{ "cells": [ { "cell_type": "markdown", "id": "048c6b14", "metadata": { "id": "048c6b14" }, "source": [ "# TCGA Histology Images Benchmarking Execution Steps\n", "\n", "This notebook follows the README instructions to:\n", "1. Clone the repository\n", "2. Set up the environment (install dependencies)\n", "3. Execute the training script (`extract_train.py`)\n", "\n", "We will explain and execute these steps.\n" ] }, { "cell_type": "markdown", "id": "e7d3f2ef", "metadata": { "id": "e7d3f2ef" }, "source": [ "## Step 1: Clone the Repository\n", "\n", "Use the following command to clone the target repository.\n" ] }, { "cell_type": "code", "source": [ "# check python version (this example is google colab environment)\n", "!python --version" ], "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "FccnVVy0GAVR", "outputId": "e90aefeb-6cd3-4875-cc53-e7241c84589a" }, "id": "FccnVVy0GAVR", "execution_count": 1, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "Python 3.11.11\n" ] } ] }, { "cell_type": "code", "source": [ "# set your huggingface token\n", "import os\n", "token = \"your huggingface token\"" ], "metadata": { "id": "48KZGOUK74nm" }, "id": "48KZGOUK74nm", "execution_count": 2, "outputs": [] }, { "cell_type": "code", "execution_count": 3, "id": "7fa0d887", "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "7fa0d887", "outputId": "9ab89093-b365-419f-96d1-c2f09929b36c" }, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "Cloning into 'demo'...\n", "remote: Enumerating objects: 199, done.\u001b[K\n", "remote: Counting objects: 100% (43/43), done.\u001b[K\n", "remote: Compressing objects: 100% (43/43), done.\u001b[K\n", "remote: Total 199 (delta 21), reused 0 (delta 0), pack-reused 156 (from 1)\u001b[K\n", "Receiving objects: 100% (199/199), 79.26 KiB | 8.81 MiB/s, done.\n", "Resolving deltas: 100% (33/33), done.\n", "Filtering content: 100% (113/113), 11.30 GiB | 45.21 MiB/s, done.\n" ] } ], "source": [ "# repository url need to be changed\n", "!git clone https://oauth2:{token}@huggingface.co/datasets/kooo-sh/demo/" ] }, { "cell_type": "markdown", "id": "86ab67ec", "metadata": { "id": "86ab67ec" }, "source": [ "## Step 2: Environment Setup\n", "\n", "Navigate to the cloned directory and install the required Python packages.\n" ] }, { "cell_type": "code", "source": [ "# move directory\n", "%cd repository_directory" ], "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "RZVfsHws-djt", "outputId": "83b081d6-9249-4b24-e451-c0347e752d03" }, "id": "RZVfsHws-djt", "execution_count": 4, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "/content/drive/MyDrive/demo\n" ] } ] }, { "cell_type": "code", "source": [ "%ls" ], "metadata": { "colab": { "base_uri": "https://localhost:8080/" }, "id": "umN5ZMRHHA7z", "outputId": "199d9667-1044-4c1a-e004-bf4f5b14a56d" }, "id": "umN5ZMRHHA7z", "execution_count": 5, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "config.yaml extract_train.py \u001b[0m\u001b[01;34mlicenses\u001b[0m/ requirements.txt train_val_test_split.csv\n", "\u001b[01;34mdata\u001b[0m/ \u001b[01;34mfeatures\u001b[0m/ README.md setup.ipynb\n" ] } ] }, { "cell_type": "code", "execution_count": 6, "id": "56b69da0", "metadata": { "id": "56b69da0", "colab": { "base_uri": "https://localhost:8080/" }, "outputId": "09cdfc42-751e-432c-c978-7ca0ef4379c4" }, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "Collecting braceexpand==0.1.7 (from -r requirements.txt (line 1))\n", " Downloading braceexpand-0.1.7-py2.py3-none-any.whl.metadata (3.0 kB)\n", "Collecting certifi==2024.8.30 (from -r requirements.txt (line 2))\n", " Downloading certifi-2024.8.30-py3-none-any.whl.metadata (2.2 kB)\n", "Collecting charset-normalizer==3.3.2 (from -r requirements.txt (line 3))\n", " Downloading charset_normalizer-3.3.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (33 kB)\n", "Collecting contourpy==1.1.1 (from -r requirements.txt (line 4))\n", " Downloading contourpy-1.1.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.9 kB)\n", "Requirement already satisfied: cycler==0.12.1 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 5)) (0.12.1)\n", "Collecting filelock==3.16.1 (from -r requirements.txt (line 6))\n", " Downloading filelock-3.16.1-py3-none-any.whl.metadata (2.9 kB)\n", "Collecting fonttools==4.54.1 (from -r requirements.txt (line 7))\n", " Downloading fonttools-4.54.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (163 kB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m163.7/163.7 kB\u001b[0m \u001b[31m1.