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byuflowlab / FLOWUnsteady

An interactional aerodynamics and acoustics solver for multirotor aircraft and wind energy
https://flow.byu.edu/FLOWUnsteady/
MIT License
256 stars 68 forks source link

Adding "other Packages" and "Testing FlowUnsteady" Fails #74

Closed ilm71 closed 1 year ago

ilm71 commented 1 year ago

Dear All,

after days of intallation of FLOWUnsteady I am currently figuring out the following issue (after running successfully the pre-defined test procedurces of FLOWExaFMM and FLOWVPM):

julia> Pkg.add([ Pkg.PackageSpec(; url=url*name, rev=v) for (name, v) in packages ]) Resolving package versions... Downloaded artifact: xfoil_light Updating ~/.julia/environments/v1.8/Project.toml [008c61af] + AirfoilPrep v2.1.2 https://github.com/byuflowlab/AirfoilPrep.jl#v2.1.2 [f91b385c] + BPM v2.0.1 https://github.com/byuflowlab/BPM.jl#v2.0.1 [d27480ee] + FLOWNoise v2.3.1 https://github.com/byuflowlab/FLOWNoise#v2.3.1 [1a3ff0be] + FLOWVLM v2.1.2 https://github.com/byuflowlab/FLOWVLM#v2.1.2 Updating ~/.julia/environments/v1.8/Manifest.toml [621f4979] + AbstractFFTs v1.3.1 [79e6a3ab] + Adapt v3.6.2 [008c61af] + AirfoilPrep v2.1.2 https://github.com/byuflowlab/AirfoilPrep.jl#v2.1.2 [13072b0f] + AxisAlgorithms v1.0.1 [f91b385c] + BPM v2.0.1 https://github.com/byuflowlab/BPM.jl#v2.0.1 ⌃ [e1828068] + CCBlade v0.1.0 [336ed68f] + CSV v0.10.11 [944b1d66] + CodecZlib v0.7.1 [a8cc5b0e] + Crayons v4.1.1 [9a962f9c] + DataAPI v1.15.0 [a93c6f00] + DataFrames v1.5.0 [e2d170a0] + DataValueInterfaces v1.0.0 [7a1cc6ca] + FFTW v1.7.0 [6cb5d3fb] + FLOWMath v0.3.3 [d27480ee] + FLOWNoise v2.3.1 https://github.com/byuflowlab/FLOWNoise#v2.3.1 [1a3ff0be] + FLOWVLM v2.1.2 https://github.com/byuflowlab/FLOWVLM#v2.1.2 [48062228] + FilePathsBase v0.9.20 [59287772] + Formatting v0.4.2 [842dd82b] + InlineStrings v1.4.0 [a98d9a8b] + Interpolations v0.14.7 [41ab1584] + InvertedIndices v1.3.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [e1d29d7a] + Missings v1.1.0 [6fe1bfb0] + OffsetArrays v1.12.9 [2dfb63ee] + PooledArrays v1.4.2 [08abe8d2] + PrettyTables v2.2.4 [c84ed2f1] + Ratios v0.4.5 [91c51154] + SentinelArrays v1.4.0 [66db9d55] + SnoopPrecompile v1.0.3 [a2af1166] + SortingAlgorithms v1.1.1 [90137ffa] + StaticArrays v1.5.26 [892a3eda] + StringManipulation v0.3.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.10.1 [3bb67fe8] + TranscodingStreams v0.9.13 [8149f6b0] + WAV v1.2.0 [ea10d353] + WeakRefStrings v1.4.2 [efce3f68] + WoodburyMatrices v0.5.5 [76eceee3] + WorkerUtilities v1.6.1 [19641d66] + Xfoil v0.5.0 [f5851436] + FFTW_jll v3.3.10+0 [1d5cc7b8] + IntelOpenMP_jll v2023.1.0+0 ⌅ [856f044c] + MKL_jll v2022.2.0+0 [70cc596b] + xfoil_light_jll v0.2.1+0 [8ba89e20] + Distributed [1a1011a3] + SharedArrays Info Packages marked with ⌃ and ⌅ have new versions available, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use status --outdated -m Precompiling project... ✗ FLOWVLM 32 dependencies successfully precompiled in 407 seconds. 81 already precompiled. 1 dependency errored. To see a full report either run import Pkg; Pkg.precompile() or load the package

