Program Listing for File preprocess_fil.cpp
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/*
* SPDX-FileCopyrightText: Copyright (c) 2021-2023, NVIDIA CORPORATION & AFFILIATES. All rights reserved.
* SPDX-License-Identifier: Apache-2.0
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*/
#include "morpheus/stages/preprocess_fil.hpp"
#include "mrc/node/rx_sink_base.hpp"
#include "mrc/node/rx_source_base.hpp"
#include "mrc/node/sink_properties.hpp"
#include "mrc/node/source_properties.hpp"
#include "mrc/segment/object.hpp"
#include "mrc/types.hpp"
#include "morpheus/messages/memory/inference_memory_fil.hpp"
#include "morpheus/messages/meta.hpp" // for MessageMeta
#include "morpheus/objects/dev_mem_info.hpp" // for DevMemInfo
#include "morpheus/objects/dtype.hpp"
#include "morpheus/objects/table_info.hpp" // for TableInfo
#include "morpheus/objects/tensor.hpp"
#include "morpheus/objects/tensor_object.hpp" // for TensorObject
#include "morpheus/types.hpp" // for TensorIndex
#include "morpheus/utilities/matx_util.hpp"
#include <cuda_runtime.h> // for cudaMemcpy, cudaMemcpyDeviceToDevice
#include <cudf/column/column.hpp> // for column, column::contents
#include <cudf/column/column_view.hpp> // for column_view
#include <cudf/types.hpp>
#include <cudf/unary.hpp>
#include <mrc/cuda/common.hpp> // for MRC_CHECK_CUDA
#include <mrc/segment/builder.hpp>
#include <pybind11/cast.h> // for object_api::operator(), operator""_a
#include <pybind11/gil.h>
#include <pybind11/pybind11.h> // for str_attr_accessor, arg
#include <pybind11/pytypes.h>
#include <pymrc/node.hpp>
#include <rmm/cuda_stream_view.hpp> // for cuda_stream_per_thread
#include <rmm/device_buffer.hpp> // for device_buffer
#include <array>
#include <cstddef>
#include <exception>
#include <functional>
#include <memory>
#include <utility>
namespace morpheus {
// Component public implementations
// ************ PreprocessFILStage ************************* //
PreprocessFILStage::PreprocessFILStage(const std::vector<std::string>& features) :
PythonNode(base_t::op_factory_from_sub_fn(build_operator())),
m_fea_cols(std::move(features))
{}
PreprocessFILStage::subscribe_fn_t PreprocessFILStage::build_operator()
{
return [this](rxcpp::observable<sink_type_t> input, rxcpp::subscriber<source_type_t> output) {
return input.subscribe(rxcpp::make_observer<sink_type_t>(
[&output, this](sink_type_t x) {
// Make sure to
auto df_meta = this->fix_bad_columns(x);
auto packed_data = std::make_shared<rmm::device_buffer>(
m_fea_cols.size() * x->mess_count * sizeof(float), rmm::cuda_stream_per_thread);
for (size_t i = 0; i < df_meta.num_columns(); ++i)
{
auto curr_col = df_meta.get_column(i);
auto curr_ptr = static_cast<float*>(packed_data->data()) + i * df_meta.num_rows();
// Check if we are something other than float
if (curr_col.type().id() != cudf::type_id::FLOAT32)
{
auto float_data = cudf::cast(curr_col, cudf::data_type(cudf::type_id::FLOAT32))->release();
// Do the copy here before it goes out of scope
MRC_CHECK_CUDA(cudaMemcpy(curr_ptr,
float_data.data->data(),
df_meta.num_rows() * sizeof(float),
cudaMemcpyDeviceToDevice));
}
else
{
MRC_CHECK_CUDA(cudaMemcpy(curr_ptr,
curr_col.data<float>(),
df_meta.num_rows() * sizeof(float),
cudaMemcpyDeviceToDevice));
}
}
// Need to do a transpose here
auto transposed_data =
MatxUtil::transpose(DevMemInfo{packed_data,
TypeId::FLOAT32,
{x->mess_count, static_cast<TensorIndex>(m_fea_cols.size())},
{1, x->mess_count}});
auto input__0 = Tensor::create(transposed_data,
DType::create<float>(),
{x->mess_count, static_cast<TensorIndex>(m_fea_cols.size())},
{},
0);
auto seq_id_dtype = DType::create<TensorIndex>();
auto seq_ids = Tensor::create(MatxUtil::create_seq_ids(x->mess_count,
m_fea_cols.size(),
seq_id_dtype.type_id(),
input__0.get_memory(),
x->mess_offset),
seq_id_dtype,
{x->mess_count, 3},
{},
0);
// Build the results
auto memory =
std::make_shared<InferenceMemoryFIL>(x->mess_count, std::move(input__0), std::move(seq_ids));
auto next = std::make_shared<MultiInferenceMessage>(
x->meta, x->mess_offset, x->mess_count, std::move(memory), 0, memory->count);
output.on_next(std::move(next));
},
[&](std::exception_ptr error_ptr) { output.on_error(error_ptr); },
[&]() { output.on_completed(); }));
};
}
TableInfo PreprocessFILStage::fix_bad_columns(sink_type_t x)
{
std::vector<std::string> bad_cols;
{
// TODO(MDD): Add some sort of lock here to prevent fixing columns after they have been accessed
auto df_meta = x->get_meta(m_fea_cols);
auto df_meta_col_names = df_meta.get_column_names();
for (size_t i = 0; i < df_meta.num_columns(); ++i)
{
if (df_meta.get_column(i).type().id() == cudf::type_id::STRING)
{
bad_cols.push_back(df_meta_col_names[i]);
}
}
// Exit early if there is nothing to do
if (bad_cols.empty())
{
return df_meta;
}
}
// Need to ensure all string columns have been converted to numbers. This requires running a
// regex which is too difficult to do from C++ at this time. So grab the GIL, make the
// conversions, and release. This is horribly inefficient, but so is the JSON lines format for
// this workflow
{
// Get the mutable info for the entire meta object so we only do this once per dataframe
auto mutable_info = x->meta->get_mutable_info();
using namespace pybind11::literals;
pybind11::gil_scoped_acquire gil;
// pybind11::object df = x->meta->get_py_table();
auto df = mutable_info.checkout_obj();
std::string regex = R"((\d+))";
for (auto c : bad_cols)
{
df[pybind11::str(c)] = df[pybind11::str(c)]
.attr("str")
.attr("extract")(pybind11::str(regex), "expand"_a = true)
.attr("astype")(pybind11::str("float32"));
}
mutable_info.return_obj(std::move(df));
}
// Now re-get the meta
return x->get_meta(m_fea_cols);
}
// ************ PreprocessFILStageInterfaceProxy *********** //
std::shared_ptr<mrc::segment::Object<PreprocessFILStage>> PreprocessFILStageInterfaceProxy::init(
mrc::segment::Builder& builder, const std::string& name, const std::vector<std::string>& features)
{
auto stage = builder.construct_object<PreprocessFILStage>(name, features);
return stage;
}
} // namespace morpheus