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[REVIEW] Improve gather performance #2775

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merged 52 commits into from
Sep 27, 2019
Merged

[REVIEW] Improve gather performance #2775

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e5386b3
First pass at using transform_iterator to handle negative indices in …
shwina Sep 10, 2019
1f8ba6e
Add version of gather that accepts gathermap as gdf_column
shwina Sep 11, 2019
9e1a7b5
Add type dispatch to map type in gather
shwina Sep 12, 2019
df8103f
Remove typecasting gathermap in Cython
shwina Sep 12, 2019
e38e36d
Merge branch 'branch-0.10' of https://github.com/rapidsai/cudf into i…
shwina Sep 12, 2019
3134cc7
Restore normalize_maps
shwina Sep 12, 2019
8ce390b
Add code path that does not transform gather map
shwina Sep 13, 2019
9beae3b
Allocate output in libcudf for gather
shwina Sep 13, 2019
d5e4c8d
Replace use of `to_gpu_array()` with `mem`
shwina Sep 13, 2019
6460ac9
Update categories on gather result
shwina Sep 16, 2019
19bd8d8
Return typed column from column_empty_like_same_mask
shwina Sep 16, 2019
fc37724
Propagate empty map case to libcudf from Cython
shwina Sep 16, 2019
e6c3846
Use as_column factory instead of Column constructor directly in colum…
shwina Sep 16, 2019
890ba64
Fix bug in column_empty_like_same_mask
shwina Sep 16, 2019
292b42d
Add `check_bounds` parmeter to gather and rename existing
shwina Sep 17, 2019
d5a597a
Replace use of thrust::all_of with thrust::count_if
shwina Sep 17, 2019
bc94c8b
Remove column_select_by_* functions
shwina Sep 17, 2019
b4a5c08
whitespace cleanup
shwina Sep 17, 2019
6491cfa
Enable scatter() to accept a gdf_column scattermap
shwina Sep 18, 2019
81d6687
Style change
shwina Sep 18, 2019
9a9db63
Add gather implementation that accepts an iterator as gathermap
shwina Sep 18, 2019
4263b47
Mark scatter_to_gather() __device__
shwina Sep 19, 2019
af72396
Revert to using materialized gathermap in scatter
shwina Sep 19, 2019
92a546c
Add bounds checking to scatter
shwina Sep 19, 2019
f272499
Some renaming and namespace fixes
shwina Sep 19, 2019
bcb085e
Documentation fixes and pass maps by const reference
shwina Sep 19, 2019
611d827
Eliminate all usage of libcudf.gather/scatter outside of Column
shwina Sep 19, 2019
6bab813
Add test for IndexError in column __setitem__, __getitem__
shwina Sep 19, 2019
37ab318
Merge branch 'branch-0.10' of https://github.com/rapidsai/cudf into i…
shwina Sep 19, 2019
68080eb
Fix a couple of getitem calls
shwina Sep 19, 2019
de07ab6
Changelog
shwina Sep 19, 2019
8c8ac12
Launch scatter kernel with source_rows threads
shwina Sep 19, 2019
8ab771a
Perform fill in invert_map kernel
shwina Sep 19, 2019
b1de01a
Merge branch 'improve-gather' of https://github.com/shwina/cudf into …
shwina Sep 19, 2019
bc73c56
Rename consider_negative_indices to allow_negative_indices
shwina Sep 20, 2019
453fa6b
Clarify `negative_index_converter` behaviour in documentation
shwina Sep 20, 2019
033bfcf
Make allow_negative_indices a template param
shwina Sep 20, 2019
01a39bb
Update gather and scatter docs
shwina Sep 20, 2019
6de1a71
Use grid_config_1d to configure grid/block size for invert_map kernel
shwina Sep 20, 2019
1cdbe67
Fix typo
shwina Sep 20, 2019
46b183a
Merge branch 'branch-0.10' of https://github.com/rapidsai/cudf into i…
shwina Sep 20, 2019
d17a89b
Remove record.txt
shwina Sep 20, 2019
0a4b168
Merge branch 'branch-0.10' of https://github.com/rapidsai/cudf into i…
shwina Sep 23, 2019
e06565d
Make call to `detail::scatter` explicit
shwina Sep 23, 2019
4f35e74
Revert to performing a fill *before* the invert kernel in scatter
shwina Sep 23, 2019
7464796
Add docs for overloaded functions in copying.hpp
shwina Sep 24, 2019
6e1594b
Merge branch 'branch-0.10' into improve-gather
harrism Sep 26, 2019
bd91806
Merge branch 'branch-0.10' of https://github.com/rapidsai/cudf into i…
shwina Sep 26, 2019
d22ec45
Consistently add `@throws` to gather/scatter docs
shwina Sep 26, 2019
fe9b04c
Merge branch 'branch-0.10' of https://github.com/rapidsai/cudf into i…
shwina Sep 26, 2019
1bb6e48
Merge branch 'improve-gather' of https://github.com/shwina/cudf into …
shwina Sep 26, 2019
6a350d4
Replace use of bool template parameter with enum parameter
shwina Sep 27, 2019
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14 changes: 12 additions & 2 deletions cpp/src/copying/gather.cu
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,9 @@
#include <algorithm>

