From 7ae5f1b954d39d51e8a5aec3b426e888641e9080 Mon Sep 17 00:00:00 2001 From: Matteo Bunino Date: Fri, 10 Jan 2025 15:56:58 +0100 Subject: [PATCH 1/4] Update itwinai user installation and remove itwinai installer --- README.md | 53 +- env-files/itwinai-installer.sh | 50 - env-files/tensorflow/Dockerfile | 2 +- env-files/tensorflow/generic_tf.sh | 8 +- env-files/torch/Dockerfile | 2 +- env-files/torch/generic_torch.sh | 2 +- ...peed.slurm => horovod-deepspeed-JSC.slurm} | 2 + env-files/torch/jupyter/Dockerfile | 2 +- env-files/torch/slim.Dockerfile | 2 +- pyproject.toml | 11 +- uv.lock | 3612 +---------------- 11 files changed, 93 insertions(+), 3653 deletions(-) delete mode 100644 env-files/itwinai-installer.sh rename env-files/torch/{horovod-deepspeed.slurm => horovod-deepspeed-JSC.slurm} (95%) diff --git a/README.md b/README.md index 778a15ae..ea5c32aa 100644 --- a/README.md +++ b/README.md @@ -95,14 +95,40 @@ following command, and follow the instructions: # Second, create a python virtual environment and activate it $ python -m venv ENV_NAME $ source ENV_NAME/bin/activate +``` + +Install itwinai with support for PyTorch using: + +```bash +pip install itwinai[torch] +``` -# Install itwinai inside the environment -(ENV_NAME) $ export ML_FRAMEWORK="pytorch" # or "tensorflow" -(ENV_NAME) $ curl -fsSL https://github.com/interTwin-eu/itwinai/raw/main/env-files/itwinai-installer.sh | bash +or with TensorFlow support using: + +```bash +pip install itwinai[tf] + +# Alternatively, if you have access to GPUs +pip install itwinai[tf-cuda] ``` -The `ML_FRAMEWORK` environment variable controls whether you are installing -itwinai for PyTorch or TensorFlow. +If you want to use Prov4ML logger, you need to install it explicitly since it is only +available on GitHub: + +```bash +# For systems with Nvidia GPUs +pip install "prov4ml[nvidia]@git+https://github.com/matbun/ProvML@new-main" + +# For MacOs +pip install "prov4ml[apple]@git+https://github.com/matbun/ProvML@new-main" +``` + +If you also want to install Horovod and Microsoft DeepSpeed for distributed ML with PyTorch, +install them *after* itwinai. You can use this command: + +```bash +curl -fsSL https://github.com/interTwin-eu/itwinai/raw/main/env-files/torch/install-horovod-deepspeed-cuda.sh | bash +``` > [!WARNING] > itwinai depends on Horovod, which requires `CMake>=1.13` and @@ -163,11 +189,9 @@ commands they will use the version from your venv. ##### Installation of packages -We provide some _extras_ that can be activated depending on which platform you are +We provide some *extras* that can be activated depending on which platform you are using. -- `macos`, `amd` or `nvidia` depending on which platform you use. Changes the version -of `prov4ML`. - `dev` for development purposes. Includes libraries for testing and tensorboard etc. - `torch` for installation with PyTorch. @@ -180,17 +204,16 @@ directory, as you can very easily reach your disk quota otherwise. An example of complete command for installing as a developer on HPC with CUDA thus becomes: ```bash -pip install -e ".[torch,dev,nvidia,tf]" \ +pip install -e ".[torch,dev,tf]" \ --no-cache-dir \ --extra-index-url https://download.pytorch.org/whl/cu121 ``` -If you wanted to install this locally on macOS (i.e. without CUDA) with PyTorch, you -would do the following instead: - -```bash -pip install -e ".