From e1bdfb3e399bb310066c8a886b273e81eefb3162 Mon Sep 17 00:00:00 2001
From: JJ Guerrette <guerrett@ucar.edu>
Date: Mon, 3 Apr 2023 11:50:04 -0600
Subject: [PATCH] Update to spack-stack-v1/skylab-3.0.0 (#208)

### Description
Updates the build to use `spack-stack-v1/skylab-3.0.0` modules on Cheyenne.  Currently this only works for GNU, but intel builds are broken with the previous version of spack-stack too.  So this does not remove any functionality.

### Issue closed

Closes #206

### Tests completed
 - [x] 3dvar_OIE120km_WarmStart
 - [x] 3denvar_OIE120km_WarmStart
 - [x] 3dvar_OIE120km_ColdStart
 - [x] 3dvar_O30kmIE60km_ColdStart
 - [x] 3denvar_O30kmIE60km_WarmStart
 - [x] eda_OIE120km_WarmStart
---
 config/environmentJEDI.csh                       |  4 ++--
 .../forecast/stream_list.atmosphere.diagnostics  | 16 ++++++++++++++++
 config/mpas/geovars.yaml                         |  9 +++++++++
 initialize/framework/Build.py                    |  4 ++--
 4 files changed, 29 insertions(+), 4 deletions(-)

diff --git a/config/environmentJEDI.csh b/config/environmentJEDI.csh
index 7744e488..eecb3408 100644
--- a/config/environmentJEDI.csh
+++ b/config/environmentJEDI.csh
@@ -14,13 +14,13 @@ module use /glade/work/jedipara/cheyenne/spack-stack/modulefiles/misc
 
 
 if ( "$compilerUsed" =~  *"gnu"* ) then
-  module use /glade/work/jedipara/cheyenne/spack-stack/spack-stack-v1/envs/skylab-2.0.0-gnu-10.1.0/install/modulefiles/Core
+  module use /glade/work/jedipara/cheyenne/spack-stack/spack-stack-v1/envs/skylab-3.0.0-gnu-10.1.0/install/modulefiles/Core
   module load stack-gcc/10.1.0
   module load stack-openmpi/4.1.1
   module load jedi-mpas-env/1.0.0
 
 else if ( "$compilerUsed" =~  *"intel"* ) then
-  module use /glade/work/jedipara/cheyenne/spack-stack/spack-stack-v1/envs/skylab-2.0.0-intel-19.1.1.217/install/modulefiles/Core
+  module use /glade/work/jedipara/cheyenne/spack-stack/spack-stack-v1/envs/skylab-3.0.0-intel-19.1.1.217/install/modulefiles/Core
   module load stack-intel/19.1.1.217
   module load stack-intel-mpi/2019.7.217
   module load jedi-mpas-env/1.0.0
diff --git a/config/mpas/forecast/stream_list.atmosphere.diagnostics b/config/mpas/forecast/stream_list.atmosphere.diagnostics
index 73276426..576290ae 100644
--- a/config/mpas/forecast/stream_list.atmosphere.diagnostics
+++ b/config/mpas/forecast/stream_list.atmosphere.diagnostics
@@ -13,48 +13,64 @@ q2
 t2m
 th2m
 mslp
+relhum_50hPa
+relhum_100hPa
 relhum_200hPa
 relhum_250hPa
 relhum_500hPa
 relhum_700hPa
 relhum_850hPa
 relhum_925hPa
+dewpoint_50hPa
+dewpoint_100hPa
 dewpoint_200hPa
 dewpoint_250hPa
 dewpoint_500hPa
 dewpoint_700hPa
 dewpoint_850hPa
 dewpoint_925hPa
+temperature_50hPa
+temperature_100hPa
 temperature_200hPa
 temperature_250hPa
 temperature_500hPa
 temperature_700hPa
 temperature_850hPa
 temperature_925hPa
+height_50hPa
+height_100hPa
 height_200hPa
 height_250hPa
 height_500hPa
 height_700hPa
 height_850hPa
 height_925hPa
+uzonal_50hPa
+uzonal_100hPa
 uzonal_200hPa
 uzonal_250hPa
 uzonal_500hPa
 uzonal_700hPa
 uzonal_850hPa
 uzonal_925hPa
+umeridional_50hPa
+umeridional_100hPa
 umeridional_200hPa
 umeridional_250hPa
 umeridional_500hPa
 umeridional_700hPa
 umeridional_850hPa
 umeridional_925hPa
+w_50hPa
+w_100hPa
 w_200hPa
 w_250hPa
 w_500hPa
 w_700hPa
 w_850hPa
 w_925hPa
+vorticity_50hPa
+vorticity_100hPa
 vorticity_200hPa
 vorticity_250hPa
 vorticity_500hPa
diff --git a/config/mpas/geovars.yaml b/config/mpas/geovars.yaml
index f442fd44..6ac59872 100644
--- a/config/mpas/geovars.yaml
+++ b/config/mpas/geovars.yaml
@@ -16,9 +16,18 @@ fields:
   - field name: air_pressure_levels
     mpas template field: w
 
+  - field name: upward_air_velocity
+    mpas template field: theta
+
+  - field name: geometric_height
+    mpas template field: theta
+
   - field name: geopotential_height
     mpas template field: theta
 
+  - field name: geopotential_height_levels
+    mpas template field: w
+
   - field name: surface_geopotential_height
     mpas template field: u10
 
diff --git a/initialize/framework/Build.py b/initialize/framework/Build.py
index a4fb97dc..d490c8e7 100644
--- a/initialize/framework/Build.py
+++ b/initialize/framework/Build.py
@@ -16,10 +16,10 @@ class Build(Component):
   variablesWithDefaults = {
     ## mpas bundle
     # mpas-bundle build directory
-    'mpas bundle': ['/glade/work/bjung/panda-c/build/mpas-bundle_gnu-openmpi_24FEB2023_single', str],
+    'mpas bundle': ['/glade/work/guerrett/pandac/build/mpas-bundle_gnu-openmpi_22MAR2023_single', str],
 
     # optional double-precision build
-    #'mpas bundle': ['/glade/work/bjung/panda-c/build/mpas-bundle_gnu-openmpi_24FEB2023', str],
+    #'mpas bundle': ['/glade/work/guerrett/pandac/build/mpas-bundle_gnu-openmpi_22MAR2023', str],
 
     ## compiler used
     # {compiler}-{mpi-implementation}/{version} combination that selects the JEDI module used to build