HDF5 output capability #7
Open
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This was tricky to track down because the program would only stall for certain numbers of communicators, and later than the call actually causing the issue. For future reference, always check that the chunk sizes are identical between MPI ranks!
At the request of the developers, making this change so that users do not need to have HDF5 installed to compile FARGO3D. If the option is selected, the appropriate source file and library are added to the build.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
HDF5 is a high-performance I/O library for scientific data. This output module produces exactly one file per run of FARGO3D, with optional compression, in an easy-to-use structured format. It includes all the time-varying fluid fields for all fluids (in the multifluid version), metadata for every array (shape and data type), and all the parameter values used in the run, attached at the root node as attributes. Combined with the Python bindings for HDF5, this has made analyzing output from my runs significantly easier. I hope it can be of use to someone else, and I'm happy to continue developing on this feature branch if the developers are interested in the new functionality.