Esempio n. 1
0
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  PetscInt       i,blocks[2],nlocal;
  PetscMPIInt    size,rank;
  PetscScalar    value;
  Vec            x,y;
  IS             is1,is2;
  VecScatter     ctx = 0;
  PetscViewer    subviewer;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);

  if (size != 2) SETERRQ(PETSC_COMM_SELF,1,"Must run with 2 processors");

  /* create two vectors */
  if (!rank) nlocal = 8;
  else nlocal = 4;
  ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
  ierr = VecSetSizes(x,nlocal,12);CHKERRQ(ierr);
  ierr = VecSetFromOptions(x);CHKERRQ(ierr);
  ierr = VecCreate(PETSC_COMM_SELF,&y);CHKERRQ(ierr);
  ierr = VecSetSizes(y,8,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(y);CHKERRQ(ierr);

  /* create two index sets */
  if (!rank) {
    blocks[0] = 0; blocks[1] = 2;
  } else {
    blocks[0] = 1; blocks[1] = 2;
  }
  ierr = ISCreateBlock(PETSC_COMM_SELF,4,2,blocks,PETSC_COPY_VALUES,&is1);CHKERRQ(ierr);
  ierr = ISCreateStride(PETSC_COMM_SELF,8,0,1,&is2);CHKERRQ(ierr);

  for (i=0; i<12; i++) {
    value = i;
    ierr  = VecSetValues(x,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
  }
  ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
  ierr = VecAssemblyEnd(x);CHKERRQ(ierr);

  ierr = VecScatterCreateWithData(x,is1,y,is2,&ctx);CHKERRQ(ierr);
  ierr = VecScatterBegin(ctx,x,y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterEnd(ctx,x,y,INSERT_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterDestroy(&ctx);CHKERRQ(ierr);

  ierr = PetscViewerGetSubViewer(PETSC_VIEWER_STDOUT_WORLD,PETSC_COMM_SELF,&subviewer);CHKERRQ(ierr);
  ierr = VecView(y,subviewer);CHKERRQ(ierr);
  ierr = PetscViewerRestoreSubViewer(PETSC_VIEWER_STDOUT_WORLD,PETSC_COMM_SELF,&subviewer);CHKERRQ(ierr);

  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = VecDestroy(&y);CHKERRQ(ierr);
  ierr = ISDestroy(&is1);CHKERRQ(ierr);
  ierr = ISDestroy(&is2);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return ierr;
}
Esempio n. 2
0
void PETSc::Create(
	MPI_Comm Comm, 
	int ilower, 
	int iupper, 
	int d_nz, 
	int o_nz)
{	
	int n	= iupper - ilower +1;
	
	comm 	= Comm;
	iLower	= ilower;	
	iUpper 	= iupper;	
	
	MatCreateAIJ(PETSC_COMM_WORLD,n,n,PETSC_DECIDE,PETSC_DECIDE,
				d_nz,PETSC_NULL,o_nz,PETSC_NULL,&A);	
	ierr = PetscObjectSetName((PetscObject) A, "A");
	ierr = MatSetFromOptions(A);		
	
	// b
	ierr = VecCreate(PETSC_COMM_WORLD, &b);	
	ierr = PetscObjectSetName((PetscObject) b, "b");
	ierr = VecSetSizes(b, n, PETSC_DECIDE);	
	ierr = VecSetFromOptions(b);
	
	ierr = VecCreate(PETSC_COMM_WORLD,&x);
	ierr = PetscObjectSetName((PetscObject) x, "X");
	ierr = VecSetSizes(x, n, PETSC_DECIDE);	
	ierr = VecSetFromOptions(x);
}
Esempio n. 3
0
int main(int argc,char **argv)
{
  Vec            v,s,r,vecs[2];               /* vectors */
  PetscInt       i,start,end,n = 20;
  PetscErrorCode ierr;
  PetscScalar    value;

  PetscInitialize(&argc,&argv,(char*)0,help);
  ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);

  /*
      Create multi-component vector with 2 components
  */
  ierr = VecCreate(PETSC_COMM_WORLD,&v);CHKERRQ(ierr);
  ierr = VecSetSizes(v,PETSC_DECIDE,n);CHKERRQ(ierr);
  ierr = VecSetBlockSize(v,4);CHKERRQ(ierr);
  ierr = VecSetFromOptions(v);CHKERRQ(ierr);

  /*
      Create double-component vectors
  */
  ierr = VecCreate(PETSC_COMM_WORLD,&s);CHKERRQ(ierr);
  ierr = VecSetSizes(s,PETSC_DECIDE,n/2);CHKERRQ(ierr);
  ierr = VecSetBlockSize(s,2);CHKERRQ(ierr);
  ierr = VecSetFromOptions(s);CHKERRQ(ierr);
  ierr = VecDuplicate(s,&r);CHKERRQ(ierr);

  vecs[0] = s;
  vecs[1] = r;
  /*
     Set the vector values
  */
  ierr = VecGetOwnershipRange(v,&start,&end);CHKERRQ(ierr);
  for (i=start; i<end; i++) {
    value = i;
    ierr  = VecSetValues(v,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
  }

  /*
     Get the components from the multi-component vector to the other vectors
  */
  ierr = VecStrideGatherAll(v,vecs,INSERT_VALUES);CHKERRQ(ierr);

  ierr = VecView(s,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecView(r,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);

  ierr = VecStrideScatterAll(vecs,v,ADD_VALUES);CHKERRQ(ierr);

  ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);

  /*
     Free work space.  All PETSc objects should be destroyed when they
     are no longer needed.
  */
  ierr = VecDestroy(&v);CHKERRQ(ierr);
  ierr = VecDestroy(&s);CHKERRQ(ierr);
  ierr = VecDestroy(&r);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return 0;
}
Esempio n. 4
0
void FETI_Operations::export_ext_solver_rhs(Vec vec_in)
{
	homemade_assert_msg(m_bScratchFolderSet,"Scratch folder not set yet!");

	Vec vec_C_micro_t_p_kkk_PETSc;
	VecCreate(m_comm.get(),&vec_C_micro_t_p_kkk_PETSc);
	VecSetSizes(vec_C_micro_t_p_kkk_PETSc,m_C_R_micro_N_local,m_C_R_micro_N);
	VecSetFromOptions(vec_C_micro_t_p_kkk_PETSc);

	Vec vec_C_BIG_t_p_kkk_PETSc;
	VecCreate(m_comm.get(),&vec_C_BIG_t_p_kkk_PETSc);
	VecSetSizes(vec_C_BIG_t_p_kkk_PETSc,m_C_R_BIG_N_local,m_C_R_BIG_N);
	VecSetFromOptions(vec_C_BIG_t_p_kkk_PETSc);

	MatMultTranspose(m_C_R_micro,vec_in,vec_C_micro_t_p_kkk_PETSc);
	MatMultTranspose(m_C_R_BIG,vec_in,vec_C_BIG_t_p_kkk_PETSc);

	write_PETSC_vector(vec_C_BIG_t_p_kkk_PETSc,m_scratch_folder_path + "/ext_solver_A_rhs.petscvec",m_comm.rank(),m_comm.get());
	write_PETSC_vector(vec_C_micro_t_p_kkk_PETSc,m_scratch_folder_path + "/ext_solver_B_rhs.petscvec",m_comm.rank(),m_comm.get());

// Print MatLab debugging output? Variable defined at "carl_headers.h"
#ifdef PRINT_MATLAB_DEBUG
	write_PETSC_vector_MATLAB(vec_C_micro_t_p_kkk_PETSc,m_scratch_folder_path + "/ext_solver_B_rhs.m",m_comm.get());
	write_PETSC_vector_MATLAB(vec_C_BIG_t_p_kkk_PETSc,m_scratch_folder_path + "/ext_solver_A_rhs.m",m_comm.get());
#endif

	VecDestroy(&vec_C_micro_t_p_kkk_PETSc);
	VecDestroy(&vec_C_BIG_t_p_kkk_PETSc);
}
Esempio n. 5
0
/*@
   MatMultEqual - Compares matrix-vector products of two matrices.

