Remove IPU (again)

.github/workflows/test.yml

@@ -16,8 +16,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.09", "3.10", "3.11"]
-        pytorch-version: ["2.0"]
+        include:
+          - python-version: "3.10"
+            pytorch-version: "2.0"
+          - python-version: "3.11"
+            pytorch-version: "2.0"
+          - python-version: "3.12"
+            pytorch-version: "2.3"
 
     runs-on: "ubuntu-latest"
     timeout-minutes: 30
@@ -55,9 +60,6 @@ jobs:
       - name: Install C++ library
         run: cd graphium/graphium_cpp && git clone https://github.com/pybind/pybind11.git && export PYTHONPATH=$PYTHONPATH:./pybind11 && python -m pip install . && cd ../..
 
-      - name: Run tests
-        run: pytest -m 'not ipu'
-
       - name: Test CLI
         run: graphium --help
 

.gitignore

@@ -55,15 +55,6 @@ debug/
 change_commits.sh
 graphium/features/test_new_pes.ipynb
 
-# IPU related ignores and profiler outputs
-*.a
-*.cbor
-*.capnp
-*.pop
-*.popart
-*.pop_cache
-*.popef
-*.pvti*
 
 ############ END graphium Custom GitIgnore ##############
 

README.md

@@ -13,7 +13,6 @@
 [![GitHub Repo stars](https://img.shields.io/github/stars/datamol-io/graphium)](https://github.com/datamol-io/graphium/stargazers)
 [![GitHub Repo stars](https://img.shields.io/github/forks/datamol-io/graphium)](https://github.com/datamol-io/graphium/network/members)
 [![test](https://github.com/datamol-io/graphium/actions/workflows/test.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/test.yml)
-[![test-ipu](https://github.com/datamol-io/graphium/actions/workflows/test_ipu.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/test_ipu.yml)
 [![release](https://github.com/datamol-io/graphium/actions/workflows/release.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/release.yml)
 [![code-check](https://github.com/datamol-io/graphium/actions/workflows/code-check.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/code-check.yml)
 [![doc](https://github.com/datamol-io/graphium/actions/workflows/doc.yml/badge.svg)](https://github.com/datamol-io/graphium/actions/workflows/doc.yml)
@@ -53,18 +52,6 @@ mamba activate graphium
 pip install --no-deps -e .
 ```
 
-### For IPU developers
-```bash
-# Install Graphcore's SDK and Graphium dependencies in a new environment called `.graphium_ipu`
-./install_ipu.sh .graphium_ipu
-```
-
-The above step needs to be done once. After that, enable the SDK and the environment as follows:
-
-```bash
-source enable_ipu.sh .graphium_ipu
-```
-
 ## Training a model
 
 To learn how to train a model, we invite you to look at the documentation, or the jupyter notebooks available [here](https://github.com/datamol-io/graphium/tree/master/docs/tutorials/model_training).

codecov.yml

@@ -16,8 +16,3 @@ component_management:
         target: auto
         branches:
           - "!main"
-  individual_components:
-    - component_id: ipu # this is an identifier that should not be changed
-      name: ipu # this is a display name, and can be changed freely
-      paths:
-        - graphium/ipu/**

docs/contribute.md

@@ -18,21 +18,6 @@ mamba activate graphium
 pip install --no-deps -e .
 ```
 
-### For IPU developers
-
-Download the SDK and use pypi to create your environment:
-
-```bash
-# Install Graphcore's SDK and Graphium dependencies in a new environment called `.graphium_ipu`
-./install_ipu.sh .graphium_ipu
-```
-
-The above step needs to be done once. After that, enable the SDK and the environment as follows:
-
-```bash
-source enable_ipu.sh .graphium_ipu
-```
-
 ## Build the documentation
 
 You can build and serve the documentation locally with:

docs/design.md

@@ -42,7 +42,6 @@ Below are a list of directory and their respective documentations:
 - [data](https://github.com/datamol-io/graphium/blob/main/graphium/data/README.md)
 - [features](https://github.com/datamol-io/graphium/tree/main/graphium/features/README.md)
 - finetuning
-- [ipu](https://github.com/datamol-io/graphium/tree/main/graphium/ipu/README.md)
 - [nn](https://github.com/datamol-io/graphium/tree/main/graphium/nn/README.md)
 - [trainer](https://github.com/datamol-io/graphium/tree/main/graphium/trainer/README.md)
 - [utils](https://github.com/datamol-io/graphium/tree/main/graphium/features/README.md)
@@ -56,7 +55,7 @@ Hence, we use [hydra](https://hydra.cc/docs/intro/) to enable splitting the conf
 
