ADIOS 2 I/O #2766
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ADIOS 2 I/O #2766
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…alise/BoutFinalise)
…DIOS. ADIOS code does not compile yet.
In general file I/O maps a logically rectangular subset of the local (nx, ny, nz) array onto a part of a global array. That global array may be sparse i.e. there might be holes in it. The mapping does not cover the entire local array because we insert communication guard cells around the outside. To perform this mapping we use ADIOS Put() function to get a span of a buffer, and then iterate over fields to copy data into those buffers.
…). Add helper functions to avoid redefining variables in an adios2::IO object.
…for restart files when using ADIOS. Replaced the use of Span and manual copy for memory selections to write data without ghost cells.
The Options tree passed to this function contains the data to be written to file, not necessarily the input settings. The output file name should be set from the Options::root() input options, not the input options tree.
Using autoconf this should be defined, but is always "no" Haven't yet regenerated configure script
Generated new configure script, updated autoconf_build_defines.hxx.in
Needs to be added to the makefile to be built.
Add --has-adios option to bout-config, and require in test-options-adios integrated test.
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| /// (MapGlobalX, MapGlobalY, MapGlobalZ) in the global index space maps to (MapLocalX, MapLocalY, MapLocalZ) locally. | ||
| /// Note that boundary cells are included in the global index space, but communication | ||
| /// guard cells are not. | ||
| int MapGlobalX, MapGlobalY, MapGlobalZ; ///< Start global indices |
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warning: member variable 'MapGlobalX' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]
int MapGlobalX, MapGlobalY, MapGlobalZ; ///< Start global indices
^| /// (MapGlobalX, MapGlobalY, MapGlobalZ) in the global index space maps to (MapLocalX, MapLocalY, MapLocalZ) locally. | ||
| /// Note that boundary cells are included in the global index space, but communication | ||
| /// guard cells are not. | ||
| int MapGlobalX, MapGlobalY, MapGlobalZ; ///< Start global indices |
There was a problem hiding this comment.
warning: member variable 'MapGlobalY' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]
int MapGlobalX, MapGlobalY, MapGlobalZ; ///< Start global indices
^| /// (MapGlobalX, MapGlobalY, MapGlobalZ) in the global index space maps to (MapLocalX, MapLocalY, MapLocalZ) locally. | ||
| /// Note that boundary cells are included in the global index space, but communication | ||
| /// guard cells are not. | ||
| int MapGlobalX, MapGlobalY, MapGlobalZ; ///< Start global indices |
There was a problem hiding this comment.
warning: member variable 'MapGlobalZ' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]
int MapGlobalX, MapGlobalY, MapGlobalZ; ///< Start global indices
^| /// Note that boundary cells are included in the global index space, but communication | ||
| /// guard cells are not. | ||
| int MapGlobalX, MapGlobalY, MapGlobalZ; ///< Start global indices | ||
| int MapLocalX, MapLocalY, MapLocalZ; ///< Start local indices |
There was a problem hiding this comment.
warning: member variable 'MapLocalX' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]
int MapLocalX, MapLocalY, MapLocalZ; ///< Start local indices
^| /// Note that boundary cells are included in the global index space, but communication | ||
| /// guard cells are not. | ||
| int MapGlobalX, MapGlobalY, MapGlobalZ; ///< Start global indices | ||
| int MapLocalX, MapLocalY, MapLocalZ; ///< Start local indices |
There was a problem hiding this comment.
warning: member variable 'MapLocalY' has public visibility [cppcoreguidelines-non-private-member-variables-in-classes]
int MapLocalX, MapLocalY, MapLocalZ; ///< Start local indices
^
|
I think the clang-tidy comments are mostly sensible, except to use |
ZedThree
reviewed
Oct 16, 2023
| template <class T> | ||
| bool readVariable(adios2::Engine& reader, adios2::IO& io, const std::string& name, | ||
| const std::string& type, Options& result) { | ||
| std::vector<T> data; |
| } | ||
|
|
||
| if (variable.ShapeID() == adios2::ShapeID::LocalArray) { | ||
| throw std::invalid_argument( |
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Worth switching to BoutException so we can use fmt to format the message?
