Problem installing and using Oceananigans w Julia 1.7 + Apple M1 chip #2485
Replies: 9 comments 3 replies
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I'm moving this to a discussion and we can continue there. :) |
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What Julia version you have? E.g., can you print out the output of
? |
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Same problem here with Julia 1.7 on MacBook Pro M1...
|
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But all seems OK on Julia 1.6 (base) navid:test_Oceananigans/ $ julia-1.6 [10:11:18]
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.6.6 (2022-03-28)
_/ |\__'_|_|_|\__'_| | Official https://julialang.org/ release
|__/ |
(@v1.6) pkg> activate .
Activating environment at `~/Research/test_Oceananigans/Project.toml`
(test_Oceananigans) pkg> add Oceananigans
Updating registry at `~/.julia/registries/General`
Resolving package versions...
Updating `~/Research/test_Oceananigans/Project.toml`
[9e8cae18] + Oceananigans v0.75.2
Updating `~/Research/test_Oceananigans/Manifest.toml`
[621f4979] + AbstractFFTs v1.1.0
[79e6a3ab] + Adapt v3.3.3
[4fba245c] + ArrayInterface v5.0.7
[ab4f0b2a] + BFloat16s v0.1.0
[fa961155] + CEnum v0.4.2
[179af706] + CFTime v0.1.2
[052768ef] + CUDA v3.3.6
[72cfdca4] + CUDAKernels v0.3.0
[49dc2e85] + Calculus v0.5.1
[7057c7e9] + Cassette v0.3.10
[d360d2e6] + ChainRulesCore v1.14.0
[9e997f8a] + ChangesOfVariables v0.1.2
[34da2185] + Compat v3.43.0
[a8cc5b0e] + Crayons v4.1.1
[7445602f] + CubedSphere v0.2.0
[9a962f9c] + DataAPI v1.10.0
[864edb3b] + DataStructures v0.18.11
[e2d170a0] + DataValueInterfaces v1.0.0
[b552c78f] + DiffRules v1.10.0
[ffbed154] + DocStringExtensions v0.8.6
[fa6b7ba4] + DualNumbers v0.6.8
[b305315f] + Elliptic v1.0.1
[e2ba6199] + ExprTools v0.1.8
[7a1cc6ca] + FFTW v1.4.6
[5789e2e9] + FileIO v1.13.0
[0c68f7d7] + GPUArrays v8.3.2
[61eb1bfa] + GPUCompiler v0.12.9
[c27321d9] + Glob v1.3.0
[615f187c] + IfElse v0.1.1
[40713840] + IncompleteLU v0.2.0
[3587e190] + InverseFunctions v0.1.3
[92d709cd] + IrrationalConstants v0.1.1
[42fd0dbc] + IterativeSolvers v0.9.2
[82899510] + IteratorInterfaceExtensions v1.0.0
[033835bb] + JLD2 v0.4.22
[692b3bcd] + JLLWrappers v1.4.1
[0f8b85d8] + JSON3 v1.9.4
[63c18a36] + KernelAbstractions v0.7.2
[929cbde3] + LLVM v4.9.1
[2ab3a3ac] + LogExpFunctions v0.3.12
[da04e1cc] + MPI v0.19.2
[1914dd2f] + MacroTools v0.5.9
[85f8d34a] + NCDatasets v0.12.4
[77ba4419] + NaNMath v1.0.0
[9e8cae18] + Oceananigans v0.75.2
[6fe1bfb0] + OffsetArrays v1.10.8
[bac558e1] + OrderedCollections v1.4.1
[69de0a69] + Parsers v2.3.1
[0e08944d] + PencilArrays v0.16.1
[4a48f351] + PencilFFTs v0.13.4
[21216c6a] + Preferences v1.3.0
[94ee1d12] + Quaternions v0.5.6
[74087812] + Random123 v1.5.0
[e6cf234a] + RandomNumbers v1.5.3
[3cdcf5f2] + RecipesBase v1.2.1
[189a3867] + Reexport v1.2.2
[ae029012] + Requires v1.3.0
[6038ab10] + Rotations v1.3.1
[1bc83da4] + SafeTestsets v0.0.1
[d496a93d] + SeawaterPolynomials v0.2.2
[276daf66] + SpecialFunctions v1.8.4
[aedffcd0] + Static v0.6.2
[90137ffa] + StaticArrays v1.4.4
[15972242] + StaticPermutations v0.3.0
[5e0ebb24] + Strided v1.2.1
[09ab397b] + StructArrays v0.6.5
[856f2bd8] + StructTypes v1.8.1
[3783bdb8] + TableTraits v1.0.1
[bd369af6] + Tables v1.7.0
[6aa5eb33] + TaylorSeries v0.10.13
[a759f4b9] + TimerOutputs v0.5.17
[3bb67fe8] + TranscodingStreams v0.9.6
[bc48ee85] + Tullio v0.3.4
[9d95972d] + TupleTools v1.3.0
[81def892] + VersionParsing v1.3.0
[f5851436] + FFTW_jll v3.3.10+0
[0234f1f7] + HDF5_jll v1.12.0+1
[1d5cc7b8] + IntelOpenMP_jll v2018.0.3+2
[dad2f222] + LLVMExtra_jll v0.0.14+2
[856f044c] + MKL_jll v2022.0.0+0
[7cb0a576] + MPICH_jll v4.0.2+0
[9237b28f] + MicrosoftMPI_jll v10.1.3+2
[7243133f] + NetCDF_jll v400.702.400+0
[fe0851c0] + OpenMPI_jll v4.1.2+0
[458c3c95] + OpenSSL_jll v1.1.14+0
[efe28fd5] + OpenSpecFun_jll v0.5.5+0
[0dad84c5] + ArgTools
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8bb1440f] + DelimitedFiles
[8ba89e20] + Distributed
[f43a241f] + Downloads
[b77e0a4c] + InteractiveUtils
[4af54fe1] + LazyArtifacts
[b27032c2] + LibCURL
[76f85450] + LibGit2
[8f399da3] + Libdl
[37e2e46d] + LinearAlgebra
[56ddb016] + Logging
[d6f4376e] + Markdown
[a63ad114] + Mmap
[ca575930] + NetworkOptions
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[1a1011a3] + SharedArrays
[6462fe0b] + Sockets
[2f01184e] + SparseArrays
[10745b16] + Statistics
[fa267f1f] + TOML
[a4e569a6] + Tar
[8dfed614] + Test
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[e66e0078] + CompilerSupportLibraries_jll
[deac9b47] + LibCURL_jll
[29816b5a] + LibSSH2_jll
[c8ffd9c3] + MbedTLS_jll
[14a3606d] + MozillaCACerts_jll
[05823500] + OpenLibm_jll
[83775a58] + Zlib_jll
[8e850ede] + nghttp2_jll
[3f19e933] + p7zip_jll
Precompiling project...
34 dependencies successfully precompiled in 49 seconds (57 already precompiled) |
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on Julia 1.7, I can't even install MPI by itself... (base) navid:test_Oceananigans/ $ julia [10:17:45]
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.7.2 (2022-02-06)
_/ |\__'_|_|_|\__'_| |
|__/ |
(@v1.7) pkg> activate .
Activating project at `~/Research/test_Oceananigans`
(test_Oceananigans) pkg> add MPI
Updating registry at `~/.julia/registries/General.toml`
Resolving package versions...
