Usage

For usage see Usage

Installation

Linux

Without conda

Creating directories

mkdir CryoViaInstallation

cd CryoViaInstallation

git clone https://github.com/philipp-schoennenbeck/CryoVia

git clone https://github.com/philipp-schoennenbeck/GridEdgeDetector

Creating python environment

Make sure you have python 3.9 installed.

python3.9 -m venv /path/to/venv/name_of_venv

source /path/to/venv/name_of_venv/bin/activate

Installing tensorflow

pip install tensorflow[and-cuda]

Verifying tensorflow install

python3 -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU'))"

Installing CryoVia

cd CryoVia

pip install .

Install GridEdgeDetector

cd ../GridEdgeDetector

pip install .

With conda

Creating directories

mkdir CryoViaInstallation

cd CryoViaInstallation

git clone https://github.com/philipp-schoennenbeck/CryoVia

git clone https://github.com/philipp-schoennenbeck/GridEdgeDetector

Creating python environment

conda create -n cryovia python=3.9.16

conda activate cryovia

Installing tensorflow

conda install -c conda-forge cudatoolkit=11.8.0

python3 -m pip install nvidia-cudnn-cu11==8.6.0.163 tensorflow==2.12.*

mkdir -p $CONDA_PREFIX/etc/conda/activate.d

echo 'CUDNN_PATH=$(dirname $(python -c "import nvidia.cudnn;print(nvidia.cudnn.__file__)"))' >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh

echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$CONDA_PREFIX/lib/:$CUDNN_PATH/lib' >> $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh

source $CONDA_PREFIX/etc/conda/activate.d/env_vars.sh

Verifying tensorflow install

python3 -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU'))"

Installing CryoVia

cd CryoVia

pip install .

Install GridEdgeDetector

cd ../GridEdgeDetector

pip install .

Windows

Creating directories

mkdir CryoViaInstallation

cd CryoViaInstallation

git clone https://github.com/philipp-schoennenbeck/CryoVia

git clone https://github.com/philipp-schoennenbeck/GridEdgeDetector

Creating python environment

conda create -n cryovia python=3.9.16

conda activate cryovia

Installing tensorflow

conda install -c conda-forge cudatoolkit=11.2 cudnn=8.1.0

pip install tensorflow==2.10

pip install numpy==1.24.1

Verifying tensorflow install

python -c "import tensorflow as tf; print(tf.config.list_physical_devices('GPU'))"

Installing CryoVia

cd CryoVia

pip install .

Install GridEdgeDetector

cd ../GridEdgeDetector

pip install .