Initial commit from pyrefine

Author: kejacobson

.gitignore

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+*pyc
+*swp
+*html
+*egg
+*egg-info
+build
+.vscode/.ropeproject/objectdb
+.vscode/.ropeproject/config.py
+tests/test_output_files
+htmlcov
+.coverage
+examples/*/*/Flow*
+examples/*/*/geom*
+examples/*/geom*
+
+*pbs
+*log
+fun3d.nml_*
+*solb
+*out
+*dat
+*.forces
+*.grid_info
+*szplt
+*meshb
+*.flow
+*.trace
+moving_body.input_*
+*.restart
+*.mapbc
+*.ugrid
+*.names
+*.tec
+sfe.cfg_*
+cov.xml

README.md

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+[![pipeline status](https://gitlab.larc.nasa.gov/sketch-to-solution/pyrefine/badges/main/pipeline.svg)](https://gitlab.larc.nasa.gov/sketch-to-solution/pyrefine/-/commits/main)
+
+# Description
+
+A python module for scripting PBS jobs
+
+# Set up
+
+## Installation with setup.py
+
+setup.py in the root directory is a setuptools script for installing pyrefine.
+It is run with `python setup.py install`.
+Typical command line arguments to this script are `--user` to install in ~/.local or `--prefix={path/to/install}`.
+
+## In place usage of pyrefine using pip
+From this root directory do `pip install -e .` to do a "developer install". This allows you to edit pbs4py without
+having to reinstall to get new changes.
+
+# Documentation
+[LaRC gitlab page](https://sketch-to-solution.gitlab-pages.larc.nasa.gov/pyrefine/)
+
+
+The pyrefine documentation is generated from the source code with Sphinx.
+If you do not already have sphinx installed, you can use `pip` or `conda` to install it.
+Once you have installed or added pyrefine to your PYTHONPATH, the documentation is built by running `make html` in the docs directory.
+The generated documentation will be in `docs/build/html`.
+
+
+# Quick Start
+
+After installation,
+
+```python
+from pbs4py import PBS
+pbs = PBS.k4()
+pbs.launch('example_job',['echo "Hello World"'])
+```

docs/Makefile

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+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

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+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/source/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+import os
+import sys
+sys.path.insert(0, os.path.abspath('../../'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'pbs4py'
+copyright = '2021, NASA'
+author = 'NASA'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx.ext.autodoc','sphinx.ext.napoleon']
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = []
+
+autoclass_content = 'both'
+autodoc_member_order = 'bysource'
+autodoc_default_flags = ['members', 'inherited-members']
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'sphinxdoc'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

docs/source/index.rst

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+pbs4py
+======
+
+
+PBS Job Submission Handler
+--------------------------
+.. toctree::
+   :maxdepth: 1
+
+   pbs.rst
+   pbs_examples.rst
+
+
+Batch Job Submission
+--------------------
+.. toctree::
+   :maxdepth: 1
+
+   pbs_batch.rst
+   batch_examples.rst
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`

docs/source/pbs.rst

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+.. _pbs_section:
+
+PBS Job Handling
+%%%%%%%%%%%%%%%%
+
+The adaptation process requires automation of creating and submitting PBS jobs.
+However each HPC machine's PBS set up is slightly different.
+The PBS class is a tool to define properties of the PBS set up you want to use
+and then launch jobs.
+
+Note: Nothing about these utility classes is specific to adaptation, so they
+could be used for other job scripting.
+
+
+PBS stand alone example
+=======================
+
+.. code-block :: python
+
+    from pbs4py import PBS
+
+    k4 = PBS.k4(time=48)
+    k4.mpiexec = 'mpiexec_mpt'
+    k4.requested_number_of_nodes = 5
+
+    fun3d_command = 'nodet_mpi --gamma 1.14'
+    fun3d_mpi_command = k4.create_mpi_command(fun3d_command, 'dog')
+
+    pbs_commands = ['echo Start', fun3d_mpi_command, 'echo Done']
+
+    # submit and move on
+    k4.launch('test_job', pbs_commands, blocking=False)
+
+    # submit and wait for job to finish before continuing script
+    k4.launch('test_job', pbs_commands)
+
+This script will launch pbs jobs with the following test_jobs.pbs script:
+
+.. code-block :: bash
+
+    #!/usr/bin/env bash
+    #PBS -N test_job
+    #PBS -q K4-route
+    #PBS -l select=5:ncpus=40:mpiprocs=40
+    #PBS -l walltime=48:00:00
+    #PBS -o test_job_pbs.log
+    #PBS -j oe
+    #PBS -r n
+
+
+    cd $PBS_O_WORKDIR
+    source ~/.bashrc
+
+    echo Start
+    mpiexec_mpt nodet_mpi --gamma 1.14 > dog.out 2>&1
+    echo Done
+
+PBS Class
+=========
+The basic queue attributes are set in the constructor, but less common ones can be adjusted by changing the attributes.
+
+.. automodule:: pbs4py.pbs
+
+.. autoclass:: PBS
+   :members:
+
+PBS's classmethod constructors
+------------------------------
+Although not captured by the sphinx's autodocumentation,
+the ``PBS`` class has several classmethods that serve as alternate constructors which fill in properties of some NASA HPC systems and queue.
+
+
+.. code-block :: python
+
+    from pbs4py import PBS
+
+    k4 = PBS.k4(time=48)
+    k3 = PBS.k3()
+    k3a = PBS.k3a()
+    nas = PBS.nas(group_list='n1337', proc_type='skylake', time = 72)
+
+FakePBS Class
+*************
+Some adaptation such as 2D problems are small enough to run everything in a single pbs job so that you avoid having to sit in the queue for each operation.
+The FakePBS object appears to the adaptation drivers as a standard PBS object, but directly runs the commands instead of putting them into a PBS job and launching the job.
+
+.. autoclass:: FakePBS
+   :members: