Skip to content

Problem installing and using Oceananigans #2480

@oseanography

Description

@oseanography

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:
Building MPI → ~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/d56a80d8cf8b9dc3050116346b3d83432b1912c0/build.log
Precompiling project...
✗ MPI
✗ PencilArrays
✗ PencilFFTs
✗ Oceananigans
89 dependencies successfully precompiled in 41 seconds
4 dependencies errored. To see a full report either run import Pkg; Pkg.precompile() or load the packages

(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:

julia> using Oceananigans
[ Info: Precompiling Oceananigans [9e8cae18-63c1-5223-a75c-80ca9d6e9a09]
ERROR: LoadError: MPI.jl not properly configured, please run Pkg.build("MPI").
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] top-level scope
@ ~/.julia/packages/MPI/08SPr/src/MPI.jl:38
[3] include
@ ./Base.jl:418 [inlined]
[4] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1318
[5] top-level scope
@ none:1
[6] eval
@ ./boot.jl:373 [inlined]
[7] eval(x::Expr)
@ Base.MainInclude ./client.jl:453
[8] top-level scope
@ none:1
in expression starting at /Users/sean/.julia/packages/MPI/08SPr/src/MPI.jl:1

caused by: LoadError: InitError: could not load library "/Users/sean/.julia/artifacts/48a9a608db31268626d8b8d4d1272c3e7ccbf7d5/lib/libmpifort.12.dylib"
dlopen(/Users/sean/.julia/artifacts/48a9a608db31268626d8b8d4d1272c3e7ccbf7d5/lib/libmpifort.12.dylib, 0x0001): Library not loaded: @rpath/libquadmath.0.dylib
Referenced from: /Users/sean/.julia/artifacts/48a9a608db31268626d8b8d4d1272c3e7ccbf7d5/lib/libmpifort.12.dylib
Reason: tried: '/Users/sean/.julia/artifacts/48a9a608db31268626d8b8d4d1272c3e7ccbf7d5/lib/./libquadmath.0.dylib' (no such file), '/Users/sean/.julia/artifacts/48a9a608db31268626d8b8d4d1272c3e7ccbf7d5/lib/./libquadmath.0.dylib' (no such file), '/Applications/Julia-1.7.app/Contents/Resources/julia/lib/julia/libquadmath.0.dylib' (no such file), '/Applications/Julia-1.7.app/Contents/Resources/julia/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] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1097
[8] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:1013
[9] require(into::Module, mod::Symbol)
@ Base ./loading.jl:997
[10] top-level scope
@ ~/.julia/packages/MPI/08SPr/deps/deps.jl:8
[11] include(mod::Module, _path::String)
@ Base ./Base.jl:418
[12] include(x::String)
@ MPI ~/.julia/packages/MPI/08SPr/src/MPI.jl:1
[13] top-level scope
@ ~/.julia/packages/MPI/08SPr/src/MPI.jl:36
[14] include
@ ./Base.jl:418 [inlined]
[15] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::String)
@ Base ./loading.jl:1318
[16] top-level scope
@ none:1
[17] eval
@ ./boot.jl:373 [inlined]
[18] eval(x::Expr)
@ Base.MainInclude ./client.jl:453
[19] top-level scope
@ none:1
during initialization of module MPICH_jll
in expression starting at /Users/sean/.julia/packages/MPI/08SPr/deps/deps.jl:1
ERROR: LoadError: Failed to precompile MPI [da04e1cc-30fd-572f-bb4f-1f8673147195] to /Users/sean/.julia/compiled/v1.7/MPI/jl_AfEwik.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:997
[7] include(mod::Module, _path::String)
@ Base ./Base.jl:418
[8] include(x::String)
@ Oceananigans ~/.julia/packages/Oceananigans/jmNfq/src/Oceananigans.jl:5
[9] top-level scope
@ ~/.julia/packages/Oceananigans/jmNfq/src/Oceananigans.jl:190
[10] include
@ ./Base.jl:418 [inlined]
[11] include_package_for_output(pkg::Base.PkgId, input::String, depot_path::Vector{String}, dl_load_path::Vector{String}, load_path::Vector{String}, concrete_deps::Vector{Pair{Base.PkgId, UInt64}}, source::Nothing)
@ Base ./loading.jl:1318
[12] top-level scope
@ none:1
[13] eval
@ ./boot.jl:373 [inlined]
[14] eval(x::Expr)
@ Base.MainInclude ./client.jl:453
[15] top-level scope
@ none:1
in expression starting at /Users/sean/.julia/packages/Oceananigans/jmNfq/src/Distributed/Distributed.jl:1
in expression starting at /Users/sean/.julia/packages/Oceananigans/jmNfq/src/Oceananigans.jl:1
ERROR: Failed to precompile Oceananigans [9e8cae18-63c1-5223-a75c-80ca9d6e9a09] to /Users/sean/.julia/compiled/v1.7/Oceananigans/jl_sx8KhM.
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:33
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, ignore_loaded_modules::Bool)
@ Base ./loading.jl:1466
[3] compilecache(pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1410
[4] _require(pkg::Base.PkgId)
@ Base ./loading.jl:1120
[5] require(uuidkey::Base.PkgId)
@ Base ./loading.jl:1013
[6] require(into::Module, mod::Symbol)
@ Base ./loading.jl:997

Any help would be greatly appreciated. Thanks

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions