Merge 4.4.1 into next #2488

ZedThree · 2022-01-21T09:52:10Z

@bendudson Could you double-check the SNES stuff? There were a couple of conflicts I had to fix

Fix BOUT_OVERRIDE_DEFAULT_OPTION()

Shared objects should be executable

Fix permission of shared objects

Enables much quicker calculation of steady-state solutions than CVODE typically can.

Recent change in commit hash broke this Fixes #2461

Ambiguous between mpark:: and std::visit when compiling with GCC 11.1 (Arch linux)

Fix SUNDIALS download git tag

Add `bout::utils::` prefix to `visit`

Fixes #2472 [skip ci]

Before this change, setting an integer/BoutReal to, for example, 'true', would yield: Cannot find variable 'true' With this change, now the error is: Couldn't get BoutReal from option conduction:chi = 'true': \ Cannot find variable 'true' Backported from next Fixes #2466

…essage Raise more descriptive error if converting Option fails

Print correct CMake build directory in configure message

This makes the output feel a bit more accurate

[skip ci]

[skip ci] Co-authored-by: johnomotani <john.omotani@ukaea.uk>

CMake: Fix using the build directory directly

Update "Running BOUT++" documentation

- Add equation_form option, to change the nonlinear equation being solved: Pseudo-transient, backward Euler (two forms) and direct Newton - Add line_search_type option, to set the SNES line search - Add stol convergence tolerance option - Use SNESSetForceIteration if PETSc >= 3.8 - Print more diagnostics if solve diverges or fails - Add forward Euler step to get out of local minima - Print more diagnostics if diagnose = true

Not needed since PETSc 3.2

Some suggestions for beuler backport

Back-port beuler/snes improvements to master

[skip ci]

Version 4.4.1 release

* master: (27 commits) Fix contributor's name Update release date Update changelog Revert SONAME/SOVERSION to 4.4.0 Fix test-bout-override-default-option for cmake Update DOI and release date for 4.4.1 Update changelog for 4.4.1 Update translation files for 4.4.1 Bump version to 4.4.1 Enable setting SNES solver PETSc options from input file Try to consolidate some loops/branches in SNESSolver Use `BOUT_ENUM_CLASS` for `SNESSolver::equation_form` Use `std::vector/array` instead of C style arrays Remove `__FUNCT__` macros for PETSc callbacks Update backport of beuler/snes solver Fix typo in docs Remove IDL section and recommend xBOUT for analysis Recommend using xBOUT for manipulating restart files Update log output in "running BOUT++" manual section Move "Initialising solver" message to top of `Solver::solve` ...

github-actions

clang-tidy made some suggestions

There were too many comments to post at once. Showing the first 25 out of 33. Check the log or trigger a new build to see more.

github-actions · 2022-01-21T12:10:03Z

src/solver/impls/snes/snes.cxx

+}
+
+static PetscErrorCode snesPCapply(PC pc, Vec x, Vec y) {
+  int ierr;


warning: variable ierr is not initialized [cppcoreguidelines-init-variables]

int ierr; ^ = 0

github-actions · 2022-01-21T12:10:03Z

src/solver/impls/snes/snes.cxx

+  int ierr;
+
+  // Get the context
+  SNESSolver* s;


warning: variable s is not initialized [cppcoreguidelines-init-variables]

SNESSolver* s; ^ = nullptr

github-actions · 2022-01-21T12:10:04Z

src/solver/impls/snes/snes.cxx

+
+  // Get the context
+  SNESSolver* s;
+  ierr = PCShellGetContext(pc, reinterpret_cast<void**>(&s));


warning: do not use reinterpret_cast [cppcoreguidelines-pro-type-reinterpret-cast]

ierr = PCShellGetContext(pc, reinterpret_cast<void**>(&s)); ^

github-actions · 2022-01-21T12:10:04Z

src/solver/impls/snes/snes.cxx

+  PetscFunctionReturn(s->precon(x, y));
+}
+
+SNESSolver::SNESSolver(Options* opt)


warning: constructor does not initialize these fields: timestep, dt, dt_min_reset, lower_its, upper_its, out_timestep, nsteps, diagnose, nlocal, neq, equation_form, snes_f, snes_x, x0, delta_x, predictor, x1, snes, Jmf, fdcoloring [cppcoreguidelines-pro-type-member-init]

SNESSolver::SNESSolver(Options* opt) ^

github-actions · 2022-01-21T12:10:04Z

src/solver/impls/snes/snes.cxx

+    .doc("Line search type: basic, bt, l2, cp, nleqerr")
+    .withDefault("default");
+  if (line_search_type != "default") {
+    SNESLineSearch linesearch;


warning: variable linesearch is not initialized [cppcoreguidelines-init-variables]

