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Updated bindings
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Devesh Sarda committed Mar 7, 2024
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3 changes: 2 additions & 1 deletion CMakeLists.txt
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Expand Up @@ -200,6 +200,7 @@ IF(CMAKE_BUILD_TYPE MATCHES Debug AND MARIUS_USE_ASAN)
set(CMAKE_MODULE_LINKER_FLAGS "{$CMAKE_MODULE_LINKER_FLAGS} -fsanitize=address -fsanitize=leak")
ENDIF(CMAKE_BUILD_TYPE MATCHES Debug AND MARIUS_USE_ASAN)


IF(BUILD_DOCS)
add_subdirectory(${project_DOCS_DIR})
ENDIF()
Expand Down Expand Up @@ -246,4 +247,4 @@ pybind11_add_module(_storage ${STORAGE_BINDINGS})
target_link_libraries(_storage PRIVATE ${PROJECT_NAME} ${TORCH_PYTHON_LIBRARY})

add_custom_target(bindings)
add_dependencies(bindings _config _data _manager _nn _pipeline _report _storage)
add_dependencies(bindings _config _data _manager _nn _pipeline _report _storage)
9 changes: 5 additions & 4 deletions examples/docker/README.md
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Expand Up @@ -19,12 +19,13 @@ although Marius and MariusGNN can run on CPU only machines as well.
**Full List of Example Commands for GPU Installation**:

```
CURRENT_DIR=`pwd`
git clone https://github.com/marius-team/marius.git
cd marius/examples/docker/
docker build -t marius:latest gpu_ubuntu/.
docker run --gpus all -it -v $CURRENT_DIR:/working_dir/ marius:latest bash
cd marius
export CURRENT_DIR=`pwd`
cd examples/docker
docker build -t marius:latest gpu_ubuntu/.
docker run --gpus all -d -v $CURRENT_DIR:/working_dir/ --name=marius marius:latest sleep infinity
docker exec -it marius bash
pip3 install . --no-build-isolation
```

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1 change: 1 addition & 0 deletions examples/docker/cpu_ubuntu/dockerfile
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Expand Up @@ -26,6 +26,7 @@ RUN ln -s /opt/cmake/bin/cmake /usr/local/bin/cmake

# install pytorch
RUN python3 -m pip install torch --index-url https://download.pytorch.org/whl/cpu
RUN git config --global --add safe.directory "*"

RUN mkdir /working_dir
WORKDIR /working_dir
1 change: 1 addition & 0 deletions examples/docker/gpu_ubuntu/dockerfile
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Expand Up @@ -29,6 +29,7 @@ RUN ln -s /opt/cmake/bin/cmake /usr/local/bin/cmake

# install pytorch
RUN python3 -m pip install torch==1.13.1+cu116 --extra-index-url https://download.pytorch.org/whl/cu116
RUN git config --global --add safe.directory "*"

RUN mkdir /working_dir
WORKDIR /working_dir
26 changes: 26 additions & 0 deletions simulator/README.md
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# Simulator

Before running the simulator, install the required dependencies using the command:
```
$
```

The following directory contains code to simulate GNN inference. The main file in this directory is `main.py` which takes in the arguments of:
```
usage: main.py [-h] [--config_file CONFIG_FILE] --save_path SAVE_PATH --graph_title GRAPH_TITLE [--log_rate LOG_RATE]
optional arguments:
-h, --help show this help message and exit
--config_file CONFIG_FILE
The config file containing the details for the simulation (default: None)
--save_path SAVE_PATH
The path to save the resulting image to (default: None)
--graph_title GRAPH_TITLE
The title of the saved graph (default: None)
--log_rate LOG_RATE Log rate of the nodes processed (default: 20)
```

