From 85fb27c545869df188ab0b76e43f70b352b92627 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Tue, 3 Mar 2020 21:58:35 +0100 Subject: [PATCH 1/2] Update ocean readme with new compass environment This is based on the metapackage from MPAS-Tools. --- testing_and_setup/compass/README_ocean.md | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/testing_and_setup/compass/README_ocean.md b/testing_and_setup/compass/README_ocean.md index 02fe3dac0e..ec007778f2 100644 --- a/testing_and_setup/compass/README_ocean.md +++ b/testing_and_setup/compass/README_ocean.md @@ -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_0.1.1 -c conda-forge -c e3sm python=3.7 compass=0.1.1 ``` Each time you want to work with COMPASS, you will need to run: ``` -conda activate compass_py3.7 +conda activate compass_0.1.1 ``` 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 /load_latest_compass.sh ``` +Values of `` 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 @@ -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 @@ -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 @@ -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 From 75a55d62dce72193ed3b7152bc7d9d620cfbea81 Mon Sep 17 00:00:00 2001 From: Xylar Asay-Davis Date: Sat, 7 Mar 2020 21:39:23 +0100 Subject: [PATCH 2/2] Update to compass 0.1.2 Just built and uploaded --- testing_and_setup/compass/README_ocean.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/testing_and_setup/compass/README_ocean.md b/testing_and_setup/compass/README_ocean.md index ec007778f2..5748ed35a7 100644 --- a/testing_and_setup/compass/README_ocean.md +++ b/testing_and_setup/compass/README_ocean.md @@ -6,11 +6,11 @@ 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_0.1.1 -c conda-forge -c e3sm python=3.7 compass=0.1.1 +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_0.1.1 +conda activate compass_0.1.2 ``` An appropriate conda environment is already available on Los Alamos National