Do things automatically for FCI #3004

dschwoerer · 2024-10-22T09:50:09Z

Many things could be done automatically to make usage of FCI easier. However that may be slower, so this is optional.

Might help with performance

Otherwise the regions aren't cached.

Might help with performance

Precalculate the matrix. This hard-codes the DDX and DDZ derivative to C2. Rather than taking derivatives, this first does the matrix-matrix multiplication and then does only a single matrix-vector operation, rather than 4. Retains a switch to go back to the old version.

release leaks the pointer, reset free's the object.

* helped finding the bug for the boundary * rather slow (around 1 minute) * needs internet connectivity

Calculating parallel fields for metrics terms does not make sense. Using such parallel fields is very, very likely a bug.

Just dumping the parallel slices does in general not work, as then collect discards that, especially if NYPE==ny

hasBndryUpperY / hasBndryLowerY does not work for FCI and thus the request does not make sense / can be configured to throw. Thus it should not be checked if it is not needed.

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 25 out of 116. Check the log or trigger a new build to see more.

github-actions · 2024-10-22T11:26:06Z

include/bout/boundary_iterator.hxx

+#include "bout/sys/parallel_stencils.hxx"
+#include "bout/sys/range.hxx"
+
+class BoundaryRegionIter {


warning: destructor of 'BoundaryRegionIter' is public and non-virtual [cppcoreguidelines-virtual-class-destructor]

class BoundaryRegionIter { ^

Additional context

include/bout/boundary_iterator.hxx:6: make it public and virtual

class BoundaryRegionIter { ^

include/bout/boundary_iterator.hxx

github-actions · 2024-10-22T11:26:06Z

include/bout/boundary_iterator.hxx

+      : dir(bx + by), x(x), y(y), bx(bx), by(by), localmesh(mesh) {
+    ASSERT3(bx * by == 0);
+  }
+  bool operator!=(const BoundaryRegionIter& rhs) { return ind() != rhs.ind(); }


warning: method 'operator!=' can be made const [readability-make-member-function-const]

Suggested change

bool operator!=(const BoundaryRegionIter& rhs) { return ind() != rhs.ind(); }

bool operator!=(const BoundaryRegionIter& rhs) const { return ind() != rhs.ind(); }

github-actions · 2024-10-22T11:26:06Z

include/bout/boundary_iterator.hxx

+  BoutReal& yprev(Field3D& f) const { return f[ind().yp(-by).xp(-bx)]; }
+  const BoutReal& yprev(const Field3D& f) const { return f[ind().yp(-by).xp(-bx)]; }
+
+  const int dir;


warning: member 'dir' of type 'const int' is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const int dir; ^

github-actions · 2024-10-22T11:26:08Z

include/bout/field.hxx

+#if BOUT_USE_FCI_AUTOMAGIC
+  if (var.isFci()) {
+    for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
+      BOUT_FOR(d, result.yup(i).getRegion(rgn)) {


warning: loop variable name 'd' is too short, expected at least 2 characters [readability-identifier-length]

{ ^

github-actions · 2024-10-22T11:26:08Z

include/bout/field.hxx

+          result.yup(i)[d] = f;
+        }
+      }
+      BOUT_FOR(d, result.ydown(i).getRegion(rgn)) {


warning: loop variable name 'd' is too short, expected at least 2 characters [readability-identifier-length]

} ^

github-actions · 2024-10-22T11:26:08Z

include/bout/field2d.hxx

  bool hasParallelSlices() const { return true; }
+  void calcParallelSlices() const {}
+  void clearParallelSlices() {}
+  int numberParallelSlices() { return 0; }


warning: method 'numberParallelSlices' can be made static [readability-convert-member-functions-to-static]

Suggested change

int numberParallelSlices() { return 0; }

static int numberParallelSlices() { return 0; }

github-actions · 2024-10-22T11:26:08Z

include/bout/interpolation_xz.hxx

@@ -26,6 +26,15 @@

 #include "bout/mask.hxx"

+#define USE_NEW_WEIGHTS 1


warning: macro 'USE_NEW_WEIGHTS' used to declare a constant; consider using a 'constexpr' constant [cppcoreguidelines-macro-usage]

#define USE_NEW_WEIGHTS 1 ^

github-actions · 2024-10-22T11:26:08Z

include/bout/interpolation_xz.hxx

@@ -26,6 +26,15 @@

 #include "bout/mask.hxx"

+#define USE_NEW_WEIGHTS 1
+#if BOUT_HAS_PETSC
+#define HS_USE_PETSC 1


warning: macro 'HS_USE_PETSC' used to declare a constant; consider using a 'constexpr' constant [cppcoreguidelines-macro-usage]

#define HS_USE_PETSC 1 ^

Otherwise it is attempted to transform it to field-aligned, which fails as the parallel transform is not set.

