Add Frierson(2006) diffusion profile

modified:   src/prognostic_equations/vertical_diffusion_boundary_layer.jl
modified:   src/utils/common_spaces.jl
modified:   src/cache/temporary_quantities.jl
modified:   src/prognostic_equations/vertical_diffusion_boundary_layer.jl
+Formatter
Update deps
Add FriersonDiffusion type

.buildkite/JuliaProject.toml

@@ -8,7 +8,8 @@ MPIPreferences = "3da0fdf6-3ccc-4f1b-acd9-58baa6c99267"
 compat = false
 
 [preferences.CUDA_Runtime_jll]
-version = "local"
+version = "12.2"
+local = "true"
 
 [preferences.HDF5_jll]
 libhdf5_path = "libhdf5"

.buildkite/gpu_pipeline/pipeline.yml

@@ -1,7 +1,7 @@
 agents:
   queue: clima
   slurm_mem: 8G
-  modules: julia/1.9.3 cuda/julia-pref openmpi/4.1.5
+  modules: julia/1.9.4 cuda/julia-pref openmpi/4.1.5
 
 env:
   OPENBLAS_NUM_THREADS: 1
@@ -21,7 +21,7 @@ steps:
 
       - echo "--- Configure CUDA"
       # force the initialization of the CUDA runtime as it is lazily loaded by default
-      - julia --project=cuda_env -e 'using Pkg; Pkg.resolve(); Pkg.instantiate(;verbose=true); using CUDA; CUDA.precompile_runtime()'
+      - julia --project=examples -e 'using CUDA; CUDA.precompile_runtime(); CUDA.versioninfo()'
 
       - echo "--- Download artifacts"
       - julia --project=examples artifacts/download_artifacts.jl

.buildkite/longruns/pipeline.yml

@@ -1,15 +1,15 @@
 agents:
   queue: central
   slurm_mem_per_cpu: 8G
-  modules: julia/1.9.3 cuda/12.2 ucx/1.14.1_cuda-12.2 openmpi/4.1.5_cuda-12.2 hdf5/1.12.2-ompi415 nsight-systems/2023.3.1
+  modules: julia/1.9.4 cuda/12.2 ucx/1.14.1_cuda-12.2 openmpi/4.1.5_cuda-12.2 hdf5/1.12.2-ompi415 nsight-systems/2023.3.1
 
 env:
   JULIA_LOAD_PATH: "${JULIA_LOAD_PATH}:${BUILDKITE_BUILD_CHECKOUT_PATH}/.buildkite"
   OPENBLAS_NUM_THREADS: 1
   JULIA_NVTX_CALLBACKS: gc
   OMPI_MCA_opal_warn_on_missing_libcuda: 0
   JULIA_MAX_NUM_PRECOMPILE_FILES: 100
-  JULIA_CPU_TARGET: 'broadwell;skylake'
+  JULIA_CPU_TARGET: 'skylake;cascadelake'
   CONFIG_PATH: "config/longrun_configs"
   SLURM_KILL_BAD_EXIT: 1
 
@@ -19,24 +19,15 @@ steps:
   - label: "init :computer:"
     key: "init_cpu_env"
     command:
-      - echo "--- Instantiate project"
-      - "julia --project -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
-      - "julia --project -e 'using Pkg; Pkg.precompile()'"
-      - "julia --project -e 'using Pkg; Pkg.status()'"
-
-      - echo "--- Configure CUDA"
-      # force the initialization of the CUDA runtime as it is lazily loaded by default
-      - "julia --project=cuda_env -e 'using Pkg; Pkg.resolve(); Pkg.instantiate(;verbose=true);using CUDA; CUDA.precompile_runtime()'"
-
-      - echo "--- Instantiate"
+      - echo "--- Instantiate examples"
       - "julia --project=examples -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
       - "julia --project=examples -e 'using Pkg; Pkg.precompile()'"
       - "julia --project=examples -e 'using Pkg; Pkg.status()'"
+      - "julia --project=examples -e 'using CUDA; CUDA.precompile_runtime(); CUDA.versioninfo()'"
       - "julia --project=examples artifacts/download_artifacts.jl"
 
     agents:
       slurm_cpus_per_task: 8
-      slurm_gpus: 1
     env:
       JULIA_NUM_PRECOMPILE_TASKS: 8
 

.buildkite/pipeline.yml

@@ -1,7 +1,7 @@
 agents:
   queue: central
   slurm_mem: 8G
-  modules: julia/1.9.3 cuda/12.2 ucx/1.14.1_cuda-12.2 openmpi/4.1.5_cuda-12.2 hdf5/1.12.2-ompi415 nsight-systems/2023.3.1
+  modules: julia/1.9.4 cuda/12.2 ucx/1.14.1_cuda-12.2 openmpi/4.1.5_cuda-12.2 hdf5/1.12.2-ompi415 nsight-systems/2023.3.1
 
 env:
   JULIA_LOAD_PATH: "${JULIA_LOAD_PATH}:${BUILDKITE_BUILD_CHECKOUT_PATH}/.buildkite"
@@ -31,20 +31,18 @@ steps:
       - "julia --project -e 'using Pkg; Pkg.precompile()'"
       - "julia --project -e 'using Pkg; Pkg.status()'"
 
