PetscErrorCode TSTrajectoryGet_Basic(TSTrajectory tj,TS ts,PetscInt stepnum,PetscReal *t)
{
Vec Sol,*Y;
PetscInt Nr,i;
PetscViewer viewer;
PetscReal timepre;
char filename[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = TSGetTotalSteps(ts,&stepnum);CHKERRQ(ierr);
ierr = PetscSNPrintf(filename,sizeof filename,"SA-data/SA-%06d.bin",stepnum);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = TSGetSolution(ts,&Sol);CHKERRQ(ierr);
ierr = VecLoad(Sol,viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,t,1,NULL,PETSC_REAL);CHKERRQ(ierr);
if (stepnum != 0) {
ierr = TSGetStages(ts,&Nr,&Y);CHKERRQ(ierr);
for (i=0;i<Nr ;i++) {
ierr = VecLoad(Y[i],viewer);CHKERRQ(ierr);
}
ierr = PetscViewerBinaryRead(viewer,&timepre,1,NULL,PETSC_REAL);CHKERRQ(ierr);
ierr = TSSetTimeStep(ts,-(*t)+timepre);CHKERRQ(ierr);
}
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
PetscInt M = PETSC_DECIDE,N = PETSC_DECIDE;
DM da;
Vec global;
PetscViewer bviewer;
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = PetscOptionsGetInt(NULL,NULL,"-M",&M,NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL,"-N",&N,NULL);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"daoutput",FILE_MODE_READ,&bviewer);CHKERRQ(ierr);
ierr = DMCreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr);
ierr = DMLoad(da,bviewer);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&global);CHKERRQ(ierr);
ierr = VecLoad(global,bviewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&bviewer);CHKERRQ(ierr);
ierr = VecView(global,PETSC_VIEWER_DRAW_WORLD);CHKERRQ(ierr);
/* Free memory */
ierr = VecDestroy(&global);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
PetscErrorCode MyVecLoad(const char fname[],PetscBool skippheader,PetscBool usempiio,Vec x)
{
MPI_Comm comm;
PetscViewer viewer;
PetscBool ismpiio,isskip;
PetscErrorCode ierr;
PetscFunctionBeginUser;
ierr = PetscObjectGetComm((PetscObject)x,&comm);CHKERRQ(ierr);
ierr = PetscViewerCreate(comm,&viewer);CHKERRQ(ierr);
ierr = PetscViewerSetType(viewer,PETSCVIEWERBINARY);CHKERRQ(ierr);
if (skippheader) { ierr = PetscViewerBinarySetSkipHeader(viewer,PETSC_TRUE);CHKERRQ(ierr); }
ierr = PetscViewerFileSetMode(viewer,FILE_MODE_READ);CHKERRQ(ierr);
if (usempiio) { ierr = PetscViewerBinarySetUseMPIIO(viewer,PETSC_TRUE);CHKERRQ(ierr); }
ierr = PetscViewerFileSetName(viewer,fname);CHKERRQ(ierr);
ierr = VecLoad(x,viewer);CHKERRQ(ierr);
ierr = PetscViewerBinaryGetSkipHeader(viewer,&isskip);CHKERRQ(ierr);
if (isskip) { ierr = PetscPrintf(comm,"*** PetscViewer[load] skipping header ***\n");CHKERRQ(ierr); }
ierr = PetscViewerBinaryGetUseMPIIO(viewer,&ismpiio);CHKERRQ(ierr);
if (ismpiio) { ierr = PetscPrintf(comm,"*** PetscViewer[load] using MPI-IO ***\n");CHKERRQ(ierr); }
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Vec x; /* exact solution, RHS, temp */
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
char file2[PETSC_MAX_PATH_LEN]; /* input file name */
PetscErrorCode ierr,ierrp;
PetscInitialize(&argc,&args,(char *)0,help);
ierr = PetscPrintf(PETSC_COMM_WORLD,"initializing...\n");CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-f1",file,PETSC_MAX_PATH_LEN-1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-f2",file2,PETSC_MAX_PATH_LEN-1,PETSC_NULL);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierrp = VecLoad(fd,PETSC_NULL,&x);CHKERRQ(ierr);
ierr = PetscViewerDestroy(fd);CHKERRQ(ierr);
PetscScalar *a;
VecGetArray(x,&a);
PetscInt n;
VecGetSize(x,&n);
std::ofstream f(file2);
for (int i=0;i<n;i++)
f << a[i] << " ";
ierr = VecDestroy(x);CHKERRQ(ierr);
ierr = PetscFinalize();CHKERRQ(ierr);
return 0;
}
int main(int argc,char **args)
{
Mat A,B;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscErrorCode ierr;
PetscBool flg;
Vec v;
PetscInitialize(&argc,&args,(char *)0,help);
/*
Determine files from which we read the two linear systems
(matrix and right-hand-side vector).
*/
ierr = PetscOptionsGetString(PETSC_NULL,"-f0",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate binary file with the -f0 option");
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&v);CHKERRQ(ierr);
ierr = VecLoad(v,fd);CHKERRQ(ierr);
ierr = MatView(A,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PadMatrix(A,v,3.0,&B);CHKERRQ(ierr);
ierr = MatView(B,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = MatDestroy(&B);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
KSP ksp; /* linear solver context */
Mat A; /* matrix */
Vec x,b; /* approx solution, RHS, exact solution */
PetscViewer fd; /* viewer */
PetscErrorCode ierr;
PetscInitialize(&argc,&args,(char *)0,help);
fd = PETSC_VIEWER_SOCKET_WORLD;
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecLoad(b,fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecDuplicate(b,&x);CHKERRQ(ierr);
ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
ierr = KSPSetOperators(ksp,A,A,SAME_NONZERO_PATTERN);CHKERRQ(ierr);
ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
ierr = KSPSetUp(ksp);CHKERRQ(ierr);
ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);
ierr = VecView(x,fd);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = KSPDestroy(&ksp);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc, char **argv)
{
PetscErrorCode ierr;
Vec U,cv,eta;
DM da,da2;
PetscViewer viewer,view_vtk_cv,view_vtk_eta;
char filename[PETSC_MAX_PATH_LEN],cv_filename[PETSC_MAX_PATH_LEN],eta_filename[PETSC_MAX_PATH_LEN];
PetscBool flg,sflg = PETSC_FALSE;
PetscInt i,n=10000;
PetscInt seed;
PetscInitialize(&argc,&argv, (char*)0, help);
ierr = PetscOptionsSetValue("-viewer_binary_skip_info","true");CHKERRQ(ierr);
ierr = PetscOptionsGetString(PETSC_NULL,"-f",filename,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (!flg) {
ierr = PetscOptionsGetInt(PETSC_NULL,"-random_seed",&seed,&sflg);CHKERRQ(ierr);
if (!sflg) {
ierr = PetscStrcpy(filename,"ex61.data");CHKERRQ(ierr);
} else {
sprintf(filename,"ex61.data.%d",seed);
}
}
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer);CHKERRQ(ierr);
/* Get physics and time parameters */
ierr = DMCreate(PETSC_COMM_WORLD,&da);CHKERRQ(ierr);
ierr = DMLoad(da,viewer);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da,&U);CHKERRQ(ierr);
