscSynchronizedFlush(PETSC_COMM_WORLD);
AO ao;
DAGetAO(da,&ao);
if( rank == 0 )
{
int *idx, len = d1*d2;
PetscReal *val;
PetscMalloc(sizeof(PetscReal)*len, &val);
PetscMalloc(sizeof(int)*len, &idx);
for (int j = 0; j < d2; ++j)
{
for (int i = 0; i < d1; ++i)
{
idx[i + d1*j] = i + d1*j;
val[i + d1*j] = i + d1*j;
}
}
AOApplicationToPetsc(ao,len,idx);
VecSetValues(vec,len,idx,val,INSERT_VALUES);
int a[2], b[2],ld[1]={0};
double c = 0;
for (int j = 0; j < d2; ++j)
{
for (int i = 0; i < d1; ++i)
{
a[0] = j;
a[1] = i;
// printf("%5.0f ",c);
NGA_Put(ga,a,a,&c,ld);
c++;
}
}
}
// GA_Print(ga);
VecAssemblyBegin(vec);
VecAssemblyEnd(vec);
int ld;
double *ptr;
NGA_Access(ga,lo,hi,&ptr,&ld);
PetscReal **d;
int c=0;
ierr = DAVecGetArray(da,vec,&d); CHKERRQ(ierr);
for (int j = info.ys; j < info.ys+info.ym; ++j)
{
for (int i = info.xs; i < info.xs+info.xm; ++i)
{
if( d[j][i] != ptr[(i-info.xs)+ld*(j-info.ys)] )
GA_Error("DA array is not equal to GA array",1);
// printf("%d (%d,%d):\t%3.0f\t%3.0f\n", c, i, j, d[j][i], ptr[(i-info.xs)+ld*(j-info.ys)]);
c++;
}
}
ierr = DAVecRestoreArray(da,vec,&d); CHKERRQ(ierr);
c=0;
PetscReal *v;
int start, end;
VecGetOwnershipRange(vec, &start, &end);
VecGetArray( vec, &v );
for( int i = start; i < end; i++)
{
// printf("%d:\t%3.0f\t%3.0f\t%s\n", start, v[i-start], ptr[i-start], (v[i-start]-ptr[i-start]==0?"":"NO") );
}
VecRestoreArray( vec, &v );
NGA_Release_update(ga,lo,hi);
Vec gada;
VecCreateMPIWithArray(((PetscObject)da)->comm,da->Nlocal,PETSC_DETERMINE,ptr,&gada);
VecView(gada,PETSC_VIEWER_STDOUT_SELF);
GA_Destroy(ga);
ierr = VecDestroy(vec); CHKERRQ(ierr);
ierr = DADestroy(da); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
PetscErrorCode ierr;
PetscInitialize(&argc,&args,(char *)0,help);
PetscInt m = 10; /* default number of rows and columns IN GRID,
but matrix is (m^2) x (m^2) */
ierr = PetscOptionsGetInt(PETSC_NULL,"-m",&m,PETSC_NULL);CHKERRQ(ierr);
MPI_Comm com = PETSC_COMM_WORLD;
PetscMPIInt rank, size;
ierr = MPI_Comm_rank(com, &rank); CHKERRQ(ierr);
ierr = MPI_Comm_size(com, &size); CHKERRQ(ierr);
/* create m x m two-dimensional grid for periodic boundary condition problem */
DA da2;
PetscInt dof=1, stencilwidth=1;
ierr = DACreate2d(com, DA_XYPERIODIC, DA_STENCIL_STAR,
m,m,PETSC_DECIDE,PETSC_DECIDE,
dof,stencilwidth,PETSC_NULL,PETSC_NULL,&da2); CHKERRQ(ierr);
/* get da2-managed Vecs */
Vec x,b,u;
ierr = DACreateGlobalVector(da2,&x); CHKERRQ(ierr);
ierr = VecDuplicate(x,&b); CHKERRQ(ierr);
ierr = VecDuplicate(x,&u); CHKERRQ(ierr);
Mat A;
ierr = DAGetMatrix(da2, MATMPIAIJ, &A); CHKERRQ(ierr);
/* alternative call below is not quite same as result from DAGetMatrix(),
because of nonzero allocation; the Mat ownership ranges are same */
/* ierr = MatCreateMPIAIJ(com, mlocal, mlocal, m*m, m*m,
5, PETSC_NULL, 4, PETSC_NULL,
&A); CHKERRQ(ierr) */
ierr = MatSetFromOptions(A);CHKERRQ(ierr);
/* report on ownership range */
PetscInt rstart,rend,mlocal;
ierr = VecGetOwnershipRange(x,&rstart,&rend);CHKERRQ(ierr);
ierr = VecGetLocalSize(x,&mlocal);CHKERRQ(ierr);
PetscInt A_rstart,A_rend;
ierr = MatGetOwnershipRange(A,&A_rstart,&A_rend);CHKERRQ(ierr);
if ((rstart != A_rstart) || (rend != A_rend)) {
ierr = PetscPrintf(com,
"Vec and Mat ownership ranges different!!! ending ...\n"); CHKERRQ(ierr);
PetscEnd();
} else {
ierr = PetscSynchronizedPrintf(com,
"rank=%d has Vec and Mat ownership: mlocal=%d, rstart=%d, rend=%d\n",
rank,mlocal,rstart,rend); CHKERRQ(ierr);
}
PetscSynchronizedFlush(com);
/* get local part of grid */
PetscInt xm,ym,xs,ys;
DAGetCorners(da2,&xs,&ys,0,&xm,&ym,0);
/* report on local part of grid */
ierr = PetscSynchronizedPrintf(com,
