Merge pull request #1112 from lzjpaul/23-10-24-v410

Add the implementation for the model selection example

CMakeLists.txt

@@ -29,10 +29,10 @@ LIST(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/Thirdparty)
 #string(REGEX REPLACE "^[0-9]+\\.[0-9]+\\.([0-9]+).*" "\\1" VERSION_PATCH "${VERSION}")
 
 
-SET(PACKAGE_VERSION 4.0.0) # ${VERSION})
-SET(VERSION 4.0.0)
+SET(PACKAGE_VERSION 4.1.0) # ${VERSION})
+SET(VERSION 4.1.0)
 SET(SINGA_MAJOR_VERSION 4)
-SET(SINGA_MINOR_VERSION 0)
+SET(SINGA_MINOR_VERSION 1)
 SET(SINGA_PATCH_VERSION 0)
 #SET(SINGA_MAJOR_VERSION ${VERSION_MAJOR})  # 0 -
 #SET(SINGA_MINOR_VERSION ${VERSION_MINOR})  # 0 - 9

LICENSE

@@ -559,3 +559,59 @@ PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
 OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+===============================================================================
+SINGA bundles the following under MIT License: 
+examples/model_selection/TRAILS-Database-Native-Model-Selection/internal/pg_extension/*
+
+MIT License
+
+Portions Copyright 2019-2021 ZomboDB, LLC.
+Portions Copyright 2021-2023 Technology Concepts & Design, Inc.
+Portions Copyright 2023 PgCentral Foundation, Inc.
+
+All rights reserved.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
+
+===============================================================================
+SINGA bundles the following under The PostgreSQL License: 
+examples/model_selection/TRAILS-Database-Native-Model-Selection/internal/pg_extension/*
+
+The PostgreSQL License
+
+Portions Copyright (c) 1996-2023, The PostgreSQL Global Development Group
+
+Portions Copyright (c) 1994, The Regents of the University of California
+
+Permission to use, copy, modify, and distribute this software and its documentation for any 
+purpose, without fee, and without a written agreement is hereby granted, provided that the above 
+copyright notice and this paragraph and the following two paragraphs appear in all copies.
+
+IN NO EVENT SHALL THE UNIVERSITY OF CALIFORNIA BE LIABLE TO ANY PARTY FOR DIRECT, INDIRECT, 
+SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST PROFITS, ARISING 
+OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF 
+THE UNIVERSITY OF CALIFORNIA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+THE UNIVERSITY OF CALIFORNIA SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, 
+BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR 
+A PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, 
+AND THE UNIVERSITY OF CALIFORNIA HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, 
+UPDATES, ENHANCEMENTS, OR MODIFICATIONS.
+

examples/model_selection/TRAILS-Database-Native-Model-Selection/Dockerfile

@@ -0,0 +1,58 @@
+FROM ubuntu:20.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install Python, Vim, and necessary libraries
+RUN apt-get update && \
+    apt-get install -y software-properties-common wget gnupg2 lsb-release git && \
+    add-apt-repository ppa:deadsnakes/ppa && \
+    apt-get install -y python3.6 python3-pip vim && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install necessary dependencies for PostgreSQL and Rust
+RUN apt-get update && \
+    apt-get install -y pkg-config libssl-dev libpq-dev libclang-dev curl && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Install necessary dependencies for pgrx
+RUN apt-get update && \
+    apt-get install -y bison flex libreadline-dev && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Create the postgres user
+USER root
+RUN adduser --disabled-password --gecos "" postgres && \
+    mkdir /project && \
+    adduser postgres sudo && \
+    chown -R postgres:postgres /project
+
+# Switch to the postgres user andInstall Rust and init the cargo
+USER postgres
+RUN curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y && \
+    echo 'source $HOME/.cargo/env' >> $HOME/.bashrc && \
+    /bin/bash -c "source $HOME/.cargo/env && cargo install cargo-pgrx --version '0.9.7' --locked" && \
+    /bin/bash -c "source $HOME/.cargo/env && cargo pgrx init"
+
+# Set environment variables for Rust and Python
+ENV PATH="/root/.cargo/bin:${PATH}"
+ENV PYTHONPATH="${PYTHONPATH}:/project/TRAILS/internal/ml/model_selection"
+
+WORKDIR /project
+COPY ./internal/ml/model_selection/requirement.txt ./requirement.txt
+RUN pip install -r requirement.txt
+
+RUN pip install https://www.comp.nus.edu.sg/~zhaojing/files/singa-3.1.0-cp38-cp38-manylinux2014_x86_64.whl
+
+# appendix
+USER root
+RUN apt-get update && apt-get install -y \
+    postgresql-client && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+USER postgres
+
+CMD ["tail", "-f", "/dev/null"]