ierr = DMDAGetReducedDA(da,1,&da2);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da2,&cv);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(da2,&eta);CHKERRQ(ierr);
for (i=0; i<n; i++) {
/* when this fails it simply means the file is finished */
ierr = VecLoad(U,viewer);CHKERRQ(ierr);
ierr = VecStrideGather(U,1,cv,INSERT_VALUES);CHKERRQ(ierr);
ierr = VecStrideGather(U,4,eta,INSERT_VALUES);CHKERRQ(ierr);
sprintf(cv_filename,"%s_cv_%d.vtk",filename,i);
sprintf(eta_filename,"%s_eta_%d.vtk",filename,i);
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,cv_filename,&view_vtk_cv);CHKERRQ(ierr);
ierr = PetscViewerASCIIOpen(PETSC_COMM_WORLD,eta_filename,&view_vtk_eta);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(view_vtk_cv, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = PetscViewerSetFormat(view_vtk_eta, PETSC_VIEWER_ASCII_VTK);CHKERRQ(ierr);
ierr = DMView(da2,view_vtk_cv);CHKERRQ(ierr);
ierr = DMView(da2,view_vtk_eta);CHKERRQ(ierr);
ierr = VecView(cv,view_vtk_cv);CHKERRQ(ierr);
ierr = VecView(eta,view_vtk_eta);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view_vtk_cv);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&view_vtk_eta);CHKERRQ(ierr);
}
ierr = VecDestroy(&U);CHKERRQ(ierr);
ierr = VecDestroy(&cv);CHKERRQ(ierr);
ierr = VecDestroy(&eta);CHKERRQ(ierr);
ierr = DMDestroy(&da);CHKERRQ(ierr);
ierr = DMDestroy(&da2);CHKERRQ(ierr);
PetscFinalize();
return 0;
}
PetscErrorCode loadVec(const char *path, Vec* v, MPI_Comm comm, PetscViewer* fd){
PetscErrorCode err;
err = PetscViewerBinaryOpen(comm, path, FILE_MODE_READ, fd); CHKERRQ(err);
err = VecCreate(comm, v); CHKERRQ(err);
err = VecSetFromOptions(*v); CHKERRQ(err);
err = VecLoad(*v, *fd); CHKERRQ(err);
err = PetscViewerDestroy(fd); CHKERRQ(err);
return err;
}
static PetscErrorCode DMLoad_Shell(DM dm,PetscViewer v)
{
PetscErrorCode ierr;
DM_Shell *shell = (DM_Shell*)dm->data;
PetscFunctionBegin;
ierr = VecCreate(PetscObjectComm((PetscObject)dm),&shell->Xglobal);CHKERRQ(ierr);
ierr = VecLoad(shell->Xglobal,v);CHKERRQ(ierr);
PetscFunctionReturn(0);
}
int main(int argc,char **argv)
{
SNES snes; /* nonlinear solver context */
Vec r; /* solution, residual vectors */
PetscErrorCode ierr;
AppCtx user; /* user-defined work context */
PetscViewer viewer;
PetscInitialize(&argc,&argv,(char*)0,help);
ierr = PetscViewerBinaryOpen(PETSC_COMM_SELF,"videfinition",FILE_MODE_READ,&viewer);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_SELF,&user.M);CHKERRQ(ierr); ierr = MatLoad(user.M,viewer);CHKERRQ(ierr);
ierr = MatDuplicate(user.M,MAT_COPY_VALUES,&user.Jac);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&user.q);CHKERRQ(ierr); ierr = VecLoad(user.q,viewer);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&user.lb);CHKERRQ(ierr); ierr = VecLoad(user.lb,viewer);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&user.ub);CHKERRQ(ierr);ierr = VecLoad(user.ub,viewer);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_SELF,&user.zz);CHKERRQ(ierr);ierr = VecLoad(user.zz,viewer);CHKERRQ(ierr);
ierr = VecView(user.zz,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
/* ierr = VecSet(user.zz,0.01);CHKERRQ(ierr);*/
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecDuplicate(user.q,&r);CHKERRQ(ierr);
/* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Create nonlinear solver context
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */
ierr = SNESCreate(PETSC_COMM_WORLD,&snes);CHKERRQ(ierr);
ierr = SNESSetFunction(snes,r,FormFunction1,&user);CHKERRQ(ierr);
ierr = SNESSetJacobian(snes,user.Jac,user.Jac,FormJacobian1,&user);CHKERRQ(ierr);
ierr = SNESVISetVariableBounds(snes,user.lb,user.ub);CHKERRQ(ierr);
ierr = SNESSetFromOptions(snes);CHKERRQ(ierr);
ierr = SNESSolve(snes,NULL,user.zz);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)user.zz,"x*");CHKERRQ(ierr);
ierr = VecView(user.zz,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)r,"f(x*)");CHKERRQ(ierr);
ierr = FormFunction1(snes,user.zz,r,&user);CHKERRQ(ierr);
ierr = VecView(r,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode DataLoad(Vec x, char *filename)
{
PetscErrorCode ierr;
PetscViewer dataviewer;
PetscFunctionBegin;
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&dataviewer); CHKERRQ(ierr);
ierr = VecLoad(x,dataviewer); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&dataviewer); CHKERRQ(ierr);
PetscFunctionReturn(0);
}
void readVec(Vec_dh *bout, char *ft, char *fn, HYPRE_Int ignore)
{
START_FUNC_DH
*bout = NULL;
if (fn == NULL) {
SET_V_ERROR("passed NULL filename; can't open for reading!");
}
if (!strcmp(ft, "csr") || !strcmp(ft, "trip"))
{
Vec_dhRead(bout, ignore, fn); CHECK_V_ERROR;
}
else if (!strcmp(ft, "ebin"))
{
Vec_dhReadBIN(bout, fn); CHECK_V_ERROR;
}
#ifdef PETSC_MODE
else if (!strcmp(ft, "petsc")) {
Viewer_DH viewer;
HYPRE_Int ierr;
Vec bb;
ierr = ViewerBinaryOpen_DH(comm_dh, fn, BINARY_WRONLY_DH, &viewer);
if (ierr) { SET_V_ERROR("ViewerBinaryOpen failed! [PETSc lib]"); }
ierr = VecLoad(viewer, &bb);
if (ierr) { SET_V_ERROR("VecLoad failed! [PETSc lib]"); }
ierr = ViewerDestroy_DH(viewer);
if (ierr) { SET_V_ERROR("ViewerDestroy failed! [PETSc lib]"); }
ierr = convertPetscToEuclidVec(bb, bout);
if (ierr) { SET_V_ERROR("convertPetscToEuclidVec failed!"); }
ierr = VecDestroy(bb);
if (ierr) { SET_V_ERROR("VecDestroy failed! [PETSc lib]"); }
}
#else
else if (!strcmp(ft, "petsc")) {
hypre_sprintf(msgBuf_dh, "must recompile Euclid using petsc mode!");
SET_V_ERROR(msgBuf_dh);
}
#endif
else
{
hypre_sprintf(msgBuf_dh, "unknown filetype: -ftin %s", ft);
SET_V_ERROR(msgBuf_dh);
}
END_FUNC_DH
}
int main(int argc,char **args)
{
Mat A;
Vec x,b;
PetscErrorCode ierr;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscBool flg;
PetscInitialize(&argc,&args,(char*)0,help);
/* 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);
flg = PETSC_FALSE;
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = PetscOptionsGetString(NULL,"-vec",file,PETSC_MAX_PATH_LEN,&flg);CHKERRQ(ierr);
if (flg) {
if (file[0] == '0') {
PetscInt m;
PetscScalar one = 1.0;
ierr = PetscInfo(0,"Using vector of ones for RHS\n");CHKERRQ(ierr);
ierr = MatGetLocalSize(A,&m,NULL);CHKERRQ(ierr);
ierr = VecSetSizes(x,m,PETSC_DECIDE);CHKERRQ(ierr);
ierr = VecSetFromOptions(x);CHKERRQ(ierr);
ierr = VecSet(x,one);CHKERRQ(ierr);
}
} else {
