Posts tagged jupyterhub

SLURM update / Memory use

Slurm config on Mistral has been updated to fix an issue related to memory use.

Prior the update, some Slurm jobs continue consuming the available memory (and even swap) of the allocated node and exceed the allocated memory (set in sbatch or srun). If this occurs, it also affect other jobs/users.

error message

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Dask jobqueue on Mistral

According to the official Web site, Dask jobqueue can be used to deploy deploy Dask on job queuing systems like PBS, Slurm, MOAB, SGE, LSF, and HTCondor. Since the queuing system on Mistral is Slurm, we are going to show how to start a Dask cluster there. The idea is simple as described here. The difference is that the workers can be distributed through multiple nodes from the same partition. Using Dask jobqueue will Dask cluster as a Slurm jobs.

In this case, Jupyterhub will often play an interface role and the Dask can use more than the allocated resources to your jupyterhub session (profiles).

Dask jobqueue

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Jupyter notebook/lab extensions

Extensions bring additional interesting features to Jupyter*. Depending on the workflow in the notebook, users can install/enable extensions when required. Although is easy to add extensions to both Jupyter notebook an lab, the process can be sometimes annoying based on where jupyter is served from.

In general, installing and enabling extensions in your laptop or using the start-jupyter script is straightforward, especially when the developers well describe their extensions. There should be no restrictions or permissions issues, just follow the instructions.

Extensions configurator

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Enable NCL Kernel in Jupyterhub

can’t use NCL (Python) as kernel in Jupyter

This tutorial won’t work

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Spawner options now savable

We introduced a new feature to the preset and advanced options form. This is a nice feature especially for the advanced options form, which contain many fields. You can also reset the options to their initial values by clicking on reset. The form options are saved in the client’s browser every 10 seconds and are not lost if:

the browser crashes

../../_images/options_saved.gif

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Connection error in your code?

Connection Error

DownloadWarning

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Jupyterhub log file

Each Jupyter notebook is running as a SLUM job on MIstral. By default, stdout and stderr of the SLURM batch job that is spawned by Jupyterhub is written to your HOME directory on the HPC system. In order to make it simple to locate the log file:

if you use the preset options form: the log file is named jupyterhub_slurmspawner_preset_<id>.log.

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Simple Dask clusters in Jupyterhub

There are multiple ways to create a dask cluster, the following is only an example. Please consult the official documentation. The Dask library is installed and can be found in any of the python3 kernels in jupyterhub. Of course, you can use your own python environment.

The simplest way to create a Dask cluster is to use the distributed module:

Dask Labextension

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