   Collective on Mat

   Input Parameters:
+  A - the first matrix
-  B - the second matrix
-  n - number of random vectors to be tested

   Output Parameter:
.  flg - PETSC_TRUE if the products are equal; PETSC_FALSE otherwise.

   Level: intermediate

   Concepts: matrices^equality between
@*/
PetscErrorCode  MatMultEqual(Mat A,Mat B,PetscInt n,PetscBool  *flg)
{
  PetscErrorCode ierr;
  Vec            x,s1,s2;
  PetscRandom    rctx;
  PetscReal      r1,r2,tol=1.e-10;
  PetscInt       am,an,bm,bn,k;
  PetscScalar    none = -1.0;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(A,MAT_CLASSID,1); 
  PetscValidHeaderSpecific(B,MAT_CLASSID,2);
  ierr = MatGetLocalSize(A,&am,&an);CHKERRQ(ierr);
  ierr = MatGetLocalSize(B,&bm,&bn);CHKERRQ(ierr);
  if (am != bm || an != bn) SETERRQ4(PETSC_COMM_SELF,PETSC_ERR_ARG_SIZ,"Mat A,Mat B: local dim %D %D %D %D",am,bm,an,bn);
  PetscCheckSameComm(A,1,B,2);

#if defined(PETSC_USE_REAL_SINGLE)
  tol  = 1.e-5;
#endif
  ierr = PetscRandomCreate(((PetscObject)A)->comm,&rctx);CHKERRQ(ierr);
  ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
  ierr = VecCreate(((PetscObject)A)->comm,&x);CHKERRQ(ierr);
  ierr = VecSetSizes(x,an,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(x);CHKERRQ(ierr);
  
  ierr = VecCreate(((PetscObject)A)->comm,&s1);CHKERRQ(ierr);
  ierr = VecSetSizes(s1,am,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(s1);CHKERRQ(ierr);
  ierr = VecDuplicate(s1,&s2);CHKERRQ(ierr);
  
  *flg = PETSC_TRUE;
  for (k=0; k<n; k++) {
    ierr = VecSetRandom(x,rctx);CHKERRQ(ierr);
    ierr = MatMult(A,x,s1);CHKERRQ(ierr);
    ierr = MatMult(B,x,s2);CHKERRQ(ierr);
    ierr = VecNorm(s2,NORM_INFINITY,&r2);CHKERRQ(ierr);
    if (r2 < tol){
      ierr = VecNorm(s1,NORM_INFINITY,&r1);CHKERRQ(ierr);
    } else {
      ierr = VecAXPY(s2,none,s1);CHKERRQ(ierr);
      ierr = VecNorm(s2,NORM_INFINITY,&r1);CHKERRQ(ierr);
      r1 /= r2;
    }
    if (r1 > tol) {
      *flg = PETSC_FALSE;
      ierr = PetscInfo2(A,"Error: %D-th MatMult() %G\n",k,r1);CHKERRQ(ierr);
      break;
    } 
  }
  ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);
  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = VecDestroy(&s1);CHKERRQ(ierr);
  ierr = VecDestroy(&s2);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
void MultigridSolver_UpdateWorkVectors( MultigridSolver* self ) {
	MultigridSolver_Level*	level;
	//unsigned		rowSize, colSize;
	PetscInt		rowSize, colSize, vecSize;
	unsigned		l_i;

	assert( self && Stg_CheckType( self, MultigridSolver ) );

	for( l_i = 0; l_i < self->nLevels - 1; l_i++ ) {
		level = self->levels + l_i;

		//Matrix_GetLocalSize( MatrixSolver_GetMatrix( level->downSolver ), &rowSize, &colSize );
		MatGetLocalSize( level->downSolver->matrix, &rowSize, &colSize );

		VecGetLocalSize( level->workSol, &vecSize );

		//if( !level->workSol || Vector_GetLocalSize( level->workSol ) != rowSize ) {
		if( !level->workSol || vecSize != rowSize ) {
			//if( level->workSol )
			//	Stg_Class_RemoveRef( level->workSol );
			//Vector_Duplicate( self->curSolution, (void**)&level->workSol );
			//Vector_SetLocalSize( level->workSol, rowSize );
			if( level->workSol != PETSC_NULL )
				Stg_VecDestroy(&level->workSol );
			VecCreate( self->mgData->comm, &level->workSol );
			VecSetSizes( level->workSol, rowSize, PETSC_DECIDE );
			VecSetFromOptions( level->workSol );
#if( PETSC_VERSION_MAJOR <= 2 && PETSC_VERSION_MINOR >= 3 && PETSC_VERSION_SUBMINOR >= 3 )
			VecSetOption( level->workSol, VEC_IGNORE_NEGATIVE_INDICES );
#elif( PETSC_VERSION_MAJOR >= 3 )
			VecSetOption( level->workSol, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE );
#endif
		}

		VecGetLocalSize( level->workRHS, &vecSize );

		if( !level->workRHS || /*Vector_GetLocalSize( level->workRHS )*/vecSize != rowSize ) {
			//if( level->workRHS )
			//	Stg_Class_RemoveRef( level->workRHS );
			//Vector_Duplicate( self->curSolution, (void**)&level->workRHS );
			//Vector_SetLocalSize( level->workRHS, rowSize );
			if( level->workRHS != PETSC_NULL )
				Stg_VecDestroy(&level->workRHS );
			VecCreate( self->mgData->comm, &level->workRHS );
			VecSetSizes( level->workRHS, rowSize, PETSC_DECIDE );
			VecSetFromOptions( level->workRHS );
#if( PETSC_VERSION_MAJOR <= 2 && PETSC_VERSION_MINOR >= 3 && PETSC_VERSION_SUBMINOR >= 3 )
			VecSetOption( level->workRHS, VEC_IGNORE_NEGATIVE_INDICES );
#elif( PETSC_VERSION_MAJOR >= 3 )
			VecSetOption( level->workRHS, VEC_IGNORE_NEGATIVE_INDICES, PETSC_TRUE );
#endif
		}
	}
}
Esempio n. 7
0
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  Vec            v,s;               /* vectors */
  PetscInt       n = 20;
  PetscScalar    one = 1.0;

  PetscInitialize(&argc,&argv,(char*)0,help);
  ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);

  /*
      Create multi-component vector with 2 components
  */
  ierr = VecCreate(PETSC_COMM_WORLD,&v);CHKERRQ(ierr);
  ierr = VecSetSizes(v,PETSC_DECIDE,n);CHKERRQ(ierr);
  ierr = VecSetBlockSize(v,2);CHKERRQ(ierr);
  ierr = VecSetFromOptions(v);CHKERRQ(ierr);