ierr = VecLoad(x,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
}
ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
ierr = MatMult(A,x,b);CHKERRQ(ierr);
/* Print (for testing only) */
ierr = MatView(A,0);CHKERRQ(ierr);
ierr = VecView(b,0);CHKERRQ(ierr);
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode DMLoad_DA(DM da,PetscViewer viewer)
{
PetscErrorCode ierr;
PetscInt dim,m,n,p,dof,swidth;
DMDAStencilType stencil;
DMDABoundaryType bx,by,bz;
PetscInt classid = DM_FILE_CLASSID,subclassid = DMDA_FILE_CLASSID;
PetscBool coors;
DM dac;
Vec c;
PetscFunctionBegin;
ierr = PetscViewerBinaryRead(viewer,&classid,1,PETSC_INT);CHKERRQ(ierr);
if (classid != DM_FILE_CLASSID) SETERRQ(((PetscObject)da)->comm,PETSC_ERR_ARG_WRONG,"Not DM next in file");
ierr = PetscViewerBinaryRead(viewer,&subclassid,1,PETSC_INT);CHKERRQ(ierr);
if (subclassid != DMDA_FILE_CLASSID) SETERRQ(((PetscObject)da)->comm,PETSC_ERR_ARG_WRONG,"Not DM DA next in file");
ierr = PetscViewerBinaryRead(viewer,&dim,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&m,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&n,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&p,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&dof,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&swidth,1,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&bx,1,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&by,1,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&bz,1,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&stencil,1,PETSC_ENUM);CHKERRQ(ierr);
ierr = DMDASetDim(da, dim);CHKERRQ(ierr);
ierr = DMDASetSizes(da, m,n,p);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, bx, by, bz);CHKERRQ(ierr);
ierr = DMDASetDof(da, dof);CHKERRQ(ierr);
ierr = DMDASetStencilType(da, stencil);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, swidth);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&coors,1,PETSC_ENUM);CHKERRQ(ierr);
if (coors) {
ierr = DMDAGetCoordinateDA(da,&dac);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dac,&c);CHKERRQ(ierr);
ierr = VecLoad(c,viewer);CHKERRQ(ierr);
ierr = DMDASetCoordinates(da,c);CHKERRQ(ierr);
ierr = VecDestroy(&c);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
PetscErrorCode UMReadNodes(UM *mesh, char *filename) {
PetscErrorCode ierr;
int twoN;
PetscViewer viewer;
if (mesh->N > 0) {
SETERRQ(PETSC_COMM_WORLD,1,"nodes already created?\n");
}
ierr = VecCreate(PETSC_COMM_WORLD,&mesh->loc); CHKERRQ(ierr);
ierr = VecSetFromOptions(mesh->loc); CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,filename,FILE_MODE_READ,&viewer); CHKERRQ(ierr);
ierr = VecLoad(mesh->loc,viewer); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer); CHKERRQ(ierr);
ierr = VecGetSize(mesh->loc,&twoN); CHKERRQ(ierr);
if (twoN % 2 != 0) {
SETERRQ1(PETSC_COMM_WORLD,2,"node locations loaded from %s are not N pairs\n",filename);
}
mesh->N = twoN / 2;
return 0;
}
-fout <output_file> : file for saving output matrix and vector\n\n";
#include <petscmat.h>
#undef __FUNCT__
#define __FUNCT__ "main"
int main(int argc,char **args)
{
PetscErrorCode ierr;
PetscBool flg;
Vec x;
Mat A;
char file[256];
PetscViewer fd;
PetscInitialize(&argc,&args,(char *)0,help);
/* Read matrix and RHS */
ierr = PetscOptionsGetString(PETSC_NULL,"-fin",file,256,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,help);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecLoad(x,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
/* Write matrix and vector */
ierr = PetscOptionsGetString(PETSC_NULL,"-fout",file,256,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,help);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_WRITE,&fd);CHKERRQ(ierr);
ierr = MatView(A,fd);CHKERRQ(ierr);
ierr = VecView(x,fd);CHKERRQ(ierr);
/* Free data structures */
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **args)
{
Vec b;
PetscViewer fd; /* viewer */
PetscErrorCode ierr;
PetscInt i;
PetscInitialize(&argc,&args,(char *)0,help);
fd = PETSC_VIEWER_SOCKET_WORLD;
for (i=0;i<1000;i++){
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecLoad(b,fd);CHKERRQ(ierr);
ierr = VecView(b,fd);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
}
ierr = PetscFinalize();
return 0;
}
PetscErrorCode H2Solve(H2 h2) {
PetscErrorCode ierr;
EEPS eps;
EEPSCreate(h2->comm, &eps);
// set operator
if(h2->s_is_id) {
ierr = EEPSSetOperators(eps, h2->H, NULL); CHKERRQ(ierr);
} else {
ierr = EEPSSetOperators(eps, h2->H, h2->S); CHKERRQ(ierr);
}
// set initial space
if(h2->eps_old) {
PrintTimeStamp(h2->comm, "set init", NULL);
EEPSSetInitSpaceFromOther(eps, PETSC_DEFAULT, h2->H, h2->eps_old->eps);
} else if(h2->init_view) {
PrintTimeStamp(h2->comm, "Read init", NULL);
Vec x[1]; MatCreateVecs(h2->H, NULL, &x[0]);
ierr = VecLoad(x[0], h2->init_view); CHKERRQ(ierr);
ierr = EPSSetInitialSpace(eps->eps, 1, x);
ierr = VecDestroy(&x[0]); CHKERRQ(ierr);
ierr = PetscViewerDestroy(&h2->init_view); CHKERRQ(ierr);
}
// set other
ierr = EEPSSetTarget(eps, -4.1); CHKERRQ(ierr);
ierr = EEPSSetFromOptions(eps); CHKERRQ(ierr);
// solve
PrintTimeStamp(h2->comm, "solve", NULL);
ierr = EEPSSolve(eps); CHKERRQ(ierr);
// finalize
if(h2->eps_old) { ierr = EEPSDestroy(&h2->eps_old); CHKERRQ(ierr); }
h2->eps_old = eps;
return 0;
}
PetscErrorCode DMLoad_DA(DM da,PetscViewer viewer)
{
PetscErrorCode ierr;
PetscInt dim,m,n,p,dof,swidth;
DMDAStencilType stencil;
DMBoundaryType bx,by,bz;
PetscBool coors;
DM dac;
Vec c;
PetscFunctionBegin;
ierr = PetscViewerBinaryRead(viewer,&dim,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&m,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&n,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&p,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&dof,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&swidth,1,NULL,PETSC_INT);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&bx,1,NULL,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&by,1,NULL,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&bz,1,NULL,PETSC_ENUM);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&stencil,1,NULL,PETSC_ENUM);CHKERRQ(ierr);
ierr = DMSetDimension(da, dim);CHKERRQ(ierr);
ierr = DMDASetSizes(da, m,n,p);CHKERRQ(ierr);
ierr = DMDASetBoundaryType(da, bx, by, bz);CHKERRQ(ierr);
