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PERF: Optimize GAMER IO #4651

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PERF: Optimize GAMER IO #4651

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3012471
Use a smaller temporary buffer for GAMER
matthewturk Aug 25, 2023
68f5787
Update yt/frontends/gamer/io.py
matthewturk Aug 25, 2023
79f3471
Use a cache and specialize with grid selector
matthewturk Aug 25, 2023
d1a1d73
Undo my nonsensical transpose attempt
matthewturk Aug 25, 2023
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28 changes: 12 additions & 16 deletions yt/frontends/gamer/io.py
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Original file line number Diff line number Diff line change
Expand Up @@ -121,24 +121,20 @@ def _read_fluid_selection(self, chunks, selector, fields, size):
start = (gs[0].id) * self.pgroup
end = (gs[-1].id + 1) * self.pgroup
buf = ds[start:end, :, :, :]
ngrid = len(gs)
data = np.empty((ngrid, ps2, ps2, ps2), dtype=self._field_dtype)

for g in range(ngrid):
pid0 = g * self.pgroup
data[g, 0:ps1, 0:ps1, 0:ps1] = buf[pid0 + 0, :, :, :]
data[g, 0:ps1, 0:ps1, ps1:ps2] = buf[pid0 + 1, :, :, :]
data[g, 0:ps1, ps1:ps2, 0:ps1] = buf[pid0 + 2, :, :, :]
data[g, ps1:ps2, 0:ps1, 0:ps1] = buf[pid0 + 3, :, :, :]
data[g, 0:ps1, ps1:ps2, ps1:ps2] = buf[pid0 + 4, :, :, :]
data[g, ps1:ps2, ps1:ps2, 0:ps1] = buf[pid0 + 5, :, :, :]
data[g, ps1:ps2, 0:ps1, ps1:ps2] = buf[pid0 + 6, :, :, :]
data[g, ps1:ps2, ps1:ps2, ps1:ps2] = buf[pid0 + 7, :, :, :]

data = data.transpose()
data = np.empty((ps2, ps2, ps2), dtype=self._field_dtype)

for i, g in enumerate(gs):
offset += g.select(selector, data[..., i], rv[field], offset)
pid0 = i * self.pgroup
data[0:ps1, 0:ps1, 0:ps1] = buf[pid0 + 0, :, :, :]
data[0:ps1, 0:ps1, ps1:ps2] = buf[pid0 + 1, :, :, :]
data[0:ps1, ps1:ps2, 0:ps1] = buf[pid0 + 2, :, :, :]
data[ps1:ps2, 0:ps1, 0:ps1] = buf[pid0 + 3, :, :, :]
data[0:ps1, ps1:ps2, ps1:ps2] = buf[pid0 + 4, :, :, :]
data[ps1:ps2, ps1:ps2, 0:ps1] = buf[pid0 + 5, :, :, :]
data[ps1:ps2, 0:ps1, ps1:ps2] = buf[pid0 + 6, :, :, :]
data[ps1:ps2, ps1:ps2, ps1:ps2] = buf[pid0 + 7, :, :, :]
offset += g.select(selector, data, rv[field], offset)
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return rv

def _read_chunk_data(self, chunk, fields):
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