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 25 out of 93. Check the log or trigger a new build to see more.

github-actions · 2024-10-22T13:48:01Z

include/bout/field.hxx

+#if BOUT_USE_FCI_AUTOMAGIC
+    if (var.isFci()) {
+      for (size_t i = 0; i < result.numberParallelSlices(); ++i) {
+        BOUT_FOR(d, result.yup(i).getRegion(rgn)) {


warning: loop variable name 'd' is too short, expected at least 2 characters [readability-identifier-length]

{ ^

github-actions · 2024-10-22T13:48:01Z

include/bout/field.hxx

+            result.yup(i)[d] = f;
+          }
+        }
+        BOUT_FOR(d, result.ydown(i).getRegion(rgn)) {


warning: loop variable name 'd' is too short, expected at least 2 characters [readability-identifier-length]

} ^

github-actions · 2024-10-22T13:48:01Z

include/bout/interpolation_xz.hxx

@@ -43,57 +52,52 @@ public:
 protected:
  Mesh* localmesh{nullptr};

-  std::string region_name;
-  std::shared_ptr<Region<Ind3D>> region{nullptr};
+  int region_id{-1};


warning: member variable 'region_id' has protected visibility [cppcoreguidelines-non-private-member-variables-in-classes]

int region_id{-1}; ^

github-actions · 2024-10-22T13:48:01Z

include/bout/interpolation_xz.hxx

-                  Mesh* mesh = nullptr)
-      : y_offset(y_offset), localmesh(mesh), region(std::move(region)) {}
+      : y_offset(y_offset), localmesh(mesh),
+        region_id(localmesh->getRegionID(region_name)) {}


warning: narrowing conversion from 'size_t' (aka 'unsigned long') to signed type 'int' is implementation-defined [bugprone-narrowing-conversions]

region_id(localmesh->getRegionID(region_name)) {} ^

github-actions · 2024-10-22T13:48:01Z

include/bout/interpolation_xz.hxx

-  void setRegion(const std::shared_ptr<Region<Ind3D>>& region) {
-    this->region_name = "";
-    this->region = region;
+    this->region_id = localmesh->getRegionID(region_name);


warning: narrowing conversion from 'size_t' (aka 'unsigned long') to signed type 'int' is implementation-defined [bugprone-narrowing-conversions]

this->region_id = localmesh->getRegionID(region_name); ^

github-actions · 2024-10-22T13:48:03Z

include/bout/parallel_boundary_region.hxx

+  }
+
+  // extrapolate the gradient into the boundary
+  inline BoutReal extrapolate_grad_o1(const Field3D& f) const { return 0; }


warning: unused parameter 'f' [clang-diagnostic-unused-parameter]

inline BoutReal extrapolate_grad_o1(const Field3D& f) const { return 0; } ^

github-actions · 2024-10-22T13:48:03Z

include/bout/parallel_boundary_region.hxx

+  }
+
+  // extrapolate the gradient into the boundary
+  inline BoutReal extrapolate_grad_o1(const Field3D& f) const { return 0; }


warning: parameter 'f' is unused [misc-unused-parameters]

Suggested change

inline BoutReal extrapolate_grad_o1(const Field3D& f) const { return 0; }

inline BoutReal extrapolate_grad_o1(const Field3D& /*f*/) const { return 0; }

github-actions · 2024-10-22T13:48:03Z

include/bout/parallel_boundary_region.hxx


 private:
+  const IndicesVec& bndry_points;


warning: member 'bndry_points' of type 'const IndicesVec &' is a reference [cppcoreguidelines-avoid-const-or-ref-data-members]

const IndicesVec& bndry_points; ^

github-actions · 2024-10-22T13:48:03Z

include/bout/parallel_boundary_region.hxx


 private:
+  const IndicesVec& bndry_points;


warning: member 'bndry_points' of type 'const std::vectorbout::parallel_boundary_region::Indices &' is a reference [cppcoreguidelines-avoid-const-or-ref-data-members]

const IndicesVec& bndry_points; ^

github-actions · 2024-10-22T13:48:03Z

include/bout/parallel_boundary_region.hxx

-  const BoutReal& yprev(const Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; }
-  BoutReal& yprev(Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; }
+public:
+  const int dir;


warning: member 'dir' of type 'const int' is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const int dir; ^

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 25 out of 68. Check the log or trigger a new build to see more.

