Fix minor HYPRE and ADIOS2 compilation issues by ZedThree · Pull Request #3022 · boutproject/BOUT-dev

ZedThree · 2024-11-07T17:20:35Z

It turns out we're not building HYPRE on CI at all, and we're silently not actually using ADIOS2, and that's let a couple of compilation issues creep in.

This fixes the compilation and CI issues (hopefully).

Caused linking issues. Also put used function in an anonymous namespace to prevent future linking issues

Also default to off

Usually installed under `usr/include/hypre` (or similar) for system packages

ZedThree · 2024-11-08T09:43:52Z

Hmm, more problems with 3D metrics and the Hypre laplacians. Guess I'll have to build that config locally to fix them all.

dschwoerer · 2024-11-12T10:38:30Z

It would be great to fix that, but I think disabling hypre with 3D is also fine. Hypre is often used - but only via PETSc, so that should be fine ...

So adding a configure time error should be fine ...

ZedThree · 2024-11-12T11:09:32Z

I think it's mostly just making some types auto instead of Field2D or whatever, but I need to find some time to look into it

dschwoerer · 2024-11-15T13:42:59Z

I have it fixed, so that it compiles.
I do not think it does the right think, as I need to change Field2D to FieldMetric in many places ...

dschwoerer · 2024-11-15T14:04:44Z

Fixes #2701

Saved to dmp files by the Laplacian savePerformance monitor. If the savePerformance() method is called to enable outputs, the mean solver and AMG iterations, and the final residual, are saved as time-varying scalars.

Default was "parallel_dirichlet", but no boundary is registered with that name. Changed to "parallel_dirichlet_o2".

Calling `phiSolver->savePerformance(...)` causes performance (e.g. iteration count) diagnostics to be saved to the output file. hypre input did have the wrong parallel transform, boundary conditions that have not been implemented. Now uses hypre3d as the phiSolver.

The combination doesn't yet work, so disable for now.

Add `override` keyword to squash warning.

- Mesh variable names are case sensitive - mpirun needs ./ to find executable on some systems

Calls a Hypre function to print the matrix elements.

ZedThree · 2025-01-22T17:54:56Z

Failing test is probably because ADIOS2 is missing from bout++Config.cmake.in -- need a find_dependency and set ADIOS2_ROOT or similar

* next: Prefer scientific notation Prefer scientific notation Prefer scientific notation Prefer scientific notation Prefer scientific notation pvpre library should link against pvode Update some copyright notices Replace finite() with std::isfinite() Use non-deprecated values also in input files update input files for deprecated options. Revert "update input files for deprecated options." update input files for deprecated options. Deprecate options that only use as default for other options.

ZedThree · 2025-01-23T15:26:24Z

Failing on test-laplacexy2-hypre with OSError: ERROR: No data files found in path data, which is not terribly helpful.

Full error message:

33/63 Test #33: test-laplacexy2-hypre ...............***Failed   63.26 sec
Making LaplaceXY inversion test
Running LaplaceXY inversion test
   8 processors....
mpiexec -np 8 ./test-laplacexy laplacexy:core_bndry_dirichlet=true laplacexy:pf_bndry_dirichlet=true laplacexy:y_bndry_dirichlet=true f:bndry_xin=dirichlet f:bndry_xout=dirichlet f:bndry_yup=dirichlet f:bndry_ydown=dirichlet
Traceback (most recent call last):
  File "/home/runner/work/BOUT-dev/BOUT-dev/build/tests/integrated/test-laplacexy2-hypre/runtest", line 58, in <module>
    error = collect("max_error", path="data", info=False)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/BOUT-dev/BOUT-dev/tools/pylib/boutdata/collect.py", line 186, in collect
    file_list, parallel, _ = findFiles(path, prefix)
                             ^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/runner/work/BOUT-dev/BOUT-dev/tools/pylib/boutdata/collect.py", line 1227, in findFiles
    raise IOError("ERROR: No data files found in path {0}".format(path))

ZedThree · 2025-01-23T16:55:20Z

The test turns out to be failing because the solver wasn't converging. Switching laplacexy:hypre_solver_type to gmres fixes this.

The default HYPRE solver is bicgstab -- is this test an indication to change the default to gmres, or are we happy to just change the type for this test?