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hCollecting fsspec==2024.9.0 (from -r requirements.txt (line 8))\n", " Downloading fsspec-2024.9.0-py3-none-any.whl.metadata (11 kB)\n", "Collecting h5py==3.11.0 (from -r requirements.txt (line 9))\n", " Downloading h5py-3.11.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)\n", "Collecting huggingface-hub==0.24.6 (from -r requirements.txt (line 10))\n", " Downloading huggingface_hub-0.24.6-py3-none-any.whl.metadata (13 kB)\n", "Requirement already satisfied: idna==3.10 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 11)) (3.10)\n", "Collecting Jinja2==3.1.4 (from -r requirements.txt (line 12))\n", " Downloading jinja2-3.1.4-py3-none-any.whl.metadata (2.6 kB)\n", "Requirement already satisfied: joblib==1.4.2 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 13)) (1.4.2)\n", "Collecting kiwisolver==1.4.7 (from -r requirements.txt (line 14))\n", " Downloading kiwisolver-1.4.7-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.3 kB)\n", "Collecting MarkupSafe==2.1.5 (from -r requirements.txt (line 15))\n", " Downloading MarkupSafe-2.1.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)\n", "Collecting matplotlib==3.6.1 (from -r requirements.txt (line 16))\n", " Downloading matplotlib-3.6.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.8 kB)\n", "Requirement already satisfied: mpmath==1.3.0 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 17)) (1.3.0)\n", "Collecting networkx==3.1 (from -r requirements.txt (line 18))\n", " Downloading networkx-3.1-py3-none-any.whl.metadata (5.3 kB)\n", "Collecting numpy==1.22.2 (from -r requirements.txt (line 19))\n", " Downloading numpy-1.22.2.zip (11.4 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m11.4/11.4 MB\u001b[0m \u001b[31m47.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25h Installing build dependencies ... \u001b[?25l\u001b[?25hdone\n", " Getting requirements to build wheel ... \u001b[?25l\u001b[?25hdone\n", " Preparing metadata (pyproject.toml) ... \u001b[?25l\u001b[?25hdone\n", "Collecting nvidia-cublas-cu11==11.10.3.66 (from -r requirements.txt (line 20))\n", " Downloading nvidia_cublas_cu11-11.10.3.66-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n", "Collecting nvidia-cuda-nvrtc-cu11==11.7.99 (from -r requirements.txt (line 21))\n", " Downloading nvidia_cuda_nvrtc_cu11-11.7.99-2-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-cuda-runtime-cu11==11.7.99 (from -r requirements.txt (line 22))\n", " Downloading nvidia_cuda_runtime_cu11-11.7.99-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n", "Collecting nvidia-cudnn-cu11==8.5.0.96 (from -r requirements.txt (line 23))\n", " Downloading nvidia_cudnn_cu11-8.5.0.96-2-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n", "Requirement already satisfied: opencv-python==4.10.0.84 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 24)) (4.10.0.84)\n", "Collecting packaging==24.1 (from -r requirements.txt (line 25))\n", " Downloading packaging-24.1-py3-none-any.whl.metadata (3.2 kB)\n", "Collecting pandas==1.4.4 (from -r requirements.txt (line 26))\n", " Downloading pandas-1.4.4.tar.gz (4.9 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m4.9/4.9 MB\u001b[0m \u001b[31m103.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25h Installing build dependencies ... \u001b[?25l\u001b[?25hdone\n", " Getting requirements to build wheel ... \u001b[?25l\u001b[?25hdone\n", " Preparing metadata (pyproject.toml) ... \u001b[?25l\u001b[?25hdone\n", "Collecting pillow==10.4.0 (from -r requirements.txt (line 27))\n", " Downloading pillow-10.4.0-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (9.2 kB)\n", "Collecting pip-licenses==4.5.1 (from -r requirements.txt (line 28))\n", " Downloading pip_licenses-4.5.1-py3-none-any.whl.metadata (34 kB)\n", "Collecting prettytable==3.11.0 (from -r requirements.txt (line 29))\n", " Downloading prettytable-3.11.0-py3-none-any.whl.metadata (30 kB)\n", "Collecting pyparsing==3.1.4 (from -r requirements.txt (line 30))\n", " Downloading pyparsing-3.1.4-py3-none-any.whl.metadata (5.1 kB)\n", "Collecting python-dateutil==2.9.0.post0 (from -r requirements.txt (line 31))\n", " Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB)\n", "Requirement already satisfied: pytz==2024.2 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 32)) (2024.2)\n", "Requirement already satisfied: PyYAML==6.0.2 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 33)) (6.0.2)\n", "Collecting regex==2024.9.11 (from -r requirements.txt (line 34))\n", " Downloading regex-2024.9.11-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (40 kB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m40.5/40.5 kB\u001b[0m \u001b[31m1.