-      - echo "--- Configure CUDA"
-      # force the initialization of the CUDA runtime as it is lazily loaded by default
-      - "julia --project=cuda_env -e 'using Pkg; Pkg.resolve(); Pkg.instantiate(;verbose=true);using CUDA; CUDA.precompile_runtime()'"
-
       - echo "--- Instantiate test"
       - "julia --project=test -e 'using Pkg; Pkg.develop(path = \".\")'"
       - "julia --project=test -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
       - "julia --project=test -e 'using Pkg; Pkg.precompile()'"
       - "julia --project=test -e 'using Pkg; Pkg.status()'"
 
       - echo "--- Instantiate examples"
+      - "julia --project=examples -e 'using Pkg; Pkg.develop(path = \".\")'"
       - "julia --project=examples -e 'using Pkg; Pkg.instantiate(;verbose=true)'"
       - "julia --project=examples -e 'using Pkg; Pkg.precompile()'"
       - "julia --project=examples -e 'using Pkg; Pkg.status()'"
+      - "julia --project=examples -e 'using CUDA; CUDA.precompile_runtime(); CUDA.versioninfo()'"
 
       - echo "--- Instantiate perf"
       - "julia --project=perf -e 'using Pkg; Pkg.instantiate(;verbose=true)'"

.buildkite/scaling/pipeline.sh

@@ -68,7 +68,7 @@ done
 cat << 'EOM'
 agents:
   queue: central
-  modules: julia/1.9.3 cuda/12.2 ucx/1.14.1_cuda-12.2 openmpi/4.1.5_cuda-12.2 hdf5/1.12.2-ompi415 nsight-systems/2023.3.1
+  modules: julia/1.9.4 cuda/12.2 ucx/1.14.1_cuda-12.2 openmpi/4.1.5_cuda-12.2 hdf5/1.12.2-ompi415 nsight-systems/2023.3.1
 
 env:
   JULIA_LOAD_PATH: "${JULIA_LOAD_PATH}:${BUILDKITE_BUILD_CHECKOUT_PATH}/.buildkite"

.dev/Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.9.3"
+julia_version = "1.9.4"
 manifest_format = "2.0"
 project_hash = "b280bcf3b481823c97fa1a62c1b5e65114b8fa18"
 
@@ -86,12 +86,12 @@ version = "1.0.42"
 [[deps.LibCURL]]
 deps = ["LibCURL_jll", "MozillaCACerts_jll"]
 uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
-version = "0.6.3"
+version = "0.6.4"
 
 [[deps.LibCURL_jll]]
 deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
 uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
-version = "7.84.0+0"
+version = "8.4.0+0"
 
 [[deps.LibGit2]]
 deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
@@ -100,7 +100,7 @@ uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 [[deps.LibSSH2_jll]]
 deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
 uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
-version = "1.10.2+0"
+version = "1.11.0+1"
 
 [[deps.Libdl]]
 uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
@@ -213,7 +213,7 @@ version = "1.2.13+0"
 [[deps.nghttp2_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
-version = "1.48.0+0"
+version = "1.52.0+1"
 
 [[deps.p7zip_jll]]
 deps = ["Artifacts", "Libdl"]

.gitignore

@@ -28,7 +28,6 @@ docs/site/
 # environment.
 /Manifest.toml
 test/Manifest.toml
-cuda_env/Manifest.toml
 
 # ignore vscode artifacts
 *.vscode

README.md

@@ -42,7 +42,7 @@ ClimaAtmos.jl is the atmosphere components of the CliMA software stack. We striv
 
 ## Installation instructions
 
-Recommended Julia: Stable release v1.9.3
+Recommended Julia: Stable release v1.9.4
 
 ClimaAtmos.jl is a [registered Julia package](https://julialang.org/packages/). To install
 

config/default_configs/default_config.yml

@@ -121,7 +121,7 @@ post_process:
   help: "Post process [`true` (default), `false`]"
   value: true
 vert_diff:
-  help: "Vertical diffusion [`false` (default), `VerticalDiffusion`, `true` (defaults to `VerticalDiffusion`)]"
+  help: "Vertical diffusion [`false` (default), `VerticalDiffusion`, `true` (defaults to `VerticalDiffusion`), `FriersonDiffusion`]"
   value: "false"
 hyperdiff:
   help: "Hyperdiffusion [`ClimaHyperdiffusion` (or `true`; default), `none` (or `false`)]"

config/model_configs/sphere_baroclinic_wave_rhoe_equilmoist_expvdiff.yml

@@ -1,6 +1,7 @@
 precip_model: "0M"
-vert_diff: "true"
-z_elem: 20
+vert_diff: "FriersonDiffusion"
+z_elem: 10
+h_elem: 6
 dz_bottom: 100
 dt_save_to_disk: "12hours"
 initial_condition: "MoistBaroclinicWave"