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Updates for PETSc 3.21 #668

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merged 4 commits into from
Jan 4, 2025
Merged

Updates for PETSc 3.21 #668

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59ca1c0
docs: update PETSc badge
andrsd Jan 1, 2025
a54fe16
feat: allow to use PETSc 3.21 with the library
andrsd Jan 1, 2025
6e3194d
cicd: adding PETSc 3.21 into testing workflow
andrsd Jan 2, 2025
965f4b9
fix: don't run 1D FV stuff with PETSc 3.21+
andrsd Jan 4, 2025
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4 changes: 4 additions & 0 deletions .github/workflows/build.yml
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Expand Up @@ -26,6 +26,10 @@ jobs:
python-version: "3.9"
petsc: 3.20.6
build: Release
- os: ubuntu-22.04
python-version: "3.9"
petsc: 3.21.6
build: Release
runs-on: ${{ matrix.os }}
steps:
- name: Set up miniconda
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -7,7 +7,7 @@ godzilla
[![github-pages](https://github.com/andrsd/godzilla/actions/workflows/gh-pages.yml/badge.svg)](https://github.com/andrsd/godzilla/actions/workflows/gh-pages.yml)
[![codecov](https://codecov.io/gh/andrsd/godzilla/branch/main/graph/badge.svg?token=7KL45W9Z4G)](https://codecov.io/gh/andrsd/godzilla)
[![License](http://img.shields.io/:license-mit-blue.svg)](https://andrsd.mit-license.org/)
[![PETSc](https://img.shields.io/badge/PETSc-3.20-red)](https://petsc.org/)
[![PETSc](https://img.shields.io/badge/PETSc-3.20,%203.21-red)](https://petsc.org/)
[![Scc Count Badge](https://sloc.xyz/github/andrsd/godzilla/)](https://github.com/andrsd/godzilla/)


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4 changes: 4 additions & 0 deletions examples/advect-eqn/test/CMakeLists.txt
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@@ -1,5 +1,7 @@
include(TesterExodusII)

if(${PETSC_VERSION} VERSION_LESS "3.21.0")

add_test_exodiff(
NAME advect
BIN ${PROJECT_NAME}
Expand All @@ -8,3 +10,5 @@ add_test_exodiff(
GOLD ${PROJECT_SOURCE_DIR}/test/gold/1d.exo
ARGS -Floor 1e-16
)

endif()
3 changes: 3 additions & 0 deletions include/godzilla/Mesh.h
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Expand Up @@ -93,6 +93,9 @@ class Mesh {
/// @param c coordinate vector
void set_coordinates_local(const Vector & c);

/// If a mesh is periodic, create local coordinates for cells having periodic faces
void localize_coordinates() const;

/// Sets up the data structures inside the `DM` object
void set_up();

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9 changes: 9 additions & 0 deletions include/godzilla/Partitioner.h
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Expand Up @@ -33,6 +33,15 @@ class Partitioner {
const Section & target_section,
Section & partSection,
IndexSet & partition);
void partition(Int n_parts,
Int n_vertices,
Int start[],
Int adjacency[],
const Section & vertex_section,
const Section & edge_section,
const Section & target_section,
Section & partSection,
IndexSet & partition);

void view(PetscViewer viewer = PETSC_VIEWER_STDOUT_WORLD) const;

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11 changes: 11 additions & 0 deletions include/godzilla/Problem.h
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Expand Up @@ -228,6 +228,17 @@ class Problem : public Object, public PrintInterface {
/// @return The global indices for the subproblem
IndexSet create_section_subis(const std::vector<Int> & fields) const;

/// Returns an IndexSet containing a Section that encapsulates a subproblem defined by
/// a subset of the fields and components in a Section in the problem.
///
/// @param fields The field numbers of the selected fields
/// @param n_comps The number of components from each field to incorporate into the subproblem
/// @param comps The component numbers of the selected fields
/// @return The global indices for the subproblem
IndexSet create_section_subis(const std::vector<Int> & fields,
const std::vector<Int> & n_comps,
const std::vector<Int> & comps) const;

protected:
/// Set vector/matrix types
virtual void set_up_types();
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3 changes: 3 additions & 0 deletions src/DGProblemInterface.cpp
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Expand Up @@ -49,6 +49,8 @@

PETSC_CHECK(DMCopyDisc(dm, cdm));
PETSC_CHECK(DMGetCoarseDM(cdm, &cdm));
if (cdm)
PETSC_CHECK(DMLocalizeCoordinates(cdm));

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}
}

Expand Down Expand Up @@ -395,6 +397,7 @@
CALL_STACK_MSG();
set_up_fields();
DiscreteProblemInterface::create();
get_unstr_mesh()->localize_coordinates();

