From 4e13869a358857765ada32177cb69b69e9de6109 Mon Sep 17 00:00:00 2001
From: Charles Kawczynski <kawczynski.charles@gmail.com>
Date: Mon, 2 Oct 2023 13:02:18 -0700
Subject: [PATCH 1/3] Add Krylov dependency

---
 Project.toml                     | 2 ++
 docs/Manifest.toml               | 2 +-
 docs/Project.toml                | 1 +
 examples/Manifest.toml           | 2 +-
 examples/Project.toml            | 1 +
 perf/Manifest.toml               | 2 +-
 perf/Project.toml                | 1 +
 src/time_stepper/time_stepper.jl | 1 +
 test/Project.toml                | 1 +
 9 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/Project.toml b/Project.toml
index d096988198b..3239b6283b7 100644
--- a/Project.toml
+++ b/Project.toml
@@ -26,6 +26,7 @@ Insolation = "e98cc03f-d57e-4e3c-b70c-8d51efe9e0d8"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+Krylov = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 LambertW = "984bce1d-4616-540c-a9ee-88d1112d94c9"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
@@ -68,6 +69,7 @@ Insolation = "0.6"
 Interpolations = "0.14"
 IntervalSets = "0.5, 0.6, 0.7"
 JLD2 = "0.4"
+Krylov = "0.9"
 LambertW = "0.4"
 NCDatasets = "0.11, 0.12"
 NVTX = "0.3"
diff --git a/docs/Manifest.toml b/docs/Manifest.toml
index 4cc92ff3a2f..c413a83019c 100644
--- a/docs/Manifest.toml
+++ b/docs/Manifest.toml
@@ -2,7 +2,7 @@
 
 julia_version = "1.9.3"
 manifest_format = "2.0"
-project_hash = "0ec43c631f23df4ba1817c10e57a9aadcc74d6ad"
+project_hash = "81c90708be1a8691c5fe6e9f23d35b4bd686a90b"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "5d2e21d7b0d8c22f67483ef95ebdc39c0e6b6003"
diff --git a/docs/Project.toml b/docs/Project.toml
index 1cc4067a0de..ecf3cf11fa4 100644
--- a/docs/Project.toml
+++ b/docs/Project.toml
@@ -5,6 +5,7 @@ CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 ClimaAtmos = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"
+Krylov = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
diff --git a/examples/Manifest.toml b/examples/Manifest.toml
index aa4542ce16f..8d2c97e3592 100644
--- a/examples/Manifest.toml
+++ b/examples/Manifest.toml
@@ -2,7 +2,7 @@
 
 julia_version = "1.9.3"
 manifest_format = "2.0"
-project_hash = "2d49c534fc32df8e020c1e281ecb638a59571404"
+project_hash = "6aafc01e3f7396811b8be3359baa437fb641dc2c"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "5d2e21d7b0d8c22f67483ef95ebdc39c0e6b6003"
diff --git a/examples/Project.toml b/examples/Project.toml
index c5fc02ab402..c8428aeaba7 100644
--- a/examples/Project.toml
+++ b/examples/Project.toml
@@ -32,6 +32,7 @@ IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+Krylov = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 LambertW = "984bce1d-4616-540c-a9ee-88d1112d94c9"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
diff --git a/perf/Manifest.toml b/perf/Manifest.toml
index fc07376d387..0c03caaf420 100644
--- a/perf/Manifest.toml
+++ b/perf/Manifest.toml
@@ -2,7 +2,7 @@
 
 julia_version = "1.9.3"
 manifest_format = "2.0"
-project_hash = "88cff4be951174939b5ca391858b2e951b1f42f8"
+project_hash = "6c95ea0b3c28ee3079f90af2e8950ed31eec87a9"
 