Thus, to run the simulator on the archive dataset with 1-hop sampling, you can run the command:
```
$ python3 main.py --config_file configs/arvix_linear.json --save_path results/arvix_linear.png --graph_title "CDF for sequentially arranged features"
```
2 changes: 1 addition & 1 deletion simulator/configs/arvix_linear.json
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{
"dataset_name" : "ogbn_arxiv",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 128,
"feature_size" : "float32"
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2 changes: 1 addition & 1 deletion simulator/configs/arvix_linear_2_hop.json
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{
"dataset_name" : "ogbn_arxiv",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 128,
"feature_size" : "float32"
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2 changes: 1 addition & 1 deletion simulator/configs/arvix_linear_2_hop_in_mem.json
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{
"dataset_name" : "ogbn_arxiv",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 128,
"feature_size" : "float32"
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2 changes: 1 addition & 1 deletion simulator/configs/arvix_linear_3_hop.json
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{
"dataset_name" : "ogbn_arxiv",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 128,
"feature_size" : "float32"
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2 changes: 1 addition & 1 deletion simulator/configs/arvix_linear_3_hop_5_in_mem.json
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{
"dataset_name" : "ogbn_arxiv",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 128,
"feature_size" : "float32"
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2 changes: 1 addition & 1 deletion simulator/configs/arvix_linear_3_hop_in_mem.json
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{
"dataset_name" : "ogbn_arxiv",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 128,
"feature_size" : "float32"
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1 change: 1 addition & 0 deletions simulator/configs/ogbn_products_benchmark/products_1_hop_0.0001_in_mem.json
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 0.0001}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 0.0005}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 0.001}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 0.005}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 0.01}
1 change: 1 addition & 0 deletions simulator/configs/ogbn_products_benchmark/products_1_hop_0.05_in_mem.json
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 0.05}
1 change: 1 addition & 0 deletions simulator/configs/ogbn_products_benchmark/products_1_hop_0.1_in_mem.json
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 0.1}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 0.5}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 1.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 10.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 100.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 20, "sampling_depth": 1, "top_percent_in_mem": 25.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 5.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 1, "top_percent_in_mem": 50.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 0.0001}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 0.0005}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 0.001}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 0.005}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 0.01}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 0.05}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 0.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 0.1}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 0.5}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 1.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 10.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 100.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 20, "sampling_depth": 2, "top_percent_in_mem": 25.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 5.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 2, "top_percent_in_mem": 50.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 0.0001}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 0.0005}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 0.001}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 0.005}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 0.01}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 0.05}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 0.0}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 0.1}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 0.5}
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 1.0}
1 change: 1 addition & 0 deletions simulator/configs/ogbn_products_benchmark/products_3_hop_10.0_in_mem.json
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 10.0}
1 change: 1 addition & 0 deletions simulator/configs/ogbn_products_benchmark/products_3_hop_100.0_in_mem.json
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 100.0}
1 change: 1 addition & 0 deletions simulator/configs/ogbn_products_benchmark/products_3_hop_25.0_in_mem.json
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 20, "sampling_depth": 3, "top_percent_in_mem": 25.0}
1 change: 1 addition & 0 deletions simulator/configs/ogbn_products_benchmark/products_3_hop_5.0_in_mem.json
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 5.0}
1 change: 1 addition & 0 deletions simulator/configs/ogbn_products_benchmark/products_3_hop_50.0_in_mem.json
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{"dataset_name": "ogbn_products", "features_stats": {"featurizer_type": "linear", "page_size": "16.384 KB", "feature_dimension": 100, "feature_size": "float32"}, "batch_size": 5, "sample_percentage": 25, "sampling_depth": 3, "top_percent_in_mem": 50.0}
3 changes: 0 additions & 3 deletions simulator/configs/papers.json
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2 changes: 1 addition & 1 deletion simulator/configs/products_linear.json
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{
"dataset_name" : "ogbn_products",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 100,
"feature_size" : "float32"
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2 changes: 1 addition & 1 deletion simulator/configs/products_linear_1_hop.json
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{
"dataset_name" : "ogbn_products",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 100,
"feature_size" : "float32"
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2 changes: 1 addition & 1 deletion simulator/configs/products_linear_1_hop_in_mem.json
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{
"dataset_name" : "ogbn_products",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 100,
"feature_size" : "float32"
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2 changes: 1 addition & 1 deletion simulator/configs/products_linear_2_hop.json
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{
"dataset_name" : "ogbn_products",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 100,
"feature_size" : "float32"
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2 changes: 1 addition & 1 deletion simulator/configs/products_linear_2_hop_in_mem.json
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@@ -1,7 +1,7 @@
{
"dataset_name" : "ogbn_products",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 100,
"feature_size" : "float32"
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2 changes: 1 addition & 1 deletion simulator/configs/products_linear_3_hop.json
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Expand Up @@ -7,6 +7,6 @@
"feature_size" : "float32"
},
"sampling_depth" : 3,
"sample_percentage" : 20,
"sample_percentage" : 25,
"batch_size" : 5
}
4 changes: 2 additions & 2 deletions simulator/configs/products_linear_3_hop_in_mem.json
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Expand Up @@ -7,7 +7,7 @@
"feature_size" : "float32"
},
"sampling_depth" : 3,
"sample_percentage" : 20,
"top_percent_in_mem" : 0.1,
"sample_percentage" : 25,
"top_percent_in_mem" : 10.0,
"batch_size" : 5
}
2 changes: 1 addition & 1 deletion simulator/configs/tree_linear_3_hop.json
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{
"dataset_name" : "tree",
"features_stats" : {
"featurizer_type" : "default",
"featurizer_type" : "linear",
"page_size" : "16.384 KB",
"feature_dimension" : 100,
"feature_size" : "float32"
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