 Examples of possibilities include:
 
-- Switching between accelerators (CPU, GPU and IPU)
+- Switching between accelerators (CPU, GPU)
 - Benchmarking different models on the same dataset
 - Fine-tuning a pre-trained model on a new dataset
 

docs/index.md

@@ -25,17 +25,6 @@ or pip:
 pip install graphium
 ```
 
-### For IPU
-```bash
-# Install Graphcore's SDK and Graphium dependencies in a new environment called `.graphium_ipu`
-./install_ipu.sh .graphium_ipu
-```
-
-The above step needs to be done once. After that, enable the SDK and the environment as follows:
-
-```bash
-source enable_ipu.sh .graphium_ipu
-```
 
 Finally, you will need to install graphium with pip
 ```bash

docs/tutorials/feature_processing/timing_parallel.ipynb

@@ -476,7 +476,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "graphium_ipu",
+   "display_name": "graphium",
    "language": "python",
    "name": "python3"
   },

docs/tutorials/model_training/simple-molecular-model.ipynb

@@ -405,9 +405,9 @@
       "    zinc:\n",
       "    - mae\n",
       "  loss_fun:\n",
-      "    qm9: mae_ipu\n",
-      "    tox21: bce_logits_ipu\n",
-      "    zinc: mae_ipu\n",
+      "    qm9: mae\n",
+      "    tox21: bce_logits\n",
+      "    zinc: mae\n",
       "  random_seed: ${constants.seed}\n",
       "  optim_kwargs:\n",
       "    lr: 4.0e-05\n",
@@ -451,28 +451,28 @@
       "metrics:\n",
       "  qm9:\n",
       "  - name: mae\n",
-      "    metric: mae_ipu\n",
+      "    metric: mae\n",
       "    target_nan_mask: null\n",
       "    multitask_handling: flatten\n",
       "    threshold_kwargs: null\n",
       "  - name: pearsonr\n",
-      "    metric: pearsonr_ipu\n",
+      "    metric: pearsonr\n",
       "    threshold_kwargs: null\n",
       "    target_nan_mask: null\n",
       "    multitask_handling: mean-per-label\n",
       "  - name: r2_score\n",
-      "    metric: r2_score_ipu\n",
+      "    metric: r2_score\n",
       "    target_nan_mask: null\n",
       "    multitask_handling: mean-per-label\n",
       "    threshold_kwargs: null\n",
       "  tox21:\n",
       "  - name: auroc\n",
-      "    metric: auroc_ipu\n",
+      "    metric: auroc\n",
       "    task: binary\n",
       "    multitask_handling: mean-per-label\n",
       "    threshold_kwargs: null\n",
       "  - name: avpr\n",
-      "    metric: average_precision_ipu\n",
+      "    metric: average_precision\n",
       "    task: binary\n",
       "    multitask_handling: mean-per-label\n",
       "    threshold_kwargs: null\n",
@@ -498,17 +498,17 @@
       "      th_on_target: true\n",
       "  zinc:\n",
       "  - name: mae\n",
-      "    metric: mae_ipu\n",
+      "    metric: mae\n",
       "    target_nan_mask: null\n",
       "    multitask_handling: flatten\n",
       "    threshold_kwargs: null\n",
       "  - name: pearsonr\n",
-      "    metric: pearsonr_ipu\n",
+      "    metric: pearsonr\n",
       "    threshold_kwargs: null\n",
       "    target_nan_mask: null\n",
       "    multitask_handling: mean-per-label\n",
       "  - name: r2_score\n",
-      "    metric: r2_score_ipu\n",
+      "    metric: r2_score\n",
       "    target_nan_mask: null\n",
       "    multitask_handling: mean-per-label\n",
       "    threshold_kwargs: null\n",

env.yml

@@ -70,7 +70,16 @@ dependencies:
   - markdown-include
   - mike >=1.0.0
 
+  # C++ dependencies
+  - gcc_linux-64 # Sometimes I find that I need to enforce `gcc_linux-64`, but that won't work with Mac, Windows, or Arm-Linux
+  - gxx_linux-64 # Sometimes I find that I need to enforce `gxx_linux-64`, but that won't work with Mac, Windows, or Arm-Linux
+  - libgcc
+  - pybind11
+  - boost
+
+  # Optional
+  - pytdc
+
   - pip:
-      - lightning-graphcore # optional, for using IPUs only
       - hydra-core>=1.3.2
       - hydra-optuna-sweeper