[torch,dev,macos,tf]" -``` +If you want to use Prov4ML logger, you need to install it explicitly since it is only +available on GitHub. Please refer to the +[users installation](#install-itwinai-for-users) +to know more on how to install +Prov4ML. diff --git a/env-files/itwinai-installer.sh b/env-files/itwinai-installer.sh deleted file mode 100644 index 6a540859..00000000 --- a/env-files/itwinai-installer.sh +++ /dev/null @@ -1,50 +0,0 @@ -#!/bin/bash - -# -------------------------------------------------------------------------------------- -# Part of the interTwin Project: https://www.intertwin.eu/ -# -# Created by: Matteo Bunino -# -# Credit: -# - Matteo Bunino - CERN -# -------------------------------------------------------------------------------------- - -# Simple installation for users -# It expects ML_FRAMEWORK env variable to be set - -if [ -z "$ML_FRAMEWORK" ]; then - echo "Error: ML_FRAMEWORK env variable not set. Accepted values are 'pytorch' and 'tensorflow'" - exit 1 -fi - -# Detect python env and CUDA env -if [ -z "$VIRTUAL_ENV" ]; then - echo "Error: Not in a Python virtual environment." - exit 1 -fi -export ENV_NAME=$VIRTUAL_ENV - -# Check if any CUDA-capable device is detected by nvidia-smi -if ! nvidia-smi > /dev/null 2>&1; then - echo "CUDA is not available. Installing cpu-only version." - export NO_CUDA=1 -fi - -# Begin installation of dependencies + itwinai -if [ "$ML_FRAMEWORK" == "pytorch" ]; then - echo "Installing itwinai with PyTorch support..." - # Skip last line (head -n -1) because it contains the istallation of itwinai - curl -fsSL https://github.com/interTwin-eu/itwinai/raw/main/env-files/torch/generic_torch.sh | sed '$d' | bash || exit 1 - # cat ../env-files/torch/generic_torch.sh | head -n -1 | bash - # Install from PyPI - pip install itwinai[torch] -elif [ "$ML_FRAMEWORK" == "tensorflow" ]; then - echo "Installing itwinai with TensorFlow support..." - # Skip last line (head -n -1) because it contains the istallation of itwinai - curl -fsSL https://github.com/interTwin-eu/itwinai/raw/main/env-files/tensorflow/generic_tf.sh | sed '$d' | bash || exit 1 - # cat ../env-files/tensorflow/generic_tf.sh | head -n -1 | bash - # Install from PyPI - pip install itwinai -else - echo "Invalid choice. Please run the script again by setting a valid ML_FRAMEWORK. Accepted values are 'pytorch' and 'tensorflow'." -fi diff --git a/env-files/tensorflow/Dockerfile b/env-files/tensorflow/Dockerfile index e848da7f..124a47f6 100644 --- a/env-files/tensorflow/Dockerfile +++ b/env-files/tensorflow/Dockerfile @@ -41,7 +41,7 @@ ENV PYTHONPATH="" # Install itwinai COPY pyproject.toml pyproject.toml COPY src src -RUN pip install --no-cache-dir .[prov4ml-nvidia] \ +RUN pip install --no-cache-dir .[tf-cuda] \ && itwinai sanity-check --tensorflow --optional-deps ray # Additional pip deps diff --git a/env-files/tensorflow/generic_tf.sh b/env-files/tensorflow/generic_tf.sh index b3e26661..870157ae 100644 --- a/env-files/tensorflow/generic_tf.sh +++ b/env-files/tensorflow/generic_tf.sh @@ -25,4 +25,10 @@ else fi source $ENV_NAME/bin/activate -pip install --no-cache-dir -e ".[dev,prov4ml-nvidia,tf]" + +if [ -z "$NO_CUDA" ]; then + TF_EXTRA="tf" +else + TF_EXTRA="tf-cuda" +fi +pip install --no-cache-dir -e ".[$TF_EXTRA,dev]" diff --git a/env-files/torch/Dockerfile b/env-files/torch/Dockerfile index 180c2c32..5e838260 100644 --- a/env-files/torch/Dockerfile +++ b/env-files/torch/Dockerfile @@ -35,7 +35,7 @@ RUN pip install --no-cache-dir --upgrade pip \ # Install itwinai with torch COPY pyproject.toml pyproject.toml COPY src src -RUN pip install --no-cache-dir .