added real project code
parent
5461990d0a
commit
7f1bbf5162
@ -1,29 +1,57 @@
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# cmake_minimum_required(VERSION 3.5.0)
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# set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
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# # set root of location to find PETSc's pkg-config
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# set(PETSC $ENV{PETSC_DIR}/$ENV{PETSC_ARCH})
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# set(ENV{PKG_CONFIG_PATH} ${PETSC}/lib/pkgconfig)
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# # Remove the lines below if you do not wish to have PETSc determine the compilers
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# execute_process ( COMMAND pkg-config PETSc --variable=ccompiler COMMAND tr -d '\n' OUTPUT_VARIABLE C_COMPILER)
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# SET(CMAKE_C_COMPILER ${C_COMPILER})
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# execute_process ( COMMAND pkg-config PETSc --variable=cxxcompiler COMMAND tr -d '\n' OUTPUT_VARIABLE CXX_COMPILER)
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# if (CXX_COMPILER)
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# SET(CMAKE_CXX_COMPILER ${CXX_COMPILER})
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# endif (CXX_COMPILER)
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# execute_process ( COMMAND pkg-config PETSc --variable=fcompiler COMMAND tr -d '\n' OUTPUT_VARIABLE FORTRAN_COMPILER)
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# if (FORTRAN_COMPILER)
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# SET(CMAKE_Fortran_COMPILER ${FORTRAN_COMPILER})
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# enable_language(Fortran)
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# endif (FORTRAN_COMPILER)
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# # tells CMake to build the application ex1 from the source file ex1.c
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# # this must appear AFTER the compilers are set
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# project(main)
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# add_executable(main main.c)
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# find_package(MPI REQUIRED)
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# include_directories(${MPI_INCLUDE_PATH})
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# find_package(PkgConfig REQUIRED)
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# pkg_search_module(PETSC REQUIRED IMPORTED_TARGET PETSc)
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# target_link_libraries(main PkgConfig::PETSC)
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cmake_minimum_required(VERSION 3.5.0)
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set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
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# set root of location to find PETSc's pkg-config
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# Set root of location to find PETSc's pkg-config
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set(PETSC $ENV{PETSC_DIR}/$ENV{PETSC_ARCH})
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set(ENV{PKG_CONFIG_PATH} ${PETSC}/lib/pkgconfig)
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# Remove the lines below if you do not wish to have PETSc determine the compilers
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execute_process ( COMMAND pkg-config PETSc --variable=ccompiler COMMAND tr -d '\n' OUTPUT_VARIABLE C_COMPILER)
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SET(CMAKE_C_COMPILER ${C_COMPILER})
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execute_process ( COMMAND pkg-config PETSc --variable=cxxcompiler COMMAND tr -d '\n' OUTPUT_VARIABLE CXX_COMPILER)
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if (CXX_COMPILER)
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SET(CMAKE_CXX_COMPILER ${CXX_COMPILER})
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endif (CXX_COMPILER)
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execute_process ( COMMAND pkg-config PETSc --variable=fcompiler COMMAND tr -d '\n' OUTPUT_VARIABLE FORTRAN_COMPILER)
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if (FORTRAN_COMPILER)
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SET(CMAKE_Fortran_COMPILER ${FORTRAN_COMPILER})
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enable_language(Fortran)
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endif (FORTRAN_COMPILER)
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# tells CMake to build the application ex1 from the source file ex1.c
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# this must appear AFTER the compilers are set
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SET(CMAKE_C_COMPILER gcc)
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SET(CMAKE_CXX_COMPILER g++)
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SET(CMAKE_Fortran_COMPILER gfortran)
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enable_language(Fortran)
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# Tells CMake to build the application ex1 from the source file ex1.c
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# This must appear AFTER the compilers are set
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project(main)
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add_executable(main main.c)
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find_package(MPI REQUIRED)
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find_package(PkgConfig REQUIRED)
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pkg_search_module(PETSC REQUIRED IMPORTED_TARGET PETSc)
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target_link_libraries(main PkgConfig::PETSC)
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target_link_libraries(main MPI::MPI_C MPI::MPI_CXX MPI::MPI_Fortran PkgConfig::PETSC)
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@ -1,173 +1,161 @@
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/*
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Laplacian in 3D. Modeled by the partial differential equation
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#include <petscmat.h>
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#include <petscsys.h>
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#include <petscsystypes.h>
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#include <petscvec.h>
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#include <petscviewer.h>
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- Laplacian u = 1,0 < x,y,z < 1,
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#include <petscdm.h>
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#include <petscdmda.h>
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#include <petscksp.h>
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with boundary conditions
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static char help[] = "Example PETSc program\n\n";
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u = 1 for x = 0, x = 1, y = 0, y = 1, z = 0, z = 1.