Using the default `bicgstab` caused the test to not converge

ZedThree · 2025-01-24T10:29:35Z

Still having a weird issue with the coverage build

ZedThree · 2025-01-24T11:00:22Z

Think this has finally fixed the issues I was originally trying to fix!

dschwoerer

Looks good, thanks 👍

dschwoerer · 2025-01-24T13:03:04Z

cmake/SetupBOUTThirdParty.cmake

 set(BOUT_HAS_NETCDF ${BOUT_USE_NETCDF})

-option(BOUT_USE_ADIOS2 "Enable support for ADIOS output" ON)
+option(BOUT_USE_ADIOS2 "Enable support for ADIOS output" OFF)


I would prefer if such feature would be automatically enabled if they are found.

ZedThree and others added 11 commits November 7, 2024 17:19

CI: Enable HYPRE in builds

ee90bee

Fix use of private variable in HYPRE laplace solver

e8adc3f

Delete (unused) duplicate private function

403fd19

Caused linking issues. Also put used function in an anonymous namespace to prevent future linking issues

CMake: Error if ADIOS2 requested and not found

ff63ff8

Also default to off

Fix missing parameter from overridden virtual function

171b7ae

CI: Fix ADIOS2 build not finding ADIOS2

237207b

CMake: Fix FindHYPRE for non-CMake builds

c3c7f46

Usually installed under `usr/include/hypre` (or similar) for system packages

Apply clang-format changes

ae8840a

Fix hypre3d laplace solver for 3D metrics

6398368

Fix a bunch of clang-tidy issues

d23cff8

Remove a couple of unused private members

9c1cfc9

bendudson and others added 12 commits January 9, 2025 10:44

Hypre3D Laplacian: Save diagnostics using outputVars

31567f9

Saved to dmp files by the Laplacian savePerformance monitor. If the savePerformance() method is called to enable outputs, the mean solver and AMG iterations, and the final residual, are saved as time-varying scalars.

ParallelTransform: Add missing space in error message

9e765b6

BoundaryFactory: Fix default for parallel boundary regions

90332a8

Default was "parallel_dirichlet", but no boundary is registered with that name. Changed to "parallel_dirichlet_o2".

Apply clang-format changes

f46d0a6

Merge branch 'next' into fix-hypre

6e1bd45

Disable hypre with 3D metrics

07603f0

The combination doesn't yet work, so disable for now.

Testing: Missed 3D + hypre combination

0012914

OptionsNetCDF: verifyTimesteps, write override base class

e3a4e1e

Add `override` keyword to squash warning.

tests/integrated: Fix hypre tests

a188682

- Mesh variable names are case sensitive - mpirun needs ./ to find executable on some systems

hypre_interface: Add print() method to HypreMatrix

9d8cae1

Calls a Hypre function to print the matrix elements.

Merge branch 'next-hypre3d-laplace' into fix-hypre

518bd4b

bendudson mentioned this pull request Jan 17, 2025

Hypre3D Laplacian diagnostics, parallel boundary default fix #3055

Closed

Apply clang-format changes

99bce95

ZedThree added 3 commits January 23, 2025 10:13

CMake: Ensure we find adios2 when linking against BOUT++

77ed8db

CMake: Reduce duplication in linking against adios2

d5c14c1

Fix laplacexy2-hypre test failing silently

dd34789

ZedThree added 5 commits January 23, 2025 16:55

Change test hypre type to gmres

acf1b5d

Using the default `bicgstab` caused the test to not converge

Remove unused x_outer_dirichlet member from LaplaceXY2 hypre

f0aea43

Remove unused header include

4172f1c

Use modern output API

e55611f

CMake: Ensure we find ADIOS2 if we downloaded it

0590870

dschwoerer previously approved these changes Jan 24, 2025

View reviewed changes

Remove coverage test from github workflow

d32c70f

bendudson dismissed dschwoerer’s stale review via d32c70f January 24, 2025 19:24

bendudson merged commit 1a002d2 into next Jan 24, 2025
26 of 27 checks passed

bendudson deleted the fix-hypre branch January 24, 2025 20:10

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Fix minor HYPRE and ADIOS2 compilation issues#3022

Fix minor HYPRE and ADIOS2 compilation issues#3022
bendudson merged 34 commits intonextfrom
fix-hypre

ZedThree commented Nov 7, 2024

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dschwoerer commented Nov 12, 2024

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ZedThree commented Nov 7, 2024

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dschwoerer commented Nov 12, 2024

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ZedThree commented Nov 12, 2024

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