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}

void
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3 changes: 3 additions & 0 deletions src/FEProblemInterface.cpp
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Expand Up @@ -89,6 +89,7 @@
this->asmbl = new AssemblyData(dim);
set_up_fields();
DiscreteProblemInterface::create();
get_unstr_mesh()->localize_coordinates();
}

void
Expand All @@ -112,6 +113,8 @@

PETSC_CHECK(DMCopyDisc(dm, cdm));
PETSC_CHECK(DMGetCoarseDM(cdm, &cdm));
if (cdm)
PETSC_CHECK(DMLocalizeCoordinates(cdm));

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}

set_up_assembly_data_aux();
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8 changes: 8 additions & 0 deletions src/FVProblemInterface.cpp
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Expand Up @@ -76,6 +76,8 @@

PETSC_CHECK(DMCopyDisc(dm, cdm));
PETSC_CHECK(DMGetCoarseDM(cdm, &cdm));
if (cdm)
PETSC_CHECK(DMLocalizeCoordinates(cdm));

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}
}

Expand Down Expand Up @@ -364,6 +366,12 @@
set_up_fields();
DiscreteProblemInterface::create();
get_unstr_mesh()->construct_ghost_cells();
get_unstr_mesh()->localize_coordinates();

#if PETSC_VERSION_GE(3, 21, 0)
if (get_unstr_mesh()->get_dimension() == 1)
throw Exception("FV in 1D is not possible due to a bug in PETSc. Use PETSc 3.20 instead.");
#endif
}

void
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7 changes: 7 additions & 0 deletions src/Mesh.cpp
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Expand Up @@ -132,6 +132,13 @@ Mesh::set_coordinates_local(const Vector & c)
PETSC_CHECK(DMSetCoordinatesLocal(this->dm, c));
}

void
Mesh::localize_coordinates() const
{
CALL_STACK_MSG();
PETSC_CHECK(DMLocalizeCoordinates(this->dm));
}

void
Mesh::set_up()
{
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42 changes: 42 additions & 0 deletions src/Partitioner.cpp
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Expand Up @@ -4,6 +4,7 @@
#include "godzilla/Partitioner.h"
#include "godzilla/CallStack.h"
#include "godzilla/Error.h"
#include "godzilla/Exception.h"

using namespace godzilla;

Expand Down Expand Up @@ -87,15 +88,56 @@
IndexSet & partition)
{
CALL_STACK_MSG();
#if PETSC_VERSION_GE(3, 21, 0)
PETSC_CHECK(PetscPartitionerPartition(this->part,
n_parts,
n_vertices,
start,
adjacency,
vertex_section,
NULL,
target_section,
part_section,
partition));
#else
PETSC_CHECK(PetscPartitionerPartition(this->part,

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n_parts,
n_vertices,
start,
adjacency,
vertex_section,
target_section,
part_section,
partition));
#endif
}

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void
Partitioner::partition(Int n_parts,

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Int n_vertices,
Int start[],
Int adjacency[],
const Section & vertex_section,
const Section & edge_section,
const Section & target_section,
Section & part_section,
IndexSet & partition)
{
CALL_STACK_MSG();

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#if PETSC_VERSION_GE(3, 21, 0)
PETSC_CHECK(PetscPartitionerPartition(this->part,

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n_parts,
n_vertices,
start,
adjacency,
vertex_section,
edge_section,
target_section,
part_section,
partition));
#else
throw Exception("PETSc 3.21+ is needed for Partitioner::partition with edge_section parameter");

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#endif
}

Partitioner::operator PetscPartitioner() const
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30 changes: 24 additions & 6 deletions src/Problem.cpp
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Expand Up @@ -437,19 +437,37 @@
{
CALL_STACK_MSG();
#if PETSC_VERSION_GE(3, 21, 0)
IS is;
PETSC_CHECK(

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DMCreateSectionSubDM(get_dm(), fields.size(), fields.data(), NULL, NULL, &is, NULL));
return IndexSet(is);

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#else
IS is;
PETSC_CHECK(DMCreateSectionSubDM(get_dm(), fields.size(), fields.data(), &is, NULL));
return IndexSet(is);

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#endif
}

IndexSet
Problem::create_section_subis(const std::vector<Int> & fields,

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const std::vector<Int> & n_comps,
const std::vector<Int> & comps) const
{
CALL_STACK_MSG();

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#if PETSC_VERSION_GE(3, 21, 0)
assert(fields.size() == n_comps.size());
IS is;
PETSC_CHECK(DMCreateSectionSubDM(get_dm(),
fields.size(),
fields.data(),
PETSC_DECIDE,
nullptr,
n_comps.data(),
comps.data(),
&is,
nullptr));
NULL));
return IndexSet(is);
#else
IS is;
PETSC_CHECK(DMCreateSectionSubDM(get_dm(), fields.size(), fields.data(), &is, nullptr));
return IndexSet(is);
throw Exception(
"PETSc 3.21+ is needed for Problem::create_section_subis with component support");