(@v1.8) pkg> add https://github.com/byuflowlab/FLOWUnsteady Updating git-repo https://github.com/byuflowlab/FLOWUnsteady Resolving package versions... Updating ~/.julia/environments/v1.8/Project.toml [b491798d] + FLOWUnsteady v3.2.1 https://github.com/byuflowlab/FLOWUnsteady#master Updating ~/.julia/environments/v1.8/Manifest.toml [b491798d] + FLOWUnsteady v3.2.1 https://github.com/byuflowlab/FLOWUnsteady#master Precompiling project... ✗ FLOWUnsteady 0 dependencies successfully precompiled in 164 seconds. 113 already precompiled. 1 skipped during auto due to previous errors. 1 dependency errored. To see a full report either run import Pkg; Pkg.precompile() or load the package

julia> import FLOWUnsteady as uns [ Info: Precompiling FLOWUnsteady [b491798d-ac6e-455f-a27c-49c10bb0a666] ERROR: LoadError: InitError: PyError ($(Expr(:escape, :(ccall(#= /home/philippmandl/.julia/packages/PyCall/ahlL0/src/pyfncall.jl:43 =# @pysym(:PyObject_Call), PyPtr, (PyPtr, PyPtr, PyPtr), o, pyargsptr, kw))))) <class 'ModuleNotFoundError'> ModuleNotFoundError("No module named 'mpmath'") File "/home/philippmandl/.julia/conda/3/x86_64/lib/python3.10/imp.py", line 235, in load_module return load_source(name, filename, file) File "/home/philippmandl/.julia/conda/3/x86_64/lib/python3.10/imp.py", line 172, in load_source module = _load(spec) File "", line 719, in _load File "", line 688, in _load_unlocked File "", line 883, in exec_module File "", line 241, in _call_with_frames_removed File "/home/philippmandl/.julia/packages/AirfoilPrep/QE29n/src/airfoilprep.py", line 27, in import cmath, mpmath

Stacktrace: [1] pyerr_check @ ~/.julia/packages/PyCall/ahlL0/src/exception.jl:75 [inlined] [2] pyerr_check @ ~/.julia/packages/PyCall/ahlL0/src/exception.jl:79 [inlined] [3] _handle_error(msg::String) @ PyCall ~/.julia/packages/PyCall/ahlL0/src/exception.jl:96 [4] macro expansion @ ~/.julia/packages/PyCall/ahlL0/src/exception.jl:110 [inlined] [5] #107 @ ~/.julia/packages/PyCall/ahlL0/src/pyfncall.jl:43 [inlined] [6] disable_sigint @ ./c.jl:473 [inlined] [7] __pycall! @ ~/.julia/packages/PyCall/ahlL0/src/pyfncall.jl:42 [inlined] [8] _pycall!(ret::PyCall.PyObject, o::PyCall.PyObject, args::Tuple{String, PyCall.PyObject, String, Tuple{String, String, Int64}}, nargs::Int64, kw::Ptr{Nothing}) @ PyCall ~/.julia/packages/PyCall/ahlL0/src/pyfncall.jl:29 [9] _pycall!(ret::PyCall.PyObject, o::PyCall.PyObject, args::Tuple{String, PyCall.PyObject, String, Tuple{String, String, Int64}}, kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ PyCall ~/.julia/packages/PyCall/ahlL0/src/pyfncall.jl:11 [10] (::PyCall.PyObject)(::String, ::Vararg{Any}; kwargs::Base.Pairs{Symbol, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ PyCall ~/.julia/packages/PyCall/ahlL0/src/pyfncall.jl:86 [11] (::PyCall.PyObject)(::String, ::Vararg{Any}) @ PyCall ~/.julia/packages/PyCall/ahlL0/src/pyfncall.jl:86 [12] init() @ AirfoilPrep ~/.julia/packages/AirfoilPrep/QE29n/src/AirfoilPrep.jl:33 [13] _include_from_serialized(pkg::Base.PkgId, path::String, depmods::Vector{Any}) @ Base ./loading.jl:831 [14] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt64) @ Base ./loading.jl:1039 [15] _require(pkg::Base.PkgId) @ Base ./loading.jl:1315 [16] _require_prelocked(uuidkey::Base.PkgId) @ Base ./loading.jl:1200 [17] macro expansion @ ./loading.jl:1180 [inlined] [18] macro expansion @ ./lock.jl:223 [inlined] [19] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [20] include @ ./Base.jl:419 [inlined] [21] 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:1554 [22] top-level scope @ stdin:1 during initialization of module AirfoilPrep in expression starting at /home/philippmandl/.julia/packages/FLOWVLM/RWw6g/src/FLOWVLM.jl:1 in expression starting at stdin:1 ERROR: LoadError: Failed to precompile FLOWVLM [1a3ff0be-0410-4572-aa62-b496bdd1f33b] to /home/philippmandl/.julia/compiled/v1.8/FLOWVLM/jl_eg56Tx. Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:1707 [3] compilecache @ ./loading.jl:1651 [inlined] [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1337 [5] _require_prelocked(uuidkey::Base.PkgId) @ Base ./loading.jl:1200 [6] macro expansion @ ./loading.jl:1180 [inlined] [7] macro expansion @ ./lock.jl:223 [inlined] [8] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144 [9] include @ ./Base.jl:419 [inlined] [10] 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:1554 [11] top-level scope @ stdin:1 in expression starting at /home/philippmandl/.julia/packages/FLOWUnsteady/Jl5A6/src/FLOWUnsteady.jl:1 in expression starting at stdin:1 ERROR: Failed to precompile FLOWUnsteady [b491798d-ac6e-455f-a27c-49c10bb0a666] to /home/philippmandl/.julia/compiled/v1.8/FLOWUnsteady/jl_HTveGV. Stacktrace: [1] error(s::String) @ Base ./error.jl:35 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, keep_loaded_modules::Bool) @ Base ./loading.jl:1707 [3] compilecache @ ./loading.jl:1651 [inlined] [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1337 [5] _require_prelocked(uuidkey::Base.PkgId) @ Base ./loading.jl:1200 [6] macro expansion @ ./loading.jl:1180 [inlined] [7] macro expansion @ ./lock.jl:223 [inlined] [8] require(into::Module, mod::Symbol) @ Base ./loading.jl:1144

