MPAS-Dev · mark-petersen · May 10, 2019 · Feb 24, 2019 · Feb 26, 2019 · Feb 26, 2019
diff --git a/testing_and_setup/compass/README_ocean.md b/testing_and_setup/compass/README_ocean.md
@@ -0,0 +1,98 @@
+# Setting up COMPASS for ocean test case
+
+## COMPASS conda environment
+
+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 python=3.7 geometric_features
+    mpas_tools jigsaw metis pyflann scikit-image basemap pyamg
+```
+Each time you want to work with COMPASS, you will need to run:
+```
+conda activate compass_py3.7
+```
+
+An appropriate conda environment is already available on Los Alamos National
+Laboratory's Institutional Computing (LANL IC) machines:
+```
+source /usr/projects/climate/SHARED_CLIMATE/anaconda_envs/base/etc/profile.d/conda.sh
+conda activate compass_py3.7
+```
+
+## Setting config options
+
+The file `general.config.ocean` is a template containing a set of config
+options that the COMPASS user must set in order to set up ocean test cases.
+Make a copy of this file (e.g. `config.ocean`) and set the options as follows.
+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 = FULL_PATH_TO_PATH_OF_CACHED_GEOMETRIC_FEATURES_DATA
+```
+In general, this can be any directory where geojson data files will be
+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)
+The easiest way to do this is with:
+```
+git clone git@github.com:MPAS-Dev/geometric_features.git
+cd geometric_features
+git checkout 0.1
+```
+Then, point `geometric_data` in your config file to
+`geometric_features/geometirc_data/` in the location you have just placed it.
+
+On LANL IC, a full checkout is already available at:
+```
+geometric_data = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/geometric_data_v0.1
+```
+
+### jigsaw-geo-matlab
+
+For any test cases using the `JIGSAW` tool to generate meshes, you will need
+a local checkout fo the repository of Matlab routines for `JIGSAW` check out
+a local copy of the repo with:
+```
+git clone git@github.com:dengwirda/jigsaw-geo-matlab.git
+```
+Then, point `jigsaw-geo-matlab` in your config file to the path to the local
+check-out of the repo.
+
+If you have already checked out `jigsaw-geo-matlab` previously, be sure to
+update to the latest master.  Changes made in early May 2019 are required in
+order for these scripts to be able to use the version of `jigsaw` from the
+conda package, rather than requiring a local build.
+
+### mesh_database and initial_condition_database
+
+These are directories for storing pre-generated mesh files and data sets for
+creating initial conditions. These can be empty directories, in which case
+meshes and other data sets will be downloaded as required during test-case
+setup.  (If a test case appears to hang during setup, it is most likely
+downloading mesh or initial-condition data.)
+
+On LANL IC, the shared data bases can be found at:
+```
+mesh_database = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/mesh_database
+initial_condition_database = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/initial_condition_database
+```
+
+### bathymetry_database
+
+This is a database for bathymetry data sets that can be used at various phases
+of mesh generation and test-case initialization.  Currently, only a few test
+cases require these data sets and they are not downloaded automatically.  Thus,
+there is not a good way for users to access these datasets.
+
+On LANL IC, the shared location of the bathymetry database is at:
+```
+bathymetry_database = /usr/projects/regionalclimate/COMMON_MPAS/ocean/grids/bathymetry_database
+```
diff --git a/testing_and_setup/compass/general.config.ocean b/testing_and_setup/compass/general.config.ocean
@@ -26,11 +26,6 @@ init    = FULL_PATH_TO_MPAS_MODEL_REPO/streams.ocean.init
 # anywhere on the machine.
 [executables]
 model = FULL_PATH_TO_MPAS_MODEL_REPO/ocean_model
-metis = FULL_PATH_TO_METIS
-mesh_converter = FULL_PATH_TO_MPAS_TOOLS_REPO/mesh_tools/mesh_conversion_tools/MpasMeshConverter.x
-cell_culler    = FULL_PATH_TO_MPAS_TOOLS_REPO/mesh_tools/mesh_conversion_tools/MpasCellCuller.x
-mask_creator   = FULL_PATH_TO_MPAS_TOOLS_REPO/mesh_tools/mesh_conversion_tools/MpasMaskCreator.x
-mesh_generator = FULL_PATH_TO_EXECUTABLE_MESH_GENERATION_SCRIPT
 