"rank=%d has da2-managed-Vec local ranges: xs=%d, xm=%d, ys=%d, ym=%d\n",
rank,xs,xm,ys,ym); CHKERRQ(ierr);
PetscSynchronizedFlush(com);
/* set up linear system */
PetscScalar **barr, **uarr; /* RHS and exact soln, resp. */
DAVecGetArray(da2, b, &barr);
DAVecGetArray(da2, u, &uarr);
PetscScalar dx = 1.0/(double)m, dy = dx, pi = 3.14159265358979;
PetscScalar xi,yj;
PetscInt diag=0,north=1,east=2,south=3,west=4;
PetscScalar vals[5] = {-4.0 + dx * dx, 1.0, 1.0, 1.0, 1.0};
MatStencil row, col[5]; /* these are not "stencils" at all, but local grid
to global indices helpers */
PetscInt i,j,num;
for (j=ys; j<ys+ym; j++) {
for(i=xs; i<xs+xm; i++) {
/* entries of matrix A */
row.i = i; row.j = j; row.c = 0; /* dof = 1 so first component;
note row.k is for 3d DAs */
for (num=0; num<5; num++) col[num].c = 0;
/* set diag first, then go through stencil neighbors */
col[diag].i = i; col[diag].j = j;
col[north].i = i; col[north].j = j+1;
col[east].i = i+1; col[east].j = j;
col[south].i = i; col[south].j = j-1;
col[west].i = i-1; col[west].j = j;
ierr = MatSetValuesStencil(A,1,&row,5,col,vals,INSERT_VALUES); CHKERRQ(ierr);
/* entries of vectors: exact solution u and right-hand-side b */
xi = (double)i * dx;
yj = (double)j * dy;
uarr[j][i] = sin(2.0 * pi * xi) * cos(4.0 * pi * yj);
barr[j][i] = (1.0 - 20.0 * pi * pi) * uarr[j][i];
barr[j][i] *= dx * dx;
}
}
DAVecRestoreArray(da2, b, &barr);
DAVecRestoreArray(da2, u, &uarr);
ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY); CHKERRQ(ierr);
ierr = VecAssemblyBegin(b); CHKERRQ(ierr);
ierr = VecAssemblyEnd(b); CHKERRQ(ierr);
ierr = VecAssemblyBegin(u); CHKERRQ(ierr);
ierr = VecAssemblyEnd(u); CHKERRQ(ierr);
/* uncomment for dense view; -mat_view default format is good enough for most purposes
PetscViewer viewer;
PetscViewerCreate(com, &viewer);
PetscViewerSetType(viewer, PETSC_VIEWER_ASCII);
PetscViewerSetFormat(viewer, PETSC_VIEWER_ASCII_DENSE);
MatView(A,viewer);
PetscViewerDestroy(viewer);
*/
/* setup solver context now that Mat and Vec are assembled */
KSP ksp;
ierr = KSPCreate(com,&ksp);CHKERRQ(ierr);
/* Set "operators". Here the matrix that defines the linear system
also serves as the preconditioning matrix. But we do not assert a
relationship between their nonzero patterns.(???) */
ierr = KSPSetOperators(ksp,A,A,DIFFERENT_NONZERO_PATTERN);CHKERRQ(ierr);
/* Following is optional; parameters could be set at runtime. */
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>
*/
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
/* Solve linear system */
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
/* Compute and report the error (and the iteration count and reason). */
PetscScalar norminf, normtwo, neg_one=-1.0;
PetscInt its;
KSPConvergedReason reason;
ierr = VecAXPY(x,neg_one,u);CHKERRQ(ierr); // x = x - u
ierr = VecNorm(x,NORM_INFINITY,&norminf);CHKERRQ(ierr);
ierr = VecNorm(x,NORM_2,&normtwo);CHKERRQ(ierr); // discrete norm
normtwo *= dx * dy; // integral norm
ierr = KSPGetIterationNumber(ksp,&its);CHKERRQ(ierr);
ierr = KSPGetConvergedReason(ksp,&reason); CHKERRQ(ierr);
ierr = PetscPrintf(com,
"Error norms ||err||_inf = %.3e, ||err||_2 = %.3e;\n"
"Iterations = %d; Reason = %d\n",
norminf, normtwo, its, (int) reason);CHKERRQ(ierr);
/* destroy */
ierr = KSPDestroy(ksp);CHKERRQ(ierr);
ierr = MatDestroy(A);CHKERRQ(ierr);
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = VecDestroy(u);CHKERRQ(ierr);
ierr = VecDestroy(b);CHKERRQ(ierr);
ierr = DADestroy(da2);CHKERRQ(ierr);
/* Always call PetscFinalize() before exiting a program. */
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