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// extern PetscErrorCode ComputeMatrix(KSP, Mat, Mat, void *);
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// extern PetscErrorCode ComputeRHS(KSP, Vec, void *);
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// extern PetscErrorCode ComputeInitialSolution(DM, Vec);
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This uses multigrid to solve the linear system
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PetscErrorCode ArnoldiIteration(Mat A, Vec b, PetscInt n, Vec *Q, Mat H);
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See src/snes/tutorials/ex50.c
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int main(int argc, char **argv) {
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Mat A;
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Vec b;
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PetscInt n, l;
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Can also be run with -pc_type exotic -ksp_type fgmres
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PetscFunctionBeginUser;
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PetscInitialize(&argc, &argv, (char *)0, help);
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PetscBool flg;
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PetscOptionsGetInt(NULL, NULL, "-n", &n, &flg);
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if (!flg)
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n = 10;
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PetscOptionsGetInt(NULL, NULL, "-l", &l, &flg);
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if (!flg)
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l = 4;
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VecCreate(PETSC_COMM_WORLD, &b);
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VecSetSizes(b, PETSC_DECIDE, n);
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VecSetType(b, VECMPI);
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VecSet(b, 1.0);
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// VecSetValue(b, 0, 1.0, INSERT_VALUES);
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MatCreate(PETSC_COMM_WORLD, &A);
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MatSetSizes(A, PETSC_DECIDE, PETSC_DECIDE, n, n);
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MatSetType(A, MATMPIAIJ);
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// A := diag(-1, 2, -1)
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for (PetscInt i = 0; i < n; i++) {
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// PetscScalar v[3] = {-1.0, 2.0, -1.0};
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// PetscInt col[3] = {i - 1, i, i + 1};
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// PetscInt ncol = 0;
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// if (i > 0) {
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// col[ncol] = i - 1;
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// v[ncol] = -1.0;
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// ncol++;
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// }
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// col[ncol] = i;
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// v[ncol] = 2.0;
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// ncol++;
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// if (i < n - 1) {
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// col[ncol] = i + 1;
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// v[ncol] = -1.0;
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// ncol++;
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// }
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// MatSetValues(A, 1, &i, ncol, col, v, INSERT_VALUES);
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MatSetValue(A, i, i, (PetscScalar)(i + 1), INSERT_VALUES);
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}
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*/
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MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY);
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MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY);
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static char help[] = "Solves 3D Laplacian using multigrid.\n\n";
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// MatView(A, PETSC_VIEWER_DRAW_WORLD);
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MatView(A, PETSC_VIEWER_STDOUT_WORLD);
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// VecView(b, PETSC_VIEWER_DRAW_WORLD);
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VecView(b, PETSC_VIEWER_STDOUT_WORLD);
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#include <petscdm.h>
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#include <petscdmda.h>
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#include <petscksp.h>
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printf("Allocating memory for Krylov subspace basis\n");
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extern PetscErrorCode ComputeMatrix(KSP, Mat, Mat, void *);
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extern PetscErrorCode ComputeRHS(KSP, Vec, void *);
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extern PetscErrorCode ComputeInitialGuess(KSP, Vec, void *);
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Vec *Q;
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PetscMalloc1(l, &Q);
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int main(int argc, char **argv) {
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KSP ksp;
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PetscReal norm;
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DM da;
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Vec x, b, r;
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Mat A;
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for (PetscInt i = 0; i < l; i++) {
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VecCreateMPI(PETSC_COMM_WORLD, PETSC_DECIDE, n, &Q[i]);
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}
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PetscFunctionBeginUser;
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PetscCall(PetscInitialize(&argc, &argv, (char *)0, help));
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PetscCall(KSPCreate(PETSC_COMM_WORLD, &ksp));
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PetscCall(DMDACreate3d(PETSC_COMM_WORLD, DM_BOUNDARY_NONE, DM_BOUNDARY_NONE,
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DM_BOUNDARY_NONE, DMDA_STENCIL_STAR, 7, 7, 7,
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PETSC_DECIDE, PETSC_DECIDE, PETSC_DECIDE, 1, 1, 0, 0,
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0, &da));