  /*
      Create single-component vector
  */
  ierr = VecCreate(PETSC_COMM_WORLD,&s);CHKERRQ(ierr);
  ierr = VecSetSizes(s,PETSC_DECIDE,n/2);CHKERRQ(ierr);
  ierr = VecSetFromOptions(s);CHKERRQ(ierr);

  /*
     Set the vectors to entries to a constant value.
  */
  ierr = VecSet(v,one);CHKERRQ(ierr);

  /*
     Get the first component from the multi-component vector to the single vector
  */
  ierr = VecStrideGather(v,0,s,INSERT_VALUES);CHKERRQ(ierr);

  ierr = VecView(s,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);

  /*
     Put the values back into the second component
  */
  ierr = VecStrideScatter(s,1,v,ADD_VALUES);CHKERRQ(ierr);

  ierr = VecView(v,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);

  /*
     Free work space.  All PETSc objects should be destroyed when they
     are no longer needed.
  */
  ierr = VecDestroy(&v);CHKERRQ(ierr);
  ierr = VecDestroy(&s);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return 0;
}
Esempio n. 8
0
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  PetscInt       n = 5,N,i;
  PetscMPIInt    size,rank;
  PetscScalar    value,zero = 0.0;
  Vec            x,y;
  IS             is1,is2;
  VecScatter     ctx = 0;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); 
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);

  /* create two vectors */
  N = size*n; 
  ierr = VecCreate(PETSC_COMM_WORLD,&y);CHKERRQ(ierr);
  ierr = VecSetSizes(y,n,PETSC_DECIDE);CHKERRQ(ierr)
  ierr = VecSetFromOptions(y);CHKERRQ(ierr);

  ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
  ierr = VecSetSizes(x,n,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(x);CHKERRQ(ierr);

  /* create two index sets */
  ierr = ISCreateStride(PETSC_COMM_WORLD,n,n*rank,1,&is1);CHKERRQ(ierr);
  ierr = ISCreateStride(PETSC_COMM_WORLD,n,(n*(rank+1))%N,1,&is2);CHKERRQ(ierr);

  /* fill local part of parallel vector x */
  value = (PetscScalar)(rank+1); 
  for (i=n*rank; i<n*(rank+1); i++) {
    ierr = VecSetValues(x,1,&i,&value,INSERT_VALUES);CHKERRQ(ierr);
  }
  ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
  ierr = VecAssemblyEnd(x);CHKERRQ(ierr);

  ierr = VecSet(y,zero);CHKERRQ(ierr);

  ierr = VecScatterCreate(x,is1,y,is2,&ctx);CHKERRQ(ierr);
  ierr = VecScatterBegin(ctx,x,y,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterEnd(ctx,x,y,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterDestroy(ctx);CHKERRQ(ierr);
  
  ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);

  ierr = VecDestroy(x);CHKERRQ(ierr);
  ierr = VecDestroy(y);CHKERRQ(ierr);
  ierr = ISDestroy(is1);CHKERRQ(ierr);
  ierr = ISDestroy(is2);CHKERRQ(ierr);

  ierr = PetscFinalize();CHKERRQ(ierr);
  return 0;
}
Esempio n. 9
0
int main(int argc,char **args)
{
  KSP            ksp;      /* linear solver context */
  Mat            A;        /* linear system matrix */
  Vec            x,b;      /* approx solution, RHS */
  PetscInt       Ii,Istart,Iend;
  PetscErrorCode ierr;
  PetscScalar    v[3] = {-1./2., 1., -1./2.};
  PetscInt       j[3];
  PetscInt       k=15;
  PetscInt       M,m=420;

  ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
  ierr = PetscOptionsGetInt(NULL,NULL,"-k",&k,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-m",&m,NULL);CHKERRQ(ierr);

  ierr = KSPCreate(PETSC_COMM_WORLD,&ksp);CHKERRQ(ierr);
  ierr = KSPSetFromOptions(ksp);CHKERRQ(ierr);
  ierr = KSPGetOperators(ksp,&A,NULL);CHKERRQ(ierr);

  ierr = MatSetSizes(A,m,m,PETSC_DETERMINE,PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);
  ierr = MatGetOwnershipRange(A,&Istart,&Iend);CHKERRQ(ierr);
  ierr = MatGetSize(A,&M,NULL);CHKERRQ(ierr);
  for (Ii=Istart; Ii<Iend; Ii++) {
    j[0] = Ii - k;
    j[1] = Ii;
    j[2] = (Ii + k) < M ? (Ii + k) : -1;
    ierr = MatSetValues(A,1,&Ii,3,j,v,INSERT_VALUES);CHKERRQ(ierr);
  }
  ierr = MatAssemblyBegin(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatAssemblyEnd(A,MAT_FINAL_ASSEMBLY);CHKERRQ(ierr);
  ierr = MatCreateVecs(A,&x,&b);CHKERRQ(ierr);

  ierr = VecSetFromOptions(b);CHKERRQ(ierr);
  ierr = VecSet(b,1.0);CHKERRQ(ierr);
  ierr = VecSetFromOptions(x);CHKERRQ(ierr);
  ierr = VecSet(x,2.0);CHKERRQ(ierr);

  ierr = KSPSolve(ksp,b,x);CHKERRQ(ierr);

  ierr = VecDestroy(&b);CHKERRQ(ierr);
  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = KSPDestroy(&ksp);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return ierr;
}
Esempio n. 10
0
void operator| (PUP::er& p, Vec& v) {
  PetscInt sz;
  if (!p.isUnpacking()) {
    VecGetSize(v, &sz);
  }
  p | sz;
  if(p.isUnpacking()) {    
	  VecCreateSeq(PETSC_COMM_WORLD, sz,  &v);
	  VecSetFromOptions(v);
	  VecGetSize(v, &sz);

	  for (int i = 0; i < sz; i++) {
		  PetscScalar d;
		  p | d;
		  VecSetValue(v, i, d, INSERT_VALUES);
	  }
	  VecAssemblyBegin(v);
	  VecAssemblyEnd(v);
  }
  else {
	  for (int i = 0; i < sz; i++) {
		  PetscScalar d;
		  VecGetValues(v, 1, &i, &d);
		  p | d;
	  }
  }
}
Esempio n. 11
0
int main(int argc,char **args)
{
  PetscErrorCode ierr;
  PetscInt       m = 10;
  int            fcomm;
  Vec            vec;

  ierr = PetscInitialize(&argc,&args,(char*)0,help);if (ierr) return ierr;
  /* This function should be called to be able to use PETSc routines
     from the FORTRAN subroutines needed by this program */

  PetscInitializeFortran();

  ierr = VecCreate(PETSC_COMM_WORLD,&vec);CHKERRQ(ierr);
  ierr = VecSetSizes(vec,PETSC_DECIDE,m);CHKERRQ(ierr);
  ierr = VecSetFromOptions(vec);CHKERRQ(ierr);

  /*
     Call Fortran routine - the use of MPI_Comm_c2f() allows
     translation of the MPI_Comm from C so that it can be properly
     interpreted from Fortran.
  */
  fcomm = MPI_Comm_c2f(PETSC_COMM_WORLD);

  ex7f_(&vec,&fcomm);

  ierr = VecView(vec,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecDestroy(&vec);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Esempio n. 12
0
File: atan.c Progetto: bueler/p4pdes
int main(int argc,char **argv) {
    PetscErrorCode ierr;
    SNES      snes;          // nonlinear solver context
    Vec       x, r;          // solution, residual vectors
    PetscReal x0 = 2.0;

