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Comment: jupyterhub mentioned for ECMWF staff

cintYou You may use the ecinteractive tool to open interactive sessions with dedicated resources on the HPCF.

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However, note that they will be time constrained and once the job has reached it's time limit they will be closed.

Table of Contents
maxLevel3

Main Features

The main features of this ecinteractive tool are the following:

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No Format
$ ecinteractive -h

Usage :  /usr/local/bin/ecinteractive [options] [--]

    -d|desktop     Submits a vnc job (default is interactive ssh job)
    -j|jupyter     Submits a jupyter job (default is interactive ssh job) 
    -J|jupyters    Submits a jupyter job with HTTPS support (default is interactive ssh job)

    More Options:
    -h|help        Display this message
    -v|version     Display script version
    -p|platform    Platform (default aa. Choices: aa, ab, ac, ad, ecs)
    -u|user        ECMWF User (default user)
    -A|account     Project account
    -c|cpus        Number of CPUs (default 2)
    -m|memory      Requested Memory (default 8G)
    -s|tmpdirsize  Requested TMPDIR size (default 3 GB)
    -t|time        Wall clock limit (default 0612:00:00)
    -k|kill        Cancel any running interactive job
    -q|query       Check running job
    -Q|quiet       Silent mode
    -o|output      Output file for the interactive job (default /dev/null)
    -x             set -x

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Excerpt

Opening a Jupyter Lab instance

Show If
groupecmwf


Tip
titleJupyterHub Service

You may find it more convenient to use ECMWF's Jupyterhub instead of ecinteractive to run Jupyter on HPCF or ECS. Only your browser is required to access this service.


You can use ecinteractive to open up a Jupyter Lab instance on the HPCFYou can use ecinteractive to open up a Jupyter Lab instance on the HPCF.  The application would effectively run on the allocated node for the job, and would allow you to conveniently interact with it from your browser. When running from VDI or your end user device, ecinteractive will try to open it in a new tab automatically. Alternatively you may manually open the URL provided to connect to your Jupyter Lab session.

No Format
[user@aa6-100 ~]$ ecinteractive -j
Using interactive job:
CLUSTER JOBID       STATE       EXEC_HOST  TIME_LIMIT  TIME_LEFT MAX_CPUS MIN_MEMORY TRES_PER_NODE
aa      10225277    RUNNING     aa6-104       6:00:00    5:58:07        2         8G     ssdtmp:3G

To cancel the job:         
        /usr/local/bin/ecinteractive -k

Attaching to Jupyterlab session...
To manually re-attach go to http://aa6-104.ecmwf.int:33698/?token=b1624da17308654986b1fd66ef82b9274401ea8982f3b747

To use your own conda environment as a kernel for Jupyter notebook you will need to have ipykernel installed in the conda environment before starting ecinteractive job. ipykernel can be installed with:

No Format
[user@aa6-100 ~]$ conda activate {myEnv}
[user@aa6-100 ~]$ conda install ipykernel
[user@aa6-100 ~]$ python3 -m ipykernel install --user --name={myEnv}

The same is true if you want to make your own Python virtual environment visible in Jupyterlab

No Format
[user@aa6-100 ~]$ source {myEnv}/bin/activate
[user@aa6-100 ~]$ pip3 install ipykernel
[user@aa6-100 ~]$ python3 -m ipykernel install --user --name={myEnv}

To remove your personal kernels from Jupyterlab once you don't need them anymore, you could do so with:

No Format
jupyter kernelspec uninstall {myEnv}


Expand
titleHow to connect to the Jupiter Lab instance from web browser on your end user device
  • Authenticate with Teleport using jump.ecmwf.int as described in the  Teleport SSH Access page

  • Copy ecinteractive script from hpc to your local machine:

    Code Block
    languagebash
    scp username@hpc-login:/usr/local/bin/ecinteractive .


  • Run ecinteractive script on your local machine:

    Code Block
    languagebash
    ./ecinteractive -u username -j

    "-u" should be used to provide ECMWF username if username on your local machine doesn't match username on the Atos HPC.

  • The ecinteractive job will start, new tab will automatically open on your web browser and attach to the Jupyter server running on the HPC. If not, you will get a link which can be used on your local machine only to paste it manually into the web browser. It should look like this:

    http://localhost:.....

  • To kill your ecinteractive job from the local machine use:

    Code Block
    languagebash
    ./ecinteractive -p hpc -k -u username


HTTPS access

If you wish to run Juptyer Lab on HTTPS instead of plain HTTP, you may use the -J option in ecinteractive. In that case, a personal SSL certificate would be created under ~/.ssl the first time, and would be used to encrypt the HTTP traffic between your browser and the compute node.

In order to avoid browser security warnings, you may fetch the ~/.ssl/selfCA.crt certificate from the HPCF and import it into your browser as a trusted Certificate Authority. This is only needed once.

Customising your jupyter version and environment

By default, ecinteractive will start the jupyterlab coming from the default version of python 3. If you wish to customise the version of python or jupyterlab, or simply want to tailor its environment in your ecinteractive session, create the following file in your Atos HPCF HOME:

No Format
~/.ecinteractive/jupyter_setup.sh

Then add in it the commands needed to set up the environment so that the jupyter and node commands can be found in the path. This would be equivalent to the default behaviour:

No Format
module load python3 node

Examples of contents for ~/.ecinteractive/jupyter_setup.sh

Code Block
languagebash
titleUsing the newest Python
module load python3/new node/new


Code Block
languagebash
titleUsing jupyter from a custom conda environment
module load conda
conda activate myjupyterenv