Updating `~/Research/test_Oceananigans/Project.toml`
[da04e1cc] + MPI v0.19.2
Updating `~/Research/test_Oceananigans/Manifest.toml`
[ffbed154] + DocStringExtensions v0.8.6
[692b3bcd] + JLLWrappers v1.4.1
[da04e1cc] + MPI v0.19.2
[21216c6a] + Preferences v1.3.0
[ae029012] + Requires v1.3.0
[7cb0a576] + MPICH_jll v4.0.2+0
[9237b28f] + MicrosoftMPI_jll v10.1.3+2
[fe0851c0] + OpenMPI_jll v4.1.2+0
[0dad84c5] + ArgTools
[56f22d72] + Artifacts
[2a0f44e3] + Base64
[ade2ca70] + Dates
[8ba89e20] + Distributed
[f43a241f] + Downloads
[b77e0a4c] + InteractiveUtils
[4af54fe1] + LazyArtifacts
[b27032c2] + LibCURL
[76f85450] + LibGit2
[8f399da3] + Libdl
[56ddb016] + Logging
[d6f4376e] + Markdown
[ca575930] + NetworkOptions
[44cfe95a] + Pkg
[de0858da] + Printf
[3fa0cd96] + REPL
[9a3f8284] + Random
[ea8e919c] + SHA
[9e88b42a] + Serialization
[6462fe0b] + Sockets
[fa267f1f] + TOML
[a4e569a6] + Tar
[cf7118a7] + UUIDs
[4ec0a83e] + Unicode
[e66e0078] + CompilerSupportLibraries_jll
[deac9b47] + LibCURL_jll
[29816b5a] + LibSSH2_jll
[c8ffd9c3] + MbedTLS_jll
[14a3606d] + MozillaCACerts_jll
[83775a58] + Zlib_jll
[8e850ede] + nghttp2_jll
[3f19e933] + p7zip_jll
(test_Oceananigans) pkg> build MPI
Building MPI → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/d56a80d8cf8b9dc3050116346b3d83432b1912c0/build.log`
julia> using MPI
ERROR: InitError: could not load library "/Users/navid/.julia/artifacts/48a9a608db31268626d8b8d4d1272c3e7ccbf7d5/lib/libmpifort.12.dylib"
dlopen(/Users/navid/.julia/artifacts/48a9a608db31268626d8b8d4d1272c3e7ccbf7d5/lib/libmpifort.12.dylib, 0x0001): Library not loaded: @rpath/libquadmath.0.dylib
Referenced from: /Users/navid/.julia/artifacts/48a9a608db31268626d8b8d4d1272c3e7ccbf7d5/lib/libmpifort.12.dylib
Reason: tried: '/Users/navid/.julia/artifacts/48a9a608db31268626d8b8d4d1272c3e7ccbf7d5/lib/./libquadmath.0.dylib' (no such file), '/Users/navid/.julia/artifacts/48a9a608db31268626d8b8d4d1272c3e7ccbf7d5/lib/./libquadmath.0.dylib' (no such file), '/Users/navid/julia-1.7/usr/lib/libquadmath.0.dylib' (no such file), '/Users/navid/julia-1.7/usr/bin/../lib/libquadmath.0.dylib' (no such file), '/usr/local/lib/libquadmath.0.dylib' (no such file), '/usr/lib/libquadmath.0.dylib' (no such file)
Stacktrace:
[1] dlopen(s::String, flags::UInt32; throw_error::Bool)
@ Base.Libc.Libdl ./libdl.jl:117
[2] dlopen(s::String, flags::UInt32)
@ Base.Libc.Libdl ./libdl.jl:117
[3] macro expansion
@ ~/.julia/packages/JLLWrappers/QpMQW/src/products/library_generators.jl:54 [inlined]
[4] __init__()
@ MPICH_jll ~/.julia/packages/MPICH_jll/dhUyI/src/wrappers/aarch64-apple-darwin-libgfortran5.jl:32
[5] _include_from_serialized(path::String, depmods::Vector{Any})
@ Base ./loading.jl:768
[6] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:854
[7] _tryrequire_from_serialized(modkey::Base.PkgId, build_id::UInt64, modpath::String)
@ Base ./loading.jl:783
[8] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String)
@ Base ./loading.jl:843
[9] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1097
[10] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:1013
[11] require(into::Module, mod::Symbol)
@ Base ./loading.jl:997
during initialization of module MPICH_jll |
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I think we should raise this issue at MPI.jl? |
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@oseanography first of all amazing github handle. You might be able to fix this problem by first adding julia> using Pkg; Pkg.add(name="MPICH_jll", version="4.0.1"); Pkg.build() then restart Julia and try again to add Oceananigans, etc. |
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So, Oceananigans v0.75.3 will resolve this and one need not be doing |
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Hello, I am having some technical trouble installing and using Oceananigans. I am new to Julia and would like to try to set up Oceananigans on a Macbook. But it is running into issues.
(1) - installation process says some things are missing:
(2) - using Oceananigans is looking for MPI, but to my knowledge if I want to run on my computer, it shouldn't need MPI, like MITgcm using serial instead of parallel. But I don't know where to change the setting? This is what happens when I call using Oceananigans:
Any help would be greatly appreciated. Thanks
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