ierr = DMDASetDof(da, dof);CHKERRQ(ierr);
ierr = DMDASetStencilType(da, stencil);CHKERRQ(ierr);
ierr = DMDASetStencilWidth(da, swidth);CHKERRQ(ierr);
ierr = DMSetUp(da);CHKERRQ(ierr);
ierr = PetscViewerBinaryRead(viewer,&coors,1,NULL,PETSC_ENUM);CHKERRQ(ierr);
if (coors) {
ierr = DMGetCoordinateDM(da,&dac);CHKERRQ(ierr);
ierr = DMCreateGlobalVector(dac,&c);CHKERRQ(ierr);
ierr = VecLoad(c,viewer);CHKERRQ(ierr);
ierr = DMSetCoordinates(da,c);CHKERRQ(ierr);
ierr = VecDestroy(&c);CHKERRQ(ierr);
}
PetscFunctionReturn(0);
}
int main(int argc,char **args)
{
Vec b;
PetscViewer fd;
PetscErrorCode ierr;
PetscInt i;
PetscInitialize(&argc,&args,(char *)0,help);
/* server indicates we WAIT for someone to connect to our socket */
ierr = PetscViewerSocketOpen(PETSC_COMM_WORLD,"server",PETSC_DEFAULT,&fd);CHKERRQ(ierr);
ierr = VecCreateMPI(PETSC_COMM_WORLD,10000,PETSC_DECIDE,&b);CHKERRQ(ierr);
for (i=0;i<1000;i++){
ierr = VecView(b,fd);CHKERRQ(ierr);
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&b);CHKERRQ(ierr);
ierr = VecLoad(b,fd);CHKERRQ(ierr);
}
ierr = VecDestroy(&b);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
PetscErrorCode loadVector(char * type_v,Vec * b){
char file[PETSC_MAX_PATH_LEN];
char err[PETSC_MAX_PATH_LEN];
PetscErrorCode ierr;
PetscBool flag;
PetscViewer fd;
PetscInt size;
// check if there is a vec file, vector is not mandatory
ierr=PetscOptionsGetString(PETSC_NULL,type_v,file,PETSC_MAX_PATH_LEN-1,&flag);CHKERRQ(ierr);
if (!flag) {
PetscPrintf(PETSC_COMM_WORLD,"Error : %s is not properly set\n",type_v);
*b = NULL;
}else{
PetscPrintf(PETSC_COMM_WORLD,"Loading Vector : %s\n",file);
ierr=PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr=VecLoad(*b,fd);CHKERRQ(ierr);
ierr=PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr=VecGetSize(*b,&size);CHKERRQ(ierr);
PetscPrintf(PETSC_COMM_WORLD,"Loaded Vector of size : %d\n",size);
}
return 0;
}
PetscErrorCode InitializeProblem(AppCtx *user)
{
PetscErrorCode ierr;
PetscViewer loader;
MPI_Comm comm;
PetscInt nrows,ncols,i;
PetscScalar one=1.0;
char filebase[128];
char filename[128];
PetscFunctionBegin;
comm = PETSC_COMM_WORLD;
ierr = PetscStrncpy(filebase,user->name,128);CHKERRQ(ierr);
ierr = PetscStrncat(filebase,"/",1);CHKERRQ(ierr);
ierr = PetscStrncpy(filename,filebase,128);CHKERRQ(ierr);
ierr = PetscStrncat(filename,"f",3);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(comm,filename,FILE_MODE_READ,&loader);CHKERRQ(ierr);
ierr = VecCreate(comm,&user->d);CHKERRQ(ierr);
ierr = VecLoad(user->d,loader);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&loader);CHKERRQ(ierr);
ierr = VecGetSize(user->d,&nrows);CHKERRQ(ierr);
ierr = VecSetFromOptions(user->d);CHKERRQ(ierr);
user->n = nrows;
ierr = PetscStrncpy(filename,filebase,128);CHKERRQ(ierr);
ierr = PetscStrncat(filename,"H",3);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(comm,filename,FILE_MODE_READ,&loader);CHKERRQ(ierr);
ierr = MatCreate(comm,&user->H);CHKERRQ(ierr);
ierr = MatSetSizes(user->H,PETSC_DECIDE,PETSC_DECIDE,nrows,nrows);CHKERRQ(ierr);
ierr = MatLoad(user->H,loader);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&loader);CHKERRQ(ierr);
ierr = MatGetSize(user->H,&nrows,&ncols);CHKERRQ(ierr);
if (nrows != user->n) SETERRQ(comm,0,"H: nrows != n\n");
if (ncols != user->n) SETERRQ(comm,0,"H: ncols != n\n");
ierr = MatSetFromOptions(user->H);CHKERRQ(ierr);
ierr = PetscStrncpy(filename,filebase,128);CHKERRQ(ierr);
ierr = PetscStrncat(filename,"Aeq",3);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(comm,filename,FILE_MODE_READ,&loader);
if (ierr) {
user->Aeq = NULL;
user->me = 0;
} else {
ierr = MatCreate(comm,&user->Aeq);CHKERRQ(ierr);
ierr = MatLoad(user->Aeq,loader);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&loader);CHKERRQ(ierr);
ierr = MatGetSize(user->Aeq,&nrows,&ncols);CHKERRQ(ierr);
if (ncols != user->n) SETERRQ(comm,0,"Aeq ncols != H nrows\n");
ierr = MatSetFromOptions(user->Aeq);CHKERRQ(ierr);
user->me = nrows;
}
ierr = PetscStrncpy(filename,filebase,128);CHKERRQ(ierr);
ierr = PetscStrncat(filename,"Beq",3);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(comm,filename,FILE_MODE_READ,&loader);CHKERRQ(ierr);
if (ierr) {
user->beq = 0;
} else {
ierr = VecCreate(comm,&user->beq);CHKERRQ(ierr);
ierr = VecLoad(user->beq,loader);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&loader);CHKERRQ(ierr);
ierr = VecGetSize(user->beq,&nrows);CHKERRQ(ierr);
if (nrows != user->me) SETERRQ(comm,0,"Aeq nrows != Beq n\n");
ierr = VecSetFromOptions(user->beq);CHKERRQ(ierr);
}
user->mi = user->n;
/* Ain = eye(n,n) */
ierr = MatCreate(comm,&user->Ain);CHKERRQ(ierr);
ierr = MatSetType(user->Ain,MATAIJ);CHKERRQ(ierr);
ierr = MatSetSizes(user->Ain,PETSC_DECIDE,PETSC_DECIDE,user->mi,user->mi);CHKERRQ(ierr);
ierr = MatMPIAIJSetPreallocation(user->Ain,1,NULL,0,NULL);CHKERRQ(ierr);
ierr = MatSeqAIJSetPreallocation(user->Ain,1,NULL);CHKERRQ(ierr);
for (i=0;i<user->mi;i++) {
ierr = MatSetValues(user->Ain,1,&i,1,&i,&one,INSERT_VALUES);CHKERRQ(ierr);
}
ierr = MatAssemblyBegin(user->Ain,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatAssemblyEnd(user->Ain,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
ierr = MatSetFromOptions(user->Ain);CHKERRQ(ierr);
/* bin = [0,0 ... 0]' */
ierr = VecCreate(comm,&user->bin);CHKERRQ(ierr);
ierr = VecSetType(user->bin,VECMPI);CHKERRQ(ierr);
ierr = VecSetSizes(user->bin,PETSC_DECIDE,user->mi);CHKERRQ(ierr);
ierr = VecSet(user->bin,0.0);CHKERRQ(ierr);
ierr = VecSetFromOptions(user->bin);CHKERRQ(ierr);
user->m = user->me + user->mi;
PetscFunctionReturn(0);
}
int main(int argc, char **argv)
{
MPI_Comm comm;
DM dm;
Vec v, nv, rv, coord;
PetscBool test_read = PETSC_FALSE, verbose = PETSC_FALSE, flg;
PetscViewer hdf5Viewer;
PetscInt dim = 2;
PetscInt numFields = 1;
PetscInt numBC = 0;
PetscInt numComp[1] = {2};
PetscInt numDof[3] = {2, 0, 0};
PetscInt bcFields[1] = {0};
IS bcPoints[1] = {NULL};
PetscSection section;
PetscReal norm;
PetscErrorCode ierr;
ierr = PetscInitialize(&argc, &argv, (char *) 0, help);CHKERRQ(ierr);
comm = PETSC_COMM_WORLD;
ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","Test Options","none");CHKERRQ(ierr);
ierr = PetscOptionsBool("-test_read","Test reading from the HDF5 file","",PETSC_FALSE,&test_read,NULL);CHKERRQ(ierr);
