Consolidate Manifests

Manifests.toml are a burden to maintain and add a lot of git diff noise.
The one benefit of Manifests.toml is that they help with tracking
version dependencies.

However:
- For `docs`, the precise version of dependencies is not important,
there is pretty much no version-dependent code being executed there
- `perf` and `examples` can be consolidated into a single `.buildkite`
environment. This environment only has to have one manifest checked, the
one for which buildkite is run (and not one for each version of Julia).
- The `perf` environment can be removed all together. It is a more niche
environment: if reproducing a specific result is required, developers
can use the `.buildkite` Manifest. If not, developers can also consider
keeping the relevant tools (mainly JET) in the base environment.

This is the same pattern we have in other repos such as ClimaCore.

.buildkite/gpu_pipeline/pipeline.yml

@@ -20,19 +20,13 @@ steps:
     key: "init_gpu_env"
     command:
       - 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 CUDA; CUDA.precompile_runtime()'
-      - julia --project=examples -e 'using Pkg; Pkg.status()'
-
-      - echo "--- Instantiate perf"
-      - julia --project=perf -e 'using Pkg; Pkg.instantiate(;verbose=true)'
-      - julia --project=perf -e 'using Pkg; Pkg.precompile()'
-      - julia --project=perf -e 'using CUDA; CUDA.precompile_runtime()'
-      - julia --project=perf -e 'using Pkg; Pkg.status()'
+      - julia --project=.buildkite -e 'using Pkg; Pkg.instantiate(;verbose=true)'
+      - julia --project=.buildkite -e 'using Pkg; Pkg.precompile()'
+      - julia --project=.buildkite -e 'using CUDA; CUDA.precompile_runtime()'
+      - julia --project=.buildkite -e 'using Pkg; Pkg.status()'
 
       - echo "--- Download artifacts"
-      - julia --project=examples artifacts/download_artifacts.jl
+      - julia --project=.buildkite artifacts/download_artifacts.jl
 