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hRequirement already satisfied: requests==2.32.3 in /usr/local/lib/python3.11/dist-packages (from -r requirements.txt (line 35)) (2.32.3)\n", "Collecting safetensors==0.4.5 (from -r requirements.txt (line 36))\n", " Downloading safetensors-0.4.5-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.8 kB)\n", "Collecting scikit-learn==0.24.2 (from -r requirements.txt (line 37))\n", " Downloading scikit-learn-0.24.2.tar.gz (7.5 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m7.5/7.5 MB\u001b[0m \u001b[31m97.8 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25h Installing build dependencies ... \u001b[?25l\u001b[?25hdone\n", " Getting requirements to build wheel ... \u001b[?25l\u001b[?25hdone\n", " \u001b[1;31merror\u001b[0m: \u001b[1msubprocess-exited-with-error\u001b[0m\n", " \n", " \u001b[31m×\u001b[0m \u001b[32mPreparing metadata \u001b[0m\u001b[1;32m(\u001b[0m\u001b[32mpyproject.toml\u001b[0m\u001b[1;32m)\u001b[0m did not run successfully.\n", " \u001b[31m│\u001b[0m exit code: \u001b[1;36m1\u001b[0m\n", " \u001b[31m╰─>\u001b[0m See above for output.\n", " \n", " \u001b[1;35mnote\u001b[0m: This error originates from a subprocess, and is likely not a problem with pip.\n", " Preparing metadata (pyproject.toml) ... \u001b[?25l\u001b[?25herror\n", "\u001b[1;31merror\u001b[0m: \u001b[1mmetadata-generation-failed\u001b[0m\n", "\n", "\u001b[31m×\u001b[0m Encountered error while generating package metadata.\n", "\u001b[31m╰─>\u001b[0m See above for output.\n", "\n", "\u001b[1;35mnote\u001b[0m: This is an issue with the package mentioned above, not pip.\n", "\u001b[1;36mhint\u001b[0m: See above for details.\n" ] } ], "source": [ "# install packages\n", "!pip install -r requirements.txt" ] }, { "cell_type": "code", "source": [ "# if scikit-leran is not installed, run this command\n", "# !pip install scikit-learn\n", "# !pip install scipy six==1.16.0" ], "metadata": { "colab": { "base_uri": "https://localhost:8080/", "height": 434 }, "id": "kvflBfrrSyU4", "outputId": "5b10426c-c3e3-4eff-cbcd-0fa1f6f96d46" }, "id": "kvflBfrrSyU4", "execution_count": 7, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "Requirement already satisfied: scikit-learn in /usr/local/lib/python3.11/dist-packages (1.6.1)\n", "Requirement already satisfied: numpy>=1.19.5 in /usr/local/lib/python3.11/dist-packages (from scikit-learn) (1.26.4)\n", "Requirement already satisfied: scipy>=1.6.0 in /usr/local/lib/python3.11/dist-packages (from scikit-learn) (1.13.1)\n", "Requirement already satisfied: joblib>=1.2.0 in /usr/local/lib/python3.11/dist-packages (from scikit-learn) (1.4.2)\n", "Requirement already satisfied: threadpoolctl>=3.1.0 in /usr/local/lib/python3.11/dist-packages (from scikit-learn) (3.5.0)\n", "Requirement already satisfied: scipy in /usr/local/lib/python3.11/dist-packages (1.13.1)\n", "Collecting six==1.16.0\n", " Downloading six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)\n", "Requirement already satisfied: numpy<2.3,>=1.22.4 in /usr/local/lib/python3.11/dist-packages (from scipy) (1.26.4)\n", "Downloading six-1.16.0-py2.py3-none-any.whl (11 kB)\n", "Installing collected packages: six\n", " Attempting uninstall: six\n", " Found existing installation: six 1.17.0\n", " Uninstalling six-1.17.0:\n", " Successfully uninstalled six-1.17.0\n", "Successfully installed six-1.16.0\n" ] }, { "output_type": "display_data", "data": { "application/vnd.colab-display-data+json": { "pip_warning": { "packages": [ "six" ] }, "id": "9f6ede4ac0cd447db545799914707e3b" } }, "metadata": {} } ] }, { "cell_type": "markdown", "id": "d725eb4d", "metadata": { "id": "d725eb4d" }, "source": [ "### Troubleshooting SPAMS Library Installation\n", "\n", "If you encounter issues installing the SPAMS library from `requirements.txt`, try executing the following alternative command.\n" ] }, { "cell_type": "code", "execution_count": 1, "id": "d3d70745", "metadata": { "id": "d3d70745", "colab": { "base_uri": "https://localhost:8080/" }, "outputId": "2c674c7b-d821-43be-aad1-8172985e9439" }, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "Collecting spams-bin\n", " Downloading spams_bin-2.6.10-cp311-cp311-manylinux_2_28_x86_64.whl.metadata (754 bytes)\n", "Requirement already satisfied: numpy>=1.21.3 in /usr/local/lib/python3.11/dist-packages (from spams-bin) (1.26.4)\n", "Requirement already satisfied: scipy>=1.5 in /usr/local/lib/python3.11/dist-packages (from spams-bin) (1.13.1)\n", "Downloading spams_bin-2.6.10-cp311-cp311-manylinux_2_28_x86_64.whl (16.6 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m16.6/16.6 MB\u001b[0m \u001b[31m53.