 # The paths section describes paths that are used within the ocean core test
 # cases.
@@ -42,8 +37,7 @@ mesh_generator = FULL_PATH_TO_EXECUTABLE_MESH_GENERATION_SCRIPT
 # some test cases might download data into them, which will then be reused if
 # the test case is run again later.
 mpas_model = FULL_PATH_TO_MPAS_MODEL_REPO
-mpas_tools = FULL_PATH_TO_MPAS_TOOLS_REPO
-geometric_features = FULL_PATH_TO_LOCAL_CHECKOUT_OF_GEOMETRIC_FEATURES_REPO
+geometric_data = FULL_PATH_TO_PATH_OF_CACHED_GEOMETRIC_FEATURES_DATA
 jigsaw-geo-matlab = FULL_PATH_TO_JIGSAW_REPO
 mesh_database = FULL_PATH_TO_LOCAL_MESH_DATABASE
 initial_condition_database = FULL_PATH_TO_LOCAL_INITIAL_CONDITION_DATABASE

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/decomp_test/config_4proc_run.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/decomp_test/config_4proc_run.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step2/graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="forward">
 		<template file="baroclinic_channel_10km_template.xml" path_base="script_resolution_dir"/>
@@ -15,7 +14,7 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./metis">
+		<step executable="gpmetis">
 			<argument flag="graph.info">4</argument>
 		</step>
 		<model_run procs="4" threads="2" namelist="namelist.ocean" streams="streams.ocean"/>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/decomp_test/config_8proc_run.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/decomp_test/config_8proc_run.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step2/graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="forward">
 		<template file="baroclinic_channel_10km_template.xml" path_base="script_resolution_dir"/>
@@ -15,7 +14,7 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./metis">
+		<step executable="gpmetis">
 			<argument flag="graph.info">8</argument>
 		</step>
 		<model_run procs="8" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/decomp_test/config_init1.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/decomp_test/config_init1.xml
@@ -8,8 +8,6 @@
 	<add_link source_path="mesh_database" source="doubly_periodic_10km_160x500km_planar.151001.nc" dest="base_mesh.nc"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="cell_culler" dest="MpasCellCuller.x"/>
-	<add_executable source="mesh_converter" dest="MpasMeshConverter.x"/>
 
 	<namelist name="namelist.ocean" mode="init">
 		<option name="config_init_configuration">'baroclinic_channel'</option>
@@ -49,14 +47,14 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./MpasMeshConverter.x">
+		<step executable="MpasMeshConverter.x">
 			<argument flag="">base_mesh.nc</argument>
 			<argument flag="">mesh.nc</argument>
 		</step>
 
 		<model_run procs="1" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
 
-		<step executable="./MpasCellCuller.x">
+		<step executable="MpasCellCuller.x">
 			<argument flag="">ocean.nc</argument>
 		</step>
 	</run_script>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/decomp_test/config_init2.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/decomp_test/config_init2.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step1/culled_graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="init">
 		<option name="config_init_configuration">'baroclinic_channel'</option>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/default/config_forward.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/default/config_forward.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step2/graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="forward">
 		<template file="baroclinic_channel_10km_template.xml" path_base="script_resolution_dir"/>
@@ -15,7 +14,7 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./metis">
+		<step executable="gpmetis">
 			<argument flag="graph.info">4</argument>
 		</step>
 		<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/default/config_init1.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/default/config_init1.xml
@@ -8,8 +8,6 @@
 	<add_link source_path="mesh_database" source="doubly_periodic_10km_160x500km_planar.151001.nc" dest="base_mesh.nc"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="cell_culler" dest="MpasCellCuller.x"/>
-	<add_executable source="mesh_converter" dest="MpasMeshConverter.x"/>
 
 	<namelist name="namelist.ocean" mode="init">
 		<option name="config_init_configuration">'baroclinic_channel'</option>
@@ -49,14 +47,14 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./MpasMeshConverter.x">
+		<step executable="MpasMeshConverter.x">
 			<argument flag="">base_mesh.nc</argument>
 			<argument flag="">mesh.nc</argument>
 		</step>
 
 		<model_run procs="1" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
 
-		<step executable="./MpasCellCuller.x">
+		<step executable="MpasCellCuller.x">
 			<argument flag="">ocean.nc</argument>
 		</step>
 	</run_script>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/default/config_init2.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/default/config_init2.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step1/culled_graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="init">
 		<option name="config_init_configuration">'baroclinic_channel'</option>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/restart_test/config_full_run.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/restart_test/config_full_run.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step2/graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="forward">
 		<template file="baroclinic_channel_10km_template.xml" path_base="script_resolution_dir"/>
@@ -17,7 +16,7 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./metis">
+		<step executable="gpmetis">
 			<argument flag="graph.info">4</argument>
 		</step>
 

