PETSc.jl
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Installation of Mac M1 ARM
Hi, I am facing a problem when testing and using PETSc. I have a friend using the same versions, and it works on his Mac M1. We can not identify any difference… if someone could point me to what I am doing wrong:
brew info openmpi
==> open-mpi: stable 4.1.4 (bottled), HEAD
brew info petsc
==> petsc: stable 3.18.3 (bottled)
julia> versioninfo()
Julia Version 1.8.5
Commit 17cfb8e65ea (2023-01-08 06:45 UTC)
Platform Info:
OS: macOS (arm64-apple-darwin21.5.0)
CPU: 8 × Apple M1 Pro
WORD_SIZE: 64
LIBM: libopenlibm
LLVM: libLLVM-13.0.1 (ORCJIT, apple-m1)
Threads: 6 on 6 virtual cores
Errors
(@v1.8) pkg> build PETSc
Building MPI → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/d56a80d8cf8b9dc3050116346b3d83432b1912c0/build.log`
(@v1.8) pkg> test PETSc
Testing PETSc
Status `/private/var/folders/xc/q9wrnbzn5hz1lmx999bcd_zm0000gn/T/jl_jGuUaB/Project.toml`
[f6369f11] ForwardDiff v0.10.34
⌅ [da04e1cc] MPI v0.19.2
[ace2c81b] PETSc v0.1.3
[91a5bcdd] Plots v1.38.2
[47a9eef4] SparseDiffTools v1.30.0
[b8865327] UnicodePlots v3.3.4
[8fa3689e] PETSc_jll v3.16.8+0
[8f399da3] Libdl `@stdlib/Libdl`
[37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra`
[de0858da] Printf `@stdlib/Printf`
[2f01184e] SparseArrays `@stdlib/SparseArrays`
[8dfed614] Test `@stdlib/Test`
Status `/private/var/folders/xc/q9wrnbzn5hz1lmx999bcd_zm0000gn/T/jl_jGuUaB/Manifest.toml`
[79e6a3ab] Adapt v3.4.0
[ec485272] ArnoldiMethod v0.2.0
[4fba245c] ArrayInterface v6.0.24
[30b0a656] ArrayInterfaceCore v0.1.28
[b0d46f97] ArrayInterfaceStaticArrays v0.1.5
[dd5226c6] ArrayInterfaceStaticArraysCore v0.1.3
[d1d4a3ce] BitFlags v0.1.7
[fa961155] CEnum v0.4.2
[d360d2e6] ChainRulesCore v1.15.6
[9e997f8a] ChangesOfVariables v0.1.4
[944b1d66] CodecZlib v0.7.0
[35d6a980] ColorSchemes v3.20.0
[3da002f7] ColorTypes v0.11.4
[c3611d14] ColorVectorSpace v0.9.10
[5ae59095] Colors v0.12.10
[bbf7d656] CommonSubexpressions v0.3.0
⌃ [34da2185] Compat v3.46.0
[187b0558] ConstructionBase v1.4.1
[d38c429a] Contour v0.6.2
[a8cc5b0e] Crayons v4.1.1
[9a962f9c] DataAPI v1.14.0
[864edb3b] DataStructures v0.18.13
[163ba53b] DiffResults v1.1.0
[b552c78f] DiffRules v1.12.2
⌅ [ffbed154] DocStringExtensions v0.8.6
[c87230d0] FFMPEG v0.4.1
[5789e2e9] FileIO v1.16.0
[6a86dc24] FiniteDiff v2.17.0
[53c48c17] FixedPointNumbers v0.8.4
[59287772] Formatting v0.4.2
[f6369f11] ForwardDiff v0.10.34
[b38be410] FreeType v4.0.0
[28b8d3ca] GR v0.71.3
[86223c79] Graphs v1.7.4
[42e2da0e] Grisu v1.0.2
[cd3eb016] HTTP v1.7.3
[615f187c] IfElse v0.1.1
[d25df0c9] Inflate v0.1.3
[83e8ac13] IniFile v0.5.1
[3587e190] InverseFunctions v0.1.8