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hInstalling collected packages: spams-bin\n", "Successfully installed spams-bin-2.6.10\n", "Requirement already satisfied: PyOpenGL in /usr/local/lib/python3.11/dist-packages (3.1.9)\n", "Collecting PyOpenGL_accelerate\n", " Downloading PyOpenGL_accelerate-3.1.9-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.9 kB)\n", "Downloading PyOpenGL_accelerate-3.1.9-cp311-cp311-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.2/3.2 MB\u001b[0m \u001b[31m27.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hInstalling collected packages: PyOpenGL_accelerate\n", "Successfully installed PyOpenGL_accelerate-3.1.9\n", "Collecting staintools==2.1.2\n", " Downloading staintools-2.1.2.tar.gz (7.0 kB)\n", " Preparing metadata (setup.py) ... \u001b[?25l\u001b[?25hdone\n", "Collecting sympy==1.13.3\n", " Downloading sympy-1.13.3-py3-none-any.whl.metadata (12 kB)\n", "Requirement already satisfied: threadpoolctl==3.5.0 in /usr/local/lib/python3.11/dist-packages (3.5.0)\n", "Collecting timm==1.0.9\n", " Downloading timm-1.0.9-py3-none-any.whl.metadata (42 kB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m42.4/42.4 kB\u001b[0m \u001b[31m1.9 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hCollecting tokenizers==0.19.1\n", " Downloading tokenizers-0.19.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.7 kB)\n", "Collecting tomli==2.0.2\n", " Downloading tomli-2.0.2-py3-none-any.whl.metadata (10.0 kB)\n", "Requirement already satisfied: torch in /usr/local/lib/python3.11/dist-packages (2.5.1+cu124)\n", "Requirement already satisfied: torchvision in /usr/local/lib/python3.11/dist-packages (0.20.1+cu124)\n", "Collecting tqdm==4.66.5\n", " Downloading tqdm-4.66.5-py3-none-any.whl.metadata (57 kB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m57.6/57.6 kB\u001b[0m \u001b[31m4.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hCollecting transformers==4.44.2\n", " Downloading transformers-4.44.2-py3-none-any.whl.metadata (43 kB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m43.7/43.7 kB\u001b[0m \u001b[31m3.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hCollecting triton==3.0.0\n", " Downloading triton-3.0.0-1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (1.3 kB)\n", "Requirement already satisfied: typing_extensions==4.12.2 in /usr/local/lib/python3.11/dist-packages (4.12.2)\n", "Collecting urllib3==2.2.3\n", " Downloading urllib3-2.2.3-py3-none-any.whl.metadata (6.5 kB)\n", "Requirement already satisfied: wcwidth==0.2.13 in /usr/local/lib/python3.11/dist-packages (0.2.13)\n", "Collecting webdataset==0.2.100\n", " Downloading webdataset-0.2.100-py3-none-any.whl.metadata (12 kB)\n", "Requirement already satisfied: numpy in /usr/local/lib/python3.11/dist-packages (from staintools==2.1.2) (1.26.4)\n", "Requirement already satisfied: matplotlib in /usr/local/lib/python3.11/dist-packages (from staintools==2.1.2) (3.10.0)\n", "Requirement already satisfied: opencv-python in /usr/local/lib/python3.11/dist-packages (from staintools==2.1.2) (4.10.0.84)\n", "Requirement already satisfied: mpmath<1.4,>=1.1.0 in /usr/local/lib/python3.11/dist-packages (from sympy==1.13.3) (1.3.0)\n", "Requirement already satisfied: pyyaml in /usr/local/lib/python3.11/dist-packages (from timm==1.0.9) (6.0.2)\n", "Requirement already satisfied: huggingface_hub in /usr/local/lib/python3.11/dist-packages (from timm==1.0.9) (0.27.1)\n", "Requirement already satisfied: safetensors in /usr/local/lib/python3.11/dist-packages (from timm==1.0.9) (0.5.2)\n", "Requirement already satisfied: filelock in /usr/local/lib/python3.11/dist-packages (from transformers==4.44.2) (3.17.0)\n", "Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.11/dist-packages (from transformers==4.44.2) (24.2)\n", "Requirement already satisfied: regex!