(@v1.8) pkg> status Status ~/.julia/environments/v1.8/Project.toml [008c61af] AirfoilPrep v2.1.2 https://github.com/byuflowlab/AirfoilPrep.jl#v2.1.2 [f91b385c] BPM v2.0.1 https://github.com/byuflowlab/BPM.jl#v2.0.1 ⌃ [1f15a43c] CxxWrap v0.11.2 [a07d1f4e] FLOWExaFMM v2.1.0 ~/Software/FLOWExaFMM [d27480ee] FLOWNoise v2.3.1 https://github.com/byuflowlab/FLOWNoise#v2.3.1 [b491798d] FLOWUnsteady v3.2.1 https://github.com/byuflowlab/FLOWUnsteady#master [1a3ff0be] FLOWVLM v2.1.2 https://github.com/byuflowlab/FLOWVLM#v2.1.2 [6e19019d] FLOWVPM v3.0.1 https://github.com/byuflowlab/FLOWVPM.jl#master [83792f5e] GeometricTools v2.1.6 [7073ff75] IJulia v1.24.2 [438e738f] PyCall v1.95.2 Info Packages marked with ⌃ have new versions available and may be upgradable.

Do you have any idea what might be wrong? Thank you so much for any help!!

EdoAlvarezR commented 1 year ago

@philippmandl, could you please comment on how you were able to resolve the issue?

ilm71 commented 1 year ago

there was a bug in the python-path to anaconda 3 which wasn't found by the system.

