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Use parallel I/O in Github Actions CI tests #277

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merged 7 commits into from
Oct 9, 2024
Merged

Use parallel I/O in Github Actions CI tests #277

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9a79f03
Remove HDF5_jll pinning
johnomotani Oct 8, 2024
04015c1
Disable "parallel_io" in Harrison-Thompson test
johnomotani Oct 8, 2024
331b9fa
Install NCDatasets for the Github Actions CI parallel checks
johnomotani Oct 8, 2024
2bc99e4
Set `parallel_io=false` for a few debug checks
johnomotani Oct 8, 2024
219f9bd
Test NetCDF I/O in a few debug checks, if available
johnomotani Oct 8, 2024
399c094
Use `--check-bounds=yes` for all commands in debug_checks.yml
johnomotani Oct 8, 2024
69faf43
Don't install NCDatasets in debug CI job
johnomotani Oct 8, 2024
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4 changes: 3 additions & 1 deletion .github/workflows/debug_checks.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -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

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4 changes: 2 additions & 2 deletions .github/workflows/parallel_test.yml
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Expand Up @@ -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
Expand All @@ -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
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2 changes: 0 additions & 2 deletions moment_kinetics/Project.toml
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Expand Up @@ -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"
Expand Down Expand Up @@ -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]
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11 changes: 9 additions & 2 deletions moment_kinetics/debug_test/sound_wave_inputs.jl
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Original file line number Diff line number Diff line change
@@ -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",
Expand Down Expand Up @@ -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 =
Expand All @@ -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 =
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3 changes: 2 additions & 1 deletion moment_kinetics/test/harrisonthompson.jl
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Expand Up @@ -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,
Expand Down