github-actions · 2024-10-22T14:39:12Z

include/bout/parallel_boundary_region.hxx

-  const BoutReal& yprev(const Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; }
-  BoutReal& yprev(Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; }
+public:
+  const int dir;


warning: member variable 'dir' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]

const int dir; ^

github-actions · 2024-10-22T14:39:12Z

include/bout/parallel_boundary_region.hxx

-  BoutReal& yprev(Field3D& f) const { return f.ynext(-dir)[ind().yp(-dir)]; }
+public:
+  const int dir;
+  Mesh* localmesh;


warning: member variable 'localmesh' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]

Mesh* localmesh; ^

github-actions · 2024-10-22T14:39:13Z

include/bout/parallel_boundary_region.hxx

+    return std::binary_search(std::begin(bndry_points), std::end(bndry_points),
+                              *bndry.bndry_position,
+                              [](const bout::parallel_boundary_region::Indices& i1,
+                                 const bout::parallel_boundary_region::Indices& i2) {


warning: parameter name 'i2' is too short, expected at least 3 characters [readability-identifier-length]

const bout::parallel_boundary_region::Indices& i2) { ^

github-actions · 2024-10-22T14:39:13Z

include/bout/parallel_boundary_region.hxx

+    return BoundaryRegionParIter(bndry_points, bndry_points.end(), dir, localmesh);
+  }
+
+  const int dir;


warning: member 'dir' of type 'const int' is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const int dir; ^

github-actions · 2024-10-22T14:39:13Z

include/bout/parallel_boundary_region.hxx

+    return BoundaryRegionParIter(bndry_points, bndry_points.end(), dir, localmesh);
+  }
+
+  const int dir;


warning: member variable 'dir' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]

const int dir; ^

github-actions · 2024-10-22T14:39:14Z

include/bout/sys/parallel_stencils.hxx

+                             BoutReal value1) {
+  return (spacing0 * value1 - spacing1 * value0) / (spacing0 - spacing1);
+}
+inline BoutReal neumann_o2(BoutReal UNUSED(spacing0), BoutReal value0, BoutReal spacing1,


warning: unknown type name 'BoutReal' [clang-diagnostic-error]

inline BoutReal neumann_o2(BoutReal UNUSED(spacing0), BoutReal value0, BoutReal spacing1, ^

github-actions · 2024-10-22T14:39:14Z

include/bout/sys/parallel_stencils.hxx

+                             BoutReal value1) {
+  return (spacing0 * value1 - spacing1 * value0) / (spacing0 - spacing1);
+}
+inline BoutReal neumann_o2(BoutReal UNUSED(spacing0), BoutReal value0, BoutReal spacing1,


warning: unknown type name 'BoutReal' [clang-diagnostic-error]

inline BoutReal neumann_o2(BoutReal UNUSED(spacing0), BoutReal value0, BoutReal spacing1, ^

github-actions · 2024-10-22T14:39:14Z

include/bout/sys/parallel_stencils.hxx

+  return (spacing0 * value1 - spacing1 * value0) / (spacing0 - spacing1);
+}
+inline BoutReal neumann_o2(BoutReal UNUSED(spacing0), BoutReal value0, BoutReal spacing1,
+                           BoutReal value1) {


warning: unknown type name 'BoutReal' [clang-diagnostic-error]

BoutReal value1) { ^

github-actions · 2024-10-22T14:39:15Z

include/bout/sys/parallel_stencils.hxx

+                           BoutReal value1) {
+  return -spacing1 * value0 + value1;
+}
+inline BoutReal dirichlet_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1,


warning: unknown type name 'BoutReal' [clang-diagnostic-error]

inline BoutReal dirichlet_o3(BoutReal spacing0, BoutReal value0, BoutReal spacing1, ^

github-actions · 2024-10-22T14:39:15Z

src/field/field.cxx

@@ -39,3 +39,14 @@ int Field::getNx() const { return getMesh()->LocalNx; }
 int Field::getNy() const { return getMesh()->LocalNy; }

 int Field::getNz() const { return getMesh()->LocalNz; }
+
+bool Field::isFci() const {
+  const auto coords = this->getCoordinates();


warning: 'const auto coords' can be declared as 'auto *const coords' [readability-qualified-auto]

Suggested change

const auto coords = this->getCoordinates();

auto *const coords = this->getCoordinates();

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 25 out of 44. Check the log or trigger a new build to see more.