An additional failure comes up when I try to install the software on Scientific Linux 7.9:

Error-Message:

pkg> test FLOWExaFMM Testing FLOWExaFMM Status /tmp/jl_aVi9OH/Project.toml [1f15a43c] CxxWrap v0.11.2 [a07d1f4e] FLOWExaFMM v2.1.0 /local/disk1/pmandl/01_Software/FLOWExaFMM [8dfed614] Test @stdlib/Test Status /tmp/jl_aVi9OH/Manifest.toml [1f15a43c] CxxWrap v0.11.2 [a07d1f4e] FLOWExaFMM v2.1.0 /local/disk1/pmandl/01_Software/FLOWExaFMM [692b3bcd] JLLWrappers v1.4.1 [1914dd2f] MacroTools v0.5.10 [21216c6a] Preferences v1.4.0 [3eaa8342] libcxxwrap_julia_jll v0.8.8+1 [0dad84c5] ArgTools @stdlib/ArgTools [56f22d72] Artifacts @stdlib/Artifacts [2a0f44e3] Base64 @stdlib/Base64 [ade2ca70] Dates @stdlib/Dates [f43a241f] Downloads @stdlib/Downloads [b77e0a4c] InteractiveUtils @stdlib/InteractiveUtils [b27032c2] LibCURL @stdlib/LibCURL [76f85450] LibGit2 @stdlib/LibGit2 [8f399da3] Libdl @stdlib/Libdl [56ddb016] Logging @stdlib/Logging [d6f4376e] Markdown @stdlib/Markdown [ca575930] NetworkOptions @stdlib/NetworkOptions [44cfe95a] Pkg @stdlib/Pkg [de0858da] Printf @stdlib/Printf [3fa0cd96] REPL @stdlib/REPL [9a3f8284] Random @stdlib/Random [ea8e919c] SHA @stdlib/SHA [9e88b42a] Serialization @stdlib/Serialization [6462fe0b] Sockets @stdlib/Sockets [fa267f1f] TOML @stdlib/TOML [a4e569a6] Tar @stdlib/Tar [8dfed614] Test @stdlib/Test [cf7118a7] UUIDs @stdlib/UUIDs [4ec0a83e] Unicode @stdlib/Unicode [deac9b47] LibCURL_jll @stdlib/LibCURL_jll [29816b5a] LibSSH2_jll @stdlib/LibSSH2_jll [c8ffd9c3] MbedTLS_jll @stdlib/MbedTLS_jll [14a3606d] MozillaCACerts_jll @stdlib/MozillaCACerts_jll [83775a58] Zlib_jll @stdlib/Zlib_jll [8e850ede] nghttp2_jll @stdlib/nghttp2_jll [3f19e933] p7zip_jll @stdlib/p7zip_jll Precompiling project... ✗ FLOWExaFMM 0 dependencies successfully precompiled in 1 seconds (8 already precompiled) 1 dependency errored. To see a full report either run import Pkg; Pkg.precompile() or load the package Testing Running tests... /local/disk1/pmandl/01_Software/julia-1.6.7/bin/julia: symbol lookup error: /local/disk1/pmandl/01_Software/FLOWExaFMM/src/fmm.so: undefined symbol: _ZN5jlcxx6Module12get_constantERKSs ERROR: LoadError: Failed to precompile FLOWExaFMM [a07d1f4e-0e34-4d8b-bfef-e5b961477d34] to /home/pmandl/.julia/compiled/v1.6/FLOWExaFMM/jl_T5D5wX. Stacktrace: [1] error(s::String) @ Base ./error.jl:33 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool) @ Base ./loading.jl:1385 [3] compilecache(pkg::Base.PkgId, path::String) @ Base ./loading.jl:1329 [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1043 [5] require(uuidkey::Base.PkgId) @ Base ./loading.jl:936 [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:923 [7] include(fname::String) @ Base.MainInclude ./client.jl:444 [8] top-level scope @ none:6 in expression starting at /local/disk1/pmandl/01_Software/FLOWExaFMM/test/runtests.jl:2 ERROR: Package FLOWExaFMM errored during testing

do you have any ideas which might help? Thank you very much for your support!

ilm71 commented 1 year ago

there was a bug in the python-path to anaconda 3 which wasn't found by the system.

