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environment notes.txt
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environment notes.txt
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***ISSUES WITH ENVIRONMENTS***
module load languages/anaconda3/2022.12-3.11.4-torch-cuda-11.7 [CANT INSTALL LIBROSA]
module load languages/anaconda3/2022.11-3.11.4 [TESTING AS BROKEN TORCH WITH ABOVE]
conda create -n ecgpcg python=3.11.4
-- check https://pytorch.org/ for cuda/python/conda compatibility
[PYTHON INSTALLATION]
# install python3.8.1/3.11.4
# WINDOWS
# install python via .exe
# add to path: {installation_directory_path}\python.exe -V
# LINUX
sudo apt-get install python3.8.1
[CHECK CUDA VERSION]
nvcc --version
[CHECK CUDA INSTALLATION]
python -c "import torch; print(torch.cuda.is_available()); print(torch.cuda.device_count()); print(torch.cuda.get_device_name(0))"
[NEW CONDA PYTHON3.11.4]
module load languages/anaconda3/2022.12-3.9.13-torch-cuda-11.7
module load apps/ffmpeg/4.3
conda create --name ecgpcg
conda activate ecgpcg
https://pytorch.org/get-started/locally/
(e.g. conda install pytorch torchvision torchaudio pytorch-cuda=11.7 -c pytorch -c nvidia)
conda env export > environment_3.11.4_linux.yml
conda env create --name ecgpcg --file=environment_3.11.4_linux.yml
[NEW CONDA PYTHON3.8.1]
module load languages/anaconda3/2022.11-3.11.4
module load apps/ffmpeg/4.3
conda create --name ecgpcg-381 python=3.8.1
conda activate ecgpcg-381
https://pytorch.org/get-started/previous-versions/
(e.g. conda install pytorch==1.12.0 torchvision==0.13.0 torchaudio==0.12.0 cudatoolkit=11.6 -c pytorch -c conda-forge)
(e.g. conda install pytorch==1.13.1 torchvision==0.14.1 torchaudio==0.13.1 pytorch-cuda=11.6 -c pytorch -c nvidia)
conda env export > environment_3.8.1_linux.yml
conda env create --name ecgpcg-test --file=environment_3.8.1_linux.yml
[NEW CONDA - ALL PYTHON VERSIONS 3.8.1/3.11.4]
python -m pip install torch-ecg
conda install matplotlib tensorboard
conda install -c conda-forge matplotlib
conda install pywavelets
conda install -c conda-forge wfdb
conda install -c conda-forge opencv
[pip install opencv-python]
conda install -c anaconda pandas
conda install seaborn -c conda-forge
conda install -c conda-forge tqdm
conda install -c conda-forge librosa
conda install -c conda-forge configargparse
conda install -c conda-forge regex
conda install -c conda-forge moviepy
conda install scikit-image
conda install -c conda-forge scikit-build
conda install scipy
#WINDOWS
conda install -c conda-forge psutil
conda install -c anaconda pywin32
[NEW PIP/VENV PYTHON3.8.1]
# install python3.8.1, then pip, then make virtualenv using path to python3.8.1, activate venv, then install packages
# WINDOWS
python -m virtualenv --python="{installation_directory_path}\python.exe" "{path_to_environment}/{environment_name}"
(e.g. python -m virtualenv --python="C:/Users/willi/AppData/Local/Programs/Python/Python38-32/python.exe" "D:/Uni/Thesis/NEWREPO/multimodal-cardiography-learning/envs/ecgpcg-new")
{path_to_environment}/{environment_name}/Scripts/Activate.ps1 [Powershell]
(e.g. D:/Uni/Thesis/NEWREPO/multimodal-cardiography-learning/envs/ecgpcg-new/Scripts/activate.bat [.ps1])
# LINUX
python -m virtualenv --python="{installation_directory_path}\python.exe" "{path_to_environment}/{environment_name}"
(e.g. python -m virtualenv --python="C:/Users/willi/AppData/Local/Programs/Python/Python38-32/python.exe" "D:/Uni/Thesis/NEWREPO/multimodal-cardiography-learning/envs/ecgpcg-new")
source {path_to_environment}/{environment_name}/bin/activate
(e.g. source D:/Uni/Thesis/NEWREPO/multimodal-cardiography-learning/envs/ecgpcg-new/bin/activate [bash])
https://pytorch.org/get-started/previous-versions/
pip install torch==1.12.0 torchvision==0.13.0 torchaudio==0.12.0 [+ cuda]
pip install matplotlib
pip install pywavelets
pip install wfdb
pip install opencv-python
pip install pandas
pip install seaborn
pip install tqdm
pip install librosa
pip install configargparse
pip install regex
pip install tensorboard
pip install moviepy
pip install torch-ecg
pip install scikit-image
pip install scikit-build
pip install scipy
#LINUX
pip install python-resources
#WINDOWS
pip install pywin32
pip install psutil
import winerror
import win32api
import win32job
# IGNORETHIS: pip install pillow==6.2
# IGNORETHIS: pip install librosa==0.8
# IGNORETHIS: pip install numba==0.53
--IF No module named XXX: pip install -U pip setuptools
--IF activate.bat NOT RUNNING: Set-ExecutionPolicy Unrestricted --Force AS ADMINISTRATOR
[AVOBJECTS]
conda create -n avobjects --file=environment_droplet.yml python=3.6
conda install -c pytorch pytorch torchvision cudatoolkit=9.2
conda install -c anaconda mkl
conda install -c conda-forge configargparse
conda install -c conda-forge tqdm
conda install -c conda-forge librosa
conda install -c conda-forge av
conda install -c conda-forge opencv
conda install -c anaconda cupy
conda install -c conda-forge moviepy
conda install -c conda-forge dataclasses
## changed line 79 in D:\anaconda\envs\avobjects\Lib\site-packages\moviepy\decorators.py
## changed line 118 in D:\anaconda\envs\avobjects\Lib\site-packages\moviepy\decorators.py
pip install google-colab
pip3 install configargparse
MZdBGGg738kzd5mE
ssh -X gg18045@bc4login.acrc.bris.ac.uk
GA+CL-ECG-NET+CL-PCG-NET
http://dx.doi.org/10.13005/bbra/2610
https://github.com/Aolibaba/ecg_pcg_ga
ECG-PCG Data (Abnormal + Normal)
https://zenodo.org/record/4263528#.YjoW203P2Uk
PCG - 2000Hz
ECG - 1000Hz
Environments: Ubuntu 18.04, Python3.6, tensorflow-gpu==1.10.1, keras==2.2.5, scikit-learn==0.23.2
AVOBJECTS LWTNet
https://doi.org/10.48550/arXiv.2008.04237
https://github.com/afourast/avobjects
Environments: check environment.yml
EPHNOGRAM ECG-PCG-Data (Normal)
https://physionet.org/content/ephnogram/1.0.0/
https://doi.org/10.13026/tjtq-5911
PCG - 8000Hz
ECG - 8000Hz
PHYSIONET ECG-PCG Data (Abnormal + Normal)
https://physionet.org/content/challenge-2016/1.0.0/#files
PCG - 2000Hz
ECG - 2000Hz