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#endif
}

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51 changes: 51 additions & 0 deletions test/src/ExplicitFVLinearProblem_test.cpp
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@@ -1,6 +1,7 @@
#include "gmock/gmock.h"
#include "godzilla/CallStack.h"
#include "godzilla/LineMesh.h"
#include "godzilla/RectangleMesh.h"
#include "godzilla/NaturalRiemannBC.h"
#include "godzilla/ExplicitFVLinearProblem.h"
#include "godzilla/Parameters.h"
Expand Down Expand Up @@ -112,10 +113,19 @@ TEST(ExplicitFVLinearProblemTest, api)
{
TestApp app;

#if PETSC_VERSION_GE(3, 21, 0)
// PETSc 3.21.0+ has a bug in forming the mass matrix in 1D, se we use 2D mesh in this test
Parameters mesh_pars = RectangleMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 2;
mesh_pars.set<Int>("ny") = 1;
RectangleMesh mesh(mesh_pars);
#else
Parameters mesh_pars = LineMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 2;
LineMesh mesh(mesh_pars);
#endif

Parameters prob_pars = TestExplicitFVLinearProblem::parameters();
prob_pars.set<App *>("_app") = &app;
Expand Down Expand Up @@ -201,10 +211,19 @@ TEST(ExplicitFVLinearProblemTest, fields)
{
TestApp app;

#if PETSC_VERSION_GE(3, 21, 0)
// PETSc 3.21.0+ has a bug in forming the mass matrix in 1D, se we use 2D mesh in this test
Parameters mesh_pars = RectangleMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 2;
mesh_pars.set<Int>("ny") = 1;
RectangleMesh mesh(mesh_pars);
#else
Parameters mesh_pars = LineMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 2;
LineMesh mesh(mesh_pars);
#endif

Parameters prob_pars = TestExplicitFVLinearProblem::parameters();
prob_pars.set<App *>("_app") = &app;
Expand Down Expand Up @@ -244,10 +263,20 @@ TEST(ExplicitFVLinearProblemTest, test_mass_matrix)
{
TestApp app;

#if PETSC_VERSION_GE(3, 21, 0)
// PETSc 3.21.0+ has a bug in forming the mass matrix in 1D, se we use 2D mesh in this test
Parameters mesh_pars = RectangleMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 3;
mesh_pars.set<Int>("ny") = 1;
mesh_pars.set<Real>("ymax") = 3.;
RectangleMesh mesh(mesh_pars);
#else
Parameters mesh_pars = LineMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 3;
LineMesh mesh(mesh_pars);
#endif

Parameters prob_pars = TestExplicitFVLinearProblem::parameters();
prob_pars.set<App *>("_app") = &app;
Expand Down Expand Up @@ -276,6 +305,9 @@ TEST(ExplicitFVLinearProblemTest, solve)
{
TestApp app;

#if PETSC_VERSION_GE(3, 21, 0)
// PETSc 3.21.0+ has a bug in forming the mass matrix in 1D, se we use 2D mesh in this test
#else
Parameters mesh_pars = LineMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 2;
Expand Down Expand Up @@ -330,16 +362,26 @@ TEST(ExplicitFVLinearProblemTest, solve)
EXPECT_NEAR(lx[2], 0., 1e-15);
EXPECT_NEAR(lx[3], 0., 1e-15);
loc_sln.restore_array_read(lx);
#endif
}

TEST(ExplicitFVLinearProblemTest, set_schemes)
{
TestApp app;

#if PETSC_VERSION_GE(3, 21, 0)
// PETSc 3.21.0+ has a bug in forming the mass matrix in 1D, se we use 2D mesh in this test
Parameters mesh_pars = RectangleMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 2;
mesh_pars.set<Int>("ny") = 1;
RectangleMesh mesh(mesh_pars);
#else
Parameters mesh_pars = LineMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 2;
LineMesh mesh(mesh_pars);
#endif

Parameters prob_pars = TestExplicitFVLinearProblem::parameters();
prob_pars.set<App *>("_app") = &app;
Expand Down Expand Up @@ -373,10 +415,19 @@ TEST(ExplicitFVLinearProblemTest, wrong_schemes)

TestApp app;

#if PETSC_VERSION_GE(3, 21, 0)
// PETSc 3.21.0+ has a bug in forming the mass matrix in 1D, se we use 2D mesh in this test
Parameters mesh_pars = RectangleMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 2;
mesh_pars.set<Int>("ny") = 1;
RectangleMesh mesh(mesh_pars);
#else
Parameters mesh_pars = LineMesh::parameters();
mesh_pars.set<App *>("_app") = &app;
mesh_pars.set<Int>("nx") = 2;
LineMesh mesh(mesh_pars);
#endif

Parameters prob_pars = TestExplicitFVLinearProblem::parameters();
prob_pars.set<App *>("_app") = &app;
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