SNESLineSearch linesearch; ^ = nullptr

github-actions · 2022-01-21T12:10:06Z

src/solver/impls/snes/snes.cxx

+    SNESType snestype;
+    SNESGetType(snes, &snestype);
+    output.write("SNES Type : %s\n", snestype);
+    if (ksptype) {


warning: implicit conversion KSPType (aka const char *) -> bool [readability-implicit-bool-conversion]

if (ksptype) { ^ != nullptr

github-actions · 2022-01-21T12:10:06Z

src/solver/impls/snes/snes.cxx

+    if (ksptype) {
+      output.write("KSP Type  : %s\n", ksptype);
+    }
+    if (pctype) {


warning: implicit conversion PCType (aka const char *) -> bool [readability-implicit-bool-conversion]

if (pctype) { ^ != nullptr

github-actions · 2022-01-21T12:10:06Z

src/solver/impls/snes/snes.cxx

      if (predictor) {
        // Save previous values: x1 <- x0
        VecCopy(x0, x1);
        time1 = simtime;
      }

+      int nl_its;


warning: variable nl_its is not initialized [cppcoreguidelines-init-variables]

int nl_its; ^ = 0

github-actions · 2022-01-21T12:10:06Z

src/solver/impls/snes/snes.cxx

+          const BoutReal* xdata = nullptr;
+          int ierr = VecGetArrayRead(snes_x, &xdata);
+          CHKERRQ(ierr);
+          load_vars(const_cast<BoutReal*>(xdata));


warning: do not use const_cast [cppcoreguidelines-pro-type-const-cast]

load_vars(const_cast<BoutReal*>(xdata)); ^

github-actions · 2022-01-21T12:10:06Z

src/solver/impls/snes/snes.cxx

-                     its);
+        // Gather and print diagnostic information
+
+        int lin_its;


warning: variable lin_its is not initialized [cppcoreguidelines-init-variables]

int lin_its; ^ = 0

- Ensure that the linear boolean flag is passed through to the rhs function - Formatting strings e.g. `%e` -> `{}`

github-actions

clang-tidy made some suggestions

github-actions · 2022-01-27T19:10:59Z

src/solver/impls/snes/snes.cxx

+    throw BoutException("No user preconditioner");
+  }
+
+  int ierr;


warning: variable ierr is not initialized [cppcoreguidelines-init-variables]

int ierr; ^ = 0

github-actions · 2022-01-27T19:10:59Z

src/solver/impls/snes/snes.cxx

+  int ierr;
+
+  // Get data from PETSc into BOUT++ fields
+  Vec solution;


warning: variable solution is not initialized [cppcoreguidelines-init-variables]

Vec solution; ^ = nullptr

github-actions · 2022-01-27T19:11:00Z

src/solver/impls/snes/snes.cxx

+  // Get data from PETSc into BOUT++ fields
+  Vec solution;
+  SNESGetSolution(snes, &solution);
+  BoutReal* soldata;


warning: variable soldata is not initialized [cppcoreguidelines-init-variables]

BoutReal* soldata; ^ = nullptr

github-actions · 2022-01-27T19:11:00Z

src/solver/impls/snes/snes.cxx

+  CHKERRQ(ierr);
+
+  // Load vector to be inverted into ddt() variables
+  const BoutReal* xdata;


warning: variable xdata is not initialized [cppcoreguidelines-init-variables]

const BoutReal* xdata; ^ = nullptr

github-actions · 2022-01-27T19:11:00Z

src/solver/impls/snes/snes.cxx

+  const BoutReal* xdata;
+  ierr = VecGetArrayRead(x, &xdata);
+  CHKERRQ(ierr);
+  load_derivs(const_cast<BoutReal*>(xdata)); // Note: load_derivs does not modify data


warning: do not use const_cast [cppcoreguidelines-pro-type-const-cast]

load_derivs(const_cast<BoutReal*>(xdata)); // Note: load_derivs does not modify data ^

github-actions · 2022-01-27T19:11:00Z

src/solver/impls/snes/snes.cxx

+  runPreconditioner(simtime + dt, dt, 0.0);
+
+  // Save the solution from F_vars
+  BoutReal* fdata;


warning: variable fdata is not initialized [cppcoreguidelines-init-variables]

BoutReal* fdata; ^ = nullptr

github-actions · 2022-01-27T19:11:00Z

src/solver/solver.cxx

@@ -1246,13 +1244,13 @@ int Solver::run_rhs(BoutReal t) {

    save_vars(tmp.begin()); // Copy variables into tmp
    pre_rhs(t);
-    status = model->runConvective(t);
+    status = model->runConvective(t, linear);


warning: Value stored to status is never read [clang-analyzer-deadcode.DeadStores]

status = model->runConvective(t, linear); ^ src/solver/solver.cxx:1247:5: note: Value stored to 'status' is never read

github-actions · 2022-01-27T19:11:00Z

src/sys/petsclib.cxx

@@ -74,6 +74,18 @@ void PetscLib::setOptionsFromInputFile(KSP& ksp) {
  }
 }

+void PetscLib::setOptionsFromInputFile(SNES& snes) {
+  auto ierr = SNESSetOptionsPrefix(snes, options_prefix.c_str());
+  if (ierr) {


warning: implicit conversion int -> bool [readability-implicit-bool-conversion]

if (ierr) { ^ != 0

github-actions · 2022-01-27T19:11:00Z

src/sys/petsclib.cxx

+  }
+
+  ierr = SNESSetFromOptions(snes);
+  if (ierr) {


warning: implicit conversion int -> bool [readability-implicit-bool-conversion]

if (ierr) { ^ != 0

API includes a `linear` flag, which is set to `true` when a linearised rhs() function can be used.