 [[deps.ADTypes]]
 git-tree-sha1 = "5d2e21d7b0d8c22f67483ef95ebdc39c0e6b6003"
diff --git a/perf/Project.toml b/perf/Project.toml
index fe9944cc768..fc0d519cfbb 100644
--- a/perf/Project.toml
+++ b/perf/Project.toml
@@ -34,6 +34,7 @@ IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+Krylov = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 LambertW = "984bce1d-4616-540c-a9ee-88d1112d94c9"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
diff --git a/src/time_stepper/time_stepper.jl b/src/time_stepper/time_stepper.jl
index db357db8fe7..4134def718c 100644
--- a/src/time_stepper/time_stepper.jl
+++ b/src/time_stepper/time_stepper.jl
@@ -1,5 +1,6 @@
 import NVTX
 import ClimaTimeSteppers as CTS
+import Krylov
 
 Base.@kwdef struct AtmosODEFunction{TL, TE, TI, L, D, PE, PI} <:
                    CTS.AbstractClimaODEFunction
diff --git a/test/Project.toml b/test/Project.toml
index 6c4a0cb15aa..6371573d1d9 100644
--- a/test/Project.toml
+++ b/test/Project.toml
@@ -33,6 +33,7 @@ Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+Krylov = "ba0b0d4f-ebba-5204-a429-3ac8c609bfb7"
 LambertW = "984bce1d-4616-540c-a9ee-88d1112d94c9"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"

From a110b32a520a1b033805f5c30a35867770278df5 Mon Sep 17 00:00:00 2001
From: Charles Kawczynski <kawczynski.charles@gmail.com>
Date: Mon, 2 Oct 2023 14:42:54 -0700
Subject: [PATCH 2/3] Update manifests

---
 docs/Manifest.toml     | 14 +++++++-------
 examples/Manifest.toml | 18 +++++++++---------
 perf/Manifest.toml     | 18 +++++++++---------
 3 files changed, 25 insertions(+), 25 deletions(-)

diff --git a/docs/Manifest.toml b/docs/Manifest.toml
index c413a83019c..a5c15768523 100644
--- a/docs/Manifest.toml
+++ b/docs/Manifest.toml
@@ -247,7 +247,7 @@ uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 version = "1.16.0"
 
 [[deps.ClimaAtmos]]
-deps = ["ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "CLIMAParameters", "CUDA", "ClimaComms", "ClimaCore", "ClimaTimeSteppers", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqCallbacks", "Distributions", "DocStringExtensions", "FastGaussQuadrature", "ImageFiltering", "Insolation", "Interpolations", "IntervalSets", "JLD2", "LambertW", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "OrdinaryDiffEq", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "TerminalLoggers", "Test", "Thermodynamics", "YAML"]
+deps = ["ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "CLIMAParameters", "CUDA", "ClimaComms", "ClimaCore", "ClimaTimeSteppers", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqCallbacks", "Distributions", "DocStringExtensions", "FastGaussQuadrature", "ImageFiltering", "Insolation", "Interpolations", "IntervalSets", "JLD2", "Krylov", "LambertW", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "OrdinaryDiffEq", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "TerminalLoggers", "Test", "Thermodynamics", "YAML"]
 path = ".."
 uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
 version = "0.16.1"
@@ -1106,9 +1106,9 @@ version = "2.28.2+0"
 
 [[deps.MicrosoftMPI_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "a8027af3d1743b3bfae34e54872359fdebb31422"
+git-tree-sha1 = "a7023883872e52bc29bcaac74f19adf39347d2d5"
 uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf"
-version = "10.1.3+4"
+version = "10.1.4+0"
 
 [[deps.Missings]]
 deps = ["DataAPI"]
@@ -1182,9 +1182,9 @@ version = "1.2.0"
 
 [[deps.NonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LineSearches", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"]
-git-tree-sha1 = "847f6b564d74422440850a99912c314595be4023"
+git-tree-sha1 = "7032be911404fe667e2a7ccd464ba5f2532797f2"
 uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
-version = "2.0.0"
+version = "2.0.1"
 
 [[deps.OffsetArrays]]
 deps = ["Adapt"]
@@ -1233,9 +1233,9 @@ version = "6.57.0"
 
 [[deps.PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "bf6085e8bd7735e68c210c6e5d81f9a6fe192060"
+git-tree-sha1 = "b7c4f29f93b548caa58f703580f4d79ab753c8ac"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
-version = "0.11.19"
+version = "0.11.21"
 
