From 7f30367b7060e542b1ea1f1db3e4f91818fa924c Mon Sep 17 00:00:00 2001 From: NeethuES-intel Date: Wed, 26 Apr 2023 21:07:41 -0700 Subject: [PATCH 1/2] [Bug: 766] Fix OpenFL MICCAI tutorials Fixes following 2 notebook in the tutorials - 1) 2D MedMNIST - added ipywidgets to make tqm work on jupyter notebook 2) OpenFL GaNDLF tutorial - added note that OpenFL needs python 3.8 to work without any errors. Google collab runs the notebook with python 3.9.16 by default, this needs to be changed to 3.8 to run without any errors Fixes #766 Co-authored-by: Emmanuel Jillela Signed-off-by: Neethu Elizabeth Simon --- .../Tutorial_1_Medmnist_2D.ipynb | 597 +++++++++++------- .../Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb | 1 + 2 files changed, 387 insertions(+), 211 deletions(-) diff --git a/tutorial_notebooks/Tutorial_1_Medmnist_2D.ipynb b/tutorial_notebooks/Tutorial_1_Medmnist_2D.ipynb index e8512f4..1ae69f7 100644 --- a/tutorial_notebooks/Tutorial_1_Medmnist_2D.ipynb +++ b/tutorial_notebooks/Tutorial_1_Medmnist_2D.ipynb @@ -8,7 +8,8 @@ }, "source": [ "# Federated Learning with BloodMNIST2D Dataset\n", - "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/intel/fl-tutorial/blob/gh-pages/tutorial_notebooks/Tutorial_1_Medmnist_2D.ipynb)" + "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/intel/fl-tutorial/blob/gh-pages/tutorial_notebooks/Tutorial_1_Medmnist_2D.ipynb)\n", + "### Note: If running the notebook on google colab, please make sure to use python version 3.8, OpenFL works with this version only." ] }, { @@ -73,7 +74,8 @@ ], "source": [ "!python -m pip install -U pip\n", - "!python -m pip install tqdm torch torchvision medmnist matplotlib" + "!python -m pip install tqdm torch torchvision medmnist matplotlib\n", + "!pip install ipywidgets" ] }, { @@ -313,7 +315,7 @@ "output_type": "stream", "text": [ "PyTorch 1.8.2+cu111\n", - "MedMNIST 2.1.0\n" + "MedMNIST 2.2.1\n" ] } ], @@ -428,7 +430,7 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 6, "id": "983adc4a", "metadata": { "colab": { @@ -453,26 +455,21 @@ }, "outputs": [ { - "data": { - "text/html": [ - "
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[15:42:51] INFO     MedMNIST data was loaded!                                                                                   medmnist_shard_descriptor.py:128\n",
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           METRIC   Round 0, collaborator validate_agg aggregated_model_validate result val_loss:   2.093000                                   experiment.py:132\n",
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[15:03:24] METRIC   Round 0, collaborator Aggregator train result train_acc:        0.857000                                                   experiment.py:132\n",
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[15:23:00] METRIC   Round 0, collaborator Aggregator train result train_acc:        0.617505                                                   experiment.py:132\n",
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           METRIC   Round 0, collaborator Aggregator aggregated_model_validate result val_acc:      0.137496                                   experiment.py:132\n",
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[15:03:31] METRIC   Round 1, collaborator trained train result train_acc:   0.714000                                                           experiment.py:132\n",
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           METRIC   Round 0, collaborator Aggregator aggregated_model_validate result val_loss:     2.091001                                   experiment.py:132\n",
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[15:23:02] METRIC   Round 1, collaborator trained train result train_acc:   0.815000                                                           experiment.py:132\n",
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           METRIC   Round 1, collaborator trained train result train_loss:  0.693000                                                           experiment.py:132\n",
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[15:03:32] METRIC   Round 1, collaborator validate_local locally_tuned_model_validate result val_acc:       0.801000                           experiment.py:132\n",
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           METRIC   Round 1, collaborator validate_agg aggregated_model_validate result val_acc:    0.751000                                   experiment.py:132\n",
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[15:23:12] METRIC   Round 1, collaborator validate_agg aggregated_model_validate result val_acc:    0.760000                                   experiment.py:132\n",
