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Manual cherry pick of chunk logic fix to devel #213

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Merged
The9Cat merged 1 commit into from
Mar 27, 2026
Merged

Manual cherry pick of chunk logic fix to devel #213

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24 changes: 20 additions & 4 deletions src/Component.cc
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Original file line number Diff line number Diff line change
Expand Up @@ -2501,13 +2501,23 @@ void Component::write_HDF5(HighFive::Group& group, bool masses, bool IDs)
auto dcplI = HighFive::DataSetCreateProps{};
auto dcplD = HighFive::DataSetCreateProps{};

if (H5compress or H5chunk) {
// Compression and chunking. Do not set chunk size larger than
// nbodies. Turn off compression altogether if nbodies = 0 to avoid
// HDF5 errors.
//
if ((H5compress or H5chunk) and nbodies > 0) {
int chunk = H5chunk;

// Sanity
// Clamp chunk to [1, nbodies]: use nbodies/8 as a downsize when
// H5chunk would exceed the dataset extent, then ensure at least 1
if (H5chunk >= nbodies) {
chunk = nbodies/8;
}
if (chunk < 1) {
chunk = 1;
} else if (static_cast<unsigned int>(chunk) > nbodies) {
chunk = static_cast<int>(nbodies);
}

dcpl1.add(HighFive::Chunking(chunk));
if (H5shuffle) dcpl1.add(HighFive::Shuffle());
Expand Down Expand Up @@ -2636,14 +2646,20 @@ void Component::write_H5(H5::Group& group)

// This could be generalized by registering a user filter, like
// blosc. Right now, we're using the default (which is gzip)
if (H5compress or H5chunk) {
//
// Do not set chunk size larger than number of particles. If the
// particle number is zero, do not compress.
//
if ((H5compress or H5chunk) and h5_particles.size() > 0) {
// Set chunking
if (H5chunk) {
// Sanity
// Clamp chunk to [1, nbodies]: use nbodies/8 as a downsize when
// H5chunk would exceed the dataset extent, then ensure at least 1
int chunk = H5chunk;
if (H5chunk >= nbodies) {
chunk = nbodies/8;
}
chunk = std::clamp<int>(chunk, 1, static_cast<int>(nbodies));
hsize_t chunk_dims[1] = {static_cast<hsize_t>(chunk)};
dcpl.setChunk(1, chunk_dims);
}
Expand Down
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