mirror of https://github.com/abinit/abipy.git
129 lines
3.6 KiB
ReStructuredText
129 lines
3.6 KiB
ReStructuredText
.. _flows-howto:
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************
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Flows How-To
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************
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This is a list of FAQs about the AbiPy flows and the :ref:`abirun.py` script.
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Feel free to suggest new entries!
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.. important::
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The execution of the flows require the proper configuration of ``manager.yml`` and,
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optionally, ``scheduler.yml``.
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Please consult the documentation available via the abidoc.py script. See FAQ below.
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Suggestions:
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* Start with the examples available in examples/flows before embarking on large scale calculations.
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* Make sure the Abinit executable compiled on the machine can be executed both on the frontend
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and the compute node (ask your sysadmin)
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* If you are running on clusters in which the architecture of the compute node is completely different
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from the one available on the frontend, use ``shell_runner``
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* Use the ``debug`` command
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Do not:
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* Change manually the input files and the submission scripts
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* Submit jobs manually when the scheduler is running
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* Use a too small delay for the scheduler
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.. contents::
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:backlinks: top
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How to get all the TaskManager options
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--------------------------------------
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The :ref:`abidoc.py` script provides three commands to get the documentation
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for the options supported in ``manager.yml`` and ``scheduler.yml``.
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Use::
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abidoc.py manager
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to document all the options supported by |TaskManager| and::
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abidoc.py scheduler
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for the scheduler options.
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If your environment is properly configured, you should be able to get
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information about the Abinit version used by the AbiPy with::
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abidoc.py abibuild
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.. code-block:: bash
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Abinit Build Information:
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Abinit version: 8.7.2
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MPI: True, MPI-IO: True, OpenMP: False
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Netcdf: True
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Use --verbose for additional info
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.. important::
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Netcdf support must be activated in Abinit as AbiPy might use
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these files to extract data and/or fix runtime errors.
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At this point, you can try to run a small flow for testing purpose with::
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abicheck.py --with-flow
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How to limit the number of cores used by the scheduler
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------------------------------------------------------
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Add the following options to scheduler.yml
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.. code-block:: yaml
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# Limit on the number of jobs that can be present in the queue. (DEFAULT: 200)
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max_njobs_inqueue: 2
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# Maximum number of cores that can be used by the scheduler.
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max_ncores_used: 4
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How to reduce the number of files produced by the Flow
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------------------------------------------------------
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When running many calculations,
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Use ``prtwf -1`` to tell Abinit to produce the wavefunction file only
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if SCF cycle didn't converged so that AbiPy can reuse the file to restart the calculation.
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Note that it's possibile to use::
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flow.use_smartio()
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to activate this mode for all tasks that are not supposed to produce WFK files
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for their children.
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How to extend tasks/works with specialized code
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-----------------------------------------------
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Remember that pickle_ does not support classes defined inside scripts.
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If you need to subclass one of the AbiPy Tasks/Works/Flows, define the subclass
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in a separated python module and import the module inside your script.
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Kill a scheduler running in background
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--------------------------------------
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Use the official API::
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abirun.py FLOWDIR cancel
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to cancel all jobs of the flow that are in queue and kill the scheduler.
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Compare multiple output files
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-----------------------------
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The :ref:`abicomp.py` script
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Try to understand why a task failed
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-----------------------------------
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There are several reasons why a task could fail.
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Some of these reasons could be related to hardaware failure, disk quota,
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OS or resource manager errors.
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others are related to Abinit-specific errors.
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