An additional failure comes up when I try to install the software on Scientific Linux 7.9:

Error-Message:

pkg> test FLOWExaFMM Testing FLOWExaFMM Status /tmp/jl_aVi9OH/Project.toml [1f15a43c] CxxWrap v0.11.2 [a07d1f4e] FLOWExaFMM v2.1.0 /local/disk1/pmandl/01_Software/FLOWExaFMM [8dfed614] Test @stdlib/Test Status /tmp/jl_aVi9OH/Manifest.toml [1f15a43c] CxxWrap v0.11.2 [a07d1f4e] FLOWExaFMM v2.1.0 /local/disk1/pmandl/01_Software/FLOWExaFMM [692b3bcd] JLLWrappers v1.4.1 [1914dd2f] MacroTools v0.5.10 [21216c6a] Preferences v1.4.0 [3eaa8342] libcxxwrap_julia_jll v0.8.8+1 [0dad84c5] ArgTools @stdlib/ArgTools [56f22d72] Artifacts @stdlib/Artifacts [2a0f44e3] Base64 @stdlib/Base64 [ade2ca70] Dates @stdlib/Dates [f43a241f] Downloads @stdlib/Downloads [b77e0a4c] InteractiveUtils @stdlib/InteractiveUtils [b27032c2] LibCURL @stdlib/LibCURL [76f85450] LibGit2 @stdlib/LibGit2 [8f399da3] Libdl @stdlib/Libdl [56ddb016] Logging @stdlib/Logging [d6f4376e] Markdown @stdlib/Markdown [ca575930] NetworkOptions @stdlib/NetworkOptions [44cfe95a] Pkg @stdlib/Pkg [de0858da] Printf @stdlib/Printf [3fa0cd96] REPL @stdlib/REPL [9a3f8284] Random @stdlib/Random [ea8e919c] SHA @stdlib/SHA [9e88b42a] Serialization @stdlib/Serialization [6462fe0b] Sockets @stdlib/Sockets [fa267f1f] TOML @stdlib/TOML [a4e569a6] Tar @stdlib/Tar [8dfed614] Test @stdlib/Test [cf7118a7] UUIDs @stdlib/UUIDs [4ec0a83e] Unicode @stdlib/Unicode [deac9b47] LibCURL_jll @stdlib/LibCURL_jll [29816b5a] LibSSH2_jll @stdlib/LibSSH2_jll [c8ffd9c3] MbedTLS_jll @stdlib/MbedTLS_jll [14a3606d] MozillaCACerts_jll @stdlib/MozillaCACerts_jll [83775a58] Zlib_jll @stdlib/Zlib_jll [8e850ede] nghttp2_jll @stdlib/nghttp2_jll [3f19e933] p7zip_jll @stdlib/p7zip_jll Precompiling project... ✗ FLOWExaFMM 0 dependencies successfully precompiled in 1 seconds (8 already precompiled) 1 dependency errored. To see a full report either run import Pkg; Pkg.precompile() or load the package Testing Running tests... /local/disk1/pmandl/01_Software/julia-1.6.7/bin/julia: symbol lookup error: /local/disk1/pmandl/01_Software/FLOWExaFMM/src/fmm.so: undefined symbol: _ZN5jlcxx6Module12get_constantERKSs ERROR: LoadError: Failed to precompile FLOWExaFMM [a07d1f4e-0e34-4d8b-bfef-e5b961477d34] to /home/pmandl/.julia/compiled/v1.6/FLOWExaFMM/jl_T5D5wX. Stacktrace: [1] error(s::String) @ Base ./error.jl:33 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool) @ Base ./loading.jl:1385 [3] compilecache(pkg::Base.PkgId, path::String) @ Base ./loading.jl:1329 [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1043 [5] require(uuidkey::Base.PkgId) @ Base ./loading.jl:936 [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:923 [7] include(fname::String) @ Base.MainInclude ./client.jl:444 [8] top-level scope @ none:6 in expression starting at /local/disk1/pmandl/01_Software/FLOWExaFMM/test/runtests.jl:2 ERROR: Package FLOWExaFMM errored during testing

do you have any ideas which might help? Thank you very much for your support!

ilm71 commented 1 year ago

there was a bug in the python-path to anaconda 3 which wasn't found by the system.

