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Pin TensorFlow according to OS; Fix DeepLabCut install in Colab to deal with new requirements. (#2862)
1 parent b8653f1 commit c483526

8 files changed

Lines changed: 262 additions & 59 deletions

‎examples/COLAB/COLAB_3miceDemo.ipynb‎

Lines changed: 45 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,9 @@
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"- a quick guide to maDLC: https://deeplabcut.github.io/DeepLabCut/docs/tutorial.html\n",
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"- a demo COLAB for how to use maDLC on your own data: https://github.com/DeepLabCut/DeepLabCut/blob/main/examples/COLAB/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb\n",
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"\n",
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"### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n"
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"### To get started, please go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
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"\n",
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"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
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]
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},
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{
@@ -43,11 +45,49 @@
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},
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"outputs": [],
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"source": [
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"# Installs a CUDA version compatible with tensorflow on COLAB\n",
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"!apt update && apt install cuda-11-8\n",
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"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
49+
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
50+
]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
59+
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
60+
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Install the latest version of DeepLabCut\n",
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"!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
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"# create symbolic links to NVIDIA shared libraries:\n",
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"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"### Important - Restart the Runtime for the updated packages to be imported!\n",
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"\n",
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"# Install the latest DeepLabCut version:\n",
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"!pip install \"deeplabcut[tf]\""
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"PLEASE, click \"restart runtime\" from the output above before proceeding!"
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]
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},
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{

‎examples/COLAB/COLAB_DEMO_SuperAnimal.ipynb‎

Lines changed: 38 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -43,19 +43,51 @@
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"\n",
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"## **Let's get going: install DeepLabCut into COLAB:**\n",
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"\n",
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"*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*\n"
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"*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*\n",
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"\n",
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"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU.\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"id": "03ylSyQ4O9Ee"
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"# Cell 1 - Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
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"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
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"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
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"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Install the latest version of DeepLabCut\n",
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"!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git#egg=deeplabcut[modelzoo]\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"!apt update && apt install cuda-11-8\n",
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"!pip install deeplabcut[tf,modelzoo]"
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"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
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"# create symbolic links to NVIDIA shared libraries:\n",
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"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
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]
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},
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{

‎examples/COLAB/COLAB_DEMO_mouse_openfield.ipynb‎

Lines changed: 28 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -42,7 +42,30 @@
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"id": "txoddlM8hLKm"
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},
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"source": [
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"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\""
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"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
46+
"\n",
47+
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
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"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
67+
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
68+
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
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]
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},
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{
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"metadata": {},
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"outputs": [],
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"source": [
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"# Installs a CUDA version compatible with tensorflow on COLAB\n",
55-
"!apt update && apt install cuda-11-8"
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"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
78+
"# create symbolic links to NVIDIA shared libraries:\n",
79+
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
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]
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},
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{
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"source": [
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"# Install the latest DeepLabCut version (this will take a few minutes to install all the dependencies!)\n",
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"%cd /content/cloned-DLC-repo/\n",
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"!pip install \".[tf]\""
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"!pip install \".\""
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]
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},
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{

‎examples/COLAB/COLAB_DLC_ModelZoo.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -45,29 +45,60 @@
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"\n",
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"## **Let's get going: install DeepLabCut into COLAB:**\n",
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"\n",
48-
"*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*"
48+
"*Also, be sure you are connected to a GPU: go to menu, click Runtime > Change Runtime Type > select \"GPU\"*\n",
49+
"\n",
50+
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
4951
]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"id": "q23BzhA6CXxu"
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},
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"metadata": {},
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"outputs": [],
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"source": [
59+
"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
60+
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
61+
]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
59-
"#click the play icon (this will take a few minutes to install all the dependencies!)\n",
60-
"!apt update && apt install cuda-11-8\n",
61-
"!pip install deeplabcut[tf,modelzoo]"
69+
"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
70+
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
71+
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
72+
]
73+
},
74+
{
75+
"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
80+
"# Install the latest version of DeepLabCut\n",
81+
"!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git#egg=deeplabcut[modelzoo]\""
82+
]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
91+
"# create symbolic links to NVIDIA shared libraries:\n",
92+
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {
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"id": "zYm6DljQB0Y7"
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},
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"metadata": {},
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"source": [
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"###proTip: be sure to click \"restart runtime button\" if it appears above ^"
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"### Important - Restart the Runtime for the updated packages to be imported!\n",
100+
"\n",
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"PLEASE, click \"restart runtime\" from the output above before proceeding!"
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]
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},
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{

‎examples/COLAB/COLAB_YOURDATA_TrainNetwork_VideoAnalysis.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -48,22 +48,51 @@
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"id": "txoddlM8hLKm"
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},
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"source": [
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"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n"
51+
"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
52+
"\n",
53+
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"colab": {},
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"colab_type": "code",
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"id": "q23BzhA6CXxu"
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
63+
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
64+
]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
73+
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
74+
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
75+
]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Install the latest version of DeepLabCut\n",
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"!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git\""
85+
]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"#(this will take a few minutes to install all the dependences!)\n",
65-
"!apt update && apt install cuda-11-8\n",
66-
"!pip install \"deeplabcut[tf]\""
93+
"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
94+
"# create symbolic links to NVIDIA shared libraries:\n",
95+
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
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]
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},
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{

‎examples/COLAB/COLAB_maDLC_TrainNetwork_VideoAnalysis.ipynb‎

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Original file line numberDiff line numberDiff line change
@@ -46,36 +46,51 @@
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"id": "txoddlM8hLKm"
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},
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"source": [
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"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n"
49+
"## First, go to \"Runtime\" ->\"change runtime type\"->select \"Python3\", and then select \"GPU\"\n",
50+
"\n",
51+
"As the COLAB environments were updated to CUDA 12.X and Python 3.11, we need to install DeepLabCut and TensorFlow in a distinct way to get TensorFlow to connect to the GPU."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"id": "q23BzhA6CXxu"
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"#(this will take a few minutes to install all the dependences!)\n",
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"!apt update && apt install cuda-11-8\n",
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"!pip install \"deeplabcut[tf]\"\n",
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"%reload_ext numpy\n",
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"%reload_ext scipy\n",
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"%reload_ext matplotlib\n",
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"%reload_ext mpl_toolkits"
60+
"# Install TensorFlow, tensorpack and tf_slim versions compatible with DeepLabCut\n",
61+
"!pip install \"tensorflow==2.12.1\" \"tensorpack>=0.11\" \"tf_slim>=1.1.0\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {
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"id": "-MVvZ13_FMvP"
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},
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"metadata": {},
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"outputs": [],
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"source": [
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"# Downgrade PyTorch to a version using CUDA 11.8 and cudnn 8\n",
71+
"# This will also install the required CUDA libraries, for both PyTorch and TensorFlow\n",
72+
"!pip install torch==2.3.1 torchvision --index-url https://download.pytorch.org/whl/cu118"
73+
]
74+
},
75+
{
76+
"cell_type": "code",
77+
"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"# Install the latest version of DeepLabCut\n",
82+
"!pip install \"git+https://github.com/DeepLabCut/DeepLabCut.git\""
83+
]
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},
85+
{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": [
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"#a few colab specific things needed:\n",
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"!pip install --upgrade scikit-image"
91+
"# As described in https://www.tensorflow.org/install/pip#step-by-step_instructions, \n",
92+
"# create symbolic links to NVIDIA shared libraries:\n",
93+
"!ln -svf /usr/local/lib/python3.11/dist-packages/nvidia/*/lib/*.so* /usr/local/lib/python3.11/dist-packages/tensorflow"
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]
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},
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{

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