 [[deps.PackageExtensionCompat]]
 git-tree-sha1 = "fb28e33b8a95c4cee25ce296c817d89cc2e53518"
diff --git a/examples/Manifest.toml b/examples/Manifest.toml
index 8d2c97e3592..ecec42bf4a4 100644
--- a/examples/Manifest.toml
+++ b/examples/Manifest.toml
@@ -286,7 +286,7 @@ uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 version = "1.16.0"
 
 [[deps.ClimaAtmos]]
-deps = ["ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "CLIMAParameters", "CUDA", "ClimaComms", "ClimaCore", "ClimaTimeSteppers", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqCallbacks", "Distributions", "DocStringExtensions", "FastGaussQuadrature", "ImageFiltering", "Insolation", "Interpolations", "IntervalSets", "JLD2", "LambertW", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "OrdinaryDiffEq", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "TerminalLoggers", "Test", "Thermodynamics", "YAML"]
+deps = ["ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "CLIMAParameters", "CUDA", "ClimaComms", "ClimaCore", "ClimaTimeSteppers", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqCallbacks", "Distributions", "DocStringExtensions", "FastGaussQuadrature", "ImageFiltering", "Insolation", "Interpolations", "IntervalSets", "JLD2", "Krylov", "LambertW", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "OrdinaryDiffEq", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "TerminalLoggers", "Test", "Thermodynamics", "YAML"]
 path = ".."
 uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
 version = "0.16.1"
@@ -904,9 +904,9 @@ version = "0.5.3"
 
 [[deps.GeoInterface]]
 deps = ["Extents"]
-git-tree-sha1 = "bb198ff907228523f3dee1070ceee63b9359b6ab"
+git-tree-sha1 = "d53480c0793b13341c40199190f92c611aa2e93c"
 uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
-version = "1.3.1"
+version = "1.3.2"
 
 [[deps.GeometryBasics]]
 deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"]
@@ -1566,9 +1566,9 @@ version = "0.3.2"
 
 [[deps.MicrosoftMPI_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "a8027af3d1743b3bfae34e54872359fdebb31422"
+git-tree-sha1 = "a7023883872e52bc29bcaac74f19adf39347d2d5"
 uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf"
-version = "10.1.3+4"
+version = "10.1.4+0"
 
 [[deps.Missings]]
 deps = ["DataAPI"]
@@ -1664,9 +1664,9 @@ version = "1.2.0"
 
 [[deps.NonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LineSearches", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"]
-git-tree-sha1 = "847f6b564d74422440850a99912c314595be4023"
+git-tree-sha1 = "7032be911404fe667e2a7ccd464ba5f2532797f2"
 uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
-version = "2.0.0"
+version = "2.0.1"
 
 [[deps.Observables]]
 git-tree-sha1 = "6862738f9796b3edc1c09d0890afce4eca9e7e93"
@@ -1767,9 +1767,9 @@ version = "10.42.0+0"
 
 [[deps.PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "bf6085e8bd7735e68c210c6e5d81f9a6fe192060"
+git-tree-sha1 = "b7c4f29f93b548caa58f703580f4d79ab753c8ac"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
-version = "0.11.19"
+version = "0.11.21"
 
 [[deps.PNGFiles]]
 deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"]
diff --git a/perf/Manifest.toml b/perf/Manifest.toml
index 0c03caaf420..65fbf786875 100644
--- a/perf/Manifest.toml
+++ b/perf/Manifest.toml
@@ -297,7 +297,7 @@ uuid = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 version = "1.16.0"
 
 [[deps.ClimaAtmos]]
-deps = ["ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "CLIMAParameters", "CUDA", "ClimaComms", "ClimaCore", "ClimaTimeSteppers", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqCallbacks", "Distributions", "DocStringExtensions", "FastGaussQuadrature", "ImageFiltering", "Insolation", "Interpolations", "IntervalSets", "JLD2", "LambertW", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "OrdinaryDiffEq", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "TerminalLoggers", "Test", "Thermodynamics", "YAML"]
+deps = ["ArgParse", "ArtifactWrappers", "Artifacts", "AtmosphericProfilesLibrary", "CLIMAParameters", "CUDA", "ClimaComms", "ClimaCore", "ClimaTimeSteppers", "CloudMicrophysics", "Colors", "Dates", "Dierckx", "DiffEqCallbacks", "Distributions", "DocStringExtensions", "FastGaussQuadrature", "ImageFiltering", "Insolation", "Interpolations", "IntervalSets", "JLD2", "Krylov", "LambertW", "LinearAlgebra", "Logging", "NCDatasets", "NVTX", "OrdinaryDiffEq", "Pkg", "Printf", "RRTMGP", "Random", "RootSolvers", "SciMLBase", "StaticArrays", "Statistics", "StatsBase", "SurfaceFluxes", "TerminalLoggers", "Test", "Thermodynamics", "YAML"]
 path = ".."
 uuid = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
 version = "0.16.1"
@@ -945,9 +945,9 @@ version = "0.5.3"
 
