Posted in 2022

JupyterDash on Jupyterhub @ DKRZ

This content is based on this notebook.

The jupyter-dash package makes it easy to develop Plotly Dash apps from the Jupyter Notebook and JupyterLab.

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Changelog slk v3.3.67

Changes from slk v3.3.21 to v3.3.67

Changlog updated on 2022-10-21 (changes in slk chmod extended)

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How big are my files?

Our server luv shows you how much storage space your project is using and also how much each individual project member is contributing. For technical reasons, we can only show the apparent size (see below) of a user’s files. For the entire project, however, we show the actually occupied disk space. We are not happy about this inconsistency but for now, we have to live with it.

Here we try to explain the difference between the two ways to measure the size of files.

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Changelog slk_helpers v1.5.7

Update from slk_helpers v1.2.x to v1.5.7

Please have a look here for a detailed description of the new features and here for an incremental changelog.

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Can I get my compute time back?

Who wouldn’t want to use all of their node hours on Levante in the most productive way? After all, this is how we present our project in the proposal. Everything will go according to plan. What could go wrong? In fact, a lot, so can I get the time back in that case? Here is an incomplete list of things we often hear.

I found a bug in my model and now I have to run all experiments again.

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Using tmux for persistent ssh connections

Tmux allows you to keep a shell session active when closing your ssh connection. So, when you close your laptop to change a room, you don’t lose the current state of your command line tools. It has many more useful features. However, you need to remember the login node you used to start tmux, and X11 applications (e.g. ncview) will not survive the disconnect. emacs will survive in command line mode (module load emacs ; emacs -nw).

The following examples will assume that you have prescribed your user name and allowed (trusted) X11 forwarding for dkrz.de machines in your ~/.ssh/config

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Basemap on levante

Basemap has reached end-of-life and we won’t install basemap system wide (python 3 module) but you can easily install it into a personal conda environment like this

On Levante:

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API for Accounting Data

As a project admin or even as a normal project user you may look from time to time into accounting data for resources we provide (Levante, archive, etc.).

For each project you participate in, you can find a table on https://luv.dkrz.de like the one shown below. Usually you only see your own entries. Other user’s names are hidden.

utilization table

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How to build ICON on Levante

The current ICON release 2.6.4 has no setup for building and running on the new HPC system levante

There are multiple options to get an ICON binary and run it:

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Using Spyder on levante

The Python IDE Spyder is hidden in the python3 module and needs additional libraries from spack to start.

Load the missing libraries via spack and load python3 (which contains spyder):

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libGL.so.1 missing

2022-10-17: This problem should be fixed with our current software stack. The workaround is not required any longer.

When trying to start a gui application like gvim, you get an error message:

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Data Migration Mistral to Levante

So that not every user or every project has to copy its data from Mistral to Levante, DKRZ will take over this in a coordinated manner. In this way, the bandwidth between the systems can be better utilised.

We will only copy data located in /work - and only for projects that have resources granted on the Levante system.

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Bus error in jobs

Update: The problem was solved by an update of the Lustre-client by our storage vendor. The workaround described below should no longer be necessary. If you one of your jobs runs into a bus error, please let us know.

When running jobs on Levante, these sometimes fail with a Bus error, similar to the example below:

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DKRZ CDP Updates Feb 22

We proudly 🥳 announce that the CDP is extended by new sets of CMIP6 data primarily published at DKRZ.

The ensemble set of simulations from the ESM MPI-ESM1-2-LR is now completed with additional 130 Simulations. For each of the following experiments, 30 Simuluations form an ensemble of different realizations with varying initial conditions:

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