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PetscCall(DMSetFromOptions(da));
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PetscCall(DMSetUp(da));
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PetscCall(KSPSetDM(ksp, da));
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PetscCall(KSPSetComputeInitialGuess(ksp, ComputeInitialGuess, NULL));
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PetscCall(KSPSetComputeRHS(ksp, ComputeRHS, NULL));
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PetscCall(KSPSetComputeOperators(ksp, ComputeMatrix, NULL));
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PetscCall(DMDestroy(&da));
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PetscCall(KSPSetFromOptions(ksp));
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PetscCall(KSPSolve(ksp, NULL, NULL));
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PetscCall(KSPGetSolution(ksp, &x));
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PetscCall(KSPGetRhs(ksp, &b));
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PetscCall(VecDuplicate(b, &r));
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PetscCall(KSPGetOperators(ksp, &A, NULL));
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PetscCall(MatMult(A, x, r));
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PetscCall(VecAXPY(r, -1.0, b));
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PetscCall(VecNorm(r, NORM_2, &norm));
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PetscCall(PetscPrintf(PETSC_COMM_WORLD, "Residual norm %g\n", (double)norm));
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PetscCall(VecDestroy(&r));
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PetscCall(KSPDestroy(&ksp));
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PetscCall(PetscFinalize());
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return 0;
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}
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printf("Constructing Hessenberg matrix\n");
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PetscErrorCode ComputeRHS(KSP ksp, Vec b, void *ctx) {
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PetscInt i, j, k, mx, my, mz, xm, ym, zm, xs, ys, zs;
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DM dm;
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PetscScalar Hx, Hy, Hz, HxHydHz, HyHzdHx, HxHzdHy;
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PetscScalar ***barray;
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Mat H;
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MatCreate(PETSC_COMM_WORLD, &H);
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MatSetSizes(H, PETSC_DECIDE, PETSC_DECIDE, l + 1, l);
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// MatSetType(H, MATMPIAIJ);
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MatSetType(H, MATDENSE);
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PetscFunctionBeginUser;
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PetscCall(KSPGetDM(ksp, &dm));
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PetscCall(DMDAGetInfo(dm, 0, &mx, &my, &mz, 0, 0, 0, 0, 0, 0, 0, 0, 0));
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Hx = 1.0 / (PetscReal)(mx - 1);
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Hy = 1.0 / (PetscReal)(my - 1);
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Hz = 1.0 / (PetscReal)(mz - 1);
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HxHydHz = Hx * Hy / Hz;
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HxHzdHy = Hx * Hz / Hy;
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HyHzdHx = Hy * Hz / Hx;
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PetscCall(DMDAGetCorners(dm, &xs, &ys, &zs, &xm, &ym, &zm));
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PetscCall(DMDAVecGetArray(dm, b, &barray));
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for (k = zs; k < zs + zm; k++) {
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for (j = ys; j < ys + ym; j++) {
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for (i = xs; i < xs + xm; i++) {
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if (i == 0 || j == 0 || k == 0 || i == mx - 1 || j == my - 1 ||
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k == mz - 1) {
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barray[k][j][i] = 2.0 * (HxHydHz + HxHzdHy + HyHzdHx);
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} else {
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barray[k][j][i] = Hx * Hy * Hz;
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}
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}
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}
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printf("Starting Arnoldi iteration\n");
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MatAssemblyBegin(H, MAT_FINAL_ASSEMBLY);
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PetscCall(ArnoldiIteration(A, b, l, Q, H));
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MatAssemblyEnd(H, MAT_FINAL_ASSEMBLY);
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for (PetscInt i = 0; i < l + 1; i++) {
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VecView(Q[i], PETSC_VIEWER_STDOUT_WORLD);
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}
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PetscCall(DMDAVecRestoreArray(dm, b, &barray));
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PetscFunctionReturn(PETSC_SUCCESS);
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MatView(H, PETSC_VIEWER_STDOUT_WORLD);
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for (PetscInt i = 0; i < l + 1; i++) {
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VecDestroy(&Q[i]);
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}
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// PetscFree(Q);
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MatDestroy(&A);
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VecDestroy(&b);
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PetscFinalize();
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return 0;
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}
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PetscErrorCode ComputeInitialGuess(KSP ksp, Vec b, void *ctx) {
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PetscErrorCode ArnoldiIteration(Mat A, Vec b, PetscInt n, Vec *Q, Mat H) {
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PetscFunctionBeginUser;
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PetscCall(VecSet(b, 0));
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PetscFunctionReturn(PETSC_SUCCESS);
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}
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PetscErrorCode ComputeMatrix(KSP ksp, Mat jac, Mat B, void *ctx) {