[torch,tf,prov4ml-nvidia,dev] --extra-index-url https://download.pytorch.org/whl/cu124 +RUN pip install --no-cache-dir .[torch,tf,dev] --extra-index-url https://download.pytorch.org/whl/cu124 # Install DeepSpeed, Horovod and Ray ENV HOROVOD_WITH_PYTORCH=1 \ diff --git a/env-files/torch/generic_torch.sh b/env-files/torch/generic_torch.sh index 3ca1e118..1c1f093a 100644 --- a/env-files/torch/generic_torch.sh +++ b/env-files/torch/generic_torch.sh @@ -26,6 +26,6 @@ fi # Activate the venv and then install itwinai as editable source $ENV_NAME/bin/activate -pip install -e ".[torch,tf,dev,prov4ml-nvidia]" \ +pip install -e ".[torch,tf,dev]" \ --no-cache-dir \ --extra-index-url https://download.pytorch.org/whl/cu121 diff --git a/env-files/torch/horovod-deepspeed.slurm b/env-files/torch/horovod-deepspeed-JSC.slurm similarity index 95% rename from env-files/torch/horovod-deepspeed.slurm rename to env-files/torch/horovod-deepspeed-JSC.slurm index 00e9934f..086ce34b 100644 --- a/env-files/torch/horovod-deepspeed.slurm +++ b/env-files/torch/horovod-deepspeed-JSC.slurm @@ -1,5 +1,7 @@ #!/bin/bash +# Installation for JSC + # Job configuration #SBATCH --job-name=setup_venv #SBATCH --account=intertwin diff --git a/env-files/torch/jupyter/Dockerfile b/env-files/torch/jupyter/Dockerfile index bee700b1..4c336cb0 100644 --- a/env-files/torch/jupyter/Dockerfile +++ b/env-files/torch/jupyter/Dockerfile @@ -216,7 +216,7 @@ RUN pip install --no-cache-dir --upgrade pip \ WORKDIR "$HOME/itwinai" COPY --chown=${NB_UID} pyproject.toml pyproject.toml COPY --chown=${NB_UID} src src -RUN pip install --no-cache-dir .[torch,prov4ml-nvidia,dev] --extra-index-url https://download.pytorch.org/whl/cu124 +RUN pip install --no-cache-dir .[torch,dev] --extra-index-url https://download.pytorch.org/whl/cu124 # Apex: https://github.com/NVIDIA/apex # (needed for DeepSpeed *_FUSED optinal build options) diff --git a/env-files/torch/slim.Dockerfile b/env-files/torch/slim.Dockerfile index add40d64..3e6a6f30 100644 --- a/env-files/torch/slim.Dockerfile +++ b/env-files/torch/slim.Dockerfile @@ -56,7 +56,7 @@ RUN /usr/bin/python3.10 -m venv /opt/venv \ WORKDIR /app COPY pyproject.toml pyproject.toml COPY src src -RUN pip install --no-cache-dir .[torch,prov4ml-nvidia,dev] --extra-index-url https://download.pytorch.org/whl/cu124 +RUN pip install --no-cache-dir .[torch,dev] --extra-index-url https://download.pytorch.org/whl/cu124 # Install DeepSpeed, Horovod and Ray RUN CONTAINER_TORCH_VERSION="$(python -c 'import torch;print(torch.__version__)')" \ diff --git a/pyproject.toml b/pyproject.toml index 174c868b..f493807c 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -78,11 +78,12 @@ hpo = [ "hpbandster>=0.7.0", "gpy>=1.13.2", ] -prov4ml = ["prov4ml@git+https://github.com/matbun/ProvML@new-main"] -prov4ml-macos = ["prov4ml[apple]@git+https://github.com/matbun/ProvML@new-main"] -prov4ml-nvidia = [ - "prov4ml[nvidia]@git+https://github.com/matbun/ProvML@new-main", -] +# Git dependencies are not supported by PyPI and will prevent pushing new versions to it. +# prov4ml = ["prov4ml@git+https://github.com/matbun/ProvML@new-main"] +# prov4ml-macos = ["prov4ml[apple]@git+https://github.com/matbun/ProvML@new-main"] +# prov4ml-nvidia = [ +# "prov4ml[nvidia]@git+https://github.com/matbun/ProvML@new-main", +# ] # prov4ml-amd = ["prov4ml[amd]@git+https://github.com/matbun/ProvML@new-main"] [project.urls] diff --git a/uv.lock b/uv.lock index a2b89c1e..3ba14fe5 100644 --- a/uv.lock +++ b/uv.lock @@ -196,48 +196,12 @@ wheels = [ { url = "https://files.pythonhosted.org/packages/78/b6/6307fbef88d9b5ee7421e68d78a9f162e0da4900bc5f5793f6d3d0e34fb8/annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53", size = 13643 }, ] -[[package]] -name = "ansicon" -version = "1.89.0" -source = { registry = "https://pypi.org/simple" } -sdist = { url = "https://files.pythonhosted.org/packages/b6/e2/1c866404ddbd280efedff4a9f15abfe943cb83cde6e895022370f3a61f85/ansicon-1.89.0.tar.gz", hash = "sha256:e4d039def5768a47e4afec8e89e83ec3ae5a26bf00ad851f914d1240b444d2b1", size = 67312 } -wheels = [ - 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Please refer to the [users installation](#install-itwinai-for-users) -to know more on how to install -Prov4ML. +to know more on how to install Prov4ML. From 2f5793915f9af26b6840529570dce10bd94dc8dd Mon Sep 17 00:00:00 2001 From: Matteo Bunino Date: Fri, 10 Jan 2025 16:10:02 +0100 Subject: [PATCH 3/4] Integrate comments --- README.md | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index cae5f601..ffec23a8 100644 --- a/README.md +++ b/README.md @@ -130,7 +130,7 @@ curl -fsSL https://github.com/interTwin-eu/itwinai/raw/main/env-files/torch/inst ``` > [!WARNING] -> itwinai depends on Horovod, which requires `CMake>=1.13` and +> Horovod requires `CMake>=1.13` and > [other packages](https://horovod.readthedocs.io/en/latest/install_include.html#requirements). > Make sure to have them installed in your environment before proceeding. @@ -208,8 +208,15 @@ pip install -e ".[torch,dev,tf]" \ --extra-index-url https://download.pytorch.org/whl/cu121 ``` -If you want to use Prov4ML logger, you need to install it explicitly since it is only -available on GitHub. Please refer to the +If you wanted to install this locally on **macOS** (i.e. without CUDA) with PyTorch, you +would do the following instead: + +```bash +pip install -e ".[torch,dev,tf]" +``` + +If you want to use [Prov4ML](https://github.com/HPCI-Lab/yProvML) logger, you need to install +it explicitly since it is only available on GitHub. Please refer to the [users installation](#install-itwinai-for-users) to know more on how to install Prov4ML. From f0ffb3388877b2ad244a2e37b450d091cab439f3 Mon Sep 17 00:00:00 2001 From: Matteo Bunino Date: Fri, 10 Jan 2025 16:15:07 +0100 Subject: [PATCH 4/4] add comment --- env-files/torch/createEnvVega.sh | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/env-files/torch/createEnvVega.sh b/env-files/torch/createEnvVega.sh index 7b859eea..cca12a0b 100644 --- a/env-files/torch/createEnvVega.sh +++ b/env-files/torch/createEnvVega.sh @@ -1,6 +1,15 @@ #!/bin/bash # -*- coding: utf-8 -*- +# -------------------------------------------------------------------------------------- +# Part of the interTwin Project: https://www.intertwin.eu/ +# +# Created by: Matteo Bunino +# +# Credit: +# - Matteo Bunino - CERN +# -------------------------------------------------------------------------------------- + if [ ! -f "env-files/torch/generic_torch.sh" ]; then echo "ERROR: env-files/torch/generic_torch.sh not found!" exit 1 @@ -13,10 +22,8 @@ ml Python/3.11.5-GCCcore-13.2.0 ml CMake/3.24.3-GCCcore-11.3.0 ml mpi4py ml OpenMPI -#ml CUDA/11.7 ml CUDA/12.3 ml GCCcore/11.3.0 -#ml NCCL/2.12.12-GCCcore-11.3.0-CUDA-11.7.0 ml NCCL ml cuDNN/8.9.7.29-CUDA-12.3.0 ml UCX-CUDA/1.15.0-GCCcore-13.2.0-CUDA-12.3.0