Merge branch 'main' of github.com:agosztolai/MARBLE into main

MARBLE/utils.py

@@ -29,6 +29,7 @@ def print_settings(model):
 
     print("\n---- Number of features to pass to the MLP: ", n_features)
     print("---- Total number of parameters: ", n_parameters)
+    print(f"\nUsing device {device}")
 
 
 def parallel_proc(fun, iterable, inputs, processes=-1, desc=""):

README.md

@@ -56,6 +56,13 @@ git clone https://github.com/agosztolai/MARBLE
     - Activate the environment `conda activate MARBLE` 
     - Install pytorch geometric
     `pip install -r requirements_osx_arm.txt`
+
+  - For Windows computers:
+  we recommend using WSL2 that allows running a (virtual) Linux machine inside your windows computer, which makes the installation simpler. If you have a NVIDIA GPU, WSL2 will allow to take advantage of the GPU (an older version of WSL will not).
+    - Follow the [instructions to install WSL2](https://learn.microsoft.com/en-us/windows/wsl/install)
+    - Open "Ubuntu" and install a compiler `sudo apt update && sudo apt install gcc g++`
+    - Proceed with conda install and environment creation as described for Linux machines.
+    - If you do not want to use WSL, this is possible albeit more complicated. You need to have a working compiler (e.g. Visual Studio or [MSYS2](https://www.msys2.org/)). Once installed, along with conda you can create the python environment using `conda env create -f environment_windows_native.yml`. 
 - All the required dependencies are now installed. Finally, activate the environment and install by running inside the main folder
 
 ```

environment_windows_native.yml

@@ -0,0 +1,119 @@
+name: MARBLE
+channels:
+  - pytorch
+  - pyg
+  - defaults
+dependencies:
+  - blas=1.0=mkl
+  - bottleneck=1.3.5=py39h080aedc_0
+  - brotli=1.0.9=h2bbff1b_7
+  - brotli-bin=1.0.9=h2bbff1b_7
+  - brotlipy=0.7.0=py39h2bbff1b_1003
+  - ca-certificates=2023.08.22=haa95532_0
+  - certifi=2023.7.22=py39haa95532_0
+  - cffi=1.15.1=py39h2bbff1b_3
+  - charset-normalizer=2.0.4=pyhd3eb1b0_0
+  - colorama=0.4.6=py39haa95532_0
+  - contourpy=1.0.5=py39h59b6b97_0
+  - cryptography=41.0.3=py39h89fc84f_0
+  - cudatoolkit=11.3.1=h59b6b97_2
+  - cycler=0.11.0=pyhd3eb1b0_0
+  - fonttools=4.25.0=pyhd3eb1b0_0
+  - freetype=2.12.1=ha860e81_0
+  - giflib=5.2.1=h8cc25b3_3
+  - glib=2.69.1=h5dc1a3c_2
+  - icc_rt=2022.1.0=h6049295_2
+  - icu=58.2=ha925a31_3
+  - idna=3.4=py39haa95532_0
+  - importlib_resources=5.2.0=pyhd3eb1b0_1
+  - intel-openmp=2023.1.0=h59b6b97_46319
+  - jinja2=3.1.2=py39haa95532_0
+  - joblib=1.2.0=py39haa95532_0
+  - jpeg=9e=h2bbff1b_1
+  - kiwisolver=1.4.4=py39hd77b12b_0
+  - krb5=1.20.1=h5b6d351_0
+  - lerc=3.0=hd77b12b_0
+  - libbrotlicommon=1.0.9=h2bbff1b_7
+  - libbrotlidec=1.0.9=h2bbff1b_7
+  - libbrotlienc=1.0.9=h2bbff1b_7
+  - libclang=14.0.6=default_hb5a9fac_1
+  - libclang13=14.0.6=default_h8e68704_1
+  - libdeflate=1.17=h2bbff1b_1
+  - libffi=3.4.4=hd77b12b_0
+  - libiconv=1.16=h2bbff1b_2
+  - libpng=1.6.39=h8cc25b3_0
+  - libpq=12.15=h906ac69_1
+  - libtiff=4.5.1=hd77b12b_0
+  - libuv=1.44.2=h2bbff1b_0
+  - libwebp=1.3.2=hbc33d0d_0
+  - libwebp-base=1.3.2=h2bbff1b_0
+  - libxml2=2.10.4=h0ad7f3c_1
+  - libxslt=1.1.37=h2bbff1b_1
+  - lz4-c=1.9.4=h2bbff1b_0
+  - markupsafe=2.1.1=py39h2bbff1b_0
+  - matplotlib=3.7.2=py39haa95532_0
+  - matplotlib-base=3.7.2=py39h4ed8f06_0
+  - mkl=2023.1.0=h6b88ed4_46357
+  - mkl-service=2.4.0=py39h2bbff1b_1
+  - mkl_fft=1.3.8=py39h2bbff1b_0
+  - mkl_random=1.2.4=py39h59b6b97_0
+  - munkres=1.1.4=py_0
+  - networkx=3.1=py39haa95532_0
+  - numexpr=2.8.7=py39h2cd9be0_0
+  - numpy=1.26.0=py39h055cbcc_0
+  - numpy-base=1.26.0=py39h65a83cf_0
+  - openjpeg=2.4.0=h4fc8c34_0
+  - openssl=3.0.11=h2bbff1b_2
+  - packaging=23.1=py39haa95532_0
+  - pandas=2.1.1=py39h4ed8f06_0
+  - pcre=8.45=hd77b12b_0
+  - pillow=10.0.1=py39h045eedc_0
+  - pip=23.3=py39haa95532_0
+  - ply=3.11=py39haa95532_0
+  - pycparser=2.21=pyhd3eb1b0_0
+  - pyg=2.1.0=py39_torch_1.12.0_cu113
+  - pyopenssl=23.2.0=py39haa95532_0
+  - pyparsing=3.0.9=py39haa95532_0
+  - pyqt=5.15.7=py39hd77b12b_0
+  - pyqt5-sip=12.11.0=py39hd77b12b_0
+  - pysocks=1.7.1=py39haa95532_0
+  - python=3.9.18=h1aa4202_0
+  - python-dateutil=2.8.2=pyhd3eb1b0_0
+  - python-tzdata=2023.3=pyhd3eb1b0_0
+  - pytorch=1.12.1=py3.9_cuda11.3_cudnn8_0
+  - pytorch-cluster=1.6.0=py39_torch_1.12.0_cu113
+  - pytorch-mutex=1.0=cuda
+  - pytorch-scatter=2.0.9=py39_torch_1.12.0_cu113
+  - pytorch-sparse=0.6.15=py39_torch_1.12.0_cu113
+  - pytz=2023.3.post1=py39haa95532_0
+  - qt-main=5.15.2=h879a1e9_9
+  - qt-webengine=5.15.9=h5bd16bc_7
+  - qtwebkit=5.212=h2bbfb41_5
+  - requests=2.31.0=py39haa95532_0
+  - scikit-learn=1.3.0=py39h4ed8f06_0
+  - scipy=1.11.3=py39h309d312_0
+  - setuptools=68.0.0=py39haa95532_0
+  - sip=6.6.2=py39hd77b12b_0
+  - six=1.16.0=pyhd3eb1b0_1
+  - sqlite=3.41.2=h2bbff1b_0
+  - tbb=2021.8.0=h59b6b97_0
+  - threadpoolctl=2.2.0=pyh0d69192_0
+  - tk=8.6.12=h2bbff1b_0
+  - toml=0.10.2=pyhd3eb1b0_0
+  - torchaudio=0.12.1=py39_cu113
+  - torchvision=0.13.1=py39_cu113
+  - tornado=6.3.3=py39h2bbff1b_0
+  - tqdm=4.65.0=py39hd4e2768_0
+  - typing_extensions=4.7.1=py39haa95532_0
+  - tzdata=2023c=h04d1e81_0
+  - urllib3=1.26.16=py39haa95532_0
+  - vc=14.2=h21ff451_1
+  - vs2015_runtime=14.27.29016=h5e58377_2
+  - wheel=0.41.2=py39haa95532_0
+  - win_inet_pton=1.1.0=py39haa95532_0
+  - xz=5.4.2=h8cc25b3_0
+  - zipp=3.11.0=py39haa95532_0
+  - zlib=1.2.13=h8cc25b3_0
+  - zstd=1.5.5=hd43e919_0
+  - pip:
+      - teaspoon==1.3.1