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DM da;
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PetscInt i, j, k, mx, my, mz, xm, ym, zm, xs, ys, zs;
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PetscScalar v[7], Hx, Hy, Hz, HxHydHz, HyHzdHx, HxHzdHy;
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MatStencil row, col[7];
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PetscScalar eps = 1e-12;
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PetscInt m;
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VecGetSize(b, &m);
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PetscFunctionBeginUser;
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PetscCall(KSPGetDM(ksp, &da));
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PetscCall(DMDAGetInfo(da, 0, &mx, &my, &mz, 0, 0, 0, 0, 0, 0, 0, 0, 0));
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Hx = 1.0 / (PetscReal)(mx - 1);
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Hy = 1.0 / (PetscReal)(my - 1);
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Hz = 1.0 / (PetscReal)(mz - 1);
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HxHydHz = Hx * Hy / Hz;
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HxHzdHy = Hx * Hz / Hy;
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HyHzdHx = Hy * Hz / Hx;
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PetscCall(DMDAGetCorners(da, &xs, &ys, &zs, &xm, &ym, &zm));
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for (k = zs; k < zs + zm; k++) {
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for (j = ys; j < ys + ym; j++) {
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for (i = xs; i < xs + xm; i++) {
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row.i = i;
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row.j = j;
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row.k = k;
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if (i == 0 || j == 0 || k == 0 || i == mx - 1 || j == my - 1 ||
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k == mz - 1) {
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v[0] = 2.0 * (HxHydHz + HxHzdHy + HyHzdHx);
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PetscCall(MatSetValuesStencil(B, 1, &row, 1, &row, v, INSERT_VALUES));
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} else {
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v[0] = -HxHydHz;
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col[0].i = i;
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col[0].j = j;
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col[0].k = k - 1;
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v[1] = -HxHzdHy;
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col[1].i = i;
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col[1].j = j - 1;
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col[1].k = k;
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v[2] = -HyHzdHx;
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col[2].i = i - 1;
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col[2].j = j;
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col[2].k = k;
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v[3] = 2.0 * (HxHydHz + HxHzdHy + HyHzdHx);
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col[3].i = row.i;
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col[3].j = row.j;
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col[3].k = row.k;
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v[4] = -HyHzdHx;
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col[4].i = i + 1;
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col[4].j = j;
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col[4].k = k;
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v[5] = -HxHzdHy;
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col[5].i = i;
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col[5].j = j + 1;
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col[5].k = k;
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v[6] = -HxHydHz;
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col[6].i = i;
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col[6].j = j;
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col[6].k = k + 1;
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PetscCall(MatSetValuesStencil(B, 1, &row, 7, col, v, INSERT_VALUES));
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}
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}
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Vec q;
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MatZeroEntries(H);
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VecDuplicate(b, &q);
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VecCopy(b, q);
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VecNormalize(q, NULL);
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Q[0] = q;
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for (PetscInt k = 1; k < n + 1; k++) {
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Vec v;
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VecDuplicate(b, &v);
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MatMult(A, Q[k - 1], v);
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for (PetscInt j = 0; j < k; j++) {
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PetscScalar h;
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VecDot(Q[j], v, &h);
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MatSetValue(H, j, k - 1, h, INSERT_VALUES);
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VecAXPY(v, -h, Q[j]);
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}
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PetscScalar h;
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VecNorm(v, NORM_2, &h);
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MatSetValue(H, k, k - 1, h, INSERT_VALUES);
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if (h > eps) {
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VecNormalize(v, NULL);
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Q[k] = v;
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} else {
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break;
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}
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}
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PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
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PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
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PetscFunctionReturn(PETSC_SUCCESS);
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}
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