Setup to install python / jupyter on BC4

Add this to .bashrc:

#This needs to be added at the end of .bashrc
module load lang/python/anaconda/3.7.7-2020-R-3.6.1
conda activate py37
cd /user/work/hb18661 #ADJUST USER NAME

In the console, run the following commands

source .bashrc
conda init bash
conda create -n py37 python=3.7
conda activate py37
pip install notebook
jupyter notebook password

Run jupyter notebook from the login node (not suitable for large calculations)

Content of file:

echo “jupyter is running on “$(hostname -i)
jupyter notebook –no-browser –ip=$(hostname -i) –port=XXXXXX

Please adjust port number (XXXXXX). I use my birthday e.g. 230289, please use a different number. Once jupyter is running, access the notebook using: localhost:51602 – or other source port as defined below – in a browser.

Run in putty:


You need to define a new port for each IP address in putty. See example snapshot:

Run jupyter notebook from a computation node (suitable for large calculations)

Submit new job, you need to open up a new port in Putty (as described above). The IP address of the new job is stored in IP_jupyter.IP.


Content of (adjust username and port number):

#SBATCH –partition short
#SBATCH –mem=1GB
#SBATCH –ntasks-per-node=1
#SBATCH –time=3-00:00:00
#SBATCH –nodes=1
#SBATCH –job-name=Jupyter
#SBATCH –output=output_jupyter

cd /user/home/hb18661/
source .bashrc
cd /user/work/hb18661/

echo “jupyter is running on “$(hostname -i) > IP_jupyter.IP
jupyter notebook –no-browser –ip=$(hostname -i) –port=XXXXXX

Packages that I typically need:

conda install -c ambermd pytraj