An additional failure comes up when I try to install the software on Scientific Linux 7.9:

* the error message is linked to the ] test FLOWExaFMM execution-

Error-Message:

pkg> test FLOWExaFMM Testing FLOWExaFMM Status /tmp/jl_aVi9OH/Project.toml [1f15a43c] CxxWrap v0.11.2 [a07d1f4e] FLOWExaFMM v2.1.0 /local/disk1/pmandl/01_Software/FLOWExaFMM [8dfed614] Test @stdlib/Test Status /tmp/jl_aVi9OH/Manifest.toml [1f15a43c] CxxWrap v0.11.2 [a07d1f4e] FLOWExaFMM v2.1.0 /local/disk1/pmandl/01_Software/FLOWExaFMM [692b3bcd] JLLWrappers v1.4.1 [1914dd2f] MacroTools v0.5.10 [21216c6a] Preferences v1.4.0 [3eaa8342] libcxxwrap_julia_jll v0.8.8+1 [0dad84c5] ArgTools @stdlib/ArgTools [56f22d72] Artifacts @stdlib/Artifacts [2a0f44e3] Base64 @stdlib/Base64 [ade2ca70] Dates @stdlib/Dates [f43a241f] Downloads @stdlib/Downloads [b77e0a4c] InteractiveUtils @stdlib/InteractiveUtils [b27032c2] LibCURL @stdlib/LibCURL [76f85450] LibGit2 @stdlib/LibGit2 [8f399da3] Libdl @stdlib/Libdl [56ddb016] Logging @stdlib/Logging [d6f4376e] Markdown @stdlib/Markdown [ca575930] NetworkOptions @stdlib/NetworkOptions [44cfe95a] Pkg @stdlib/Pkg [de0858da] Printf @stdlib/Printf [3fa0cd96] REPL @stdlib/REPL [9a3f8284] Random @stdlib/Random [ea8e919c] SHA @stdlib/SHA [9e88b42a] Serialization @stdlib/Serialization [6462fe0b] Sockets @stdlib/Sockets [fa267f1f] TOML @stdlib/TOML [a4e569a6] Tar @stdlib/Tar [8dfed614] Test @stdlib/Test [cf7118a7] UUIDs @stdlib/UUIDs [4ec0a83e] Unicode @stdlib/Unicode [deac9b47] LibCURL_jll @stdlib/LibCURL_jll [29816b5a] LibSSH2_jll @stdlib/LibSSH2_jll [c8ffd9c3] MbedTLS_jll @stdlib/MbedTLS_jll [14a3606d] MozillaCACerts_jll @stdlib/MozillaCACerts_jll [83775a58] Zlib_jll @stdlib/Zlib_jll [8e850ede] nghttp2_jll @stdlib/nghttp2_jll [3f19e933] p7zip_jll @stdlib/p7zip_jll Precompiling project... ✗ FLOWExaFMM 0 dependencies successfully precompiled in 1 seconds (8 already precompiled) 1 dependency errored. To see a full report either run import Pkg; Pkg.precompile() or load the package Testing Running tests... /local/disk1/pmandl/01_Software/julia-1.6.7/bin/julia: symbol lookup error: /local/disk1/pmandl/01_Software/FLOWExaFMM/src/fmm.so: undefined symbol: _ZN5jlcxx6Module12get_constantERKSs ERROR: LoadError: Failed to precompile FLOWExaFMM [a07d1f4e-0e34-4d8b-bfef-e5b961477d34] to /home/pmandl/.julia/compiled/v1.6/FLOWExaFMM/jl_T5D5wX. Stacktrace: [1] error(s::String) @ Base ./error.jl:33 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool) @ Base ./loading.jl:1385 [3] compilecache(pkg::Base.PkgId, path::String) @ Base ./loading.jl:1329 [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1043 [5] require(uuidkey::Base.PkgId) @ Base ./loading.jl:936 [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:923 [7] include(fname::String) @ Base.MainInclude ./client.jl:444 [8] top-level scope @ none:6 in expression starting at /local/disk1/pmandl/01_Software/FLOWExaFMM/test/runtests.jl:2 ERROR: Package FLOWExaFMM errored during testing

do you have any ideas which might help? Thank you very much for your support!

EdoAlvarezR commented 1 year ago

Are you following the instructions in the docs? https://flow.byu.edu/FLOWUnsteady/installation/general/#FLOWVPM

As indicated in the docs:

Test that you can correctly compile C++ code wrapped for Julia following these instructions: LINK

ilm71 commented 1 year ago

yes, I followed both instructions and the C++ wrapper works correctly - all the tests are passed. I have tried it with Juli 1.6.7, 1.8.5 and 1.9.1 - but always the same problem at the scientific linux system - do you have any ideas?

