autosubmit-templates

Dummy project to use with autosubmit

Setup

The script setup.py installs autosubmit in a virtual environment and initializes autosubmit. It will create a folder called autosubmit in the home directory.

Create and run an autosubmit experiment

Once installed, to use autosubmit we have to activate the virtual environment. Check that autosubmit is usable with:

autosubmit -h

We can find how autosubmit works in the documentation.

However, we will reproduce some of the steps here:

To create a new experiment, we first need an experiment id. We can obtain that using the command:

autosubmit expid -H HPCname -d Description

In our case it could be something like:

autosubmit expid -H LMU -d "Running a first test example."

If everything works well we will obtain an output that looks like:

The new experiment "a000" has been registered.
Copying config files...
Experiment registered successfully

In this case a000 would be our experiment id.

Besides the expid itself, autosubmit will also create a new folder in the autosubmit folder.

💡 If we don't change the configuration the autosubmit folder will be ~/autosubmit

In this case it will be ~/autosubmit/a000/.

If we take a look in this folder we can see that there are few folders:

conf
plot
pkl
tmp

We are interested in the files inside conf.

💡 Look here for a more detailed explanation on what's in each file.

As we want to test how to get all the required information from a git project, we will modify the file expdef_xxxx.conf" to point to this very same repository. To do so we will go to section [project], set PROJCET_TYPE = git and under the [git] section we will set PROJECT_ORIGIN = git@gitlab.physik.uni-muenchen.de:Oriol.Tinto/autosubmit-templates.git.

Also, we need to modify the file platforms_xxxx.conf to add information about the platforms that we want to use.

In the case of using the LMU cluster our file would need the following content:

[LMU]
TYPE = SLURM
HOST = workstation
PROJECT = ls-craig
USER = oriol.tinto
SCRATCH_DIR = /project/meteo-scratch/Oriol.Tinto/tmp/autosubmit

autosubmit create a000 -np

⚠️ At the moment of writting this documentation autosubmit has a problem using Graphviz 2.40, to bypass this we use the flag -np to skip plot generation.

Troubleshooting

Scheduler not available

In our system sbatch is not available when using non-interactive shells. Like the one that you get with autosubmit. To solve that, we have to add this to .bashrc:

PATH=${PATH}:/opt/slurm/bin/

Current host is not allowed

In case of seeing this error:

 [CRITICAL] The current host is not allowed to run Autosubmit [eCode=7004]

We need to modify the file .autosubmitrc that can be found in our home directory and just comment the line with whitelist:

-whitelist =  localhost # Add your machine names
+# whitelist =  localhost # Add your machine names