 [[deps.GeoInterface]]
 deps = ["Extents"]
-git-tree-sha1 = "bb198ff907228523f3dee1070ceee63b9359b6ab"
+git-tree-sha1 = "d53480c0793b13341c40199190f92c611aa2e93c"
 uuid = "cf35fbd7-0cd7-5166-be24-54bfbe79505f"
-version = "1.3.1"
+version = "1.3.2"
 
 [[deps.GeometryBasics]]
 deps = ["EarCut_jll", "Extents", "GeoInterface", "IterTools", "LinearAlgebra", "StaticArrays", "StructArrays", "Tables"]
@@ -1618,9 +1618,9 @@ version = "0.3.2"
 
 [[deps.MicrosoftMPI_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "a8027af3d1743b3bfae34e54872359fdebb31422"
+git-tree-sha1 = "a7023883872e52bc29bcaac74f19adf39347d2d5"
 uuid = "9237b28f-5490-5468-be7b-bb81f5f5e6cf"
-version = "10.1.3+4"
+version = "10.1.4+0"
 
 [[deps.Missings]]
 deps = ["DataAPI"]
@@ -1710,9 +1710,9 @@ version = "1.2.0"
 
 [[deps.NonlinearSolve]]
 deps = ["ADTypes", "ArrayInterface", "ConcreteStructs", "DiffEqBase", "EnumX", "FiniteDiff", "ForwardDiff", "LineSearches", "LinearAlgebra", "LinearSolve", "PrecompileTools", "RecursiveArrayTools", "Reexport", "SciMLBase", "SimpleNonlinearSolve", "SparseArrays", "SparseDiffTools", "StaticArraysCore", "UnPack"]
-git-tree-sha1 = "847f6b564d74422440850a99912c314595be4023"
+git-tree-sha1 = "7032be911404fe667e2a7ccd464ba5f2532797f2"
 uuid = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
-version = "2.0.0"
+version = "2.0.1"
 
 [[deps.Observables]]
 git-tree-sha1 = "6862738f9796b3edc1c09d0890afce4eca9e7e93"
@@ -1813,9 +1813,9 @@ version = "10.42.0+0"
 
 [[deps.PDMats]]
 deps = ["LinearAlgebra", "SparseArrays", "SuiteSparse"]
-git-tree-sha1 = "bf6085e8bd7735e68c210c6e5d81f9a6fe192060"
+git-tree-sha1 = "b7c4f29f93b548caa58f703580f4d79ab753c8ac"
 uuid = "90014a1f-27ba-587c-ab20-58faa44d9150"
-version = "0.11.19"
+version = "0.11.21"
 
 [[deps.PNGFiles]]
 deps = ["Base64", "CEnum", "ImageCore", "IndirectArrays", "OffsetArrays", "libpng_jll"]

From a0f88353311fcab8b70501d5ade42737fb5a51dc Mon Sep 17 00:00:00 2001
From: Charles Kawczynski <kawczynski.charles@gmail.com>
Date: Mon, 2 Oct 2023 15:53:21 -0700
Subject: [PATCH 3/3] Increment ref counter

---
 regression_tests/ref_counter.jl | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/regression_tests/ref_counter.jl b/regression_tests/ref_counter.jl
index fd03ab2a61f..a57f6ce7bc2 100644
--- a/regression_tests/ref_counter.jl
+++ b/regression_tests/ref_counter.jl
@@ -1 +1 @@
-130
+131