ierr = PetscOptionsBool("-verbose","print the Vecs","",PETSC_FALSE,&verbose,NULL);CHKERRQ(ierr);
ierr = PetscOptionsInt("-dim","the dimension of the problem","",2,&dim,NULL);CHKERRQ(ierr);
ierr = PetscOptionsEnd();
ierr = DMPlexCreateBoxMesh(comm, dim, PETSC_TRUE, &dm);CHKERRQ(ierr);
ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr);
numDof[0] = dim;
ierr = DMPlexCreateSection(dm, dim, numFields, numComp, numDof, numBC, bcFields, bcPoints, NULL, NULL, §ion);CHKERRQ(ierr);
ierr = DMSetDefaultSection(dm, section);CHKERRQ(ierr);
ierr = PetscSectionDestroy(§ion);CHKERRQ(ierr);
ierr = DMSetUseNatural(dm, PETSC_TRUE);CHKERRQ(ierr);
{
DM dmDist;
ierr = DMPlexDistribute(dm, 0, NULL, &dmDist);CHKERRQ(ierr);
if (dmDist) {
ierr = DMDestroy(&dm);CHKERRQ(ierr);
dm = dmDist;
}
}
ierr = DMCreateGlobalVector(dm, &v);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) v, "V");CHKERRQ(ierr);
ierr = DMGetCoordinates(dm, &coord);CHKERRQ(ierr);
ierr = VecCopy(coord, v);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(v, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(v, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== original V in global ordering. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(v, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = DMCreateGlobalVector(dm, &nv);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) nv, "NV");CHKERRQ(ierr);
ierr = DMPlexGlobalToNaturalBegin(dm, v, nv);CHKERRQ(ierr);
ierr = DMPlexGlobalToNaturalEnd(dm, v, nv);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(nv, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(nv, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== V in natural ordering. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(nv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecViewFromOptions(v, NULL, "-global_vec_view");CHKERRQ(ierr);
if (test_read) {
ierr = DMCreateGlobalVector(dm, &rv);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) rv, "V");CHKERRQ(ierr);
/* Test native read */
ierr = PetscViewerHDF5Open(comm, "V.h5", FILE_MODE_READ, &hdf5Viewer);CHKERRQ(ierr);
ierr = PetscViewerPushFormat(hdf5Viewer, PETSC_VIEWER_NATIVE);CHKERRQ(ierr);
ierr = VecLoad(rv, hdf5Viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&hdf5Viewer);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(rv, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(rv, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== Vector from file. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecEqual(rv, v, &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "V and RV are equal\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "V and RV are not equal\n\n");CHKERRQ(ierr);
ierr = VecAXPY(rv, -1.0, v);CHKERRQ(ierr);
ierr = VecNorm(rv, NORM_INFINITY, &norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "diff norm is = %g\n", (double) norm);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
/* Test raw read */
ierr = PetscViewerHDF5Open(comm, "V.h5", FILE_MODE_READ, &hdf5Viewer);CHKERRQ(ierr);
ierr = VecLoad(rv, hdf5Viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&hdf5Viewer);CHKERRQ(ierr);
if (verbose) {
PetscInt size, bs;
ierr = VecGetSize(rv, &size);CHKERRQ(ierr);
ierr = VecGetBlockSize(rv, &bs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "==== Vector from file. size==%d\tblock size=%d\n", size, bs);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecEqual(rv, nv, &flg);CHKERRQ(ierr);
if (flg) {
ierr = PetscPrintf(PETSC_COMM_WORLD, "NV and RV are equal\n");CHKERRQ(ierr);
} else {
ierr = PetscPrintf(PETSC_COMM_WORLD, "NV and RV are not equal\n\n");CHKERRQ(ierr);
ierr = VecAXPY(rv, -1.0, v);CHKERRQ(ierr);
ierr = VecNorm(rv, NORM_INFINITY, &norm);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD, "diff norm is = %g\n", (double) norm);CHKERRQ(ierr);
ierr = VecView(rv, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
}
ierr = VecDestroy(&rv);CHKERRQ(ierr);
}
ierr = VecDestroy(&nv);CHKERRQ(ierr);
ierr = VecDestroy(&v);CHKERRQ(ierr);
ierr = DMDestroy(&dm);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
Example: mpiexec -n <np> ./ex130 -f <matrix binary file> -mat_solver_package 1 -mat_superlu_equil \n\n";
#include <petscmat.h>
int main(int argc,char **args)
{
Mat A,F;
Vec u,x,b;
PetscErrorCode ierr;
PetscMPIInt rank,size;
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 */
ierr = PetscInitialize(&argc,&args,(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);
/* Determine file from which we read the matrix A */
ierr = PetscOptionsGetString(NULL,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,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 ierr;
}
PetscErrorCode iniCalcBC(PetscScalar tc, PetscInt Iterc, PetscScalar tf, PetscInt Iterf, PetscInt numTracers, Vec *v, Vec *bcc, Vec *bcf)
{
PetscErrorCode ierr;
PetscInt itr;
PetscViewer fd;
PetscBool flg;
PetscInt it;
PetscScalar myTime;
PetscScalar zero = 0.0;
/* v[0]=TR1,v[1]=TR2,... */
ierr = VecGetArray(TR,&localTR);CHKERRQ(ierr);
for (itr=0; itr<numTracers; itr++) {
ierr = VecSet(bcc[itr],zero); CHKERRQ(ierr);
ierr = VecSet(bcf[itr],zero); CHKERRQ(ierr);
}
ierr = VecGetArray(BCc,&localBCc);CHKERRQ(ierr);
ierr = VecGetArray(BCf,&localBCf);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(PETSC_NULL,"-inert_gas_id",&gasID,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate inert gas tracer ID with the -inert_gas_id option");
ierr = PetscOptionsGetReal(PETSC_NULL,"-biogeochem_deltat",&DeltaT,&flg);CHKERRQ(ierr);
if (!flg) SETERRQ(PETSC_COMM_WORLD,1,"Must indicate biogeochemical time step in seconds with the -biogeochem_deltat option");
ierr = PetscOptionsHasName(PETSC_NULL,"-periodic_biogeochem_forcing",&periodicBiogeochemForcing);CHKERRQ(ierr);
if (periodicBiogeochemForcing) {
ierr=PetscPrintf(PETSC_COMM_WORLD,"Periodic biogeochemical forcing specified\n");CHKERRQ(ierr);
ierr = iniPeriodicTimer("periodic_biogeochem_", &biogeochemTimer);CHKERRQ(ierr);
}
/* Grid arrays */
/* Forcing fields */
ierr = VecDuplicate(BCc,&Tss);CHKERRQ(ierr);
ierr = VecDuplicate(BCc,&Sss);CHKERRQ(ierr);
ierr = VecDuplicate(BCc,&atmosp);CHKERRQ(ierr);
if (periodicBiogeochemForcing) {
Tssp.firstTime = PETSC_TRUE;
Sssp.firstTime = PETSC_TRUE;
