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add chainslurm links
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zingale committed Sep 17, 2023
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2 changes: 1 addition & 1 deletion sphinx_docs/source/conf.py
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Expand Up @@ -76,7 +76,7 @@
#
# This is also used if you do content translation via gettext catalogs.
# Usually you set "language" from the command line for these cases.
language = None
language = "en"

# List of patterns, relative to source directory, that match files and
# directories to ignore when looking for source files.
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2 changes: 1 addition & 1 deletion sphinx_docs/source/nersc-workflow.rst
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Expand Up @@ -67,7 +67,7 @@ Chaining
^^^^^^^^

To chain jobs, such that one queues up after the previous job
finished, use the ``chainslurm.sh`` script in that same directory:
finished, use the `chainslurm.sh <https://github.com/AMReX-Astro/workflow/blob/main/job_scripts/slurm/chainslurm.sh>`_ script in that same directory:

.. prompt:: bash

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15 changes: 9 additions & 6 deletions sphinx_docs/source/olcf-workflow.rst
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Expand Up @@ -179,12 +179,15 @@ from the 480 resources available, 398 resources will remain idle until the two w
Writting a Job Script:
^^^^^^^^^^^^^^^^^^^^^^

In order to make our life easier, instead of submitting an allocation command line, loading the modules, setting the threads/MPI process, and writing
another command line to submit our jobs, we can make an script to pack all these command into one executable ``.sh`` file, that can be submitted
via ``bsub`` just once.
In order to make our life easier, instead of submitting an allocation
command line, loading the modules, setting the threads/MPI process,
and writing another command line to submit our jobs, we can make an
script to pack all these command into one executable ``.sh`` file,
that can be submitted via ``bsub`` just once.

We start our job script, summoning the shell with the statement ``!/bin/bash``. Then we add the ``bsub`` allocations flags, starting with ``#BSUB``
as follows:
We start our job script, summoning the shell with the statement
``!/bin/bash``. Then we add the ``bsub`` allocations flags, starting
with ``#BSUB`` as follows:

.. code-block:: bash
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Job Chaining
^^^^^^^^^^^^

The script `chainslurm.sh </ccs/home/zingale/bin/chainslurm.sh>`_ can be used to start
The script `chainslurm.sh <https://github.com/AMReX-Astro/workflow/blob/main/job_scripts/slurm/chainslurm.sh>`_ can be used to start
a job chain, with each job depending on the previous. For example, to start up
10 jobs:

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