General/Jupyternotebook

Introduction

The Jupyter Notebook is an interactive computing environment that enables users to author notebook documents that include: - Live code - Interactive widgets - Plots - Narrative text - Equations - Images - Video

Setting up

Interactive mode (GPU)

Below is the console output of using jupyter notebook in an interactive session

[pysdlb@login01 ~]$ interactive -pgpu
salloc: Granted job allocation 2216487
Job ID 2216487 connecting to gpu03, please wait...
Last login: Tue Jan 14 12:01:33 2020 from login01
[pysdlb@gpu03 ~]$ module load python/anaconda/4.6/miniconda/3.7
[pysdlb@gpu03 ~]$ conda create -n jupyter

Collecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /home/pysdlb/.conda/envs/jupyter



Proceed ([y]/n)? y

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
#
# To activate this environment, use
#
#     $ conda activate jupyter
#
# To deactivate an active environment, use
#
#     $ conda deactivate

[pysdlb@gpu03 ~]$ conda activate jupyter
(jupyter) [pysdlb@gpu03 ~]$ conda install -c anaconda jupyter
Collecting package metadata (current_repodata.json): done
Solving environment: done
......
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(jupyter) [pysdlb@gpu03 ~]$ conda install -c fastai fastai
Collecting package metadata (current_repodata.json): done
Solving environment: -
.....
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(jupyter) [pysdlb@gpu03 ~]$ conda install -c conda-forge nibabel
Collecting package metadata (current_repodata.json): done
Solving environment: done
.....
Preparing transaction: done
Verifying transaction: done
Executing transaction: done
(jupyter) [pysdlb@gpu03 ~]$ jupyter notebook
[I 13:33:59.573 NotebookApp] The port 8888 is already in use, trying another port.
[I 13:33:59.715 NotebookApp] Serving notebooks from local directory: /home/pysdlb
[I 13:33:59.715 NotebookApp] The Jupyter Notebook is running at:
[I 13:33:59.715 NotebookApp] http://localhost:8889/?token=50b345a31008ba2913678140c6aa4f85d0217bce6b1f83e5
[I 13:33:59.715 NotebookApp]  or http://127.0.0.1:8889/?token=50b345a31008ba2913678140c6aa4f85d0217bce6b1f83e5
[I 13:33:59.715 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 13:34:01.967 NotebookApp]

    To access the notebook, open this file in a browser:
        file:///home/pysdlb/.local/share/jupyter/runtime/nbserver-10504-open.html
    Or copy and paste one of these URLs:
        http://localhost:8889/?token=50b345a31008ba2913678140c6aa4f85d0217bce6b1f83e5
     or http://127.0.0.1:8889/?token=50b345a31008ba2913678140c6aa4f85d0217bce6b1f83e5
START /usr/bin/firefox "/home/pysdlb/.local/share/jupyter/runtime/nbserver-10504-open.html"

• Prepare SLURM batch script for jupyter notebook backend

CPU based

#!/bin/sh
#SBATCH -p compute
#SBATCH --ntasks=1
#SBATCH -t 04:00:00             # max runtime is 4 hours
#SBATCH -J ipy_server    # name
#SBATCH -o QQQ.out

let ipnport=($UID-6025)%65274
echo ipnport=$ipnport

ipnip=$(hostname -i)
echo ipnip=$ipnip

module purge
module load python/anaconda/4.6/miniconda/3.7

# Use virtual environment for python customization (change <user>)

source activate /home/user/.conda/envs/jupyter

export I_MPI_DEBUG=5
export I_MPI_FABRICS=shm:tmi
export I_MPI_FALLBACK=no

unset XDG_RUNTIME_DIR
jupyter notebook --ip=$ipnip --port=$ipnport --no-browser

This generates an output file with the URL required to connect to the jupyter notebook backend

ipnport=1487
ipnip=10.254.5.93
[I 09:53:13.302 NotebookApp] Serving notebooks from local directory: /home/pysdlb
[I 09:53:13.302 NotebookApp] 0 active kernels
[I 09:53:13.303 NotebookApp] The Jupyter Notebook is running at:
[I 09:53:13.303 NotebookApp] http://10.254.5.93:1487/?token=b71e38e053bd44e62ba340aff5a5b9b68c74cd0d0883d582
[I 09:53:13.303 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
[C 09:53:13.345 NotebookApp]

    Copy/paste this URL into your browser when you connect for the first time,
    to login with a token:
        http://10.254.5.93:1487/?token=b71e38e053bd44e62ba340aff5a5b9b68c74cd0d0883d582
[I 09:55:58.597 NotebookApp] 302 GET /?token=b71e38e053bd44e62ba340aff5a5b9b68c74cd0d0883d582 (10.254.5.247) 3.56ms

• Going to a browser on visualisation nodes or at time of writing login02.hpc.hull.ac.uk

 $ firefox  http://10.254.5.93:1487/?token=b71e38e053bd44e62ba340aff5a5b9b68c74cd0d0883d582

• It should be possible to combine these two steps into one script

GPU Configuration

• the SLURM batch script would slightly different

#!/bin/sh
#SBATCH --ntasks=1
#SBATCH -t 04:00:00             # max runtime is 4 hours
#SBATCH -J ipy_server    # name
#SBATCH -o QQQ.out
#SBATCH --gres=gpu          # use the GPU resource not the CPU
#SBATCH -p gpu              # Slurm partition, where you want the job to be queued 

let ipnport=($UID-6025)%65274
echo ipnport=$ipnport

ipnip=$(hostname -i)
echo ipnip=$ipnip

module purge
module load python/anaconda/4.6/miniconda/3.7

# Use virtual environment for python customization (change <user>)

source activate /home/user/.conda/envs/jupyter

export I_MPI_DEBUG=5
export I_MPI_FABRICS=shm:tmi
export I_MPI_FALLBACK=no

unset XDG_RUNTIME_DIR
jupyter notebook --ip=$ipnip --port=$ipnport --no-browser

• Get Python to detect GPU Correctly (within Tensorflow here)

sess = tf.Session(config=tf.ConfigProto(log_device_placement=True))

Using jupyter configuration file

Jupyter notebook can be run using a configuration file to ease the number of command line option needed.

Defaults for these options can also be set by creating a file named jupyter_notebook_config.py in your Jupyter folder. The Jupyter folder is in your home directory, ~/.jupyter.

To create a jupyter_notebook_config.py file, with all the defaults commented out, you can use the following command line:

$ jupyter notebook --generate-config

Then for example add/modify the following lines to allow connection from any host, set a default port (5050 in this example), tell Jupyter not to try to open a browser, and set a default password.

c.NotebookApp.ip = '*'
c.NotebookApp.port = 5050
c.NotebookApp.open_browser = False
c.NotebookApp.password = u'sha1:a1d634eb9a3c:fa1e22d81b2b456be67d3b59810c335b33c223134'

To get your password you can use the following in python:

In [1]: from notebook.auth import passwd
In [2]: passwd()
Enter password:
Verify password:
Out[2]: 'sha1:a1d634eb9a3c:fa1e22d81b2b456be67d3b59810c335b33c223134'

Resources

• Anaconda python
• Jupyter notebook
• Jupyter viewer

Other Links

• Main page

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