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Update ocean readme with new compass environment #462

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Mar 9, 2020
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Update ocean readme with new compass environment #462

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85fb27c
Update ocean readme with new compass environment
xylar Mar 3, 2020
75a55d6
Update to compass 0.1.2
xylar Mar 7, 2020
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23 changes: 13 additions & 10 deletions testing_and_setup/compass/README_ocean.md
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Original file line number Diff line number Diff line change
Expand Up @@ -6,21 +6,24 @@ To set up and run ocean test cases from COMPASS, you will need a conda
environment. First, install Miniconda3 (if miniconda is not already
installed), then create a new conda environment as follows:
``` bash
conda create -n compass_py3.7 -c conda-forge -c xylar python=3.7 \
geometric_features=0.1.4 mpas_tools=0.0.6 jigsaw=0.9.11 jigsawpy=0.0.2 \
metis pyflann scikit-image basemap pyamg ffmpeg
conda create -n compass_0.1.2 -c conda-forge -c e3sm python=3.7 compass=0.1.2
```
Each time you want to work with COMPASS, you will need to run:
```
conda activate compass_py3.7
conda activate compass_0.1.2
```

An appropriate conda environment is already available on Los Alamos National
Laboratory's Institutional Computing (LANL IC) machines:
Laboratory's Institutional Computing (LANL IC) machines as well as Anvil, Compy
and Cori. In each case, you will run:
```
source /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/etc/profile.d/conda.sh
conda activate compass_py3.7
source <base_path>/load_latest_compass.sh
```
Values of `<base_path>` are:
* grizzly and badger - `/usr/projects/climate/SHARED_CLIMATE/anaconda_envs`
* anvil (blues) - `/lcrc/soft/climate/e3sm-unified/`
* compy - `/share/apps/E3SM/conda_envs`
* cori - `/global/cfs/cdirs/acme/software/anaconda_envs`

## Setting config options

Expand All @@ -31,7 +34,7 @@ In six places, replace `FULL_PATH_TO_MPAS_MODEL_REPO` with the path where you
have checked out (and built) the branch of MPAS-Model you are planning to use.
Five other paths are required, as explained below.

### geometric_data
### geometric\_data

```
geometric_data = FULL_PATH_TO_PATH_OF_CACHED_GEOMETRIC_FEATURES_DATA
Expand All @@ -41,7 +44,7 @@ automatically downloaded and cached as test cases require them. However, if
working on compute nodes that cannot get to the internet (specifically GitHub),
it may be necessary to download the full set of `geometric_data` ahead of time
from:
[https://github.com/MPAS-Dev/geometric_features/tree/0.1/geometric_data](https://github.com/MPAS-Dev/geometric_features/tree/0.1/geometric_data)
[https://github.com/MPAS-Dev/geometric\_features/tree/0.1/geometric\_data](https://github.com/MPAS-Dev/geometric_features/tree/0.1/geometric_data)
The easiest way to do this is with:
```
git clone git@github.com:MPAS-Dev/geometric_features.git
Expand All @@ -56,7 +59,7 @@ On LANL IC, a full checkout is already available at:
geometric_data = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/geometric_data_v0.1
```

### mesh_database, initial_condition_database and bathymetry_database
### mesh\_database, initial\_condition\_database and bathymetry\_database

These are directories for storing pre-generated mesh files, data sets for
creating initial conditions, and bathymetry data. These can be empty directories, in which case
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