Jupyter

Note

Quick link

Triton’s JupyterHub is available at https://jupyter.triton.aalto.fi.

Note

For new users

Are you new to Triton and want to access JupyterHub? Triton is a high-performance computing cluster, and JupyterHub is just one of our services - one of the easiest ways to get started. You still need a Triton account. This site has many instructions, but you should read at least:

If you want to use Triton more, you should finish the entire tutorials section.

alternate text

< Triton JupyterHub Demo >

Jupyter notebooks are a way of interactive, web-based computing: instead of either scripts or interactive shells, the notebooks allow you to see a whole script + output and experiment interactively and visually. They are good for developing and testing things, but once things work and you need to scale up, it is best to put your code into proper programs (more info). You must do this if you are going to large parallel computing.

Triton’s JupyterHub is available at https://jupyter.triton.aalto.fi. You can try them online at try.jupyter.org (there is a temporary notebook with no saving).

You can always run notebooks yourself on your own (or remote) computers, but on Triton we have some facilities already set up to make it easier.

How Jupyter notebooks work

  • Start a notebook

  • Enter some code into a cell.

  • Run it with the buttons or Control-enter or Shift-enter to run a cell.

  • Edit/create new cells, run again. Repeat indefinitely.

  • You have a visual history of what you have run, with code and results nicely interspersed. With certain languages such as Python, you can plots and other things embedded, so that it becomes a complete reproducible story.

JupyterLab is the next iteration of this and has many more features, making it closer to an IDE or RStudio.

Notebooks are without a doubt a great tool. However, they are only one tool, and you need to know their limitations. See our other page on limitations of notebooks.

JupyterHub

Note

JupyterHub on Triton is still under development, and features will be added as they are needed or requested. Please use the Triton issue tracker.

The easiest way of using Jupyter is through JupyterHub - it is a multi-user jupyter server which takes a web-based login and spawns your own single-user server. This is available on Triton.

Connecting and starting

Currently jupyterHub is available only within Aalto networks, or from the rest of the internet after a first Aalto login: https://jupyter.triton.aalto.fi.

Once you log in, you must start your single-user server. There are several options available that trade off between long run time and short run time but more memory available. Your server runs in the Slurm queue, so the first start-up takes a few seconds but after that it will stay running even if you log out. The resources you request are managed by slurm: if you go over the memory limit, your server will be killed without warning or notification (but you can see it in the output log, ~/'jupyterhub_slurmspawner_*.log). The Jupyter server nodes are oversubscribed, which means that we can allocate more memory and CPU than is actually available. We will monitor the nodes to try to ensure that there are enough resources available, so do report problems to us. Please request the minimum amount of memory you think you need - you can always restart with more memory. You can go over your memory request a little bit before you get problems.

When you use Jupyter via this interface, the slurm billing weights are lower, so that the rest of your Triton priority does not decrease by as much.

Usage

Once you get to your single-user server Jupyter running as your own user on Triton. You begin in a convenience directory which has links to home, scratch, etc. You can not make files in this directory (it is read-only), but you can navigate to the other folders to create your notebooks. You have access to all the Triton filesystems (not project/archive) and all normal software.

We have some basic extensions installed:

  • Jupyterlab (to use it, change /tree in the URL to /lab). Jupyterlab will eventually be made the default.

  • modules integration

  • jupyter_contrib_nbextensions - check out the variable inspector

  • diff and merge tools (currently does not work somehow)

The log files for your single-user servers can be found in, see ~/jupyterhub_slurmspawner_*.log. When a new server starts, these are automatically cleaned up when they are one week old.

For reasons of web security, you can’t install your own extensions (but you can install your own kernels). Send your requests to us instead.

Problems? Requests?

This service is currently in beta and under active development. If you notice problems or would like any more extensions or features, let us know. If this is useful to you, please let us know your user store, too. In the current development stage, the threshold for feedback should be very low.