     agents:
       slurm_gpus: 1
@@ -52,7 +46,7 @@ steps:
           - mkdir -p target_gpu_implicit_baroclinic_wave
           - >
             nsys profile --delay 100 --trace=nvtx,mpi,cuda,osrt --output=target_gpu_implicit_baroclinic_wave/output_active/report
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}target_gpu_implicit_baroclinic_wave.yml
             --job_id target_gpu_implicit_baroclinic_wave
         artifact_paths: "target_gpu_implicit_baroclinic_wave/output_active/*"
@@ -69,7 +63,7 @@ steps:
           - mkdir -p gpu_hs_rhoe_equil_55km_nz63_0M
           - >
             nsys profile --delay 100 --trace=nvtx,mpi,cuda,osrt --output=gpu_hs_rhoe_equil_55km_nz63_0M/output_active/report
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}gpu_hs_rhoe_equil_0M.yml
             --job_id gpu_hs_rhoe_equil_55km_nz63_0M
         artifact_paths: "gpu_hs_rhoe_equil_55km_nz63_0M/output_active/*"
@@ -87,7 +81,7 @@ steps:
           - >
             srun --cpu-bind=threads --cpus-per-task=4
             nsys profile --delay 100 --trace=nvtx,mpi,cuda,osrt --output=gpu_hs_rhoe_equil_55km_nz63_0M_4process/output_active/report-%q{PMI_RANK}
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}gpu_hs_rhoe_equil_0M.yml
             --job_id gpu_hs_rhoe_equil_55km_nz63_0M_4process
         artifact_paths: "gpu_hs_rhoe_equil_55km_nz63_0M_4process/output_active/*"
@@ -107,7 +101,7 @@ steps:
           - >
             srun --cpu-bind=threads --cpus-per-task=4
             nsys profile --delay 100 --trace=osrt,nvtx,cuda,mpi,ucx --output=target_gpu_implicit_baroclinic_wave_4process/output_active/report-%q{PMI_RANK}
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}target_gpu_implicit_baroclinic_wave.yml
             --job_id target_gpu_implicit_baroclinic_wave_4process
         artifact_paths: "target_gpu_implicit_baroclinic_wave_4process/output_active/*"
@@ -128,7 +122,7 @@ steps:
           - mkdir -p gpu_aquaplanet_dyamond_diag_1process
           - >
             srun --cpu-bind=threads --cpus-per-task=4
-            nsys profile --delay 100 --trace=nvtx,mpi,cuda,osrt --output=gpu_aquaplanet_dyamond_diag_1process/output_active/report julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            nsys profile --delay 100 --trace=nvtx,mpi,cuda,osrt --output=gpu_aquaplanet_dyamond_diag_1process/output_active/report julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}gpu_aquaplanet_dyamond_diag_1process.yml
             --job_id gpu_aquaplanet_dyamond_diag_1process
         artifact_paths: "gpu_aquaplanet_dyamond_diag_1process/output_active/*"
@@ -149,7 +143,7 @@ steps:
           - >
             srun --cpu-bind=threads --cpus-per-task=4
             nsys profile --delay 100 --trace=nvtx,mpi,cuda,osrt --output=gpu_aquaplanet_dyamond_ss_1process/output_active/report
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}gpu_aquaplanet_dyamond_ss.yml
             --job_id gpu_aquaplanet_dyamond_ss_1process
         artifact_paths: "gpu_aquaplanet_dyamond_ss_1process/output_active/*"
@@ -169,7 +163,7 @@ steps:
           - mkdir -p gpu_aquaplanet_dyamond_ss_2process
           - >
             srun --cpu-bind=threads --cpus-per-task=4
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}gpu_aquaplanet_dyamond_ss.yml
             --job_id gpu_aquaplanet_dyamond_ss_2process
         artifact_paths: "gpu_aquaplanet_dyamond_ss_2process/output_active/*"
@@ -189,7 +183,7 @@ steps:
           - mkdir -p gpu_aquaplanet_dyamond_ss_4process
           - >
             srun --cpu-bind=threads --cpus-per-task=4
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}gpu_aquaplanet_dyamond_ss.yml
             --job_id gpu_aquaplanet_dyamond_ss_4process
         artifact_paths: "gpu_aquaplanet_dyamond_ss_4process/output_active/*"
@@ -210,7 +204,7 @@ steps:
         command:
           - mkdir -p gpu_aquaplanet_dyamond_ss
           - >
-            julia --color=yes --project=examples post_processing/plot_gpu_strong_scaling.jl gpu_aquaplanet_dyamond_ss
+            julia --color=yes --project=.buildkite post_processing/plot_gpu_strong_scaling.jl gpu_aquaplanet_dyamond_ss
         artifact_paths: "gpu_aquaplanet_dyamond_ss/*"
         env:
           CLIMACOMMS_CONTEXT: "MPI"
@@ -227,7 +221,7 @@ steps:
           - mkdir -p gpu_aquaplanet_dyamond_ws_1process
           - >
             srun --cpu-bind=threads --cpus-per-task=4
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}gpu_aquaplanet_dyamond_ws_1process.yml
             --job_id gpu_aquaplanet_dyamond_ws_1process
         artifact_paths: "gpu_aquaplanet_dyamond_ws_1process/output_active/*"
@@ -247,7 +241,7 @@ steps:
           - mkdir -p gpu_aquaplanet_dyamond_ws_2process
           - >
             srun --cpu-bind=threads --cpus-per-task=4
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}gpu_aquaplanet_dyamond_ws_2process.yml
             --job_id gpu_aquaplanet_dyamond_ws_2process
         artifact_paths: "gpu_aquaplanet_dyamond_ws_2process/output_active/*"
@@ -267,7 +261,7 @@ steps:
           - mkdir -p gpu_aquaplanet_dyamond_ws_4process
           - >
             srun --cpu-bind=threads --cpus-per-task=4
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${GPU_CONFIG_PATH}gpu_aquaplanet_dyamond_ws_4process.yml
             --job_id gpu_aquaplanet_dyamond_ws_4process
         artifact_paths: "gpu_aquaplanet_dyamond_ws_4process/output_active/*"
@@ -288,7 +282,7 @@ steps:
         command:
           - mkdir -p gpu_aquaplanet_dyamond_ws
           - >
-            julia --color=yes --project=examples post_processing/plot_gpu_weak_scaling.jl gpu_aquaplanet_dyamond_ws
+            julia --color=yes --project=.buildkite post_processing/plot_gpu_weak_scaling.jl gpu_aquaplanet_dyamond_ws
         artifact_paths: "gpu_aquaplanet_dyamond_ws/*"
         env:
           CLIMACOMMS_DEVICE: "CUDA"
@@ -308,7 +302,7 @@ steps:
           - mkdir -p gpu_aquaplanet_diagedmf
           - >
             nsys profile --delay 200 --trace=nvtx,mpi,cuda,osrt --output=gpu_aquaplanet_diagedmf/output_active/report
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${MODEL_CONFIG_PATH}aquaplanet_diagedmf.yml
             --job_id gpu_aquaplanet_diagedmf
         artifact_paths: "gpu_aquaplanet_diagedmf/output_active/*"
@@ -324,7 +318,7 @@ steps:
 
       - label: "gpu_aquaplanet_diagedmf_benchmark"
         command: >
-          julia --color=yes --project=perf perf/benchmark.jl
+          julia --color=yes --project=.buildkite perf/benchmark.jl
           --config_file ${MODEL_CONFIG_PATH}aquaplanet_diagedmf.yml
           --job_id gpu_aquaplanet_diagedmf_benchmark
         artifact_paths: "gpu_aquaplanet_diagedmf_benchmark/output_active/*"
@@ -342,7 +336,7 @@ steps:
           - mkdir -p gpu_aquaplanet_progedmf
           - >
             nsys profile --delay 100 --trace=nvtx,mpi,cuda,osrt --output=gpu_aquaplanet_progedmf/output_active/report
-            julia --threads=3 --color=yes --project=examples examples/hybrid/driver.jl
+            julia --threads=3 --color=yes --project=.buildkite examples/hybrid/driver.jl
             --config_file ${MODEL_CONFIG_PATH}aquaplanet_progedmf.yml
             --job_id gpu_aquaplanet_progedmf
         artifact_paths: "gpu_aquaplanet_progedmf/output_active/*"
@@ -358,7 +352,7 @@ steps:
 
       - label: "gpu_aquaplanet_progedmf_benchmark"
         command: >
-          julia --color=yes --project=perf perf/benchmark.jl
+          julia --color=yes --project=.buildkite perf/benchmark.jl
           --config_file ${MODEL_CONFIG_PATH}aquaplanet_progedmf.yml
           --job_id gpu_aquaplanet_progedmf_benchmark
         artifact_paths: "gpu_aquaplanet_progedmf_benchmark/output_active/*"