atmospp.firstTime = PETSC_TRUE;
} else {
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Tss.petsc",FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = VecLoad(Tss,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Sss.petsc",FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = VecLoad(Sss,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"atmosp.petsc",FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = VecLoad(atmosp,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
}
ierr = VecGetArray(Tss,&localTss);CHKERRQ(ierr);
ierr = VecGetArray(Sss,&localSss);CHKERRQ(ierr);
ierr = VecGetArray(atmosp,&localatmosp);CHKERRQ(ierr);
/* ierr = PetscPrintf(PETSC_COMM_WORLD,"Done reading surface T, S, and atmospheric pressure\n");CHKERRQ(ierr); */
ierr = PetscOptionsHasName(PETSC_NULL,"-calc_diagnostics",&calcDiagnostics);CHKERRQ(ierr);
if (calcDiagnostics) {
/* Read T and S */
ierr = VecDuplicate(TR,&Ts);CHKERRQ(ierr);
ierr = VecDuplicate(TR,&Ss);CHKERRQ(ierr);
if (periodicBiogeochemForcing) {
Tsp.firstTime = PETSC_TRUE;
Ssp.firstTime = PETSC_TRUE;
ierr = interpPeriodicVector(tc,&Ts,biogeochemTimer.cyclePeriod,biogeochemTimer.numPerPeriod,biogeochemTimer.tdp,&Tsp,"Ts_");
ierr = interpPeriodicVector(tc,&Ss,biogeochemTimer.cyclePeriod,biogeochemTimer.numPerPeriod,biogeochemTimer.tdp,&Ssp,"Ss_");
} else {
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Ts.petsc",FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = VecLoad(Ts,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,"Ss.petsc",FILE_MODE_READ,&fd);CHKERRQ(ierr);
ierr = VecLoad(Ss,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
}
ierr = VecGetArray(Ts,&localTs);CHKERRQ(ierr);
ierr = VecGetArray(Ss,&localSs);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Done reading T/S\n");CHKERRQ(ierr);
ierr = VecDuplicate(TR,&TReqdiag);CHKERRQ(ierr);
ierr = VecSet(TReqdiag,zero);CHKERRQ(ierr);
ierr = VecGetArray(TReqdiag,&localTReqdiag);CHKERRQ(ierr);
/*Data for diagnostics */
ierr = iniStepTimer("diag_", Iter0, &diagTimer);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Diagnostics will be computed starting at (and including) time step: %d\n", diagTimer.startTimeStep);CHKERRQ(ierr);
ierr = PetscPrintf(PETSC_COMM_WORLD,"Diagnostics will be computed over %d time steps\n", diagTimer.numTimeSteps);CHKERRQ(ierr);
ierr = VecDuplicate(TR,&TRsatanomdiag);CHKERRQ(ierr);
ierr = VecSet(TRsatanomdiag,zero);CHKERRQ(ierr);
ierr = VecGetArray(TRsatanomdiag,&localTRsatanomdiag);CHKERRQ(ierr);
ierr = VecDuplicate(TR,&TRsatanomdiagavg);CHKERRQ(ierr);
ierr = VecSet(TRsatanomdiagavg,zero);CHKERRQ(ierr);
ierr = VecDuplicate(TR,&TReqdiagavg);CHKERRQ(ierr);
ierr = VecSet(TReqdiagavg,zero);CHKERRQ(ierr);
ierr = VecDuplicate(BCc,&BCdiagavg);CHKERRQ(ierr);
ierr = VecSet(BCdiagavg,zero);CHKERRQ(ierr);
// diagCount=0;
}
/* Initialize biogeochem model */
if (periodicBiogeochemForcing) {
ierr = interpPeriodicVector(tc,&Tss,biogeochemTimer.cyclePeriod,biogeochemTimer.numPerPeriod,biogeochemTimer.tdp,&Tssp,"Tss_");
ierr = interpPeriodicVector(tc,&Sss,biogeochemTimer.cyclePeriod,biogeochemTimer.numPerPeriod,biogeochemTimer.tdp,&Sssp,"Sss_");
ierr = interpPeriodicVector(tc,&atmosp,biogeochemTimer.cyclePeriod,biogeochemTimer.numPerPeriod,biogeochemTimer.tdp,&atmospp,"atmosp_");
}
myTime = DeltaT*Iterc; /* Iter should start at 0 */
inert_gas_bc_(&lBCSize,&Iterc,&myTime,&localTss[0],&localSss[0],
&localatmosp[0],&gasID,
&localBCc[0]);
if (periodicBiogeochemForcing) {
ierr = interpPeriodicVector(tf,&Tss,biogeochemTimer.cyclePeriod,biogeochemTimer.numPerPeriod,biogeochemTimer.tdp,&Tssp,"Tss_");
ierr = interpPeriodicVector(tf,&Sss,biogeochemTimer.cyclePeriod,biogeochemTimer.numPerPeriod,biogeochemTimer.tdp,&Sssp,"Sss_");
ierr = interpPeriodicVector(tf,&atmosp,biogeochemTimer.cyclePeriod,biogeochemTimer.numPerPeriod,biogeochemTimer.tdp,&atmospp,"atmosp_");
}
myTime = DeltaT*Iterf; /* Iter should start at 0 */
inert_gas_bc_(&lBCSize,&Iterf,&myTime,&localTss[0],&localSss[0],
&localatmosp[0],&gasID,
&localBCf[0]);
return 0;
}
int main(int argc,char **args)
{
Mat A,F;
PetscViewer fd; /* viewer */
char file[PETSC_MAX_PATH_LEN]; /* input file name */
PetscErrorCode ierr;
PetscBool flg;
Vec x,y,w;
MatFactorInfo iluinfo;
IS perm;
PetscInt m;
PetscReal norm;
PetscInitialize(&argc,&args,(char*)0,help);
/*
Determine file from which we read the matrix
*/
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");
/*
Open binary file. Note that we use FILE_MODE_READ to indicate
reading from this file.
*/
ierr = PetscViewerBinaryOpen(PETSC_COMM_WORLD,file,FILE_MODE_READ,&fd);CHKERRQ(ierr);
/*
Load the matrix; then destroy the viewer.
*/
ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
ierr = MatSetType(A,MATSEQBAIJ);CHKERRQ(ierr);
ierr = MatLoad(A,fd);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
ierr = VecLoad(x,fd);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&fd);CHKERRQ(ierr);
ierr = VecDuplicate(x,&y);CHKERRQ(ierr);
ierr = VecDuplicate(x,&w);CHKERRQ(ierr);
ierr = MatGetFactor(A,"petsc",MAT_FACTOR_ILU,&F);CHKERRQ(ierr);
iluinfo.fill = 1.0;
ierr = MatGetSize(A,&m,0);CHKERRQ(ierr);
ierr = ISCreateStride(PETSC_COMM_WORLD,m,0,1,&perm);CHKERRQ(ierr);
ierr = MatLUFactorSymbolic(F,A,perm,perm,&iluinfo);CHKERRQ(ierr);
ierr = MatLUFactorNumeric(F,A,&iluinfo);CHKERRQ(ierr);
ierr = MatSolveTranspose(F,x,y);CHKERRQ(ierr);
F->ops->solvetranspose = MatSolveTranspose_SeqBAIJ_N;
ierr = MatSolveTranspose(F,x,w);CHKERRQ(ierr);
/* VecView(w,0);VecView(y,0); */
ierr = VecAXPY(w,-1.0,y);CHKERRQ(ierr);
ierr = VecNorm(w,NORM_2,&norm);CHKERRQ(ierr);
if (norm) {
ierr = PetscPrintf(PETSC_COMM_SELF,"Norm of difference is nonzero %g\n",norm);CHKERRQ(ierr);
}
ierr = ISDestroy(&perm);CHKERRQ(ierr);
ierr = MatDestroy(&A);CHKERRQ(ierr);
ierr = MatDestroy(&F);CHKERRQ(ierr);
ierr = VecDestroy(&x);CHKERRQ(ierr);
ierr = VecDestroy(&y);CHKERRQ(ierr);
ierr = VecDestroy(&w);CHKERRQ(ierr);
ierr = PetscFinalize();
return 0;
}
int main(int argc,char **argv)
{
Vec x1, x2, y1, y2, y3, y4;
PetscViewer viewer;
PetscMPIInt rank;
PetscInt i, nlocal, n = 6;
PetscScalar *array;
PetscBool equal;
PetscErrorCode ierr;
PetscFunctionBegin;
ierr = PetscInitialize(&argc, &argv, (char*) 0, help);if (ierr) return ierr;