=2019.12.17 in /usr/local/lib/python3.11/dist-packages (from transformers==4.44.2) (2024.11.6)\n", "Requirement already satisfied: requests in /usr/local/lib/python3.11/dist-packages (from transformers==4.44.2) (2.32.3)\n", "Collecting braceexpand (from webdataset==0.2.100)\n", " Using cached braceexpand-0.1.7-py2.py3-none-any.whl.metadata (3.0 kB)\n", "Requirement already satisfied: networkx in /usr/local/lib/python3.11/dist-packages (from torch) (3.4.2)\n", "Requirement already satisfied: jinja2 in /usr/local/lib/python3.11/dist-packages (from torch) (3.1.5)\n", "Requirement already satisfied: fsspec in /usr/local/lib/python3.11/dist-packages (from torch) (2024.10.0)\n", "Collecting nvidia-cuda-nvrtc-cu12==12.4.127 (from torch)\n", " Downloading nvidia_cuda_nvrtc_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-cuda-runtime-cu12==12.4.127 (from torch)\n", " Downloading nvidia_cuda_runtime_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-cuda-cupti-cu12==12.4.127 (from torch)\n", " Downloading nvidia_cuda_cupti_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl.metadata (1.6 kB)\n", "Collecting nvidia-cudnn-cu12==9.1.0.70 (from torch)\n", " Downloading nvidia_cudnn_cu12-9.1.0.70-py3-none-manylinux2014_x86_64.whl.metadata (1.6 kB)\n", "Collecting nvidia-cublas-cu12==12.4.5.8 (from torch)\n", " Downloading nvidia_cublas_cu12-12.4.5.8-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-cufft-cu12==11.2.1.3 (from torch)\n", " Downloading nvidia_cufft_cu12-11.2.1.3-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-curand-cu12==10.3.5.147 (from torch)\n", " Downloading nvidia_curand_cu12-10.3.5.147-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-cusolver-cu12==11.6.1.9 (from torch)\n", " Downloading nvidia_cusolver_cu12-11.6.1.9-py3-none-manylinux2014_x86_64.whl.metadata (1.6 kB)\n", "Collecting nvidia-cusparse-cu12==12.3.1.170 (from torch)\n", " Downloading nvidia_cusparse_cu12-12.3.1.170-py3-none-manylinux2014_x86_64.whl.metadata (1.6 kB)\n", "Requirement already satisfied: nvidia-nccl-cu12==2.21.5 in /usr/local/lib/python3.11/dist-packages (from torch) (2.21.5)\n", "Requirement already satisfied: nvidia-nvtx-cu12==12.4.127 in /usr/local/lib/python3.11/dist-packages (from torch) (12.4.127)\n", "Collecting nvidia-nvjitlink-cu12==12.4.127 (from torch)\n", " Downloading nvidia_nvjitlink_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)\n", "INFO: pip is looking at multiple versions of torch to determine which version is compatible with other requirements. This could take a while.\n", "Collecting torch\n", " Downloading torch-2.6.0-cp311-cp311-manylinux1_x86_64.whl.metadata (28 kB)\n", "Collecting nvidia-cusparselt-cu12==0.6.2 (from torch)\n", " Downloading nvidia_cusparselt_cu12-0.6.2-py3-none-manylinux2014_x86_64.whl.metadata (6.8 kB)\n", "Collecting torch\n", " Downloading torch-2.5.1-cp311-cp311-manylinux1_x86_64.whl.metadata (28 kB)\n", " Downloading torch-2.5.0-cp311-cp311-manylinux1_x86_64.whl.metadata (28 kB)\n", " Downloading torch-2.4.1-cp311-cp311-manylinux1_x86_64.whl.metadata (26 kB)\n", "Collecting nvidia-cuda-nvrtc-cu12==12.1.105 (from torch)\n", " Downloading nvidia_cuda_nvrtc_cu12-12.1.105-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-cuda-runtime-cu12==12.1.105 (from torch)\n", " Downloading nvidia_cuda_runtime_cu12-12.1.105-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-cuda-cupti-cu12==12.1.105 (from torch)\n", " Downloading nvidia_cuda_cupti_cu12-12.1.105-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n", "Collecting nvidia-cublas-cu12==12.1.3.1 (from torch)\n", " Downloading nvidia_cublas_cu12-12.1.3.1-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-cufft-cu12==11.0.2.54 (from torch)\n", " Downloading nvidia_cufft_cu12-11.0.2.54-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-curand-cu12==10.3.2.106 (from torch)\n", " Downloading nvidia_curand_cu12-10.3.2.106-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n", "Collecting nvidia-cusolver-cu12==11.4.5.107 (from torch)\n", " Downloading nvidia_cusolver_cu12-11.4.5.107-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n", "Collecting nvidia-cusparse-cu12==12.1.0.106 (from torch)\n", " Downloading nvidia_cusparse_cu12-12.1.0.106-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n", "Collecting nvidia-nccl-cu12==2.20.5 (from torch)\n", " Downloading nvidia_nccl_cu12-2.20.5-py3-none-manylinux2014_x86_64.whl.metadata (1.8 kB)\n", "Collecting nvidia-nvtx-cu12==12.1.105 (from torch)\n", " Downloading nvidia_nvtx_cu12-12.1.105-py3-none-manylinux1_x86_64.whl.metadata (1.7 kB)\n", "Requirement already satisfied: nvidia-nvjitlink-cu12 in /usr/local/lib/python3.11/dist-packages (from nvidia-cusolver-cu12==11.4.5.107->torch) (12.5.82)\n", "Requirement already satisfied: pillow!=8.3.