Currently, the service level is best effort. The service may go down at any time and/or notebooks may be killed whenever there is a shortage of resources or need of maintenance. However, notebooks auto-save and do survive service restarts, and we will try to avoid killing things unnecessarily.

Software and kernels

A Jupyter Kernel is the runtime which actually executes the code in the notebook (and it is separate from JupyterHub/Jupyter itself). We have various kernels automatically installed (these instructions should apply to both JupyterHub and sjupyter):

  • Python (2 and 3 via some recent anaconda modules + a few more Python modules.)

  • Matlab (latest module)

  • Bash kernel

  • R (a default R environment you can get by module load r-triton. (“R (safe)” is similar but tries to block some local user configuration which sometimes breaks things, see FAQ for more hints.)

  • We do not yet have a kernel management policy. Kernels may be added or removed over time. We would like to keep them synced with the most common Triton modules, but it will take some time to get this automatic. Send requests and problem reports.

Since these are the normal Triton modules, you can submit installation requests for software in these so that it is automatically available.

What’s a kernel? Where are they?

As stated at the start of this section, the kernel is what actually runs the code. An example of a kernel command line is 'python -m ipykernel_launcher -f{connection_file}. What python starts?: that depends on the environment or adding an absolute path.

You can list your installed kernels with jupyter kernelspec list (to ensure the list is the same as jupyter.triton sees, module load jupyterhub/live first). Look in these directories, at kernel.json, to see just what it does.

You can remove kernels by removing their directory or jupyter kernelspec remove.

The program envkernel can serve as a wrapper to a) modify kernel.json files and b) adjust the environment (e.g. loading modules) at runtime, which can be hard to fully emulate by statically defining environment variables in kernel.json.

Installing kernels from virtualenvs or Anaconda environments

If you want to use Jupyter with your own packages, you can do that. First, make a conda environment / virtual environment on Triton and install the software you need in it (see Anaconda and conda environments or Python: virtualenv). This environment can be used for other things, such as your own development outside of Jupyter.

You have to have the package ipykernel installed in the environment: Add it to your requirements/environment, or activate the environment and do pip install ipykernel.

Then, you need to make the environment visible inside of Jupyter. For conda environments, you can do:

module load jupyterhub/live
envkernel conda --user --name INTERNAL_NAME --display-name="My conda" /path/to/conda_env

Or for Python virtualenvs:

module load jupyterhub/live
envkernel virtualenv --user --name INTERNAL_NAME --display-name="My virtualenv" /path/to/virtualenv

Installing a different R module as a kernel

Load your R modules, install R kernel normally (to some NAME), use envkernel as a wrapper to re-write the kernel (reading the NAME and rewriting to the same NAME), after it loads the modules you need:

# Load jupyterhub/live, and R 3.6.1 with IRkernel.
module load r-irkernel/1.1-python3
module load jupyterhub/live

# Use Rscript to install jupyter kernel
Rscript -e "library(IRkernel); IRkernel::installspec(name='NAME', displayname='R 3.6.1')"

# Use envkernel to re-write, loading the R modules.
envkernel lmod --user --kernel-template=NAME --name=NAME r-irkernel/1.1-python3

Installing a different R version as a kernel

There are two ways to install a different R version kernel for jupyter. One relies on you building your own conda environment. The disadvantage is that you will need to create a kernel, the advantage is that you can add additional packages. The other option is to use the existing R installations on Triton.

You will need to create your own conda environment with all packages that are necessary to deploy the environment as a kernel.:

# Load and miniconda before creating your environment - this provides mamba that is used to create your environment
module load miniconda

Create your conda environment, selecting a NAME for the environment.:

# This will use the latest R version on conda-forge. If you need a specific version you can specify it
# as r-essentials=X.X.X, where X.X.X is your required R version number
mamba create -n NAME -c conda-forge r-essentials r-irkernel
# If Mamba doesn't work you can also replace it with conda, but usually mamba is a lot faster

The next steps are the same as building a Kernel, except for activating the environment instead of loading the r-irkernel module, since this module depends on the R version. the displayname will be what will be displayed on jupyter

