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improve slurm instruction
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ilkilic committed Oct 12, 2023
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5 changes: 3 additions & 2 deletions examples/emodel_pipeline_local_python/README.rst
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Expand Up @@ -239,15 +239,16 @@ The ``githash`` provided by this operation will uniquely characterize the run, a
Running the different steps
~~~~~~~~~~~~~~~~~~~~~~~~~~~

We provide Auxiliary scripts specifically designed to facilitate the execution of various pipeline stages on Slurm. These scripts are ``./extract.sh``, ``./optimisation.sh`` and ``./analysis.sh``. Each of these scripts can be run by the command line:
Refer to the local counteract for the configuration of the recipes and targets files.

To facilitate the execution of the different steps of the pipeline on Slurm, we provide the following auxiliary scripts that can be executed in the following order:

.. code-block:: shell
./extract.sh
./optimisation.sh
./analysis.sh
Make sure to configure the necessary variables within these scripts, including setting the ``OPT_EMODEL`` value as well as configuring their sbatch counterpart by setting the #SBATCH directives according to your job requirements.

These scripts will also generates logs of the different steps for each run to track its progress and capture any issues that may arise during execution. These log files are stored in the ``./logs`` with a naming convention reflective of the operation and its corresponding job identifier (e.g., ``opt_jobid.log``). In addition to individual log files, each step maintains its own historical record (e.g., ``extract_list.log``, ``opt_list.log`` ``analyse_list.log``) . These files are also situated within the ``./logs`` directory, serving as cumulative logs that document the series of runs pertinent to that particular step. Please ensure to check these logs if you encounter issues during the pipeline execution.
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