#include <table/legacy/device_table.cuh>
#include <thrust/functional.h>
#include <thrust/gather.h>
#include <thrust/iterator/transform_iterator.h>

#include <cub/cub.cuh>
#include <nvstrings/NVCategory.h>
Expand Down Expand Up @@ -129,6 +131,7 @@ __global__ void gather_bitmask_kernel(const bit_mask_t *const *source_valid,
}
}


/**---------------------------------------------------------------------------*
* @brief Function object for gathering a type-erased
* gdf_column. To be used with the cudf::type_dispatcher.
Expand Down Expand Up @@ -191,14 +194,21 @@ struct column_gatherer {
destination_data = in_place_buffer.data().get();
}

auto source_column_size = source_column->size;
auto gather_map_iterator = thrust::make_transform_iterator(
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gather_map,
[source_column_size] __device__ (gdf_index_type in) -> gdf_index_type {
return ((in % source_column_size) + source_column_size) % source_column_size;
});

if (check_bounds) {
thrust::gather_if(rmm::exec_policy(stream)->on(stream), gather_map,
gather_map + num_destination_rows, gather_map,
source_data, destination_data,
bounds_checker{0, source_column->size});
} else {
thrust::gather(rmm::exec_policy(stream)->on(stream), gather_map,
gather_map + num_destination_rows, source_data,
thrust::gather(rmm::exec_policy(stream)->on(stream), gather_map_iterator,
gather_map_iterator+num_destination_rows, source_data,
destination_data);
}

Expand Down
2 changes: 0 additions & 2 deletions python/cudf/cudf/_lib/copying.pyx
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Original file line number Diff line number Diff line change
Expand Up @@ -51,9 +51,7 @@ def clone_columns_with_size(in_cols, row_size):

def _normalize_maps(maps, size):
from cudf.core.column import column

maps = column.as_column(maps).astype("int32")
maps = maps.binary_operator("mod", np.int32(size))
maps = maps.data.mem
return maps

Expand Down
6 changes: 6 additions & 0 deletions python/cudf/cudf/tests/test_indexing.py
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Original file line number Diff line number Diff line change
Expand Up @@ -867,3 +867,9 @@ def test_dataframe_setitem_iloc_multiindex(key, value, pdf_gdf_multi):
gdf.iloc[key] = value

assert_eq(pdf, gdf)


def test_iloc_negative_indices():
psr = pd.Series([1, 2, 3, 4, 5])
gsr = cudf.from_pandas(psr)
assert_eq(psr.iloc[[-1, -2, -4]], gsr.iloc[[-1, -2, -4]])
130 changes: 65 additions & 65 deletions python/dask_cudf/record.txt
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@@ -1,65 +1,65 @@
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/core.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/backends.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/__init__.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/_version.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/accessor.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/join_impl.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/batcher_sortnet.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_join.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_accessor.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_groupby.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/__init__.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_reductions.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_onehot.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_delayed_io.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_binops.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_batcher_sortnet.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_sort.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_distributed.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/tests/test_core.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/io/orc.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/io/json.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/io/__init__.py
/conda/envs/gdf/lib/python3.7/site-packages/dask_cudf/io/csv.py
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/home/ashwint/miniconda3/envs/cudf_dev/lib/python3.7/site-packages/dask_cudf/_version.py
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/home/ashwint/miniconda3/envs/cudf_dev/lib/python3.7/site-packages/dask_cudf/batcher_sortnet.py
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/home/ashwint/miniconda3/envs/cudf_dev/lib/python3.7/site-packages/dask_cudf/io/json.py
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