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hestia_cloud_setup.md

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Steps to configure a jupyter notebook server on Hestia

  1. login to hestia

  2. I created a shell script to simplify installation of miniconda. cp /home/kamran/Dropbox/install_miniconda.sh .

  3. Make sure it is executable. chmod +x install_miniconda.sh

  4. Run the script ./install_miniconda.sh or bash install_miniconda.sh

  5. Make sure your .bashrc has a line that points to miniconda python vi .bashrc add this line export PATH="/home/$your_account$/miniconda/bin:$PATH" source .bashrc

  6. Confirm that your python distribution is indeed the one from miniconda python The header should say Anaconda python 3.6

  7. Now we add some useful python packages/libraries. First we add the channels that contains these packages.

conda config --add channels conda-forge
conda config --add channels omnia
conda install numpy scipy pandas scikit-learn matplotlib jupyter mdtraj parmed
  1. Let's also install pymcce
conda install pymcce -c kam_haider
  1. Finally, let's set up a jupyter notebook server that we can use to interact with our files on hestia and create analysis scripts for our data. We have to use different ports for every user
jupyter notebook --no-browser --port=8889
  1. On your local machine, create an ssh tunnel that links localhost on hestia to your localhost.
ssh -N -L localhost:8888:localhost:8889 kamran@hestia