XIOS: Add File I/O To & From XIOS Grid/Axis #291
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This issue should target the diagnostics files rather than restart files. Diagnostic output is the main reason for us to use XIOS because writing and reading restart files are much less frequent and always contain the same variables, so most of the "nice" features of XIOS are not needed. So, we should prioritise diagnostic outputs for XIOS and leave restart I/O to the native functionality that already exists. We can then return to the question of XIOS vs. native I/O for restart files later. |
TomMelt
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May 2, 2024
# 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 adding the file I/O capability of the XIOS class
We need to be able to write restart files via XIOS using data stored within the XIOS Grid/Axis framework using XIOS Library calls.
This requires Issues #293 and #292
For the XIOS Integration, see the design spec or the master pull request
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