bendudson

Thanks @ZedThree ! LGTM

ZedThree and others added 30 commits September 7, 2021 17:54

Merge pull request #2417 from boutproject/default-override-macro-fix

639d581

Fix BOUT_OVERRIDE_DEFAULT_OPTION()

Fix permission of shared objects

b7064cd

Shared objects should be executable

Merge pull request #2433 from boutproject/install-perm

796caab

Fix permission of shared objects

Back-port beuler/snes improvements to master

b8cad53

Enables much quicker calculation of steady-state solutions than CVODE typically can.

Fix SUNDIALS download git tag

e64df08

Recent change in commit hash broke this Fixes #2461

Add bout::utils:: prefix to visit

a03b66e

Ambiguous between mpark:: and std::visit when compiling with GCC 11.1 (Arch linux)

Merge pull request #2462 from boutproject/fix-download-sundials

43b94fa

Fix SUNDIALS download git tag

CMake: Fix using the build directory directly

cf996aa

Merge pull request #2463 from boutproject/fix-variant-gcc11-master

15ead42

Add `bout::utils::` prefix to `visit`

Provide correct build instructions

8d99d1d

Fixes #2472 [skip ci]

Merge pull request #2474 from boutproject/master-better-parse-error-m…

6f19552

…essage Raise more descriptive error if converting Option fails

Merge pull request #2473 from boutproject/master-cmake-build

2211a91

Print correct CMake build directory in configure message

Move "Initialising solver" message to top of Solver::solve

ead8b6d

This makes the output feel a bit more accurate

Update log output in "running BOUT++" manual section

6c9d37e

[skip ci]

Recommend using xBOUT for manipulating restart files

36a15e2

[skip ci]

Remove IDL section and recommend xBOUT for analysis

00017b2

[skip ci]

Fix typo in docs

6735657

[skip ci] Co-authored-by: johnomotani <john.omotani@ukaea.uk>

Merge pull request #2464 from boutproject/cmake-fix-use-build-dir

706fb97

CMake: Fix using the build directory directly

Merge pull request #2475 from boutproject/update-running-bout-docs

66206b8

Update "Running BOUT++" documentation

Remove __FUNCT__ macros for PETSc callbacks

ca3c17c

Not needed since PETSc 3.2

Use std::vector/array instead of C style arrays

420ef27

Use BOUT_ENUM_CLASS for SNESSolver::equation_form

e46b068

Try to consolidate some loops/branches in SNESSolver

8046108

Enable setting SNES solver PETSc options from input file

145d2ba

Bump version to 4.4.1

9423a1d

Update translation files for 4.4.1

de47f69

Update changelog for 4.4.1

0012283

Update DOI and release date for 4.4.1

f02b54b

ZedThree and others added 8 commits December 13, 2021 15:52

Fix test-bout-override-default-option for cmake

e7148f0

Revert SONAME/SOVERSION to 4.4.0

3e5c412

Merge pull request #2479 from boutproject/beuler-backport-tidy

149877d

Some suggestions for beuler backport

Merge pull request #2459 from boutproject/master-beuler-backport

ecced94

Back-port beuler/snes improvements to master

Update changelog

91eda06

Update release date

6055edc

Fix contributor's name

2a35cf1

[skip ci]

Merge pull request #2480 from boutproject/v4.4.1-rc

43ca9d7

Version 4.4.1 release

ZedThree requested a review from bendudson January 21, 2022 09:52

ZedThree force-pushed the merge-441 branch from 5a19408 to 80dfb06 Compare January 21, 2022 12:03

github-actions bot reviewed Jan 21, 2022

View reviewed changes

bendudson previously approved these changes Jan 27, 2022

View reviewed changes

SNES solver merges

3afc1d2

- Ensure that the linear boolean flag is passed through to the rhs function - Formatting strings e.g. `%e` -> `{}`

bendudson dismissed their stale review via 4997887 January 27, 2022 19:03

github-actions bot reviewed Jan 27, 2022

View reviewed changes

Merge in Solver and PhysicsModel changes from next

4997887

API includes a `linear` flag, which is set to `true` when a linearised rhs() function can be used.

bendudson approved these changes Jan 27, 2022

View reviewed changes

ZedThree merged commit 7f733f9 into next Feb 2, 2022

ZedThree deleted the merge-441 branch February 2, 2022 10:09

bendudson reviewed Feb 16, 2022

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Merge 4.4.1 into next #2488

Merge 4.4.1 into next #2488

ZedThree commented Jan 21, 2022

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Merge 4.4.1 into next #2488

Merge 4.4.1 into next #2488

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