    PetscInitialize(&argc,&argv,(char*)0,help);

    ierr = PetscOptionsBegin(PETSC_COMM_WORLD,"","options to atan","");CHKERRQ(ierr);
    ierr = PetscOptionsReal("-x0","initial value","atan.c",x0,&x0,NULL); CHKERRQ(ierr);
    ierr = PetscOptionsEnd();CHKERRQ(ierr);

    ierr = VecCreate(PETSC_COMM_WORLD,&x); CHKERRQ(ierr);
    ierr = VecSetSizes(x,PETSC_DECIDE,1); CHKERRQ(ierr);
    ierr = VecSetFromOptions(x); CHKERRQ(ierr);
    ierr = VecSet(x,x0); CHKERRQ(ierr);
    ierr = VecDuplicate(x,&r); CHKERRQ(ierr);

    ierr = SNESCreate(PETSC_COMM_WORLD,&snes); CHKERRQ(ierr);
    ierr = SNESSetFunction(snes,r,FormFunction,NULL); CHKERRQ(ierr);
    ierr = SNESSetFromOptions(snes); CHKERRQ(ierr);
    ierr = SNESSolve(snes,NULL,x); CHKERRQ(ierr);
    ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD); CHKERRQ(ierr);

    VecDestroy(&x);  VecDestroy(&r);  SNESDestroy(&snes);
    PetscFinalize();
    return 0;
}
Esempio n. 13
0
PetscErrorCode DistributeCoordinates(DM dm, PetscSF pointSF, DM parallelDM)
{
  PetscSF        coordSF;
  PetscSection   originalCoordSection, newCoordSection;
  Vec            coordinates, newCoordinates;
  PetscScalar   *coords,     *newCoords;
  PetscInt      *remoteOffsets, coordSize;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMMeshGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr);
  ierr = DMMeshGetCoordinateSection(parallelDM, &newCoordSection);CHKERRQ(ierr);
  ierr = PetscSFDistributeSection(pointSF, originalCoordSection, &remoteOffsets, newCoordSection);CHKERRQ(ierr);

  ierr = DMMeshGetCoordinateVec(dm, &coordinates);CHKERRQ(ierr);
  ierr = DMMeshGetCoordinateVec(parallelDM, &newCoordinates);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(newCoordSection, &coordSize);CHKERRQ(ierr);
  ierr = VecSetSizes(newCoordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(newCoordinates);CHKERRQ(ierr);

  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = VecGetArray(newCoordinates, &newCoords);CHKERRQ(ierr);
  ierr = PetscSFCreateSectionSF(pointSF, originalCoordSection, remoteOffsets, newCoordSection, &coordSF);CHKERRQ(ierr);
  ierr = PetscSFBcastBegin(coordSF, MPIU_SCALAR, coords, newCoords);CHKERRQ(ierr);
  ierr = PetscSFBcastEnd(coordSF, MPIU_SCALAR, coords, newCoords);CHKERRQ(ierr);
  ierr = PetscSFDestroy(&coordSF);CHKERRQ(ierr);
  ierr = VecRestoreArray(newCoordinates, &newCoords);CHKERRQ(ierr);
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Esempio n. 14
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SparseGp *
SparseGp_create (AcfrKern *kern, int rank, gsl_matrix *trainObs, 
                 gsl_vector *trainLabels, gsl_matrix *testObs, 
                 gsl_vector *testLabels)
{
    PetscErrorCode ierr;        /* not used here - not returning int */
    (void) ierr;

    SparseGp *gp = calloc (1, sizeof (*gp));

    gp->kern = kern;

    gp->trainObs = trainObs;
    gp->trainLabels = trainLabels;
    gp->testObs = testObs;
    gp->testLabels = testLabels;

    PetscInt N = gp->trainLabels->size;
    ierr = VecCreate (PETSC_COMM_WORLD, &(gp->_trainLabels)); /* CHKERRQ (ierr); */
    ierr = VecSetSizes (gp->_trainLabels, PETSC_DECIDE, N); /* CHKERRQ (ierr); */
    ierr = VecSetFromOptions (gp->_trainLabels); /* CHKERRQ (ierr); */

    ierr = VecGetOwnershipRange (gp->_trainLabels, &(gp->rstart), &(gp->rend)); /* CHKERRQ (ierr); */
    ierr = VecGetLocalSize (gp->_trainLabels, &(gp->nlocal)); /* CHKERRQ (ierr); */
    petsc_util_fillVec (gp->trainLabels, &gp->_trainLabels, gp->rstart, gp->rend);

    gp->rank = rank;

    return gp;
}
Esempio n. 15
0
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  PetscMPIInt    rank;
  PetscInt       n = 5;
  char           *output;
  Vec            x;

  PetscInitialize(&argc,&argv,(char *)0,0);

  ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
  ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
  ierr = VecSetFromOptions(x);CHKERRQ(ierr);

  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);
  ierr = PetscMatlabEngineGetOutput(PETSC_MATLAB_ENGINE_WORLD,&output);
  ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"MPI_Comm_rank");
  ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d]Processor rank is %s",rank,output);CHKERRQ(ierr);
  ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD);CHKERRQ(ierr);

  ierr = PetscObjectSetName((PetscObject)x,"x");CHKERRQ(ierr);
  ierr = PetscMatlabEnginePut(PETSC_MATLAB_ENGINE_WORLD,(PetscObject)x);CHKERRQ(ierr);
  ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"x = x + MPI_Comm_rank;\n");
  ierr = PetscMatlabEngineGet(PETSC_MATLAB_ENGINE_WORLD,(PetscObject)x);CHKERRQ(ierr);

  ierr = PetscMatlabEngineEvaluate(PETSC_MATLAB_ENGINE_WORLD,"whos\n");
  ierr = PetscSynchronizedPrintf(PETSC_COMM_WORLD,"[%d]The result is %s",rank,output);CHKERRQ(ierr);
  ierr = PetscSynchronizedFlush(PETSC_COMM_WORLD);CHKERRQ(ierr);

  ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecDestroy(x);CHKERRQ(ierr);
  ierr = PetscFinalize();CHKERRQ(ierr);
  return 0;
}
Esempio n. 16
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File: ex25.c Progetto: Kun-Qu/petsc
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  PetscInt       n = 5,N,low,high,iglobal,i;
  PetscMPIInt    size,rank;
  PetscScalar    value,zero = 0.0;
  Vec            x,y;
  IS             is1,is2;
  VecScatter     ctx;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr); 
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);

  /* create two vectors */
  N = size*n;
  ierr = VecCreate(PETSC_COMM_WORLD,&y);CHKERRQ(ierr);
  ierr = VecSetSizes(y,PETSC_DECIDE,N);CHKERRQ(ierr);
  ierr = VecSetFromOptions(y);CHKERRQ(ierr);
  if (!rank) {
    ierr = VecCreateSeq(PETSC_COMM_SELF,N,&x);CHKERRQ(ierr);
  } else {
    ierr = VecCreateSeq(PETSC_COMM_SELF,0,&x);CHKERRQ(ierr);
  }

