add installation notes for CUDA 12.4, pyenv, and PyTorch; include useful links

.gitignore

@@ -1,5 +1,4 @@
 src/**/*.ini
-pypho
 
 # VSCode
 .vscode

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "pypho"]
+	path = pypho
+	url = git@gitlab.lrz.de:000000003B9B3E61/pypho.git

README.md

@@ -13,10 +13,19 @@ Full license text in LICENSE file
 
 # optical-regeneration
 
-This repo has about 7.5GB of datasets in it. The download will take a while.
+## Notes on cloning:
+
+- `pypho` is added as a submodule -> `--recurse-submodules`
+- This repo has about 7.5GB of datasets in it. The `git lfs fetch` step will take a while.
 
 ```bash
-git clone https://git.suuppl.dev/seppl/optical-regeneration.git
+apt install git-lfs
+# only necessary once per user account
+git lfs install
+
+git clone --recurse-submodules https://git.suuppl.dev/seppl/optical-regeneration.git && cd optical-regeneration
+git lfs fetch
+git lfs checkout
 ```
 
 ## License

notes/cuda-12-4-install.md

@@ -0,0 +1,74 @@
+# CUDA 12.4 Install
+
+> https://unknowndba.blogspot.com/2024/04/cuda-getting-started-on-wsl.html (@\_freddenis\_, 2024)
+
+```bash
+# get md5sums
+wget https://developer.download.nvidia.com/compute/cuda/12.4.1/docs/sidebar/md5sum.txt
+#
+# setup cuda apt repo
+wget https://developer.download.nvidia.com/compute/cuda/repos/wsl-ubuntu/x86_64/cuda-wsl-ubuntu.pin
+sudo mv cuda-wsl-ubuntu.pin /etc/apt/preferences.d/cuda-repository-pin-600
+#
+# download installer and check md5sum
+wget https://developer.download.nvidia.com/compute/cuda/12.4.1/local_installers/cuda-repo-wsl-ubuntu-12-4-local_12.4.1-1_amd64.deb
+md5sum --check --ignore-missing md5sum.txt
+#
+# try to install cuda (this will fail, but it puts the keyring file in the correct spot)
+sudo dpkg -i cuda-repo-wsl-ubuntu-12-4-local_12.4.1-1_amd64.deb
+#
+# copy cuda gpg keyring to keyrings 
+sudo cp /var/cuda-repo-wsl-ubuntu-12-4-local/cuda-*-keyring.gpg /usr/share/keyrings/
+#
+# install cuda (this time for real)
+sudo dpkg -i cuda-repo-wsl-ubuntu-12-4-local_12.4.1-1_amd64.deb
+#
+# install cuda-toolkit
+sudo apt update
+sudo apt install cuda-toolkit-12-4
+#
+# setup path
+# sudo apt install plocate
+locate nvcc
+# -> returns /usr/local/cuda-12.4
+# add these lines to your .profile (.zshrc, ...)
+#
+# export PATH="/usr/local/cuda-12.4/bin:$PATH"
+# export LD_LIBRARY_PATH="/usr/local/cuda-12.4/lib64:$LD_LIBRARY_PATH"
+#
+# after source-ing, check version of nvcc
+nvcc -V
+```
+
+## check cuda installation with cuda samples
+
+```bash
+git clone https://github.com/NVIDIA/cuda-samples
+cd cuda-samples/Samples/1_Utilities/deviceQuery
+make
+./devicequery
+```
+
+
+### if the cuda-toolkit install fails with unmet dependencies
+
+>https://askubuntu.com/a/1493087 (jspinella, 2023, CC BY-SA 4.0)
+
+1. Open the *new* file for storing the sources list
+
+    ```bash
+    sudo nano /etc/apt/sources.list.d/ubuntu.sources
+    ```
+
+2. Paste in the following at the end of the file: 
+
+    ```raw
+    Types: deb
+    URIs: http://archive.ubuntu.com/ubuntu/
+    Suites: lunar
+    Components: universe
+    Signed-By: /usr/share/keyrings/ubuntu-archive-keyring.gpg
+    ```
+
+3. Save the file and run `sudo apt update` - now the install command for CUDA should work.
+