*,>=5.3.0 in /usr/local/lib/python3.11/dist-packages (from torchvision) (11.1.0)\n", "Collecting torchvision\n", " Downloading torchvision-0.21.0-cp311-cp311-manylinux1_x86_64.whl.metadata (6.1 kB)\n", " Downloading torchvision-0.20.1-cp311-cp311-manylinux1_x86_64.whl.metadata (6.1 kB)\n", "INFO: pip is still looking at multiple versions of torch to determine which version is compatible with other requirements. This could take a while.\n", " Downloading torchvision-0.20.0-cp311-cp311-manylinux1_x86_64.whl.metadata (6.1 kB)\n", " Downloading torchvision-0.19.1-cp311-cp311-manylinux1_x86_64.whl.metadata (6.0 kB)\n", "Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.11/dist-packages (from jinja2->torch) (3.0.2)\n", "Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.11/dist-packages (from matplotlib->staintools==2.1.2) (1.3.1)\n", "Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.11/dist-packages (from matplotlib->staintools==2.1.2) (0.12.1)\n", "Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.11/dist-packages (from matplotlib->staintools==2.1.2) (4.55.7)\n", "Requirement already satisfied: kiwisolver>=1.3.1 in /usr/local/lib/python3.11/dist-packages (from matplotlib->staintools==2.1.2) (1.4.8)\n", "Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.11/dist-packages (from matplotlib->staintools==2.1.2) (3.2.1)\n", "Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.11/dist-packages (from matplotlib->staintools==2.1.2) (2.8.2)\n", "Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.11/dist-packages (from requests->transformers==4.44.2) (3.4.1)\n", "Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.11/dist-packages (from requests->transformers==4.44.2) (3.10)\n", "Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.11/dist-packages (from requests->transformers==4.44.2) (2024.12.14)\n", "Requirement already satisfied: six>=1.5 in /usr/local/lib/python3.11/dist-packages (from python-dateutil>=2.7->matplotlib->staintools==2.1.2) (1.16.0)\n", "Downloading sympy-1.13.3-py3-none-any.whl (6.2 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m6.2/6.2 MB\u001b[0m \u001b[31m58.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading timm-1.0.9-py3-none-any.whl (2.3 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m2.3/2.3 MB\u001b[0m \u001b[31m54.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading tokenizers-0.19.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.6 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m3.6/3.6 MB\u001b[0m \u001b[31m38.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading tomli-2.0.2-py3-none-any.whl (13 kB)\n", "Downloading tqdm-4.66.5-py3-none-any.whl (78 kB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m78.4/78.4 kB\u001b[0m \u001b[31m6.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading transformers-4.44.2-py3-none-any.whl (9.5 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m9.5/9.5 MB\u001b[0m \u001b[31m112.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading triton-3.0.0-1-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (209.4 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m209.4/209.4 MB\u001b[0m \u001b[31m6.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading urllib3-2.2.3-py3-none-any.whl (126 kB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m126.3/126.3 kB\u001b[0m \u001b[31m10.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading webdataset-0.2.100-py3-none-any.whl (74 kB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m74.8/74.8 kB\u001b[0m \u001b[31m6.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading torch-2.4.1-cp311-cp311-manylinux1_x86_64.whl (797.1 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m797.1/797.1 MB\u001b[0m \u001b[31m1.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_cublas_cu12-12.1.3.1-py3-none-manylinux1_x86_64.whl (410.6 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m410.6/410.6 MB\u001b[0m \u001b[31m4.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_cuda_cupti_cu12-12.1.105-py3-none-manylinux1_x86_64.whl (14.1 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m14.1/14.1 MB\u001b[0m \u001b[31m61.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_cuda_nvrtc_cu12-12.1.105-py3-none-manylinux1_x86_64.whl (23.7 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m23.7/23.7 MB\u001b[0m \u001b[31m56.4 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_cuda_runtime_cu12-12.1.105-py3-none-manylinux1_x86_64.whl (823 kB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m823.6/823.6 kB\u001b[0m \u001b[31m47.5 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_cudnn_cu12-9.1.0.70-py3-none-manylinux2014_x86_64.whl (664.8 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m664.8/664.8 MB\u001b[0m \u001b[31m2.