  /* create two index sets */
  if (!rank) {
    ierr = ISCreateStride(PETSC_COMM_SELF,N,0,1,&is1);CHKERRQ(ierr);
    ierr = ISCreateStride(PETSC_COMM_SELF,N,0,1,&is2);CHKERRQ(ierr);
  } else {
    ierr = ISCreateStride(PETSC_COMM_SELF,0,0,1,&is1);CHKERRQ(ierr);
    ierr = ISCreateStride(PETSC_COMM_SELF,0,0,1,&is2);CHKERRQ(ierr);
  }

  ierr = VecSet(x,zero);CHKERRQ(ierr);
  ierr = VecGetOwnershipRange(y,&low,&high);CHKERRQ(ierr);
  for (i=0; i<n; i++) {
    iglobal = i + low; value = (PetscScalar) (i + 10*rank);
    ierr = VecSetValues(y,1,&iglobal,&value,INSERT_VALUES);CHKERRQ(ierr);
  }
  ierr = VecAssemblyBegin(y);CHKERRQ(ierr);
  ierr = VecAssemblyEnd(y);CHKERRQ(ierr);
  ierr = VecView(y,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);

  ierr = VecScatterCreate(y,is2,x,is1,&ctx);CHKERRQ(ierr);
  ierr = VecScatterBegin(ctx,y,x,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterEnd(ctx,y,x,ADD_VALUES,SCATTER_FORWARD);CHKERRQ(ierr);
  ierr = VecScatterDestroy(&ctx);CHKERRQ(ierr);
  
  if (!rank) 
    {printf("----\n"); ierr = VecView(x,PETSC_VIEWER_STDOUT_SELF);CHKERRQ(ierr);}

  ierr = VecDestroy(&x);CHKERRQ(ierr);
  ierr = VecDestroy(&y);CHKERRQ(ierr);
  ierr = ISDestroy(&is1);CHKERRQ(ierr);
  ierr = ISDestroy(&is2);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return 0;
}
Esempio n. 17
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/*
  This takes as input the coordinates for each vertex
*/
PetscErrorCode DMPlexBuildCoordinates_Private(DM dm, PetscInt spaceDim, PetscInt numCells, PetscInt numVertices, const double vertexCoords[])
{
  PetscSection   coordSection;
  Vec            coordinates;
  PetscScalar   *coords;
  PetscInt       coordSize, v, d;
  PetscErrorCode ierr;

  PetscFunctionBegin;
  ierr = DMPlexGetCoordinateSection(dm, &coordSection);CHKERRQ(ierr);
  ierr = PetscSectionSetNumFields(coordSection, 1);CHKERRQ(ierr);
  ierr = PetscSectionSetFieldComponents(coordSection, 0, spaceDim);CHKERRQ(ierr);
  ierr = PetscSectionSetChart(coordSection, numCells, numCells + numVertices);CHKERRQ(ierr);
  for (v = numCells; v < numCells+numVertices; ++v) {
    ierr = PetscSectionSetDof(coordSection, v, spaceDim);CHKERRQ(ierr);
    ierr = PetscSectionSetFieldDof(coordSection, v, 0, spaceDim);CHKERRQ(ierr);
  }
  ierr = PetscSectionSetUp(coordSection);CHKERRQ(ierr);
  ierr = PetscSectionGetStorageSize(coordSection, &coordSize);CHKERRQ(ierr);
  ierr = VecCreate(PetscObjectComm((PetscObject)dm), &coordinates);CHKERRQ(ierr);
  ierr = PetscObjectSetName((PetscObject) coordinates, "coordinates");CHKERRQ(ierr);
  ierr = VecSetSizes(coordinates, coordSize, PETSC_DETERMINE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(coordinates);CHKERRQ(ierr);
  ierr = VecGetArray(coordinates, &coords);CHKERRQ(ierr);
  for (v = 0; v < numVertices; ++v) {
    for (d = 0; d < spaceDim; ++d) {
      coords[v*spaceDim+d] = vertexCoords[v*spaceDim+d];
    }
  }
  ierr = VecRestoreArray(coordinates, &coords);CHKERRQ(ierr);
  ierr = DMSetCoordinatesLocal(dm, coordinates);CHKERRQ(ierr);
  ierr = VecDestroy(&coordinates);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Esempio n. 18
0
PetscErrorCode MatSetLocalToGlobalMapping_IS(Mat A,ISLocalToGlobalMapping rmapping,ISLocalToGlobalMapping cmapping)
{
  PetscErrorCode ierr;
  PetscInt       n,bs;
  Mat_IS         *is = (Mat_IS*)A->data;
  IS             from,to;
  Vec            global;

  PetscFunctionBegin;
  PetscCheckSameComm(A,1,rmapping,2);
  if (rmapping != cmapping) SETERRQ(PetscObjectComm((PetscObject)A),PETSC_ERR_ARG_INCOMP,"MATIS requires the row and column mappings to be identical");
  if (is->mapping) { /* Currenly destroys the objects that will be created by this routine. Is there anything else that should be checked? */
    ierr = ISLocalToGlobalMappingDestroy(&is->mapping);CHKERRQ(ierr);
    ierr = VecDestroy(&is->x);CHKERRQ(ierr);
    ierr = VecDestroy(&is->y);CHKERRQ(ierr);
    ierr = VecScatterDestroy(&is->ctx);CHKERRQ(ierr);
    ierr = MatDestroy(&is->A);CHKERRQ(ierr);
  }
  ierr = PetscObjectReference((PetscObject)rmapping);CHKERRQ(ierr);
  ierr = ISLocalToGlobalMappingDestroy(&is->mapping);CHKERRQ(ierr);
  is->mapping = rmapping;
/*
  ierr = PetscLayoutSetISLocalToGlobalMapping(A->rmap,rmapping);CHKERRQ(ierr);
  ierr = PetscLayoutSetISLocalToGlobalMapping(A->cmap,cmapping);CHKERRQ(ierr);
*/

  /* Create the local matrix A */
  ierr = ISLocalToGlobalMappingGetSize(rmapping,&n);CHKERRQ(ierr);
  ierr = ISLocalToGlobalMappingGetBlockSize(rmapping,&bs);CHKERRQ(ierr);
  ierr = MatCreate(PETSC_COMM_SELF,&is->A);CHKERRQ(ierr);
  if (bs > 1) {
    ierr = MatSetType(is->A,MATSEQBAIJ);CHKERRQ(ierr);
  } else {
    ierr = MatSetType(is->A,MATSEQAIJ);CHKERRQ(ierr);
  }
  ierr = MatSetSizes(is->A,n,n,n,n);CHKERRQ(ierr);
  ierr = MatSetBlockSize(is->A,bs);CHKERRQ(ierr);
  ierr = MatSetOptionsPrefix(is->A,((PetscObject)A)->prefix);CHKERRQ(ierr);
  ierr = MatAppendOptionsPrefix(is->A,"is_");CHKERRQ(ierr);
  ierr = MatSetFromOptions(is->A);CHKERRQ(ierr);

  /* Create the local work vectors */
  ierr = VecCreate(PETSC_COMM_SELF,&is->x);CHKERRQ(ierr);
  ierr = VecSetBlockSize(is->x,bs);CHKERRQ(ierr);
  ierr = VecSetSizes(is->x,n,n);CHKERRQ(ierr);
  ierr = VecSetOptionsPrefix(is->x,((PetscObject)A)->prefix);CHKERRQ(ierr);
  ierr = VecAppendOptionsPrefix(is->x,"is_");CHKERRQ(ierr);
  ierr = VecSetFromOptions(is->x);CHKERRQ(ierr);
  ierr = VecDuplicate(is->x,&is->y);CHKERRQ(ierr);

