XIOS: Add Handler/Interface Class & Calendar Management (and include in CMake) #293
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This was referenced Apr 27, 2023
TomMelt
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# Nextsim XIOS Interface The previous XIOS work has diverged from the current development branch. This PR has a minimum working example (MWE) in the form of a test `testXiosInit` (source `./core/test/XiosInit_test.cpp`). The test checks most of the functionality added by the XIOS C++ interface * `./core/src/Xios.cpp` * `./core/src/include/Xios.hpp` which depend on a C interface included here: `./core/src/include/xios_c_interface.hpp` The core functionality of XIOS is included as part of this PR as the other two components will require it. ## XIOS functionality Still to discuss: - [x] we need to discuss Dockerfile because building without one will become more complicated going forward (more dependencies, `lxios`, `lpnetcdf` etc. - [x] ~Also how do we want to handle mac builds going forward? I cannot simulate mac (virt OS/docker) so it's not easy for me to "fix" CI~ we will not support MPI/xios on mac This PR does the following: - [x] add `XIOS` to `cmake` - [x] add `XIOS` to the CI workflow - [x] add unit tests to check core functionality of the C++ wrapper - [x] uses mpi-aware `doctest` I think this can be merged in relatively soon. The remaining steps are (for a future PR): - [ ] to actually integrate XIOS into nextsim (because `testXiosInit` is a stand-alone binary) - [ ] to replace the `XIOS` datetime types with `nextsim`'s - [ ] produce diagnostic output files ## Steps required to run `testXiosInit` * Install `XIOS` (see the github workflow for an idea how to install `XIOS`) * Build `nextsim` with `XIOS` support using `-DENABLE_XIOS=ON` and `-Dxios_DIR=/path/to/xios/install` * `cd` to `build/core/test` and run `mpirun -n 2 ./testXiosInit` The test should pass all tests: ``` [doctest] doctest version is "2.4.11" [doctest] run with "--help" for options step 0=============================================================================== [doctest] test cases: 1 | 1 passed | 0 failed | 0 skipped [doctest] assertions: 19 | 19 passed | 0 failed | [doctest] Status: SUCCESS! =============================================================================== [doctest] assertions on all processes: 38 | 38 passed | 0 failed | =============================================================================== [doctest] Status: SUCCESS! ``` And produce the following output: ``` xios_client_1.err xios_client_0.err diagnostic.nc xios_client_1.out xios_client_0.out doctest_1.log doctest_0.log ``` I don't currently verify the output of `diagnostic.nc` as part of `testXiosInit` but this can be added. This PR is to update the state of XIOS related PRs and Issues. This will close some stale issues closes #218 closes #291 closes #293
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Closed by #496. |
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This is a sub-feature of issue #218 tracking the addition of a new XIOS class that interfaces with the XIOS library and server process. The first step is to initialise the calendar and advance time, this is the pilot issue that navigates interfacing with undocumented XIOS library methods.
See xios-cpp-toy repository for more information
This provides the foundation for adding grid & axis data tracked in issue #292 (see parent issue #218)
This will require MPI initialisation - either via new feature or a temporary localised implementation.
For the XIOS Integration, see the design spec or the master pull request
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