examples/model_selection/TRAILS-Database-Native-Model-Selection/README.md

@@ -0,0 +1,148 @@
+# Database-Native Model Selection 
+
+​																																																		-- based on Singa
+
+
+
+![image-20231020174425377](documents/image-20231020174425377.png)
+
+## Build Docker Image
+
+```bash
+git clone https://github.com/apache/singa.git
+cd singa/examples/model_selection/TRAILS-Database-Native-Model-Selection/
+docker build -t trails-singa .
+```
+
+## Run Docker Image
+Download exp_data.zip from https://www.dropbox.com/scl/fi/xz4teosklwmfc5j4x2ug6/exp_data.zip?rlkey=5fk2ttib0zt49suyppcjhsrn2&dl=0
+and unzip the exp_data/ folder to a specific directory (path_to_exp_data_folder)
+```bash
+docker run -d --name trails-singa \
+  --network="host" \
+  -v path_to_exp_data_folder:/project/exp_data \
+  trails-singa
+```
+
+## Start PostgreSQL Instance
+
+```bash
+# 1. Run docker container
+docker exec -it trails-singa bash 
+# 2. Clone the code
+cd ~
+git clone https://github.com/apache/singa.git
+cd singa/examples/model_selection/TRAILS-Database-Native-Model-Selection/
+# 3. Export PYTHONPATH
+export PYTHONPATH=$PYTHONPATH:./internal/ml/model_selection
+# 4. Start the RDBMS and then exit
+cd internal/pg_extension
+cargo pgrx run
+exit
+cd ../..
+# 5. Load data into RDBMS
+bash internal/ml/model_selection/scripts/database/load_data_to_db.sh /project/exp_data/data/structure_data/frappe frappe
+# 6. Run database server
+cd internal/pg_extension
+cargo pgrx run
+
+```
+
+
+## Register Stored Procedure
+
+```sql
+CREATE OR REPLACE
+PROCEDURE model_selection_sp(
+    dataset TEXT,               --dataset name
+    selected_columns TEXT[],    --used columns
+    N INTEGER,                  --number of models to evaluate
+    batch_size INTEGER,         --batch size, for profiling, filtering
+    config_file TEXT            --config file path
+)
+LANGUAGE plpgsql
+AS $$
+DECLARE
+    -- global inputs/outputs
+    result_status TEXT;
+    column_list TEXT;
+BEGIN
+    -- combine the columns into a string
+    column_list := array_to_string(selected_columns, ', ');
+
+    -- 4. Run filtering phase to get top K models.
+    EXECUTE format('
+                WITH batch_rows AS (
+                    SELECT %s
+                    FROM %I
+                    ORDER BY RANDOM()
+                    LIMIT %s OFFSET 0
+                )
+                SELECT filtering_phase(
+                    json_agg(row_to_json(t))::text, %s, %s, %L
+                )
+                FROM batch_rows AS t', column_list, dataset, batch_size, N, 1, config_file) INTO result_status;
+    RAISE NOTICE '4. run filtering phase, k models = %', result_status;
+
+END; $$;
+```
+
+# Compile the UDF
+
+```bash
+# Try compile the UDF
+DROP EXTENSION IF EXISTS pg_extension;
+CREATE EXTENSION pg_extension;
+```
+
+If the above fails, open another terminal and go into the docker via docker exec -it trails-singa bash
+Then run the following 
+```bash
+rm /home/postgres/.pgrx/14.9/pgrx-install/share/extension/pg_extension--0.1.0.sql
+vi /home/postgres/.pgrx/14.9/pgrx-install/share/extension/pg_extension--0.1.0.sql
+# Copy the following to the /home/postgres/.pgrx/14.9/pgrx-install/share/extension/pg_extension--0.1.0.sql
+-- src/lib.rs:66
+-- pg_extension::filtering_phase
+CREATE  FUNCTION "filtering_phase"(
+    "mini_batch" TEXT, /* alloc::string::String */
+    "n" INT, /* i32 */
+    "k" INT, /* i32 */
+    "config_file" TEXT /* alloc::string::String */
+) RETURNS TEXT /* alloc::string::String */
+    IMMUTABLE STRICT PARALLEL SAFE
+LANGUAGE c /* Rust */
+AS 'MODULE_PATHNAME', 'filtering_phase_wrapper';
+```
+
+Go back to the first terminal and run the following in the database server again  
+```bash
+# Try compile the UDF
+DROP EXTENSION IF EXISTS pg_extension;
+CREATE EXTENSION pg_extension;
+```
+
+## Run Model Selection 
+
+```sql
+-- Template for calling 'model_selection_sp' stored procedure
+CALL model_selection_sp(
+    <TABLE_NAME>,             -- The name of the table or dataset from which data should be retrieved.
+    <COLUMN_NAMES_ARRAY>,     -- An array of column names to be considered in the model selection process.
+    <PARAMETER_1>,            -- Number of models to explore
+    <PARAMETER_2>,            -- Batch size
+    <CONFIG_FILE_PATH>        -- The file path to a configuration file needed for the process.
+);
+
+
+# For example
+CALL model_selection_sp(
+       'frappe_train',
+       ARRAY['col1', 'col2', 'col3', 'label'], 
+    10, 
+    32, 
+  '/home/postgres/singa/examples/model_selection/TRAILS-Database-Native-Model-Selection/internal/ml/model_selection/config.ini');
+```
+
+# Example Result
+
+![image-20231020174945226](documents/image-20231020174945226.png)