github-actions · 2024-10-22T15:16:45Z

src/mesh/coordinates.cxx

+  {
+    std::vector<Field3D> fields{dx,  dy,   dz,   g11,  g22,  g33,  g12,  g13,
+                                g23, g_11, g_22, g_33, g_12, g_13, g_23, J};
+    for (auto& f : fields) {


warning: variable name 'f' is too short, expected at least 3 characters [readability-identifier-length]

for (auto& f : fields) { ^

github-actions · 2024-10-22T15:16:45Z

src/mesh/interpolation/hermite_spline_xz.cxx

+private:
+  // number of procs
+  BoutMesh* mesh;
+  const int nxpe;


warning: member 'nxpe' of type 'const int' is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const int nxpe; ^

github-actions · 2024-10-22T15:16:46Z

src/mesh/interpolation/hermite_spline_xz.cxx

+  // number of procs
+  BoutMesh* mesh;
+  const int nxpe;
+  const int nype;


warning: member 'nype' of type 'const int' is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const int nype; ^

github-actions · 2024-10-22T15:16:46Z

src/mesh/interpolation/hermite_spline_xz.cxx

+  BoutMesh* mesh;
+  const int nxpe;
+  const int nype;
+  const int nzpe{1};


warning: member 'nzpe' of type 'const int' is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const int nzpe{1}; ^

github-actions · 2024-10-22T15:16:46Z

src/mesh/interpolation/hermite_spline_xz.cxx

+  const int nxpe;
+  const int nype;
+  const int nzpe{1};
+  const int xstart, ystart, zstart;


warning: member 'xstart' of type 'const int' is const qualified [cppcoreguidelines-avoid-const-or-ref-data-members]

const int xstart, ystart, zstart; ^

github-actions · 2024-10-22T15:16:47Z

src/mesh/interpolation/hermite_spline_xz.cxx

+    //     x, z, i_corn, k_corner(x, y, z));
+    // ixstep = mesh->LocalNx * mesh->LocalNz;
+    for (int j = 0; j < 4; ++j) {
+      PetscInt idxm[4];


warning: do not declare C-style arrays, use std::array<> instead [cppcoreguidelines-avoid-c-arrays]

PetscInt idxm[4]; ^

github-actions · 2024-10-22T15:16:47Z

src/mesh/interpolation/hermite_spline_xz.cxx

+    // ixstep = mesh->LocalNx * mesh->LocalNz;
+    for (int j = 0; j < 4; ++j) {
+      PetscInt idxm[4];
+      PetscScalar vals[4];


warning: do not declare C-style arrays, use std::array<> instead [cppcoreguidelines-avoid-c-arrays]

PetscScalar vals[4]; ^

github-actions · 2024-10-22T15:16:48Z

src/mesh/interpolation/hermite_spline_xz.cxx

+      PetscInt idxm[4];
+      PetscScalar vals[4];
+      for (int k = 0; k < 4; ++k) {
+        idxm[k] = conv.fromMeshToGlobal(i_corn - 1 + j, y + y_offset,


warning: do not use array subscript when the index is not an integer constant expression [cppcoreguidelines-pro-bounds-constant-array-index]

idxm[k] = conv.fromMeshToGlobal(i_corn - 1 + j, y + y_offset, ^

github-actions · 2024-10-22T15:16:48Z

src/mesh/interpolation/hermite_spline_xz.cxx

+      for (int k = 0; k < 4; ++k) {
+        idxm[k] = conv.fromMeshToGlobal(i_corn - 1 + j, y + y_offset,
+                                        k_corner(x, y, z) - 1 + k);
+        vals[k] = newWeights[j * 4 + k][i];


warning: do not use array subscript when the index is not an integer constant expression [cppcoreguidelines-pro-bounds-constant-array-index]

vals[k] = newWeights[j * 4 + k][i]; ^

github-actions · 2024-10-22T15:16:48Z

src/mesh/interpolation/hermite_spline_xz.cxx

+                                        k_corner(x, y, z) - 1 + k);
+        vals[k] = newWeights[j * 4 + k][i];
+      }
+      MatSetValues(petscWeights, 1, idxn, 4, idxm, vals, INSERT_VALUES);


warning: do not implicitly decay an array into a pointer; consider using gsl::array_view or an explicit cast instead [cppcoreguidelines-pro-bounds-array-to-pointer-decay]

MatSetValues(petscWeights, 1, idxn, 4, idxm, vals, INSERT_VALUES); ^

dschwoerer · 2024-10-22T15:27:26Z

test-laplace-petsc3d is failing, I am not sure why.
I tried changing the PETSc options, but that does not seem to impact the error.

dschwoerer and others added 30 commits February 8, 2023 10:05

Switch hermite_spline_xz to index

3583476

Might help with performance

Switch toward regions

4ec74ef

Switch to regions for FCI regions

d096020

Use region_id in interpolation

d2a81bf

Otherwise the regions aren't cached.