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/restart_test/config_init1.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/restart_test/config_init1.xml
@@ -8,8 +8,6 @@
 	<add_link source_path="mesh_database" source="doubly_periodic_10km_160x500km_planar.151001.nc" dest="base_mesh.nc"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="cell_culler" dest="MpasCellCuller.x"/>
-	<add_executable source="mesh_converter" dest="MpasMeshConverter.x"/>
 
 	<namelist name="namelist.ocean" mode="init">
 		<option name="config_init_configuration">'baroclinic_channel'</option>
@@ -49,14 +47,14 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./MpasMeshConverter.x">
+		<step executable="MpasMeshConverter.x">
 			<argument flag="">base_mesh.nc</argument>
 			<argument flag="">mesh.nc</argument>
 		</step>
 
 		<model_run procs="1" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
 
-		<step executable="./MpasCellCuller.x">
+		<step executable="MpasCellCuller.x">
 			<argument flag="">ocean.nc</argument>
 		</step>
 	</run_script>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/restart_test/config_init2.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/restart_test/config_init2.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step1/culled_graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="init">
 		<option name="config_init_configuration">'baroclinic_channel'</option>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/restart_test/config_restart_run.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/restart_test/config_restart_run.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step2/graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="forward">
 		<template file="baroclinic_channel_10km_template.xml" path_base="script_resolution_dir"/>
@@ -23,7 +22,7 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./metis">
+		<step executable="gpmetis">
 			<argument flag="graph.info">4</argument>
 		</step>
 		<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/threads_test/config_4proc_run.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/threads_test/config_4proc_run.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step2/graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="forward">
 		<template file="baroclinic_channel_10km_template.xml" path_base="script_resolution_dir"/>
@@ -15,7 +14,7 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./metis">
+		<step executable="gpmetis">
 			<argument flag="graph.info">4</argument>
 		</step>
 		<model_run procs="4" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/threads_test/config_8proc_run.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/threads_test/config_8proc_run.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step2/graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="forward">
 		<template file="baroclinic_channel_10km_template.xml" path_base="script_resolution_dir"/>
@@ -15,7 +14,7 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./metis">
+		<step executable="gpmetis">
 			<argument flag="graph.info">4</argument>
 		</step>
 		<model_run procs="4" threads="2" namelist="namelist.ocean" streams="streams.ocean"/>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/threads_test/config_init1.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/threads_test/config_init1.xml
@@ -8,8 +8,6 @@
 	<add_link source_path="mesh_database" source="doubly_periodic_10km_160x500km_planar.151001.nc" dest="base_mesh.nc"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="cell_culler" dest="MpasCellCuller.x"/>
-	<add_executable source="mesh_converter" dest="MpasMeshConverter.x"/>
 
 	<namelist name="namelist.ocean" mode="init">
 		<option name="config_init_configuration">'baroclinic_channel'</option>
@@ -49,14 +47,14 @@
 	</streams>
 
 	<run_script name="run.py">
-		<step executable="./MpasMeshConverter.x">
+		<step executable="MpasMeshConverter.x">
 			<argument flag="">base_mesh.nc</argument>
 			<argument flag="">mesh.nc</argument>
 		</step>
 
 		<model_run procs="1" threads="1" namelist="namelist.ocean" streams="streams.ocean"/>
 
-		<step executable="./MpasCellCuller.x">
+		<step executable="MpasCellCuller.x">
 			<argument flag="">ocean.nc</argument>
 		</step>
 	</run_script>

diff --git a/testing_and_setup/compass/ocean/baroclinic_channel/10km/threads_test/config_init2.xml b/testing_and_setup/compass/ocean/baroclinic_channel/10km/threads_test/config_init2.xml
@@ -4,7 +4,6 @@
 	<add_link source="../init_step1/culled_graph.info" dest="graph.info"/>
 
 	<add_executable source="model" dest="ocean_model"/>
-	<add_executable source="metis" dest="metis"/>
 
 	<namelist name="namelist.ocean" mode="init">
 		<option name="config_init_configuration">'baroclinic_channel'</option>