Add XIOS IO Capability #218
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a-smith-github
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This was referenced Apr 27, 2023
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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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Tracking XIOS integration into Nextsim-DG
Design Document: https://github.com/nextsimdg/nextsimdg/wiki/XIOS-Integration
Branch: https://github.com/nextsimdg/nextsimdg/tree/feature218_xios_io (Thanks Dom)
PR: #265
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