ierr = MPI_Comm_rank(PETSC_COMM_WORLD, &rank);CHKERRQ(ierr);
ierr = PetscOptionsGetInt(NULL,NULL, "-n", &n, NULL);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD, &x1);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) x1, "TestVec");CHKERRQ(ierr);
ierr = VecSetSizes(x1, PETSC_DECIDE, n);CHKERRQ(ierr);
ierr = VecSetFromOptions(x1);CHKERRQ(ierr);
/* initialize x1 */
ierr = VecGetLocalSize(x1, &nlocal);CHKERRQ(ierr);
ierr = VecGetArray(x1, &array);CHKERRQ(ierr);
for (i = 0; i < nlocal; i++) array[i] = rank + 1;
ierr = VecRestoreArray(x1, &array);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD, &x2);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) x2, "TestVec2");CHKERRQ(ierr);
ierr = VecSetSizes(x2, PETSC_DECIDE, n);CHKERRQ(ierr);
ierr = VecSetBlockSize(x2, 2);CHKERRQ(ierr);
ierr = VecSetFromOptions(x2);CHKERRQ(ierr);
/* initialize x2 */
ierr = VecGetLocalSize(x2, &nlocal);CHKERRQ(ierr);
ierr = VecGetArray(x2, &array);CHKERRQ(ierr);
for (i = 0; i < nlocal; i++) array[i] = rank + 1;
ierr = VecRestoreArray(x2, &array);CHKERRQ(ierr);
ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD, "ex19.h5", FILE_MODE_WRITE, &viewer);CHKERRQ(ierr);
ierr = VecView(x1, viewer);CHKERRQ(ierr);
ierr = PetscViewerHDF5PushGroup(viewer, "/testBlockSize");CHKERRQ(ierr);
ierr = VecView(x2, viewer);CHKERRQ(ierr);
ierr = PetscViewerHDF5PushGroup(viewer, "/testTimestep");CHKERRQ(ierr);
ierr = PetscViewerHDF5SetTimestep(viewer, 0);CHKERRQ(ierr);
ierr = VecView(x2, viewer);CHKERRQ(ierr);
ierr = PetscViewerHDF5SetTimestep(viewer, 1);CHKERRQ(ierr);
ierr = VecView(x2, viewer);CHKERRQ(ierr);
ierr = PetscViewerHDF5PopGroup(viewer);CHKERRQ(ierr);
ierr = PetscViewerHDF5PopGroup(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD, &y1);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) y1, "TestVec");CHKERRQ(ierr);
ierr = VecSetSizes(y1, PETSC_DECIDE, n);CHKERRQ(ierr);
ierr = VecSetFromOptions(y1);CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&y2);CHKERRQ(ierr);
ierr = VecSetBlockSize(y2, 2);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) y2, "TestVec2");CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&y3);CHKERRQ(ierr);
ierr = VecSetBlockSize(y3, 2);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) y3, "TestVec2");CHKERRQ(ierr);
ierr = VecCreate(PETSC_COMM_WORLD,&y4);CHKERRQ(ierr);
ierr = VecSetBlockSize(y4, 2);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) y4, "TestVec2");CHKERRQ(ierr);
ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD, "ex19.h5", FILE_MODE_READ, &viewer);CHKERRQ(ierr);
ierr = VecLoad(y1, viewer);CHKERRQ(ierr);
ierr = PetscViewerHDF5PushGroup(viewer, "/testBlockSize");CHKERRQ(ierr);
ierr = VecLoad(y2, viewer);CHKERRQ(ierr);
ierr = PetscViewerHDF5PushGroup(viewer, "/testTimestep");CHKERRQ(ierr);
ierr = PetscViewerHDF5SetTimestep(viewer, 0);CHKERRQ(ierr);
ierr = VecLoad(y3, viewer);CHKERRQ(ierr);
ierr = PetscViewerHDF5SetTimestep(viewer, 1);CHKERRQ(ierr);
ierr = VecLoad(y4, viewer);CHKERRQ(ierr);
ierr = PetscViewerHDF5PopGroup(viewer);CHKERRQ(ierr);
ierr = PetscViewerHDF5PopGroup(viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&viewer);CHKERRQ(ierr);
ierr = VecEqual(x1, y1, &equal);CHKERRQ(ierr);
if (!equal) {
ierr = VecView(x1, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecView(y1, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Error in HDF5 viewer");
}
ierr = VecEqual(x2, y2, &equal);CHKERRQ(ierr);
if (!equal) {
ierr = VecView(x2, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
ierr = VecView(y2, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB, "Error in HDF5 viewer");
}
ierr = VecDestroy(&x1);CHKERRQ(ierr);
ierr = VecDestroy(&x2);CHKERRQ(ierr);
ierr = VecDestroy(&y1);CHKERRQ(ierr);
ierr = VecDestroy(&y2);CHKERRQ(ierr);
ierr = VecDestroy(&y3);CHKERRQ(ierr);
ierr = VecDestroy(&y4);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
bool TestAltivecOps()
{
std::cout << "\nTesting Altivec operations...\n\n";
if (HasAltivec() == false)
{
std::cout << "\nAltivec not available, skipping test." << std::endl;
return true;
}
// These tests may seem superflous, but we really want to test the
// Altivec/POWER4 implementation. That does not happen when POWER7
// or POWER8 is available because we use POWER7's unaligned loads
// and stores with POWER8's AES, SHA, etc. These tests enage
// Altivec/POWER4 without POWER7, like on an old PowerMac.
//********** Unaligned loads and stores **********//
bool pass1=true;
CRYPTOPP_ALIGN_DATA(16)
byte dest[20], src[20] = {23,22,21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5,4};
const byte st1[16] = {22,21,20,19,18,17,16,15,14,13,12,11,10,9,8,7};
const byte st2[16] = {21,20,19,18,17,16,15,14,13,12,11,10,9,8,7,6};
const byte st3[16] = {20,19,18,17,16,15,14,13,12,11,10,9,8,7,6,5};
VecStore(VecLoad(src), dest);
pass1 = (0 == std::memcmp(src, dest, 16)) && pass1;
CRYPTOPP_ASSERT(pass1);
VecStore(VecLoad(src+1), dest+1);
pass1 = (0 == std::memcmp(st1, dest+1, 16)) && pass1;
CRYPTOPP_ASSERT(pass1);
VecStore(VecLoad(src+2), dest+2);
pass1 = (0 == std::memcmp(st2, dest+2, 16)) && pass1;
CRYPTOPP_ASSERT(pass1);
VecStore(VecLoad(src+3), dest+3);
pass1 = (0 == std::memcmp(st3, dest+3, 16)) && pass1;
CRYPTOPP_ASSERT(pass1);
VecStoreBE(VecLoadBE(src), dest);
pass1 = (0 == std::memcmp(src, dest, 16)) && pass1;
CRYPTOPP_ASSERT(pass1);
VecStoreBE(VecLoadBE(src+1), dest+1);
pass1 = (0 == std::memcmp(st1, dest+1, 16)) && pass1;
CRYPTOPP_ASSERT(pass1);
VecStoreBE(VecLoadBE(src+2), dest+2);
pass1 = (0 == std::memcmp(st2, dest+2, 16)) && pass1;
CRYPTOPP_ASSERT(pass1);
VecStoreBE(VecLoadBE(src+3), dest+3);
pass1 = (0 == std::memcmp(st3, dest+3, 16)) && pass1;
CRYPTOPP_ASSERT(pass1);
#if (CRYPTOPP_LITTLE_ENDIAN)
VecStore(VecLoadBE(src), dest);
pass1 = (0 != std::memcmp(src, dest, 16)) && pass1;
CRYPTOPP_ASSERT(pass1);
VecStoreBE(VecLoad(src), dest);
pass1 = (0 != std::memcmp(src, dest, 16)) && pass1;
CRYPTOPP_ASSERT(pass1);
#endif
if (!pass1)
std::cout << "FAILED:";
else
std::cout << "passed:";
std::cout << " Altivec loads and stores" << std::endl;
//********** Shifts **********//
bool pass2=true;
uint8x16_p val = {0xff,0xff,0xff,0xff, 0xff,0xff,0xff,0xff,
0xff,0xff,0xff,0xff, 0xff,0xff,0xff,0xff};
pass2 = (VecEqual(val, VecShiftLeftOctet<0>(val))) && pass2;