* next: Set oversubscribe flags for openmpi 5 CI: Replace pip script with requirements.txt Add BOUT_HOST_DEVICE to accessor operators for GPU hypre3d: Replace finite() with std::isfinite() hypre3d: Remove reference to datafile Use latest python in CI Bump externalpackages/boutdata from `ab59ef9` to `908a4c2` Bump externalpackages/googletest from `2dd1c13` to `829c199` Bump externalpackages/fmt from `f0903ad` to `2ac6c5c` Bump externalpackages/mpark.variant from `3c7fc82` to `23cb94f` CI: run only once per week Increase shm size in container CI: Also build slepc from devel branch CI: Run on PETSc developement branch Fix test-laplace-petsc3d CI: user master branch for OCI workflow [RTD] specify tool [RTD] add os too read the docs config Bump ZedThree/clang-tidy-review from 0.13.1 to 0.14.0 Bump stefanzweifel/git-auto-commit-action from 4 to 5 Bump actions/setup-python from 1 to 4 Increase MG levels for Petsc3DAMG test Don't include headers for petsc interface if we're not building it Apply clang-format changes Fix a whole bunch of clang-tidy issues in petsc interface/AMG solver Apply clang-format Add defaulted move ctor/assignment for `PetscMatrix::Element` Fix getting correct parallel slice for `getWeightsForYApproximation` Stop clang-tidy complaining about some short names Change some variable names to keep clang-tidy happy Apply clang-format changes Delete unneeded PetscVectorElement test Refactor setting boundary conditions in LaplacePetsc3dAmg Set LaplacePetsc3damg options in initialiser list Print error in laplace-petsc3d test Add a utility function for checking flags in bitsets Make sure guard cells in PetscVector buffer are -1 Fix some clang-tidy issues, mostly multiple declarations on one line Replace direct calls to `VecSetValue` with buffered calls Make `Field2D::data` private Collect all test failures for petsc3d Add `size()` method to Fields to get total number of points Simplify getting parallel slice interpolation weights Use `BoutException` formatted message instead of `std::cout` Use default constructor for `Vec/Mat` deleters WIP convert petscvector Fix lots of clang-tidy issues in PETSc interface Docs: Note removal of `./configure` build system Remove all autoconf files Docs: Remove remaining references to `./configure` from docs Fix sphinx configuration Bump docker/build-push-action Ensure also lower case is accepted Bump externalpackages/googletest from `6092810` to `2dd1c13` Apply clang-format changes Cast reason to int for formatting Do not try to print KSPConvergedReason CI: Use more system packages CI: Reenable petsc Try disabeling PETSc Bump actions/cache from 2 to 3 Bump docker/metadata-action Bump actions/checkout from 2 to 4 Bump codecov/codecov-action from 1 to 3 Bump externalpackages/boututils from `c2e97a2` to `433995f` Also give a backtrace if we are hitting a bus error Switch back to openmpi CI: switch to mpich to workaround openmpi issue Switch to fedora packes Default to current working directory Ensure submodules are present for local testing Change default to rawhide Prefer dnf5 Bump required C++ standard to 17
Mainly unused parameters, moving definitions to the header, adding override keywords. Note that there is a GCC compiler bug with [[maybe_unused]] on first argument of a constructor: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=81429
Automatic formatting
Sorry for the large commit; this touches quite a few places.
The OptionsNetCDF and OptionsADIOS classes are now private,
so that OptionsIO is now the interface to both.
The generic Factory is used to implement OptionsIOFactory,
and the "netcdf" and "adios" types are registered in their
separate header files.
The OptionsIOFactory handles the choice of default section
("restart_files" for restarts, "output" for dump/output files),
and sets the default path and prefix. This simplifies both
the PhysicsModel and the separate implementations by putting
that logic in one place.
…nstead of ADIOS2_DIR
Now tested with ADIOS enabled.
If configured with `-DBOUT_DOWNLOAD_ADIOS=ON`, CMake will download ADIOS2 from github, configure and build it with BOUT++.
Some documentation in the comments, and in the manual.
The unit tests require GMock, so set BUILD_GMOCK=ON by default.
Now always need to pass the data to be written, rather than implicitly writing Options::root().
Changing from OptionsNetCDF to OptionsIO interface.
Output file needs MZ and other mesh variables for collect() to work.
Needed in post-processing when reading data
collect needs to know BOUT_VERSION or it assumes pre-0.2 format.
ADIOS uses '/' as a separator, but BOUT++ options uses ':'. When reading variables, we now split on '/' separator and navigate to the correct subsection. Attributes are also named using the final part of the name after the last '/'. solver and beuler integrated tests weren't calling BoutInitialise, so failed when ADIOSFinalize is called.
BoutFinalise throws an exception when ADIOS is enabled but BoutInitialise is not called. BoutInitialise throws an exception if the "data" directory doesn't exist. For this test neither BoutInitialise nor BoutFinalise are needed, so removed.
Not required, and BoutInitialise throws an exception because the "data" directory doesn't exist.
Using $HOME/local rather than $HOME/local/adios2. Hopefully cmake can find it.
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After an extended game of whack-a-mole, I think this is now ready for merging. I don't know what's going on with clang-tidy-review, but I don't think it's related to the changes. |
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Work in progress to enable BOUT++ to write and read data using ADIOS-2 (https://adios2.readthedocs.io/en/v2.9.1/).
Rebased #2739 on the
nextbranch.BOUT++ can now be configured with
-DBOUT_DOWNLOAD_ADIOS=ONto download, configure and build ADIOS.Once configured, the output and restart file data format can be set with
output:typeandrestart_files:typesettings e.g.outputs a
BOUT.dmp.bpADIOS2 dataset.