# Use Rscript to install jupyter kernel, you need the environment for this.
# You need the Python `jupyter` command so R can know the right place to
# install the kernel (provided by jupyterhub/live)
module load jupyterhub/live
source activate NAME
Rscript -e "library(IRkernel); IRkernel::installspec(name='NAME', displayname='YOUR R Version')"
conda deactivate NAME

# For R versions before 4, you need to install the kernel. After version 4 IRkernel automatically installs it.
envkernel lmod --user --kernel-template=NAME --name=NAME

Note

Installing R packages for jupyter

Installing packages via jupyter can be problematic, as they require interactivity, which jupyter does not readily support. To install packages therefore go directly to triton. Load the environment or R module you use and install the packages ineractively. After that is done, restart your jupyter session and reload your kernel, all packages that you installed should then be available.

Install your own kernels from other Python modules

This works if the module provides the command python and ipykernel is installed. This has to be done once in any Triton shell:

module load jupyterhub/live
envkernel lmod --user --name INTERNAL_NAME --display-name="Python from my module" MODULE_NAME
module purge

Install your own kernels from Singularity image

First, find the .simg file name. If you are using this from one of the Triton modules, you can use module show MODULE_NAME and look for SING_IMAGE in the output.

Then, install a kernel for your own user using envkernel. This has to be done once in any Triton shell:

module load jupyterhub/live
envkernel singularity --user --name KERNEL_NAME --display-name="Singularity my kernel" SIMG_IMAGE
module purge

As with the above, the image has to provide a python command and have ipykernel installed (assuming you want to use Python, other kernels have different requirements).

Julia

Julia: currently doesn’t seem to play nicely with global installations (so we can’t install it for you, if anyone knows something otherwise, let us know). Roughly, these steps should work to install the kernel yourself:

module load julia
module load jupyterhub/live
julia

julia> Pkg.add("IJulia")

If this doesn’t work, it may think it is already installed. Force it with this:

julia> using IJulia
julia> installkernel("julia")

Install your own non-Python kernels

  • First, module load jupyterhub/live. This loads the anaconda environment which contains all the server code and configuration. (This step may not be needed for all kernels)

  • Follow the instructions you find for your kernel. You may need to specify --user or some such to have it install in your user directory.

  • You can check your own kernels in ~/.local/share/jupyter/kernels/.

If your kernel involves loading a module, you can either a) load the modules within the notebook server (“softwares” tab in the menu), or b) update your kernel.json to include the required environment variables (see kernelspec). (We need to do some work to figure out just how this works). Check /share/apps/jupyterhub/live/miniconda/share/jupyter/kernels/ir/kernel.json for an example of a kernel that loads a module first.

From Jupyter notebooks to running on the queue

While jupyter is great to interactively run code, it can become a problem if you need to run multiple parameter sets through a jupyter notebook or you need a specific resource which is not available for jupyter. The latter might be because the resource is sparse enough that having an open jupyter session that finished a part and is waiting for the user to start the next is idly blocking the resource. At this point you will likely want to move your code to pure python and run it via the queue.

Here are the steps necessary to do so:

  1. Log into Triton via ssh ( Tutorials can be found here and here ).

  2. In the resulting terminal session, load the jupyterhub module to have jupyter available ( module load jupyterhub )

  3. Navigate to the folder where your jupyter notebooks are located. You can see the path by moving your mouse over the files tab on jupyterlab.

  4. Convert the notebook(s) you want to run on the cluster ( jupyter nbconvert yourScriptName.ipynb --to python).

    • If you need to run your code for multiple different parameters, modify the python code to allow input parameter parsing (e.g. using argparse, or docopt ) You should include both input and output arguments as you want to save files to different result folders or have them have indicative filenames. There are two main reasons for this approach: A) it makes your code more maintainable, since you don’t need to modify the code when changing parameters and B) you are less likely to use the wrong version of your code (and thus getting the wrong results).

