Merge pull request #277 from mabarnes/ci-parallel-io

Use parallel I/O in Github Actions CI tests
mabarnes · Oct 9, 2024 · f933306 · f933306
2 parents 097ee11 + 69faf43
commit f933306
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Showing 5 changed files with 16 additions and 8 deletions.
diff --git a/.github/workflows/debug_checks.yml b/.github/workflows/debug_checks.yml
@@ -28,8 +28,10 @@ jobs:
           sed -i -e "s/_debug_level = get_options.*/_debug_level = 2/" moment_kinetics/src/debugging.jl
 
           touch Project.toml
+          # Not sure why installing "NCDatasets" fails at the moment (8/10/2024), but precompilation hangs for this job if it is included, so skip for now.
+          #julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.add(["MPI", "MPIPreferences", "NCDatasets", "PackageCompiler", "Symbolics"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
           julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.add(["MPI", "MPIPreferences", "PackageCompiler", "Symbolics"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
-          julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
+          julia --project -O3 --check-bounds=yes -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
           julia --project -O3 --check-bounds=yes -e 'using Pkg; Pkg.develop(path="moment_kinetics/"); Pkg.precompile()'
           julia --project -O3 --check-bounds=yes precompile-with-check-bounds.jl --debug 2
 

diff --git a/.github/workflows/parallel_test.yml b/.github/workflows/parallel_test.yml
@@ -23,7 +23,7 @@ jobs:
           touch Project.toml
           julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["MPI", "MPIPreferences"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
           julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
-          julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["Random", "SpecialFunctions", "StatsBase", "Test"]); Pkg.develop(path="moment_kinetics/")'
+          julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["NCDatasets", "Random", "SpecialFunctions", "StatsBase", "Test"]); Pkg.develop(path="moment_kinetics/")'
           julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.precompile()'
           # Need to use openmpi so that we can use `--oversubscribe` to allow using more MPI ranks than physical cores
           ./mpiexecjl -np 3 --oversubscribe julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --ci --debug 1
@@ -48,7 +48,7 @@ jobs:
           touch Project.toml
           julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["MPI", "MPIPreferences"]); using MPIPreferences; MPIPreferences.use_jll_binary("OpenMPI_jll")'
           julia --project -O3 --check-bounds=no -e 'using MPI; MPI.install_mpiexecjl(; destdir=".")'
-          julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["Random", "SpecialFunctions", "StatsBase", "Test"]); Pkg.develop(path="moment_kinetics/")'
+          julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.add(["NCDatasets", "Random", "SpecialFunctions", "StatsBase", "Test"]); Pkg.develop(path="moment_kinetics/")'
           julia --project -O3 --check-bounds=no -e 'import Pkg; Pkg.precompile()'
           # Need to use openmpi so that we can use `--oversubscribe` to allow using more MPI ranks than physical cores
           ./mpiexecjl -np 4 --oversubscribe julia --project -O3 --check-bounds=no moment_kinetics/test/runtests.jl --ci --debug 1

diff --git a/moment_kinetics/Project.toml b/moment_kinetics/Project.toml
@@ -11,7 +11,6 @@ FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
 FastGaussQuadrature = "442a2c76-b920-505d-bb47-c5924d526838"
 Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
 HDF5 = "f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f"
-HDF5_jll = "0234f1f7-429e-5d53-9886-15a909be8d59"
 Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
 LegendrePolynomials = "3db4a2ba-fc88-11e8-3e01-49c72059a882"
 LibGit2 = "76f85450-5226-5b5a-8eaa-529ad045b433"
@@ -50,7 +49,6 @@ file_io_netcdf = "NCDatasets"
 manufactured_solns_ext = ["Symbolics", "IfElse"]
 
 [compat]
-HDF5_jll = "<1.14, >=1.15"
 julia = "1.9.0"
 
 [extras]

diff --git a/moment_kinetics/debug_test/sound_wave_inputs.jl b/moment_kinetics/debug_test/sound_wave_inputs.jl
@@ -1,6 +1,8 @@
 test_type = "sound_wave"
 using moment_kinetics.type_definitions: OptionsDict
 using moment_kinetics.utils: recursive_merge
+using moment_kinetics.file_io: io_has_implementation
+using moment_kinetics.input_structs: netcdf
 
 # default inputs for tests
 test_input_finite_difference_1D1V = OptionsDict("output" => OptionsDict("run_name" => "finite_difference_1D1V",
@@ -210,7 +212,8 @@ recursive_merge(test_input_finite_difference_1D1V,
 
 test_input_chebyshev_1D1V_split_1_moment =
 recursive_merge(test_input_chebyshev_1D1V,
-                OptionsDict("output" => OptionsDict("run_name" => "chebyshev_pseudospectral_1D1V_split_1_moment"),
+                OptionsDict("output" => OptionsDict("run_name" => "chebyshev_pseudospectral_1D1V_split_1_moment",
+                                                    "parallel_io" => false),
                             "evolve_moments" => OptionsDict("density" => true)))
 
 test_input_chebyshev_1D1V_split_2_moments =
@@ -223,9 +226,13 @@ recursive_merge(test_input_chebyshev_1D1V_split_2_moments,
                 OptionsDict("output" => OptionsDict("run_name" => "chebyshev_pseudospectral_1D1V_split_3_moments"),
                             "evolve_moments" => OptionsDict("parallel_pressure" => true)))
 
+# Use "netcdf" for a few tests to test the NetCDF I/O if it is available.
+const binary_format = io_has_implementation(netcdf) ? "netcdf" : "hdf5"
+
 test_input_chebyshev_cx0_1D1V =
 recursive_merge(test_input_chebyshev_1D1V,
-                OptionsDict("output" => OptionsDict("run_name" => "chebyshev_pseudospectral_cx0_1D1V"),
+                OptionsDict("output" => OptionsDict("run_name" => "chebyshev_pseudospectral_cx0_1D1V",
+                                                    "binary_format" => binary_format),
                             "reactions" => OptionsDict("charge_exchange_frequency" => 0.0)))
 
 test_input_chebyshev_cx0_1D1V_split_1_moment =

diff --git a/moment_kinetics/test/harrisonthompson.jl b/moment_kinetics/test/harrisonthompson.jl
@@ -83,7 +83,8 @@ test_input_finite_difference = Dict("composition" => OptionsDict("n_ion_species"
                                                                              "upar_phase" => 0.0,
                                                                              "temperature_amplitude" => 0.0,
                                                                              "temperature_phase" => 0.0),
-                                    "output" => OptionsDict("run_name" => "finite_difference"),
+                                    "output" => OptionsDict("run_name" => "finite_difference",
+                                                            "parallel_io" => false),
                                     "evolve_moments" => OptionsDict("density" => false,
                                                                     "parallel_flow" => false,
                                                                     "parallel_pressure" => false,