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_cufft_cu12-11.0.2.54-py3-none-manylinux1_x86_64.whl (121.6 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m121.6/121.6 MB\u001b[0m \u001b[31m7.7 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_curand_cu12-10.3.2.106-py3-none-manylinux1_x86_64.whl (56.5 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m56.5/56.5 MB\u001b[0m \u001b[31m12.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_cusolver_cu12-11.4.5.107-py3-none-manylinux1_x86_64.whl (124.2 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m124.2/124.2 MB\u001b[0m \u001b[31m8.6 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_cusparse_cu12-12.1.0.106-py3-none-manylinux1_x86_64.whl (196.0 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m196.0/196.0 MB\u001b[0m \u001b[31m6.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_nccl_cu12-2.20.5-py3-none-manylinux2014_x86_64.whl (176.2 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m176.2/176.2 MB\u001b[0m \u001b[31m6.1 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading nvidia_nvtx_cu12-12.1.105-py3-none-manylinux1_x86_64.whl (99 kB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m99.1/99.1 kB\u001b[0m \u001b[31m8.0 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading torchvision-0.19.1-cp311-cp311-manylinux1_x86_64.whl (7.0 MB)\n", "\u001b[2K \u001b[90m━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━\u001b[0m \u001b[32m7.0/7.0 MB\u001b[0m \u001b[31m21.3 MB/s\u001b[0m eta \u001b[36m0:00:00\u001b[0m\n", "\u001b[?25hDownloading braceexpand-0.1.7-py2.py3-none-any.whl (5.9 kB)\n", "Building wheels for collected packages: staintools\n", " Building wheel for staintools (setup.py) ... \u001b[?25l\u001b[?25hdone\n", " Created wheel for staintools: filename=staintools-2.1.2-py3-none-any.whl size=14051 sha256=6034d47a7b5770d1df676df5a81768c52bd79b644f8b330025603148bc15249e\n", " Stored in directory: /root/.cache/pip/wheels/0c/c4/69/fc8068103fe40879db0187cd442d181b1e741e849f33814600\n", "Successfully built staintools\n", "Installing collected packages: braceexpand, webdataset, urllib3, triton, tqdm, tomli, sympy, nvidia-nvtx-cu12, nvidia-nccl-cu12, nvidia-cusparse-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, nvidia-cusolver-cu12, nvidia-cudnn-cu12, torch, staintools, torchvision, tokenizers, transformers, timm\n", " Attempting uninstall: urllib3\n", " Found existing installation: urllib3 2.3.0\n", " Uninstalling urllib3-2.3.0:\n", " Successfully uninstalled urllib3-2.3.0\n", " Attempting uninstall: triton\n", " Found existing installation: triton 3.1.0\n", " Uninstalling triton-3.1.0:\n", " Successfully uninstalled triton-3.1.0\n", " Attempting uninstall: tqdm\n", " Found existing installation: tqdm 4.67.1\n", " Uninstalling tqdm-4.67.1:\n", " Successfully uninstalled tqdm-4.67.1\n", " Attempting uninstall: sympy\n", " Found existing installation: sympy 1.13.1\n", " Uninstalling sympy-1.13.1:\n", " Successfully uninstalled sympy-1.13.1\n", " Attempting uninstall: nvidia-nvtx-cu12\n", " Found existing installation: nvidia-nvtx-cu12 12.4.127\n", " Uninstalling nvidia-nvtx-cu12-12.4.127:\n", " Successfully uninstalled nvidia-nvtx-cu12-12.4.127\n", " Attempting uninstall: nvidia-nccl-cu12\n", " Found existing installation: nvidia-nccl-cu12 2.21.5\n", " Uninstalling nvidia-nccl-cu12-2.21.5:\n", " Successfully uninstalled nvidia-nccl-cu12-2.21.5\n", " Attempting uninstall: nvidia-cusparse-cu12\n", " Found existing installation: nvidia-cusparse-cu12 12.5.1.3\n", " Uninstalling nvidia-cusparse-cu12-12.5.1.3:\n", " Successfully uninstalled nvidia-cusparse-cu12-12.5.1.3\n", " Attempting uninstall: nvidia-curand-cu12\n", " Found existing installation: nvidia-curand-cu12 10.3.6.82\n", " Uninstalling nvidia-curand-cu12-10.3.6.82:\n", " Successfully uninstalled nvidia-curand-cu12-10.3.6.82\n", " Attempting uninstall: nvidia-cufft-cu12\n", " Found existing installation: nvidia-cufft-cu12 11.2.3.61\n", " Uninstalling nvidia-cufft-cu12-11.2.3.61:\n", " Successfully uninstalled nvidia-cufft-cu12-11.2.3.61\n", " Attempting uninstall: nvidia-cuda-runtime-cu12\n", " Found existing installation: nvidia-cuda-runtime-cu12 12.5.82\n", " Uninstalling nvidia-cuda-runtime-cu12-12.5.82:\n", " Successfully uninstalled nvidia-cuda-runtime-cu12-12.5.82\n", " Attempting