[92d709cd] IrrationalConstants v0.1.1
[1019f520] JLFzf v0.1.5
[692b3bcd] JLLWrappers v1.4.1
[682c06a0] JSON v0.21.3
[b964fa9f] LaTeXStrings v1.3.0
[23fbe1c1] Latexify v0.15.18
[2ab3a3ac] LogExpFunctions v0.3.19
[e6f89c97] LoggingExtras v1.0.0
⌅ [da04e1cc] MPI v0.19.2
[3da0fdf6] MPIPreferences v0.1.7
[1914dd2f] MacroTools v0.5.10
[299715c1] MarchingCubes v0.1.4
[739be429] MbedTLS v1.1.7
[442fdcdd] Measures v0.3.2
[e1d29d7a] Missings v1.1.0
[77ba4419] NaNMath v1.0.1
[4d8831e6] OpenSSL v1.3.3
[bac558e1] OrderedCollections v1.4.1
[ace2c81b] PETSc v0.1.3
[69de0a69] Parsers v2.5.3
[b98c9c47] Pipe v1.3.0
[ccf2f8ad] PlotThemes v3.1.0
[995b91a9] PlotUtils v1.3.2
[91a5bcdd] Plots v1.38.2
[21216c6a] Preferences v1.3.0
[3cdcf5f2] RecipesBase v1.3.3
[01d81517] RecipesPipeline v0.6.11
[189a3867] Reexport v1.2.2
[05181044] RelocatableFolders v1.0.0
[ae029012] Requires v1.3.0
[6c6a2e73] Scratch v1.1.1
[efcf1570] Setfield v1.1.1
[992d4aef] Showoff v1.0.3
[777ac1f9] SimpleBufferStream v1.1.0
[699a6c99] SimpleTraits v0.9.4
[66db9d55] SnoopPrecompile v1.0.3
[a2af1166] SortingAlgorithms v1.1.0
[47a9eef4] SparseDiffTools v1.30.0
[276daf66] SpecialFunctions v2.1.7
[aedffcd0] Static v0.8.3
[90137ffa] StaticArrays v1.5.12
[1e83bf80] StaticArraysCore v1.4.0
[82ae8749] StatsAPI v1.5.0
[2913bbd2] StatsBase v0.33.21
[62fd8b95] TensorCore v0.1.1
[3bb67fe8] TranscodingStreams v0.9.11
[5c2747f8] URIs v1.4.1
[1cfade01] UnicodeFun v0.4.1
[b8865327] UnicodePlots v3.3.4
[1986cc42] Unitful v1.12.2
[41fe7b60] Unzip v0.2.0
[19fa3120] VertexSafeGraphs v0.2.0
[6e34b625] Bzip2_jll v1.0.8+0
[83423d85] Cairo_jll v1.16.1+1
[2e619515] Expat_jll v2.4.8+0
[b22a6f82] FFMPEG_jll v4.4.2+2
[a3f928ae] Fontconfig_jll v2.13.93+0
[d7e528f0] FreeType2_jll v2.10.4+0
[559328eb] FriBidi_jll v1.0.10+0
[0656b61e] GLFW_jll v3.3.8+0
[d2c73de3] GR_jll v0.71.3+0
[78b55507] Gettext_jll v0.21.0+0
[7746bdde] Glib_jll v2.74.0+2
[3b182d85] Graphite2_jll v1.3.14+0
[2e76f6c2] HarfBuzz_jll v2.8.1+1
[aacddb02] JpegTurbo_jll v2.1.2+0
[c1c5ebd0] LAME_jll v3.100.1+0
[88015f11] LERC_jll v3.0.0+1
[1d63c593] LLVMOpenMP_jll v15.0.4+0
[dd4b983a] LZO_jll v2.10.1+0
⌅ [e9f186c6] Libffi_jll v3.2.2+1
[d4300ac3] Libgcrypt_jll v1.8.7+0
[7e76a0d4] Libglvnd_jll v1.6.0+0
[7add5ba3] Libgpg_error_jll v1.42.0+0
[94ce4f54] Libiconv_jll v1.16.1+2
[4b2f31a3] Libmount_jll v2.35.0+0
[89763e89] Libtiff_jll v4.4.0+0
[38a345b3] Libuuid_jll v2.36.0+0
[d00139f3] METIS_jll v5.1.2+0
[7cb0a576] MPICH_jll v4.0.2+5
[f1f71cc9] MPItrampoline_jll v5.0.2+1
[ca64183c] MUMPS_jll v5.5.1+1
[9237b28f] MicrosoftMPI_jll v10.1.3+2
[e7412a2a] Ogg_jll v1.3.5+1
⌅ [656ef2d0] OpenBLAS32_jll v0.3.17+0
[fe0851c0] OpenMPI_jll v4.1.3+3
[458c3c95] OpenSSL_jll v1.1.19+0