  /* setup the global to local scatter */
  ierr = ISCreateStride(PETSC_COMM_SELF,n,0,1,&to);CHKERRQ(ierr);
  ierr = ISLocalToGlobalMappingApplyIS(rmapping,to,&from);CHKERRQ(ierr);
  ierr = MatCreateVecs(A,&global,NULL);CHKERRQ(ierr);
  ierr = VecScatterCreate(global,from,is->x,to,&is->ctx);CHKERRQ(ierr);
  ierr = VecDestroy(&global);CHKERRQ(ierr);
  ierr = ISDestroy(&to);CHKERRQ(ierr);
  ierr = ISDestroy(&from);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Esempio n. 19
0
void FETI_Operations::set_jacobi_precond_vector()
{
	homemade_assert_msg(m_bC_RR_MatrixSet,"Preconditioner matrix not set yet!");

	// Create and set the vector
	VecCreate(m_comm.get(),&m_coupling_jacobi_precond_vec);
	VecSetSizes(m_coupling_jacobi_precond_vec,m_C_RR_M_local,m_C_RR_M);
	VecSetFromOptions(m_coupling_jacobi_precond_vec);

	// Get the diagonal
	MatGetDiagonal(m_C_RR,m_coupling_jacobi_precond_vec);

	// Calculate the reciprocal
	VecReciprocal(m_coupling_jacobi_precond_vec);

	// Export it
	write_PETSC_vector(m_coupling_jacobi_precond_vec,m_scratch_folder_path + "/precond_Jacobi_vector.petscvec",m_comm.rank(),m_comm.get());

// Print MatLab debugging output? Variable defined at "carl_headers.h"
#ifdef PRINT_MATLAB_DEBUG
	write_PETSC_vector_MATLAB(m_coupling_jacobi_precond_vec,m_scratch_folder_path + "/precond_Jacobi_vector.m",m_comm.get());
#endif

	// Set flag
	m_bCreatedPrecondJacobiVec = true;
}
Esempio n. 20
0
int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  PetscInt       time_steps = 100,steps;
  PetscMPIInt    size;
  Vec            global;
  PetscReal      dt,ftime;
  TS             ts;
  MatStructure   A_structure;
  Mat            A = 0;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);CHKERRQ(ierr);
  ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);

  ierr = PetscOptionsGetInt(NULL,"-time",&time_steps,NULL);CHKERRQ(ierr);

  /* set initial conditions */
  ierr = VecCreate(PETSC_COMM_WORLD,&global);CHKERRQ(ierr);
  ierr = VecSetSizes(global,PETSC_DECIDE,3);CHKERRQ(ierr);
  ierr = VecSetFromOptions(global);CHKERRQ(ierr);
  ierr = Initial(global,NULL);CHKERRQ(ierr);

  /* make timestep context */
  ierr = TSCreate(PETSC_COMM_WORLD,&ts);CHKERRQ(ierr);
  ierr = TSSetProblemType(ts,TS_NONLINEAR);CHKERRQ(ierr);
  ierr = TSMonitorSet(ts,Monitor,NULL,NULL);CHKERRQ(ierr);

  dt = 0.1;

  /*
    The user provides the RHS and Jacobian
  */
  ierr = TSSetRHSFunction(ts,NULL,RHSFunction,NULL);CHKERRQ(ierr);
  ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
  ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,3,3);CHKERRQ(ierr);
  ierr = MatSetFromOptions(A);CHKERRQ(ierr);
  ierr = MatSetUp(A);CHKERRQ(ierr);
  ierr = RHSJacobian(ts,0.0,global,&A,&A,&A_structure,NULL);CHKERRQ(ierr);
  ierr = TSSetRHSJacobian(ts,A,A,RHSJacobian,NULL);CHKERRQ(ierr);

  ierr = TSSetFromOptions(ts);CHKERRQ(ierr);

  ierr = TSSetInitialTimeStep(ts,0.0,dt);CHKERRQ(ierr);
  ierr = TSSetDuration(ts,time_steps,1);CHKERRQ(ierr);
  ierr = TSSetSolution(ts,global);CHKERRQ(ierr);

  ierr = TSSolve(ts,global);CHKERRQ(ierr);
  ierr = TSGetSolveTime(ts,&ftime);CHKERRQ(ierr);
  ierr = TSGetTimeStepNumber(ts,&steps);CHKERRQ(ierr);


  /* free the memories */

  ierr = TSDestroy(&ts);CHKERRQ(ierr);
  ierr = VecDestroy(&global);CHKERRQ(ierr);
  ierr = MatDestroy(&A);CHKERRQ(ierr);

  ierr = PetscFinalize();
  return 0;
}
Esempio n. 21
0
PetscErrorCode  DMCreateGlobalVector_DA(DM da,Vec* g)
{
  PetscErrorCode ierr;
  DM_DA          *dd = (DM_DA*)da->data;

  PetscFunctionBegin;
  PetscValidHeaderSpecific(da,DM_CLASSID,1);
  PetscValidPointer(g,2);
  if (da->defaultSection) {
    ierr = DMCreateGlobalVector_Section_Private(da,g);CHKERRQ(ierr);
  } else {
    ierr = VecCreate(((PetscObject)da)->comm,g);CHKERRQ(ierr);
    ierr = VecSetSizes(*g,dd->Nlocal,PETSC_DETERMINE);CHKERRQ(ierr);
    ierr = VecSetBlockSize(*g,dd->w);CHKERRQ(ierr);
    ierr = VecSetType(*g,da->vectype);CHKERRQ(ierr);
    ierr = VecSetFromOptions(*g);CHKERRQ(ierr);
    ierr = VecSetDM(*g, da);CHKERRQ(ierr);
    ierr = VecSetLocalToGlobalMapping(*g,da->ltogmap);CHKERRQ(ierr);
    ierr = VecSetLocalToGlobalMappingBlock(*g,da->ltogmapb);CHKERRQ(ierr);
  }
  ierr = VecSetOperation(*g,VECOP_VIEW,(void(*)(void))VecView_MPI_DA);CHKERRQ(ierr);
  ierr = VecSetOperation(*g,VECOP_LOAD,(void(*)(void))VecLoad_Default_DA);CHKERRQ(ierr);
  ierr = VecSetOperation(*g,VECOP_DUPLICATE,(void(*)(void))VecDuplicate_MPI_DA);CHKERRQ(ierr);
  PetscFunctionReturn(0);
}
Esempio n. 22
0
File: ml.c Progetto: Kun-Qu/petsc
static PetscErrorCode MatWrapML_SHELL(ML_Operator *mlmat,MatReuse reuse,Mat *newmat) 
{
  PetscErrorCode ierr;
  PetscInt       m,n;
  ML_Comm        *MLcomm;
  Mat_MLShell    *shellctx;

  PetscFunctionBegin;
  m = mlmat->outvec_leng; 
  n = mlmat->invec_leng;

  if (reuse){
    ierr = MatShellGetContext(*newmat,(void **)&shellctx);CHKERRQ(ierr);
    shellctx->mlmat = mlmat;
    PetscFunctionReturn(0);
  }

