From 270cbc8c09d1155bf48ecd162891b0d0601fb434 Mon Sep 17 00:00:00 2001 From: "MARDA Science: Analytics" <53406404+MARDAScience@users.noreply.github.com> Date: Sat, 21 Sep 2019 18:23:59 -0700 Subject: [PATCH] Update README.md --- README.md | 51 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 51 insertions(+) diff --git a/README.md b/README.md index 84352bf..0752de5 100644 --- a/README.md +++ b/README.md @@ -133,6 +133,57 @@ and python sedinet_predict_continuous.py -c config_sievedsand_sieve_plus.json ``` + +-------------------------------------------------------------------------------- +## Fork this repo and run on Google Cloud Platform (GCP) + +First, follow instructions [here](https://tudip.com/blog-post/run-jupyter-notebook-on-google-cloud-platform/) for how to set up an instance to run in GCP. Make sure to set a static IP address, as per the instructions, and make a note of that because you'll need it later + +Then open a shell into the VM and set it up to + +``` +ssh-keygen -t rsa -b 4096 -C "yourname@youremail.com" + +eval "$(ssh-agent -s)" + +ssh-add ~/.ssh/id_rsa + +cat ~/.ssh/id_rsa.pub +``` + +Then copy the key into your github profile keys. For more information about how to do that, see [here](https://help.github.com/en/articles/adding-a-new-ssh-key-to-your-github-account). xclip likely won't work, but you can simply copy (Ctrl-C) the text printed to screen + + +You will be cloning your fork of the main repo, so replace ```YOURUSERNAME``` in the below code to clone the repo and set up a conda environment to run in + +``` +git clone --depth 1 git@github.com:YOURUSERNAME/SediNet.git +cd SediNet + +pip install --upgrade pip + +conda env create -f conda_env/sedinet.yml + +source activate sedinet +``` + +Now you can run sedinet on the cloud. + +To run the jupyter notebooks, run the following command to run the jupyter notebook server + +``` +jupyter notebook --NotebookApp.iopub_data_rate_limit=10000000 +``` + +The jupyterlab server will be displayed at + +``` +http://IP:8888 +``` + +where ```IP``` is the static IP of the VM that you noted earlier. + + -------------------------------------------------------------------------------- ## Install and run on your computer You must have python 3, pip for python 3, git and conda. On Windows I recommend the latest [Anaconda](https://www.anaconda.com/distribution/) release. On Linux, git should come as standard and miniconda would be the way to go. Personally, I don't use conda but system builds (deb, yum, apt) within a virtual environment, but either way a VM of some description to contain SediNet would be a good idea. Mac users: ?