up SurfaceFluxes in examples

[trontrytel]

Update ClimaAtmos to SurfaceFluxes v 0.12

[trontrytel]

My plan is to update the mse based on the outcome of this CI and merge it in

[trontrytel]

Bumping the ref_counter for mse tests. There were changes in:

• no lim held suarez (ρe) equilmoist hightop sponge and aquaplanet (ρe_tot) equil allsky monin_obukhov varying insol gravity wave (raw_topo) high top zonally asymmetric that showed up in mse test but not to the huma eye when looking at plots.

• Diagnostic EDMFX aquaplanet with TKE that showed up in fluctuations in TKE profiles. But they are also fluctuating in the current main, just differently.

[trontrytel]

Timed out in calibration test. Waiting for #3353

[trontrytel]

Timed out when uploading artifacts for GPU: gpu_aquaplanet_dyamond. The artifact upload started at 14:39 and was still not done at 15:10. Followed by an additional error below. Will re run the CI

ving profiler information | 1m 24s
-- | --
  | Generating '/tmp/slurm-44195061/nsys-report-6d8c.qdstrm'
  | [1/1] [=17%                        ] report.nsys-rep
  | Importer error status: An unknown error occurred.
  | Import Failed with unexpected exception: /dvs/p4/build/sw/devtools/Agora/Rel/QuadD_Main/QuadD/Host/QdstrmImporter/main.cpp(34): Throw in function {anonymous}::Importer::Importer(const boost::filesystem::path&, const boost::filesystem::path&)
  | Dynamic exception type: boost::wrapexcept<QuadDCommon::RuntimeException>
  | std::exception::what: RuntimeException
  | [QuadDCommon::tag_message*] = Status: AnalysisFailed
  | Error {
  | Type: RuntimeError
  | SubError {
  | Type: InvalidArgument
  | Props {
  | Items {
  | Type: OriginalExceptionClass
  | Value: "N5boost10wrapexceptIN11QuadDCommon24InvalidArgumentExceptionEEE"
  | }
  | Items {
  | Type: OriginalFile
  | Value: "/dvs/p4/build/sw/devtools/Agora/Rel/QuadD_Main/QuadD/Host/Analysis/Modules/EventCollection.cpp"
  | }
  | Items {
  | Type: OriginalLine
  | Value: "1055"
  | }
  | Items {
  | Type: OriginalFunction
  | Value: "void QuadDAnalysis::EventCollection::CheckOrder(QuadDAnalysis::EventCollectionHelper::EventContainer&, const QuadDAnalysis::ConstEvent&) const"
  | }
  | Items {
  | Type: ErrorText
  | Value: "Wrong event order has been detected when adding events to the collection:\nnew event ={ StartNs=250462919571 StopNs=250462919699 GlobalId=295604044224942 Event={ TraceProcessEvent=[{ Correlation=19255 EventClass=1 TextId=683 ReturnValue=0 },] } Type=48 }\nlast event ={ StartNs=1520111314000 StopNs=1520112075037 GlobalId=295604044224942 Event={ TraceProcessEvent=[{ Correlation=97105 EventClass=1 TextId=686 ReturnValue=0 },] } Type=48 }"
  | }
  | }
  | }
  | }
  | Generated:
  | /central/scratch/esm/slurm-buildkite/climaatmos-ci/20947/climaatmos-ci/gpu_aquaplanet_dyamond/output_active/report.qdstrm
  | Running global post-command hook | 0s
  | Uploading artifacts |  
  | $ buildkite-agent artifact upload gpu_aquaplanet_dyamond/output_active/*
  | 2024-10-02 14:39:21 INFO   Found 8 files that match "gpu_aquaplanet_dyamond/output_active/*"
  | 2024-10-02 14:39:21 INFO   Uploading to default Buildkite artifact storage
  | 2024-10-02 14:39:21 INFO   Creating (0-8)/8 artifacts
  | 2024-10-02 14:39:22 INFO   Uploading artifact 01924f2c-6367-47a6-abc0-fb38d9edf286 gpu_aquaplanet_dyamond/output_active/summary.pdf (364 KiB)
  | 2024-10-02 14:39:22 INFO   Uploading artifact 01924f2c-6362-4e4c-b0d6-f2f647cd7758 gpu_aquaplanet_dyamond/output_active/gpu_aquaplanet_dyamond_parameters.toml (25 KiB)
  | 2024-10-02 14:39:22 INFO   Uploading artifact 01924f2c-6362-4272-bc0b-b0ad58422e70 gpu_aquaplanet_dyamond/output_active/hdf5_files.tar (512 B)
  | 2024-10-02 14:39:22 INFO   Uploading artifact 01924f2c-6363-4362-b37a-cd199b852d75 gpu_aquaplanet_dyamond/output_active/summary_2D.pdf (1.6 MiB)
  | 2024-10-02 14:39:22 INFO   Uploading artifact 01924f2c-6364-4cf5-a727-8007980e6b44 gpu_aquaplanet_dyamond/output_active/report.qdstrm (223 MiB)
  | 2024-10-02 14:39:22 INFO   Uploading artifact 01924f2c-6366-4e2a-9371-bd4cb86db581 gpu_aquaplanet_dyamond/output_active/graceful_exit.dat (1 B)
  | 2024-10-02 14:39:22 INFO   Uploading artifact 01924f2c-6366-4c5a-aead-339d3115a57e gpu_aquaplanet_dyamond/output_active/nc_files.tar (378 MiB)
  | 2024-10-02 14:39:22 INFO   Uploading artifact 01924f2c-6366-4492-bb62-44feb3b1c3b2 gpu_aquaplanet_dyamond/output_active/gpu_aquaplanet_dyamond.yml (2.7 KiB)
  | 2024-10-02 14:39:22 INFO   Successfully uploaded artifact "gpu_aquaplanet_dyamond/output_active/hdf5_files.tar"
  | 2024-10-02 14:39:22 INFO   Successfully uploaded artifact "gpu_aquaplanet_dyamond/output_active/graceful_exit.dat"
  | 2024-10-02 14:39:22 INFO   Successfully uploaded artifact "gpu_aquaplanet_dyamond/output_active/gpu_aquaplanet_dyamond_parameters.toml"
  | 2024-10-02 14:39:22 INFO   Successfully uploaded artifact "gpu_aquaplanet_dyamond/output_active/gpu_aquaplanet_dyamond.yml"
  | 2024-10-02 14:39:22 INFO   Successfully uploaded artifact "gpu_aquaplanet_dyamond/output_active/summary.pdf"
  | 2024-10-02 14:39:23 INFO   Successfully uploaded artifact "gpu_aquaplanet_dyamond/output_active/summary_2D.pdf"
  | 2024-10-02 14:39:28 INFO   Successfully uploaded artifact "gpu_aquaplanet_dyamond/output_active/report.qdstrm"