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[15:03:42] METRIC   Round 2, collaborator trained train result train_acc:   0.821000                                                           experiment.py:132\n",
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           METRIC   Round 1, collaborator Aggregator locally_tuned_model_validate result val_loss:  0.537001                                   experiment.py:132\n",
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           METRIC   Round 2, collaborator trained train result train_loss:  0.552000                                                           experiment.py:132\n",
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           METRIC   Round 1, collaborator Aggregator aggregated_model_validate result val_acc:      0.755501                                   experiment.py:132\n",
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           METRIC   Round 1, collaborator Aggregator aggregated_model_validate result val_loss:     0.751500                                   experiment.py:132\n",
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[15:03:44] METRIC   Round 2, collaborator validate_local locally_tuned_model_validate result val_acc:       0.822000                           experiment.py:132\n",
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[15:23:14] METRIC   Round 2, collaborator trained train result train_acc:   0.857000                                                           experiment.py:132\n",
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           METRIC   Round 2, collaborator validate_local locally_tuned_model_validate result val_loss:      0.474000                           experiment.py:132\n",
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           METRIC   Round 2, collaborator trained train result train_loss:  0.557000                                                           experiment.py:132\n",
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[15:23:15] METRIC   Round 2, collaborator validate_local locally_tuned_model_validate result val_acc:       0.842000                           experiment.py:132\n",
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[15:03:45] METRIC   Round 2, collaborator validate_agg aggregated_model_validate result val_acc:    0.801000                                   experiment.py:132\n",
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           METRIC   Round 2, collaborator validate_local locally_tuned_model_validate result val_loss:      0.468000                           experiment.py:132\n",
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[15:03:46] METRIC   Round 2, collaborator Aggregator train result train_acc:        0.821000                                                   experiment.py:132\n",
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           METRIC   Round 2, collaborator Aggregator train result train_loss:       0.552000                                                   experiment.py:132\n",
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[15:23:24] METRIC   Round 2, collaborator trained train result train_acc:   0.778000                                                           experiment.py:132\n",
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[15:03:47] METRIC   Round 2, collaborator Aggregator locally_tuned_model_validate result val_acc:   0.822000                                   experiment.py:132\n",
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           METRIC   Round 2, collaborator trained train result train_loss:  0.559000                                                           experiment.py:132\n",
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           METRIC   Round 2, collaborator Aggregator aggregated_model_validate result val_acc:      0.825500                                   experiment.py:132\n",
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           METRIC   Round 2, collaborator Aggregator aggregated_model_validate result val_loss:     0.531502                                   experiment.py:132\n",
