Rename "doc" folder to "docs". This is standard for ReadTheDocs

Signed-off-by: Bob Yantosca <yantosca@seas.harvard.edu>
geoschem · May 26, 2022 · 08b37c6 · 08b37c6
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diff --git a/doc/Makefile → docs/Makefile b/doc/Makefile → docs/Makefile
diff --git a/doc/environment.yml → docs/environment.yml b/doc/environment.yml → docs/environment.yml
diff --git a/docs/gchp.txt b/docs/gchp.txt
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+Bonus: Running GEOS-Chem High Performance (GCHP)
+------------------------------------------------
+
+GCHP is also fully functioning on the cloud. Running it on a single EC2 instance (equivalent to a single node on HPC clusters) is extremely easy. The biggest instance on AWS is ``x1.32xlarge`` with `64 physical cores <https://aws.amazon.com/ec2/physicalcores/>`_ and 2 TB memory. (Multi-node setup is quite cumbersome right now and we are actively looking into this.)
+
+Go to the pre-configured run directory::
+
+  $ cd ~/tutorial/gchp_standard
+
+Just run the pre-compiled the model by::
+
+  $ mpirun -np 6 -oversubscribe ./geos
+
+``-oversubscribe`` is needed when the number of physical cores is less than the number of MPI processes (6 here). No need for this option on bigger instances.
+
+.. warning::
+  Make sure that the geoscience Python environment is **deactivated** (``source deactivate geo``) before calling ``mpirun``. Otherwise the incorrect ``mpirun`` coming with Anaconda will be used. Use ``which mpirun`` and ``mpirun --version`` to make sure the correct executable is called. It should be OpenMPI 3 at ``/usr/local/bin/mpirun``.
+
+  Remember to use ``r5.2xlarge`` or even bigger instances, otherwise the run will crash at the middle due to inadequate memory.
+
+After a successful run (takes ~10 min), GCHP also produces NetCDF diagnostics inside ``OutputDir/`` of the run directory. Again a pre-generated output file is already contained in the AMI. Use this :doc:`example notebook <../chapter06_appendix/plot_GCHP_data>` located at ``~/tutorial/python_example/plot_GCHP.ipynb`` to plot GCHP output data directly on the native `Cubed-Sphere grid <http://acmg.seas.harvard.edu/geos/cubed_sphere.html>`_.
+
+See https://github.com/lizziel/geoschem_data_visualization for more comprehensive examples of GCHP data analysis. See `GCHP main page <http://wiki.seas.harvard.edu/geos-chem/index.php/GEOS-Chem_HP>`_ for more tutorials on GCHP.
+
+
+.. _terminate-label:
diff --git a/doc/requirements.txt → docs/requirements.txt b/doc/requirements.txt → docs/requirements.txt
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diff --git a/...ter02_beginner-tutorial/awscli-config.rst → ...ter02_beginner-tutorial/awscli-config.rst b/...ter02_beginner-tutorial/awscli-config.rst → ...ter02_beginner-tutorial/awscli-config.rst
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diff --git a/...er02_beginner-tutorial/spot-instances.rst → ...er02_beginner-tutorial/spot-instances.rst b/...er02_beginner-tutorial/spot-instances.rst → ...er02_beginner-tutorial/spot-instances.rst
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diff --git a/...ce/chapter02_beginner-tutorial/use-s3.rst → ...ce/chapter02_beginner-tutorial/use-s3.rst b/...ce/chapter02_beginner-tutorial/use-s3.rst → ...ce/chapter02_beginner-tutorial/use-s3.rst
diff --git a/...r03_advanced-tutorial/advanced-awscli.rst → ...r03_advanced-tutorial/advanced-awscli.rst b/...r03_advanced-tutorial/advanced-awscli.rst → ...r03_advanced-tutorial/advanced-awscli.rst
diff --git a/...chapter03_advanced-tutorial/container.rst → ...chapter03_advanced-tutorial/container.rst b/...chapter03_advanced-tutorial/container.rst → ...chapter03_advanced-tutorial/container.rst
diff --git a/...pter03_advanced-tutorial/hpc-overview.rst → ...pter03_advanced-tutorial/hpc-overview.rst b/...pter03_advanced-tutorial/hpc-overview.rst → ...pter03_advanced-tutorial/hpc-overview.rst
diff --git a/.../chapter03_advanced-tutorial/iam-role.rst → .../chapter03_advanced-tutorial/iam-role.rst b/.../chapter03_advanced-tutorial/iam-role.rst → .../chapter03_advanced-tutorial/iam-role.rst
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diff --git a/...rce/chapter03_advanced-tutorial/index.rst → ...rce/chapter03_advanced-tutorial/index.rst b/...rce/chapter03_advanced-tutorial/index.rst → ...rce/chapter03_advanced-tutorial/index.rst
diff --git a/...urce/chapter04_developer-guide/gc-env.rst → ...urce/chapter04_developer-guide/gc-env.rst b/...urce/chapter04_developer-guide/gc-env.rst → ...urce/chapter04_developer-guide/gc-env.rst
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diff --git a/...e/chapter04_developer-guide/share-ami.rst → ...e/chapter04_developer-guide/share-ami.rst b/...e/chapter04_developer-guide/share-ami.rst → ...e/chapter04_developer-guide/share-ami.rst
diff --git a/...apter05_aws-in-detail/common-concepts.rst → ...apter05_aws-in-detail/common-concepts.rst b/...apter05_aws-in-detail/common-concepts.rst → ...apter05_aws-in-detail/common-concepts.rst
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diff --git a/doc/source/chapter05_aws-in-detail/index.rst → .../source/chapter05_aws-in-detail/index.rst b/doc/source/chapter05_aws-in-detail/index.rst → .../source/chapter05_aws-in-detail/index.rst
diff --git a/.../chapter05_aws-in-detail/monitor-cost.rst → .../chapter05_aws-in-detail/monitor-cost.rst b/.../chapter05_aws-in-detail/monitor-cost.rst → .../chapter05_aws-in-detail/monitor-cost.rst
diff --git a/...apter06_appendix/aws-resources-for-gc.rst → ...apter06_appendix/aws-resources-for-gc.rst b/...apter06_appendix/aws-resources-for-gc.rst → ...apter06_appendix/aws-resources-for-gc.rst
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diff --git a/...rce/chapter06_appendix/plot_NASANEX.ipynb → ...rce/chapter06_appendix/plot_NASANEX.ipynb b/...rce/chapter06_appendix/plot_NASANEX.ipynb → ...rce/chapter06_appendix/plot_NASANEX.ipynb
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