CRYPTOPP_ASSERT(pass2);
pass2 = (VecEqual(val, VecShiftRightOctet<0>(val))) && pass2;
CRYPTOPP_ASSERT(pass2);
uint8x16_p lsh1 = {0xff,0xff,0xff,0xff, 0xff,0xff,0xff,0xff,
0xff,0xff,0xff,0xff, 0xff,0xff,0xff,0x00};
uint8x16_p rsh1 = {0x00,0xff,0xff,0xff, 0xff,0xff,0xff,0xff,
0xff,0xff,0xff,0xff, 0xff,0xff,0xff,0xff};
pass2 = (VecEqual(lsh1, VecShiftLeftOctet<1>(val))) && pass2;
CRYPTOPP_ASSERT(pass2);
pass2 = (VecEqual(rsh1, VecShiftRightOctet<1>(val))) && pass2;
CRYPTOPP_ASSERT(pass2);
uint8x16_p lsh15 = {0xff,0x00,0x00,0x00, 0x00,0x00,0x00,0x00,
0x00,0x00,0x00,0x00, 0x00,0x00,0x00,0x00};
uint8x16_p rsh15 = {0x00,0x00,0x00,0x00, 0x00,0x00,0x00,0x00,
0x00,0x00,0x00,0x00, 0x00,0x00,0x00,0xff};
pass2 = (VecEqual(lsh15, VecShiftLeftOctet<15>(val))) && pass2;
CRYPTOPP_ASSERT(pass2);
pass2 = (VecEqual(rsh15, VecShiftRightOctet<15>(val))) && pass2;
CRYPTOPP_ASSERT(pass2);
uint8x16_p lsh16 = {0x00,0x00,0x00,0x00, 0x00,0x00,0x00,0x00,
0x00,0x00,0x00,0x00, 0x00,0x00,0x00,0x00};
uint8x16_p rsh16 = {0x00,0x00,0x00,0x00, 0x00,0x00,0x00,0x00,
0x00,0x00,0x00,0x00, 0x00,0x00,0x00,0x00};
pass2 = (VecEqual(lsh16, VecShiftLeftOctet<16>(val))) && pass2;
CRYPTOPP_ASSERT(pass2);
pass2 = (VecEqual(rsh16, VecShiftRightOctet<16>(val))) && pass2;
CRYPTOPP_ASSERT(pass2);
if (!pass2)
std::cout << "FAILED:";
else
std::cout << "passed:";
std::cout << " Altivec left and right shifts" << std::endl;
//********** Extraction **********//
bool pass3=true;
const byte bex1[] = {0x1f,0x1e,0x1d,0x1c, 0x1b,0x1a,0x19,0x18,
0x17,0x16,0x15,0x14, 0x13,0x12,0x11,0x10};
const byte bex2[] = {0x00,0x00,0x00,0x00, 0x00,0x00,0x00,0x00,
0x17,0x16,0x15,0x14, 0x13,0x12,0x11,0x10};
const byte bex3[] = {0x00,0x00,0x00,0x00, 0x00,0x00,0x00,0x00,
0x1f,0x1e,0x1d,0x1c, 0x1b,0x1a,0x19,0x18};
const uint8x16_p ex1 = (uint8x16_p)VecLoad(bex1);
const uint8x16_p ex2 = (uint8x16_p)VecLoad(bex2);
const uint8x16_p ex3 = (uint8x16_p)VecLoad(bex3);
pass3 = VecEqual(ex2, VecGetLow(ex1)) && pass3;
CRYPTOPP_ASSERT(pass3);
pass3 = VecEqual(ex3, VecGetHigh(ex1)) && pass3;
CRYPTOPP_ASSERT(pass3);
uint8x16_p ex4 = VecShiftRightOctet<8>(VecShiftLeftOctet<8>(ex1));
pass3 = VecEqual(ex4, VecGetLow(ex1)) && pass3;
CRYPTOPP_ASSERT(pass3);
uint8x16_p ex5 = VecShiftRightOctet<8>(ex1);
pass3 = VecEqual(ex5, VecGetHigh(ex1)) && pass3;
CRYPTOPP_ASSERT(pass3);
if (!pass3)
std::cout << "FAILED:";
else
std::cout << "passed:";
std::cout << " Altivec vector extraction" << std::endl;
return pass1 && pass2 && pass3;
}
Example: mpiexec -n <np> ./ex168 -f <matrix binary file> \n\n";
#include <petscmat.h>
int main(int argc,char **args)
{
Mat A,F;
Vec u,x,b;
PetscErrorCode ierr;
PetscMPIInt rank,size;
PetscInt m,n,nfact;
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 */
ierr = PetscInitialize(&argc,&args,(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);
/* Determine file from which we read the matrix A */
ierr = PetscOptionsGetString(NULL,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 Cholesky Factorization */
ierr = MatGetOrdering(A,MATORDERINGNATURAL,&perm,&iperm);CHKERRQ(ierr);
if (!rank) printf(" Clique Cholesky:\n");
ierr = MatGetFactor(A,MATSOLVERCLIQUE,MAT_FACTOR_CHOLESKY,&F);CHKERRQ(ierr);
info.fill = 5.0;
ierr = MatCholeskyFactorSymbolic(F,A,perm,&info);CHKERRQ(ierr);
for (nfact = 0; nfact < 1; nfact++) {
if (!rank) printf(" %d-the Cholesky numfactorization \n",nfact);
ierr = MatCholeskyFactorNumeric(F,A,&info);CHKERRQ(ierr);
/* Test MatSolve() */
if (testMatSolve && nfact == 2) {
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 ierr;
}
int main(int argc,char **argv)
{
PetscErrorCode ierr;
DM da2D;
PetscInt i,j,ixs, ixm, iys, iym;;
PetscViewer H5viewer;
PetscScalar xm = -1.0, xp=1.0;
PetscScalar ym = -1.0, yp=1.0;
PetscScalar value = 1.0,dx,dy;
PetscInt Nx = 40, Ny=40;
Vec gauss,input;
PetscScalar **gauss_ptr;
PetscReal norm;
const char *vecname;
dx=(xp-xm)/(Nx-1);
dy=(yp-ym)/(Ny-1);
/* Initialize the Petsc context */
ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
ierr = DMDACreate2d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,DMDA_STENCIL_STAR,Nx,Ny,PETSC_DECIDE,PETSC_DECIDE,1,1,NULL,NULL,&da2D);CHKERRQ(ierr);
ierr = DMSetFromOptions(da2D);CHKERRQ(ierr);
ierr = DMSetUp(da2D);CHKERRQ(ierr);
/* Set the coordinates */
ierr = DMDASetUniformCoordinates(da2D, 0.0, 1.0, 0.0, 1.0, 0.0, 0.0);CHKERRQ(ierr);
/* Declare gauss as a DMDA component */
ierr = DMCreateGlobalVector(da2D,&gauss);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject) gauss, "pressure");CHKERRQ(ierr);
/* Initialize vector gauss with a constant value (=1) */
ierr = VecSet(gauss,value);CHKERRQ(ierr);
/* Get the coordinates of the corners for each process */
ierr = DMDAGetCorners(da2D, &ixs, &iys, 0, &ixm, &iym, 0);CHKERRQ(ierr);
/* Build the gaussian profile (exp(-x^2-y^2)) */
ierr = DMDAVecGetArray(da2D,gauss,&gauss_ptr);CHKERRQ(ierr);
for (j=iys; j<iys+iym; j++) {
for (i=ixs; i<ixs+ixm; i++) {
gauss_ptr[j][i]=PetscExpScalar(-(xm+i*dx)*(xm+i*dx)-(ym+j*dy)*(ym+j*dy));
}
}
ierr = DMDAVecRestoreArray(da2D,gauss,&gauss_ptr);CHKERRQ(ierr);
/* Create the HDF5 viewer */
ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD,"gauss.h5",FILE_MODE_WRITE,&H5viewer);CHKERRQ(ierr);
ierr = PetscViewerSetFromOptions(H5viewer);CHKERRQ(ierr);
/* Write the H5 file */
ierr = VecView(gauss,H5viewer);CHKERRQ(ierr);
/* Close the viewer */
ierr = PetscViewerDestroy(&H5viewer);CHKERRQ(ierr);
ierr = VecDuplicate(gauss,&input);CHKERRQ(ierr);
ierr = PetscObjectGetName((PetscObject)gauss,&vecname);CHKERRQ(ierr);
ierr = PetscObjectSetName((PetscObject)input,vecname);CHKERRQ(ierr);
/* Create the HDF5 viewer for reading */
ierr = PetscViewerHDF5Open(PETSC_COMM_WORLD,"gauss.h5",FILE_MODE_READ,&H5viewer);CHKERRQ(ierr);
ierr = PetscViewerSetFromOptions(H5viewer);CHKERRQ(ierr);
ierr = VecLoad(input,H5viewer);CHKERRQ(ierr);
ierr = PetscViewerDestroy(&H5viewer);CHKERRQ(ierr);
ierr = VecAXPY(input,-1.0,gauss);CHKERRQ(ierr);
ierr = VecNorm(input,NORM_2,&norm);CHKERRQ(ierr);
if (norm > 1.e-6) SETERRQ(PETSC_COMM_WORLD,PETSC_ERR_PLIB,"Vec read in does not match vector written out");
ierr = VecDestroy(&input);CHKERRQ(ierr);
ierr = VecDestroy(&gauss);CHKERRQ(ierr);
ierr = DMDestroy(&da2D);CHKERRQ(ierr);
ierr = PetscFinalize();
return ierr;
}