  MLcomm = mlmat->comm;
  ierr = PetscNew(Mat_MLShell,&shellctx);CHKERRQ(ierr);
  ierr = MatCreateShell(MLcomm->USR_comm,m,n,PETSC_DETERMINE,PETSC_DETERMINE,shellctx,newmat);CHKERRQ(ierr);
  ierr = MatShellSetOperation(*newmat,MATOP_MULT,(void(*)(void))MatMult_ML);CHKERRQ(ierr); 
  ierr = MatShellSetOperation(*newmat,MATOP_MULT_ADD,(void(*)(void))MatMultAdd_ML);CHKERRQ(ierr); 
  shellctx->A         = *newmat;
  shellctx->mlmat     = mlmat;
  shellctx->work      = PETSC_NULL;
  ierr = VecCreate(MLcomm->USR_comm,&shellctx->y);CHKERRQ(ierr);
  ierr = VecSetSizes(shellctx->y,m,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(shellctx->y);CHKERRQ(ierr);
  (*newmat)->ops->destroy = MatDestroy_ML;
  PetscFunctionReturn(0);
}
Esempio n. 23
0
void linearSystemPETSc<scalar>::allocate(int nbRows)
{
  int commSize;
  MPI_Comm_size(_comm, &commSize);
  int blockSize = _getBlockSizeFromParameters();
  clear();
  _try(MatCreate(_comm, &_a));
  _try(MatSetSizes(_a, blockSize * nbRows, blockSize * nbRows, PETSC_DETERMINE, PETSC_DETERMINE));
  if (blockSize > 1) {
    if (commSize > 1) {
      _try(MatSetType(_a, MATMPIBAIJ));
    }
    else {
      _try(MatSetType(_a, MATSEQBAIJ));
    }
  }
  // override the default options with the ones from the option
  // database (if any)
  if (this->_parameters.count("petscOptions"))
    _try(PetscOptionsInsertString(this->_parameters["petscOptions"].c_str()));
  if (this->_parameters.count("petscPrefix"))
    _try(MatAppendOptionsPrefix(_a, this->_parameters["petscPrefix"].c_str()));
  _try(MatSetFromOptions(_a));
  //since PETSc 3.3 GetOwnershipRange and MatGetSize cannot be called before MatXXXSetPreallocation
  _localSize = nbRows;
  #ifdef HAVE_MPI
  if (commSize>1){
    _localRowStart = 0;
    if (Msg::GetCommRank() != 0) {
      MPI_Status status;
      MPI_Recv((void*)&_localRowStart, 1, MPI_INT, Msg::GetCommRank() - 1, 1, MPI_COMM_WORLD, &status);
    }
    _localRowEnd = _localRowStart + nbRows;
    if (Msg::GetCommRank() != Msg::GetCommSize() - 1) {
      MPI_Send((void*)&_localRowEnd, 1, MPI_INT, Msg::GetCommRank() + 1, 1, MPI_COMM_WORLD);
    }
    MPI_Allreduce((void*)&_localSize, (void*)&_globalSize, 1, MPI_INT, MPI_SUM, MPI_COMM_WORLD);
  }
  else{
    _localRowStart = 0;
    _localRowEnd = nbRows;
    _globalSize = _localSize;
  }
  #else
  _localRowStart = 0;
  _localRowEnd = nbRows;
  _globalSize = _localSize;
  #endif
  // preallocation option must be set after other options
  _try(VecCreate(_comm, &_x));
  _try(VecSetSizes(_x, blockSize * nbRows, PETSC_DETERMINE));
  // override the default options with the ones from the option
  // database (if any)
  if (this->_parameters.count("petscPrefix"))
    _try(VecAppendOptionsPrefix(_x, this->_parameters["petscPrefix"].c_str()));
  _try(VecSetFromOptions(_x));
  _try(VecDuplicate(_x, &_b));
  _isAllocated = true;
  _entriesPreAllocated = false;
}
Esempio n. 24
0
Real SAMpatchPETSc::normL2(const Vector& x, char dofType) const
{
#ifdef HAVE_MPI
  if (adm.isParallel()) {
    if (dofIS.find(dofType) == dofIS.end())
      setupIS(dofType);

    Vec lx;
    VecCreateSeqWithArray(PETSC_COMM_SELF, 1, x.size(), x.data(), &lx);
    Vec gx;
    VecCreate(*adm.getCommunicator(), &gx);
    VecSetSizes(gx, dofIS[dofType].nDofs, PETSC_DETERMINE);
    VecSetFromOptions(gx);
    PetscInt n;
    VecGetSize(gx, &n);

    if (!dofIS[dofType].scatterCreated) {
      VecScatterCreate(lx, dofIS[dofType].local, gx, dofIS[dofType].global, &dofIS[dofType].ctx);
      dofIS[dofType].scatterCreated = true;
    }

    VecScatterBegin(dofIS[dofType].ctx, lx, gx, INSERT_VALUES, SCATTER_FORWARD);
    VecScatterEnd(dofIS[dofType].ctx, lx, gx, INSERT_VALUES, SCATTER_FORWARD);
    PetscReal d;
    VecNorm(gx, NORM_2, &d);
    VecDestroy(&lx);
    VecDestroy(&gx);

    return d / sqrt(double(n));
  }
#endif

  return this->SAM::normL2(x, dofType);
}
  long initialize(long numele)
  {
    initialized = true;

    n = numele;
    neg_one = -1.0;
    one = 1.0;
    argc = 0;
    args = 0;


    // -------------------
    PetscInitialize(&argc,&args,(char *)0,help);
    ierr = MPI_Comm_size(PETSC_COMM_WORLD,&size);CHKERRQ(ierr);
    if (size != 1) SETERRQ(1,"This is a uniprocessor example only!");
    ierr = PetscOptionsGetInt(PETSC_NULL,"-n",&n,PETSC_NULL);CHKERRQ(ierr);

    /* - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 
       Compute the matrix and right-hand-side vector that define
       the linear system, Ax = b.
       - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - */

    ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
    ierr = PetscObjectSetName((PetscObject) x, "Solution");CHKERRQ(ierr);
    ierr = VecSetSizes(x,PETSC_DECIDE,n);CHKERRQ(ierr);
    ierr = VecSetFromOptions(x);CHKERRQ(ierr);
    ierr = VecDuplicate(x,&b);CHKERRQ(ierr);
    //    ierr = VecDuplicate(x,&u);CHKERRQ(ierr);

    ierr = MatCreate(PETSC_COMM_WORLD,&A);CHKERRQ(ierr);
    ierr = MatSetSizes(A,PETSC_DECIDE,PETSC_DECIDE,n,n);CHKERRQ(ierr);
    ierr = MatSetFromOptions(A);CHKERRQ(ierr);