Switch hermite_spline_xz to index

ea5640f

Might help with performance

Cleanup

de7d1de

Enable splitting in X using PETSc

8a1c230

Test parallised interpolation if PETSc is found

8234ccf

Fall back to region if not shifted

9525e2c

Split in X only if we have PETSc

b62082c

Add test-interpolate for splitting in X

e147bc5

Cleanup

62d5bbe

Only run in parallel if we split in X

5c32415

Delete object

a4a28c6

release leaks the pointer, reset free's the object.

Create PetscVecs only once

0e28dc1

Be more general about cleaning up before BoutFinialise

66bde04

Run different interpolations in the fci test

adba877

Fix parallel boundary region with x splitting

cbaf894

Add integrated test for FCI X splitting

5673f0c

* helped finding the bug for the boundary * rather slow (around 1 minute) * needs internet connectivity

Apply black changes

9149bf4

Apply clang-format changes

a088700

Apply clang-format changes

32ea2fd

Apply clang-format changes

faac69c

Merge remote-tracking branch 'origin/next' into fci-splitting

0ee0d07

Merge remote-tracking branch 'origin/next' into fci-splitting

49cd985

Apply black changes

4566405

CI: install wget

4935742

Merge remote-tracking branch 'origin/next' into fci-splitting

01a436c

Apply clang-format changes

147a872

dschwoerer added 11 commits October 22, 2024 11:21

Add isFci also to mesh

44084cc

fixup again

81dcc62

fixup fv_ops

fa27812

Always set region for hermite_spline_xz

175f8d7

Avoid using FV in y direction with FCI

f189d4f

Add option to disallow calculating parallel fields

697c89e

Calculating parallel fields for metrics terms does not make sense. Using such parallel fields is very, very likely a bug.

Add const version for getCoordinates

2b47ecd

Add simple interface to store parallel fields

78611d0

Just dumping the parallel slices does in general not work, as then collect discards that, especially if NYPE==ny

ensure we dont mix non-fci BCs with fci

0149bd0

Only check hasBndry*Y if they would be included

a307426

hasBndryUpperY / hasBndryLowerY does not work for FCI and thus the request does not make sense / can be configured to throw. Thus it should not be checked if it is not needed.

Add const version for getCoordinates

cd288e9

dschwoerer added the FCI label Oct 22, 2024

dschwoerer and others added 4 commits October 22, 2024 12:11

Merge branch 'next' of github.com:boutproject/BOUT-dev into fci-auto

003c466

Remove duplicate functions

089baa8

Merge branch 'is-fci-mesh' into fci-auto

992681d

Apply clang-format changes

1d6ecb0

github-actions bot reviewed Oct 22, 2024

View reviewed changes

dschwoerer added 3 commits October 22, 2024 14:36

Fix floor() for non-Field3D

a63ecfc

Avoid warning from unused-argument

2d9d524

Set field to be aligned

7aa8d01

Otherwise it is attempted to transform it to field-aligned, which fails as the parallel transform is not set.

github-actions bot reviewed Oct 22, 2024

View reviewed changes

Use new iterator

25fe475

dschwoerer force-pushed the fci-auto branch from b50e9e2 to 25fe475 Compare October 22, 2024 14:21

Apply clang-format changes

255eccb

github-actions bot reviewed Oct 22, 2024

View reviewed changes

dschwoerer added 3 commits October 22, 2024 17:00

Fix default region name

c69bff5

Update boundary name

1505840

Ensure we have a valid region

ae578be

github-actions bot reviewed Oct 22, 2024

View reviewed changes

	bool operator!=(const BoundaryRegionIter& rhs) { return ind() != rhs.ind(); }
	bool operator!=(const BoundaryRegionIter& rhs) const { return ind() != rhs.ind(); }

	int numberParallelSlices() { return 0; }
	static int numberParallelSlices() { return 0; }

		@@ -26,6 +26,15 @@

		#include "bout/mask.hxx"

		#define USE_NEW_WEIGHTS 1

	inline BoutReal extrapolate_grad_o1(const Field3D& f) const { return 0; }
	inline BoutReal extrapolate_grad_o1(const Field3D& /f/) const { return 0; }

	const auto coords = this->getCoordinates();
	auto *const coords = this->getCoordinates();

Do things automatically for FCI #3004

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Do things automatically for FCI #3004

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dschwoerer commented Oct 22, 2024

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