Issue264 netcdf strings #330
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timspainNERSC
requested changes
Jun 12, 2023
core/src/CommonRestartMetadata.cpp
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| // All other configuration data | ||
| netCDF::NcGroup configGroup = metaGroup.addGroup(configurationNode()); | ||
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| for (auto entry : metadata.m_config) { | ||
| switch (entry.second.index()) { | ||
| case (CONFIGMAP_DOUBLE): { | ||
| netCDF::NcVar dblVar = configGroup.addVar(entry.first, netCDF::ncDouble); | ||
| dblVar.putVar(std::get_if<double>(&entry.second)); | ||
| double value = 1.5; |
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I don't think this is doing anything? Unless it is really subtle.
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Thanks for spotting it. It was leftover from my debugging. I've pushed the fixed version (debc4bf).
Parallel netCDF4 does not support writing string variables in parallel mode so the formatted time needs to be recorded as an attribute.
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timspainNERSC
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Jun 14, 2023
TomMelt
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## Background This PR is part of #120, where the basis of strategy for MPI parallelisation is described. ## Change description As all thermodynamics operations are local to a grid cell all required MPI communication, is handled by NetCDF4 library. Therefore the only required steps are: - [x] Initialize and finalize MPI stack - [x] Read decomposition metadata on each rank - [x] Read and write the necessary part of the grid on each rank (depends on #330) - [x] Tests for parallel I/O **NOTE** PR #432 should be merged into this branch before it is merged into develop To run `run_simple_example.sh` you will need to generate the following netcdf file ``` $ ncdump partition.nc netcdf partition { dimensions: P = 1 ; L = 1 ; globalX = 30 ; globalY = 30 ; group: bounding_boxes { variables: int global_x(P) ; int global_y(P) ; int local_extent_x(P) ; int local_extent_y(P) ; data: global_x = 0 ; global_y = 0 ; local_extent_x = 30 ; local_extent_y = 30 ; } // group bounding_boxes } ```
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Fixes #264
Change description
The PR replaces NetCDF4 string variables with attributes as writing such variables is not supported in parallel mode. For consistency it also writes all other members of configuration group as attributes.