EdoAlvarezR commented 1 year ago

Can you please confirm that the file /local/disk1/pmandl/01_Software/FLOWExaFMM/src/fmm.so exists? If not, the compilation didn't work.

ilm71 commented 1 year ago

Yes, this file does exist - that's why I am wondering, why the Test fails.

ilm71 commented 1 year ago

when running the precompiler, following error is still present

julia> import Pkg; Pkg.precompile() Precompiling project... ✗ FLOWExaFMM ✗ FLOWVPM 66 dependencies successfully precompiled in 29 seconds

ERROR: The following 2 direct dependencies failed to precompile:

FLOWExaFMM [a07d1f4e-0e34-4d8b-bfef-e5b961477d34]

Failed to precompile FLOWExaFMM [a07d1f4e-0e34-4d8b-bfef-e5b961477d34] to /home/pmandl/.julia/compiled/v1.6/FLOWExaFMM/jl_Nn0DUu. /local/disk1/pmandl/01_Software/julia-1.6.7/bin/julia: symbol lookup error: /local/disk1/pmandl/01_Software/FLOWExaFMM/src/fmm.so: undefined symbol: _ZN5jlcxx6Module12get_constantERKSs

FLOWVPM [6e19019d-7c31-4940-9d16-c3f15dfe6020]

Failed to precompile FLOWVPM [6e19019d-7c31-4940-9d16-c3f15dfe6020] to /home/pmandl/.julia/compiled/v1.6/FLOWVPM/jl_EC2Pyj. /local/disk1/pmandl/01_Software/julia-1.6.7/bin/julia: symbol lookup error: /local/disk1/pmandl/01_Software/FLOWExaFMM/src/fmm.so: undefined symbol: _ZN5jlcxx6Module12get_constantERKSs ERROR: LoadError: Failed to precompile FLOWExaFMM [a07d1f4e-0e34-4d8b-bfef-e5b961477d34] to /home/pmandl/.julia/compiled/v1.6/FLOWExaFMM/jl_8ibDQS. Stacktrace: [1] error(s::String) @ Base ./error.jl:33 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IOContext{Base.PipeEndpoint}, internal_stdout::IOContext{IOStream}, ignore_loaded_modules::Bool) @ Base ./loading.jl:1385 [3] compilecache(pkg::Base.PkgId, path::String) @ Base ./loading.jl:1329 [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1043 [5] require(uuidkey::Base.PkgId) @ Base ./loading.jl:936 [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:923 [7] include @ ./Base.jl:384 [inlined] [8] 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:1235 [9] top-level scope @ none:1 [10] eval @ ./boot.jl:360 [inlined] [11] eval(x::Expr) @ Base.MainInclude ./client.jl:446 [12] top-level scope @ none:1 in expression starting at /home/pmandl/.julia/packages/FLOWVPM/WA9ug/src/FLOWVPM.jl:1

Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/Types.jl:55 [2] precompile(ctx::Pkg.Types.Context; internal_call::Bool, strict::Bool, warn_loaded::Bool, kwargs::Base.Iterators.Pairs{Union{}, Union{}, Tuple{}, NamedTuple{(), Tuple{}}}) @ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:1265 [3] precompile @ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:921 [inlined] [4] #precompile#196 @ /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:919 [inlined] [5] precompile() @ Pkg.API /buildworker/worker/package_linux64/build/usr/share/julia/stdlib/v1.6/Pkg/src/API.jl:919 [6] top-level scope @ REPL[7]:1

do you have any ideas regarding this problem? I am running out of ideas currently