uninstall: nvidia-cuda-nvrtc-cu12\n", " Found existing installation: nvidia-cuda-nvrtc-cu12 12.5.82\n", " Uninstalling nvidia-cuda-nvrtc-cu12-12.5.82:\n", " Successfully uninstalled nvidia-cuda-nvrtc-cu12-12.5.82\n", " Attempting uninstall: nvidia-cuda-cupti-cu12\n", " Found existing installation: nvidia-cuda-cupti-cu12 12.5.82\n", " Uninstalling nvidia-cuda-cupti-cu12-12.5.82:\n", " Successfully uninstalled nvidia-cuda-cupti-cu12-12.5.82\n", " Attempting uninstall: nvidia-cublas-cu12\n", " Found existing installation: nvidia-cublas-cu12 12.5.3.2\n", " Uninstalling nvidia-cublas-cu12-12.5.3.2:\n", " Successfully uninstalled nvidia-cublas-cu12-12.5.3.2\n", " Attempting uninstall: nvidia-cusolver-cu12\n", " Found existing installation: nvidia-cusolver-cu12 11.6.3.83\n", " Uninstalling nvidia-cusolver-cu12-11.6.3.83:\n", " Successfully uninstalled nvidia-cusolver-cu12-11.6.3.83\n", " Attempting uninstall: nvidia-cudnn-cu12\n", " Found existing installation: nvidia-cudnn-cu12 9.3.0.75\n", " Uninstalling nvidia-cudnn-cu12-9.3.0.75:\n", " Successfully uninstalled nvidia-cudnn-cu12-9.3.0.75\n", " Attempting uninstall: torch\n", " Found existing installation: torch 2.5.1+cu124\n", " Uninstalling torch-2.5.1+cu124:\n", " Successfully uninstalled torch-2.5.1+cu124\n", " Attempting uninstall: torchvision\n", " Found existing installation: torchvision 0.20.1+cu124\n", " Uninstalling torchvision-0.20.1+cu124:\n", " Successfully uninstalled torchvision-0.20.1+cu124\n", " Attempting uninstall: tokenizers\n", " Found existing installation: tokenizers 0.21.0\n", " Uninstalling tokenizers-0.21.0:\n", " Successfully uninstalled tokenizers-0.21.0\n", " Attempting uninstall: transformers\n", " Found existing installation: transformers 4.47.1\n", " Uninstalling transformers-4.47.1:\n", " Successfully uninstalled transformers-4.47.1\n", " Attempting uninstall: timm\n", " Found existing installation: timm 1.0.14\n", " Uninstalling timm-1.0.14:\n", " Successfully uninstalled timm-1.0.14\n", "\u001b[31mERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.\n", "torchaudio 2.5.1+cu124 requires torch==2.5.1, but you have torch 2.4.1 which is incompatible.\u001b[0m\u001b[31m\n", "\u001b[0mSuccessfully installed braceexpand-0.1.7 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-9.1.0.70 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.20.5 nvidia-nvtx-cu12-12.1.105 staintools-2.1.2 sympy-1.13.3 timm-1.0.9 tokenizers-0.19.1 tomli-2.0.2 torch-2.4.1 torchvision-0.19.1 tqdm-4.66.5 transformers-4.44.2 triton-3.0.0 urllib3-2.2.3 webdataset-0.2.100\n" ] } ], "source": [ "!pip install spams-bin\n", "!pip install PyOpenGL PyOpenGL_accelerate\n", "!pip install staintools==2.1.2 sympy==1.13.3 threadpoolctl==3.5.0 timm==1.0.9 tokenizers==0.19.1 tomli==2.0.2 torch torchvision tqdm==4.66.5 transformers==4.44.2 triton==3.0.0 typing_extensions==4.12.2 urllib3==2.2.3 wcwidth==0.2.13 webdataset==0.2.100" ] }, { "cell_type": "markdown", "id": "d86a7b1c", "metadata": { "id": "d86a7b1c" }, "source": [ "## Step 3: Execute the Training Script\n", "\n", "Run `extract_train.py` to start the following processes:\n", "\n", "- Feature extraction using the specified foundation model\n", "- Saving features in H5 format\n", "- Linear probing evaluation (outputting Accuracy and Balanced Accuracy)\n" ] }, { "cell_type": "code", "execution_count": 2, "id": "5f3a7c3e", "metadata": { "id": "5f3a7c3e", "colab": { "base_uri": "https://localhost:8080/" }, "outputId": "b7639582-b37b-4e71-e459-8b56266c7ef4" }, "outputs": [ { "output_type": "stream", "name": "stdout", "text": [ "{'model_name': 'h_optimus', 'split_type': 'internal', 'device': 'cuda', 'feature_exist': True, 'max_iter': 1000, 'cost': 0.0001, 'model_path': 'hf-hub:bioptimus/H-optimus-0'}\n", "Directory already exists: ./features\n", "Accuracy = 0.830, Balanced Accuracy = 0.739\n" ] } ], "source": [ "!python extract_train.py" ] }, { "cell_type": "markdown", "id": "5873d257", "metadata": { "id": "5873d257" }, "source": [ "This completes the repository cloning, environment setup, and training script execution.\n", "\n", "If you encounter any errors during any step, follow the error messages and take necessary actions such as adjusting package versions or installing system libraries.\n" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "name": "python3" }, "language_info": { "name": "python", "version": "3.x" }, "colab": { "provenance": [], "gpuType": "T4" }, "accelerator": "GPU" }, "nbformat": 4, "nbformat_minor": 5 }