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\n" + ], + "text/plain": [ + "\u001b[2;36m \u001b[0m\u001b[2;36m \u001b[0mMETRIC Round \u001b[1;36m2\u001b[0m, collaborator Aggregator aggregated_model_validate result val_loss: \u001b[1;36m0.531502\u001b[0m \u001b]8;id=457378;file:///home/nesubuntu20nvda/miniconda3/envs/hack_openfl/lib/python3.8/site-packages/openfl/interface/interactive_api/experiment.py\u001b\\\u001b[2mexperiment.py\u001b[0m\u001b]8;;\u001b\\\u001b[2m:\u001b[0m\u001b]8;id=620827;file:///home/nesubuntu20nvda/miniconda3/envs/hack_openfl/lib/python3.8/site-packages/openfl/interface/interactive_api/experiment.py#132\u001b\\\u001b[2m132\u001b[0m\u001b]8;;\u001b\\\n" ] }, "metadata": {}, @@ -2132,12 +2296,23 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 22, "id": "e5d793be-6c20-4a22-bad7-c082c1ee76ca", "metadata": { "id": "e5d793be-6c20-4a22-bad7-c082c1ee76ca" }, - "outputs": [], + "outputs": [ + { + "data": { + "text/plain": [ + "[None, None]" + ] + }, + "execution_count": 22, + "metadata": {}, + "output_type": "execute_result" + } + ], "source": [ "# To stop all services run\n", "!pkill fx\n", @@ -2151,7 +2326,7 @@ "provenance": [] }, "kernelspec": { - "display_name": "Python 3.8.0 ('venv': venv)", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -2165,7 +2340,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.0" + "version": "3.8.16" }, "vscode": { "interpreter": { diff --git a/tutorial_notebooks/Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb b/tutorial_notebooks/Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb index 8aa6844..442d0f9 100644 --- a/tutorial_notebooks/Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb +++ b/tutorial_notebooks/Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb @@ -8,6 +8,7 @@ "source": [ "# Federated GaNDLF Tutorial with PathMNIST Dataset\n", "[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/intel/fl-tutorial/blob/gh-pages/tutorial_notebooks/Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb)\n", + "### Note: If running the notebook on google colab, please make sure to use python version 3.8, OpenFL works with this version only.\n", "\n", "In this tutorial, we will be using the **Generally Nuanced Deep Learning Framework** (GaNDLF) to perform training and inference on a ResNet architecture, with PathMNIST, a dataset of colon pathology images, using [OpenFL](https://github.com/intel/openfl) in a federated learning fashion. This is a multi-class classification task: there are 9 different types of colon tissue displayed in the pathology images, each represented by its own class.\n", "\n", From b1320883ec623e5f312619b13fe9b182c2c46b1b Mon Sep 17 00:00:00 2001 From: NeethuES-intel Date: Mon, 22 May 2023 22:46:02 -0700 Subject: [PATCH 2/2] fix(bug 766): added python version update --- .../Tutorial_1_Medmnist_2D.ipynb | 17 ++++++++++++++++ .../Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb | 20 +++++++++++++++++-- 2 files changed, 35 insertions(+), 2 deletions(-) diff --git a/tutorial_notebooks/Tutorial_1_Medmnist_2D.ipynb b/tutorial_notebooks/Tutorial_1_Medmnist_2D.ipynb index 1ae69f7..8a38b83 100644 --- a/tutorial_notebooks/Tutorial_1_Medmnist_2D.ipynb +++ b/tutorial_notebooks/Tutorial_1_Medmnist_2D.ipynb @@ -22,6 +22,23 @@ "Let's get these out of the way first." ] }, + { + "cell_type": "code", + "execution_count": null, + "id": "415e25ee", + "metadata": {}, + "outputs": [], + "source": [ + "#If python version != 3.8, then uncomment & run the following code to change the python version to 3.8\n", + "!python --version\n", + "\n", + "#!sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1\n", + "#!sudo update-alternatives --config python3\n", + "#!python3 --version\n", + "#!sudo apt install python3-pip\n", + "#!python --version" + ] + }, { "cell_type": "code", "execution_count": 1, diff --git a/tutorial_notebooks/Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb b/tutorial_notebooks/Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb index 442d0f9..dd715a5 100644 --- a/tutorial_notebooks/Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb +++ b/tutorial_notebooks/Tutorial_3_GaNDLF_OpenFL_tutorial.ipynb @@ -26,6 +26,22 @@ "Let's get these out of the way first." ] }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [ + "#If python version != 3.8, then uncomment & run the following code to change the python version to 3.8\n", + "!python --version\n", + "\n", + "#!sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1\n", + "#!sudo update-alternatives --config python3\n", + "#!python3 --version\n", + "#!sudo apt install python3-pip\n", + "#!python --version" + ] + }, { "cell_type": "code", "execution_count": 1, @@ -2044,7 +2060,7 @@ }, "gpuClass": "standard", "kernelspec": { - "display_name": "Python 3.8.0 ('venv': venv)", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -2058,7 +2074,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.0" + "version": "3.8.16" }, "vscode": { "interpreter": {