Add HDF5 file writing to `exp` and HDF file reading to `pyEXP` [WIP]#148

Merged

michael-petersen merged 50 commits into

develfrom

Jul 28, 2025

Commits on May 28, 2025

Preliminarly, incomplete check-in of HDF5 phase-space implementation
Martin D. Weinberg
committed
Add some metadata writing; make it compile
Martin D. Weinberg
committed
Some white space for readability
Martin D. Weinberg
committed
A few additional tweaks; ready for testing
Martin D. Weinberg
committed

Commits on May 29, 2025

Implemented a HDF5 ParticleReader class; implemented compression; additional clean up
Martin D. Weinberg
committed
Fix a few mistakes in logic; add a default particle type
Martin D. Weinberg
committed
Add some data compression
Martin D. Weinberg
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Add some data compression
Martin D. Weinberg
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Removed debug output
Martin D. Weinberg
committed

Commits on May 31, 2025

Added native-style PSP HDF5; this is now the default
Martin D. Weinberg
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Some more comments only
Martin D. Weinberg
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Try to keep Clang happy...
Martin D. Weinberg
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Clean up H5 property settings
The9Cat
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Commits on Jun 1, 2025

Preliminary untested restart from PSPhdf5
Martin D. Weinberg
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Preliminary, partially tested implementation of restart from PSPhdf5
Martin D. Weinberg
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Version bump
Martin D. Weinberg
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Added a checkpoint-file writing mode
Martin D. Weinberg
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Check found HDF5 files with expected HDF5 files as a sanity check
Martin D. Weinberg
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Check found HDF5 files with expected HDF5 files as a sanity check
Martin D. Weinberg
committed

Commits on Jun 2, 2025

Set default HDF5 write mode to 'trunc' (overwrite) with an option for 'excl' (no overwrite) selective with the {preserve: bool} option
Martin D. Weinberg
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stdout log changes
Martin D. Weinberg
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Make HDF5 overwrite the default
Martin D. Weinberg
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Cache the entire EXP yaml config in the snapshot; controlled by the 'expconfig' boolean flag
Martin D. Weinberg
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Fix typo; consolidate metadata
Martin D. Weinberg
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Generalize diffpsp for PSPhdf5
Martin D. Weinberg
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Option to add metadata to all HDF5 files
Martin D. Weinberg
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Commits on Jun 3, 2025

Add directory organization of HDF5 snapshots (enabled by default)
Martin D. Weinberg
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Enable PSPhdf5 input
Martin D. Weinberg
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Additional check on Orient restart
Martin D. Weinberg
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Ignore .bak files
Martin D. Weinberg
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Comments and output changes only
Martin D. Weinberg
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Add missing PSP pot and potext fields
Martin D. Weinberg
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Commits on Jun 5, 2025

Pretty-up some log output only
Martin D. Weinberg
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Commits on Jun 16, 2025

Throw runtime exception if the user tries to write an HDF5 coefficient file from an empty Coefs instance
Martin D. Weinberg
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Commits on Jun 18, 2025

Generalize histo1dlog to return velocity dispersion
Martin D. Weinberg
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Add static functions to read and parse HDF5 directories to save the user the trouble of having to pass full file lists (which will still work)
Martin D. Weinberg
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Additional commenting only
Martin D. Weinberg
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Added directory file listing to Gadget and Tipsy readers
Martin D. Weinberg
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Commits on Jun 20, 2025

Commits on Jul 1, 2025

Output log changes for ortho test results only
Martin D. Weinberg
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Another minor output log change for ortho test results only
Martin D. Weinberg
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Commits on Jul 22, 2025

Update src/Orient.cc

The9Cat
and
Copilot
authored
Update src/OutHDF5.H

The9Cat
and
Copilot
authored
Update src/OutHDF5.cc

The9Cat
and
Copilot
authored
Update exputil/ParticleReader.cc

The9Cat
and
Copilot
authored
Update exputil/ParticleReader.cc

The9Cat
and
Copilot
authored
Do an all-process reduction rather than look for masses on a sngle processes
Martin D. Weinberg
committed
Add some comments to OutHDF5 about the global reduction
Martin D. Weinberg
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Merge branch 'devel' into HDF5 to fix synchronization
Martin D. Weinberg
committed