ilm71 commented 1 year ago

running test FLOWExaFMM leads to the error

Testing FLOWExaFMM Status /tmp/jl_MB0FLT/Project.toml [1f15a43c] CxxWrap v0.11.2 [a07d1f4e] FLOWExaFMM v2.1.0 /local/disk1/pmandl/01_Software/FLOWExaFMM [8dfed614] Test @stdlib/Test Status /tmp/jl_MB0FLT/Manifest.toml [1f15a43c] CxxWrap v0.11.2 [a07d1f4e] FLOWExaFMM v2.1.0 /local/disk1/pmandl/01_Software/FLOWExaFMM [692b3bcd] JLLWrappers v1.4.1 [1914dd2f] MacroTools v0.5.10 [21216c6a] Preferences v1.4.0 [3eaa8342] libcxxwrap_julia_jll v0.8.8+1 [0dad84c5] ArgTools @stdlib/ArgTools [56f22d72] Artifacts @stdlib/Artifacts [2a0f44e3] Base64 @stdlib/Base64 [ade2ca70] Dates @stdlib/Dates [f43a241f] Downloads @stdlib/Downloads [b77e0a4c] InteractiveUtils @stdlib/InteractiveUtils [b27032c2] LibCURL @stdlib/LibCURL [76f85450] LibGit2 @stdlib/LibGit2 [8f399da3] Libdl @stdlib/Libdl [56ddb016] Logging @stdlib/Logging [d6f4376e] Markdown @stdlib/Markdown [ca575930] NetworkOptions @stdlib/NetworkOptions [44cfe95a] Pkg @stdlib/Pkg [de0858da] Printf @stdlib/Printf [3fa0cd96] REPL @stdlib/REPL [9a3f8284] Random @stdlib/Random [ea8e919c] SHA @stdlib/SHA [9e88b42a] Serialization @stdlib/Serialization [6462fe0b] Sockets @stdlib/Sockets [fa267f1f] TOML @stdlib/TOML [a4e569a6] Tar @stdlib/Tar [8dfed614] Test @stdlib/Test [cf7118a7] UUIDs @stdlib/UUIDs [4ec0a83e] Unicode @stdlib/Unicode [deac9b47] LibCURL_jll @stdlib/LibCURL_jll [29816b5a] LibSSH2_jll @stdlib/LibSSH2_jll [c8ffd9c3] MbedTLS_jll @stdlib/MbedTLS_jll [14a3606d] MozillaCACerts_jll @stdlib/MozillaCACerts_jll [83775a58] Zlib_jll @stdlib/Zlib_jll [8e850ede] nghttp2_jll @stdlib/nghttp2_jll [3f19e933] p7zip_jll @stdlib/p7zip_jll Precompiling project... ✗ FLOWExaFMM 0 dependencies successfully precompiled in 1 seconds (8 already precompiled) 1 dependency errored. To see a full report either run import Pkg; Pkg.precompile() or load the package Testing Running tests... /local/disk1/pmandl/01_Software/julia-1.6.7/bin/julia: symbol lookup error: /local/disk1/pmandl/01_Software/FLOWExaFMM/src/fmm.so: undefined symbol: _ZN5jlcxx6Module12get_constantERKSs ERROR: LoadError: Failed to precompile FLOWExaFMM [a07d1f4e-0e34-4d8b-bfef-e5b961477d34] to /home/pmandl/.julia/compiled/v1.6/FLOWExaFMM/jl_xaHY8X. Stacktrace: [1] error(s::String) @ Base ./error.jl:33 [2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::Base.TTY, internal_stdout::Base.TTY, ignore_loaded_modules::Bool) @ Base ./loading.jl:1385 [3] compilecache(pkg::Base.PkgId, path::String) @ Base ./loading.jl:1329 [4] _require(pkg::Base.PkgId) @ Base ./loading.jl:1043 [5] require(uuidkey::Base.PkgId) @ Base ./loading.jl:936 [6] require(into::Module, mod::Symbol) @ Base ./loading.jl:923 [7] include(fname::String) @ Base.MainInclude ./client.jl:444 [8] top-level scope @ none:6 in expression starting at /local/disk1/pmandl/01_Software/FLOWExaFMM/test/runtests.jl:2 ERROR: Package FLOWExaFMM errored during testing

EdoAlvarezR commented 1 year ago

Is the Hello World test mentioned here in the manual compilation passing? https://nbviewer.org/github/byuflowlab/FLOWVPM.jl/blob/master/docs/installation-linux.ipynb

ilm71 commented 1 year ago

¥es, it is passing the test, as well as the test

_julia> ] add CxxWrap@0.11.2

You might get an error complaining that you don't have CMake installed on your system. If so go ahead and get that set up. In a Linux machine it's done with

sudo apt-get install cmake

After installing CMake, make sure your CxxWrap package is getting built:

julia> ] test CxxWrap_

is passing

EdoAlvarezR commented 1 year ago

@philippmandl, would you mind commenting on how you solved this issue?