notes/links.md

@@ -0,0 +1,4 @@
+# useful links
+
+- (Optuna)[https://optuna.org] Hyperparameter optimization framework
+  `pip install optuna`

notes/pyenv-install.md

@@ -0,0 +1,46 @@
+# pyenv install
+
+## install
+
+nice to have:
+
+```bash
+sudo apt install python-is-python3
+```
+
+```bash
+curl https://pyenv.run | bash
+```
+
+## setup zsh
+
+add the following to `.zshrc`:
+
+```bash
+export PYENV_ROOT="$HOME/.pyenv"
+[[ -d $PYENV_ROOT/bin ]] && export PATH="$PYENV_ROOT/bin:$PATH"
+eval "$(pyenv init -)"
+```
+
+## pyenv install
+
+prerequisites:
+
+```bash
+sudo apt update
+sudo apt install build-essential libssl-dev zlib1g-dev \
+libbz2-dev libreadline-dev libsqlite3-dev curl git \
+libncursesw5-dev xz-utils tk-dev libxml2-dev libxmlsec1-dev \
+libffi-dev liblzma-dev python3-pip
+```
+
+install:
+
+```bash
+# using python 3.12.7 as an example
+pyenv install 3.12.7
+
+# optional
+pyenv global 3.12.7
+pyenv versions
+```

notes/pytorch-install.md

@@ -0,0 +1,25 @@
+# pytorch install
+
+## create venv
+
+```bash
+python -m venv ./.venv
+source ./.venv/bin/activate
+```
+
+## install pytorch
+> https://pytorch.org/get-started/locally/
+
+```bash
+pip install torch torchvision torchaudio
+```
+
+## test pytorch install
+
+```python
+import torch
+x = torch.rand(5, 3)
+print(x)
+
+torch.cuda.is_available()
+```

src/single-core-regen/_path_fix.py

@@ -3,7 +3,7 @@ from pathlib import Path
 
 # hack to add the parent directory to the path -> pypho doesn't have to be installed as package
 parent_dir = Path(__file__).parent
-while not (parent_dir / "pypho").exists() and parent_dir != Path("/"):
+while not (parent_dir / "pypho" / "pypho").exists() and parent_dir != Path("/"):
     parent_dir = parent_dir.parent
-print(f"Adding '{parent_dir}' to 'sys.path' to enable import of '{parent_dir / 'pypho'}'")
+print(f"Adding '{parent_dir / "pypho"}' to 'sys.path' to enable import of '{parent_dir / 'pypho' / 'pypho'}'")
-sys.path.append(str(parent_dir))
+sys.path.append(str(parent_dir / "pypho"))

src/single-core-regen/generate_signal.py

@@ -387,7 +387,7 @@ def length_loop(config, lengths, incremental=False):
     in_out_eyes(cfiber, cdata)
 
 
-def single_run_with_plot(config):
+def single_run_with_plot(config, save=True):
     cfiber, cdata, noise, edfa = initialize_fiber_and_data(config)
 
     mean_power_in = np.sum(pypho.functions.getpower_W(cdata.E_in))
@@ -405,6 +405,7 @@ def single_run_with_plot(config):
     E_tmp = [{'E': cdata.E_out, 'noise': noise*(-cfiber.params.l*cfiber.params.alpha)}]
     E_tmp = edfa(E=E_tmp)
     cdata.E_out = E_tmp[0]['E']
+    if save:
         save_data(cdata, config)
 
     in_out_eyes(cfiber, cdata)
@@ -509,7 +510,7 @@ if __name__ == "__main__":
     ]
     lengths.append(max(length_ranges)*10)
 
-    length_loop(config, lengths)
+    # length_loop(config, lengths)
 
-    # single_run_with_plot(config)
+    single_run_with_plot(config, save=False)