    VecCreate(PETSC_COMM_WORLD,&temp_input);
    ierr = PetscObjectSetName((PetscObject) temp_input, "Tempinput");CHKERRQ(ierr);
    VecSetSizes(temp_input,PETSC_DECIDE,n);
    ierr = VecSetFromOptions(temp_input);CHKERRQ(ierr);
    VecCreate(PETSC_COMM_WORLD,&temp_output);
    ierr = PetscObjectSetName((PetscObject) temp_output, "Tempoutput");CHKERRQ(ierr);
    VecSetSizes(temp_output,PETSC_DECIDE,n);
    ierr = VecSetFromOptions(temp_output);CHKERRQ(ierr);


    return 0;
  }
Esempio n. 26
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void Field_solver::alloc_petsc_vector( Vec *x, int size, const char *name )
{
    PetscErrorCode ierr;
    ierr = VecCreate( PETSC_COMM_WORLD, x ); CHKERRXX( ierr );
    ierr = PetscObjectSetName( (PetscObject) *x, name ); CHKERRXX( ierr );
    ierr = VecSetSizes( *x, PETSC_DECIDE, size ); CHKERRXX( ierr );
    ierr = VecSetFromOptions( *x ); CHKERRXX( ierr );
    return;
}
Esempio n. 27
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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;
}
Esempio n. 28
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int main(int argc, char **argv)
{
  PetscErrorCode ierr;
  Vec            *V,t;
  PetscInt       i,j,reps,n=15,k=6;
  PetscRandom    rctx;
  PetscScalar    *val_dot,*val_mdot,*tval_dot,*tval_mdot;

  ierr = PetscInitialize(&argc,&argv,(char*)0,help);if (ierr) return ierr;
  ierr = PetscOptionsGetInt(NULL,NULL,"-n",&n,NULL);CHKERRQ(ierr);
  ierr = PetscOptionsGetInt(NULL,NULL,"-k",&k,NULL);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"Test with %D random vectors of length %D",k,n);CHKERRQ(ierr);
  ierr = PetscPrintf(PETSC_COMM_WORLD,"\n",k,n);CHKERRQ(ierr);
  ierr = PetscRandomCreate(PETSC_COMM_WORLD,&rctx);CHKERRQ(ierr);
  ierr = PetscRandomSetFromOptions(rctx);CHKERRQ(ierr);
  ierr = VecCreate(PETSC_COMM_WORLD,&t);CHKERRQ(ierr);
  ierr = VecSetSizes(t,n,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(t);CHKERRQ(ierr);
  ierr = VecDuplicateVecs(t,k,&V);CHKERRQ(ierr);
  ierr = VecSetRandom(t,rctx);CHKERRQ(ierr);
  ierr = PetscMalloc1(k,&val_dot);CHKERRQ(ierr);
  ierr = PetscMalloc1(k,&val_mdot);CHKERRQ(ierr);
  ierr = PetscMalloc1(k,&tval_dot);CHKERRQ(ierr);
  ierr = PetscMalloc1(k,&tval_mdot);CHKERRQ(ierr);
  for (i=0; i<k; i++) { ierr = VecSetRandom(V[i],rctx);CHKERRQ(ierr); }
  for (reps=0; reps<20; reps++) {
    for (i=1; i<k; i++) {
      ierr = VecMDot(t,i,V,val_mdot);CHKERRQ(ierr);
      ierr = VecMTDot(t,i,V,tval_mdot);CHKERRQ(ierr);
      for (j=0;j<i;j++) {
        ierr = VecDot(t,V[j],&val_dot[j]);CHKERRQ(ierr);
        ierr = VecTDot(t,V[j],&tval_dot[j]);CHKERRQ(ierr);
      }
      /* Check result */
      for (j=0;j<i;j++) {
        if (PetscAbsScalar(val_mdot[j] - val_dot[j])/PetscAbsScalar(val_dot[j]) > 1e-5) {
          ierr = PetscPrintf(PETSC_COMM_WORLD, "[TEST FAILED] i=%D, j=%D, val_mdot[j]=%g, val_dot[j]=%g\n",i,j,(double)PetscAbsScalar(val_mdot[j]), (double)PetscAbsScalar(val_dot[j]));CHKERRQ(ierr);
          break;
        }
        if (PetscAbsScalar(tval_mdot[j] - tval_dot[j])/PetscAbsScalar(tval_dot[j]) > 1e-5) {
          ierr = PetscPrintf(PETSC_COMM_WORLD, "[TEST FAILED] i=%D, j=%D, tval_mdot[j]=%g, tval_dot[j]=%g\n",i,j,(double)PetscAbsScalar(tval_mdot[j]), (double)PetscAbsScalar(tval_dot[j]));CHKERRQ(ierr);
          break;
        }
      }
    }
  }
  ierr = PetscPrintf(PETSC_COMM_WORLD,"Test completed successfully!\n",k,n);CHKERRQ(ierr);
  ierr = PetscFree(val_dot);CHKERRQ(ierr);
  ierr = PetscFree(val_mdot);CHKERRQ(ierr);
  ierr = PetscFree(tval_dot);CHKERRQ(ierr);
  ierr = PetscFree(tval_mdot);CHKERRQ(ierr);
  ierr = VecDestroyVecs(k,&V);CHKERRQ(ierr);
  ierr = VecDestroy(&t);CHKERRQ(ierr);
  ierr = PetscRandomDestroy(&rctx);CHKERRQ(ierr);
  ierr = PetscFinalize();
  return ierr;
}
Esempio n. 29
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int main(int argc,char **argv)
{
  PetscErrorCode ierr;
  PetscMPIInt    rank;
  PetscInt       i,N;
  PetscScalar    one = 1.0;
  Vec            x;

  PetscInitialize(&argc,&argv,(char *)0,help);
  ierr = MPI_Comm_rank(PETSC_COMM_WORLD,&rank);CHKERRQ(ierr);

  /*
     Create a parallel vector.
      - In this case, we specify the size of each processor's local
        portion, and PETSc computes the global size.  Alternatively,
        if we pass the global size and use PETSC_DECIDE for the 
        local size PETSc will choose a reasonable partition trying 
        to put nearly an equal number of elements on each processor.
  */
  ierr = VecCreate(PETSC_COMM_WORLD,&x);CHKERRQ(ierr);
  ierr = VecSetSizes(x,rank+1,PETSC_DECIDE);CHKERRQ(ierr);
  ierr = VecSetFromOptions(x);CHKERRQ(ierr);
  ierr = VecGetSize(x,&N);CHKERRQ(ierr);
  ierr = VecSet(x,one);CHKERRQ(ierr);

  /*
     Set the vector elements.
      - Always specify global locations of vector entries.
      - Each processor can contribute any vector entries,
        regardless of which processor "owns" them; any nonlocal
        contributions will be transferred to the appropriate processor
        during the assembly process.
      - In this example, the flag ADD_VALUES indicates that all
        contributions will be added together.
  */
  for (i=0; i<N-rank; i++) {
    ierr = VecSetValues(x,1,&i,&one,ADD_VALUES);CHKERRQ(ierr);  
  }

  /* 
     Assemble vector, using the 2-step process:
       VecAssemblyBegin(), VecAssemblyEnd()
     Computations can be done while messages are in transition
     by placing code between these two statements.
  */
  ierr = VecAssemblyBegin(x);CHKERRQ(ierr);
  ierr = VecAssemblyEnd(x);CHKERRQ(ierr);

  /*
      View the vector; then destroy it.
  */
  ierr = VecView(x,PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);
  ierr = VecDestroy(x);CHKERRQ(ierr);

  ierr = PetscFinalize();CHKERRQ(ierr);
  return 0;
}
Esempio n. 30
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PetscErrorCode generateVector(int size, Vec * v){
	PetscErrorCode ierr;

	ierr=VecCreate(PETSC_COMM_WORLD,v);CHKERRQ(ierr);
	ierr=VecSetSizes(*v,PETSC_DECIDE,size);CHKERRQ(ierr);
	ierr=VecSetFromOptions(*v);CHKERRQ(ierr);
	/*initiate the vector to its norm*/

	return 0;
}