  5. (Optional) Set up a conda environment. This is mainly necessary if you have multiple conda or pip installable packages that are required for your job and which are not part of the normal anaconda module. Try it via module load anaconda. You can’t install into the anaconda environment provided by the anaconda module and you should NOT use pip install --user as it will bite you later (and can cause difficult to debug problems). If you need to set up your own environment follow this guide

  6. Set up a slurm batch script in a file e.g. simple_python_gpu.sh. You can do this either with nano simple_python_gpu.sh (to save the file press ctrl+x, type y to save the file and press Enter to accept the file name), or you can mount the triton file system and use your favorite editor, for guides on how to mount the file system have a look here and here). Depending on your OS, it might be difficult to mount home and it is anyways best practice to use /scratch/work/<username> for your code. Here is an example:

    #!/bin/bash
#SBATCH --cpus-per-task 1       # The number of CPUs your code can use, if in doubt, use 1 for CPU only code or 6 if you run on GPUs (since code running on GPUs commonly allows parallelization of data provision to the GPU)
#SBATCH --mem 10G               # The amount of memory you expect your code to need. Format is 10G for 10 Gigabyte, 500M for 500 Megabyte etc
#SBATCH --time=01:00:00         # Time in HH:MM:SS or DD-HH of your job. the maximum is 120 hours or 5 days.
#SBATCH --gres=gpu:1            # Additional specific ressources can be requested via gres. Mainly used for requesting GPUs format is: gres=RessourceType:Number
module load anaconda            # or module load miniconda if you use your own environment.
source activate yourEnvironment # if you use your own environment
python yourScriptName.py ARG

    This is a minimalistic example. If you have parameter sets that you want to use have a look at array jobs here)

  7. Submit your batch script to the queue : sbatch simple_python_gpu.sh This call will print a message like: Submitted batch job <jobid> You can use e.g. slurm q to see your current jobs and their status in the queue, or monitor your jobs as described here.

Git integration

You can enable git integration on Triton by using the following lines from inside a git repository. (This is normal nbdime, but uses the centrally installed one so that you don’t have to load a particular conda environment first. The sed command fixes relative paths to absolute paths, so that you use the tools no matter what modules you have loaded):

/share/apps/jupyterhub/live/miniconda/bin/nbdime config-git --enable
sed --in-place -r 's@(= )[ a-z/-]*(git-nb)@\1/share/apps/jupyterhub/live/miniconda/bin/\2@' .git/config

FAQ/common problems

  • Jupyterhub won’t spawn my server: “Error: HTTP 500: Internal Server Error (Spawner failed to start [status=1].”. Is your home directory quota exceeded? If that’s not it, check the ~/jupyterhub_slurmspawner_* logs then contact us.

  • My server has died mysteriously. This may happen if resource usage becomes too much and exceed the limits - Slurm will kill your notebook. You can check the ~/jupyterhub_slurmspawner_* log files for jupyterhub to be sure.

  • My server seems inaccessible / I can’t get to the control panel to restart my server. Especially with JupyterLab. In JupyterLab, use File→Hub Control Panel. If you can’t get there, you can change the URL to /hub/home.

  • My R kernel keeps dying. Some people seem to have global R configuration, either in .bashrc or .Renviron or some such which globally, which even affects the R kernel here. Things we have seen: pre-loading modules in .bashrc which conflict with the kernel R module; changing RLIBS in .Renviron. You can either (temporarily or permanently) remove these changes, or you could install your own R kernel. If you install your own, it is up to you to maintain it (and remember that you installed it).

  • “Spawner pending” when you try to start - this is hopefully fixed in issue #1534/#1533 in JupyterHub. Current recommendation: wait a bit and return to JupyterHub home page and see if the server has started. Don’t click the button twice!

See also

Our configuration is available on Github. Theoretically, all the pieces are here but it is not yet documented well and not yet generalizable. The Ansible role is a good start but the jupyterhub config and setup is hackish.