[efe28fd5] OpenSpecFun_jll v0.5.5+0
[91d4177d] Opus_jll v1.3.2+0
[b247a4be] PARMETIS_jll v4.0.6+0
[8fa3689e] PETSc_jll v3.16.8+0
[30392449] Pixman_jll v0.40.1+0
[ea2cea3b] Qt5Base_jll v5.15.3+2
[aabda75e] SCALAPACK32_jll v2.2.1+0
[a8d0f55d] SCOTCH_jll v6.1.3+0
[9a1356b0] SuperLU_DIST_jll v8.0.2+0
[a2964d1f] Wayland_jll v1.21.0+0
[2381bf8a] Wayland_protocols_jll v1.25.0+0
[02c8fc9c] XML2_jll v2.10.3+0
[aed1982a] XSLT_jll v1.1.34+0
[4f6342f7] Xorg_libX11_jll v1.6.9+4
[0c0b7dd1] Xorg_libXau_jll v1.0.9+4
[935fb764] Xorg_libXcursor_jll v1.2.0+4
[a3789734] Xorg_libXdmcp_jll v1.1.3+4
[1082639a] Xorg_libXext_jll v1.3.4+4
[d091e8ba] Xorg_libXfixes_jll v5.0.3+4
[a51aa0fd] Xorg_libXi_jll v1.7.10+4
[d1454406] Xorg_libXinerama_jll v1.1.4+4
[ec84b674] Xorg_libXrandr_jll v1.5.2+4
[ea2f1a96] Xorg_libXrender_jll v0.9.10+4
[14d82f49] Xorg_libpthread_stubs_jll v0.1.0+3
[c7cfdc94] Xorg_libxcb_jll v1.13.0+3
[cc61e674] Xorg_libxkbfile_jll v1.1.0+4
[12413925] Xorg_xcb_util_image_jll v0.4.0+1
[2def613f] Xorg_xcb_util_jll v0.4.0+1
[975044d2] Xorg_xcb_util_keysyms_jll v0.4.0+1
[0d47668e] Xorg_xcb_util_renderutil_jll v0.3.9+1
[c22f9ab0] Xorg_xcb_util_wm_jll v0.4.1+1
[35661453] Xorg_xkbcomp_jll v1.4.2+4
[33bec58e] Xorg_xkeyboard_config_jll v2.27.0+4
[c5fb5394] Xorg_xtrans_jll v1.4.0+3
[3161d3a3] Zstd_jll v1.5.2+0
⌅ [214eeab7] fzf_jll v0.29.0+0
[a4ae2306] libaom_jll v3.4.0+0
[0ac62f75] libass_jll v0.15.1+0
[f638f0a6] libfdk_aac_jll v2.0.2+0
[b53b4c65] libpng_jll v1.6.38+0
[f27f6e37] libvorbis_jll v1.3.7+1
[1270edf5] x264_jll v2021.5.5+0
[dfaa095f] x265_jll v3.5.0+0
[d8fb68d0] xkbcommon_jll v1.4.1+0
[0dad84c5] ArgTools v1.1.1 `@stdlib/ArgTools`
[56f22d72] Artifacts `@stdlib/Artifacts`
[2a0f44e3] Base64 `@stdlib/Base64`
[ade2ca70] Dates `@stdlib/Dates`
[8bb1440f] DelimitedFiles `@stdlib/DelimitedFiles`
[8ba89e20] Distributed `@stdlib/Distributed`
[f43a241f] Downloads v1.6.0 `@stdlib/Downloads`
[7b1f6079] FileWatching `@stdlib/FileWatching`
[9fa8497b] Future `@stdlib/Future`
[b77e0a4c] InteractiveUtils `@stdlib/InteractiveUtils`
[4af54fe1] LazyArtifacts `@stdlib/LazyArtifacts`
[b27032c2] LibCURL v0.6.3 `@stdlib/LibCURL`
[76f85450] LibGit2 `@stdlib/LibGit2`
[8f399da3] Libdl `@stdlib/Libdl`
[37e2e46d] LinearAlgebra `@stdlib/LinearAlgebra`
[56ddb016] Logging `@stdlib/Logging`
[d6f4376e] Markdown `@stdlib/Markdown`
[a63ad114] Mmap `@stdlib/Mmap`
[ca575930] NetworkOptions v1.2.0 `@stdlib/NetworkOptions`
[44cfe95a] Pkg v1.8.0 `@stdlib/Pkg`
[de0858da] Printf `@stdlib/Printf`
[3fa0cd96] REPL `@stdlib/REPL`
[9a3f8284] Random `@stdlib/Random`
[ea8e919c] SHA v0.7.0 `@stdlib/SHA`
[9e88b42a] Serialization `@stdlib/Serialization`
[1a1011a3] SharedArrays `@stdlib/SharedArrays`
[6462fe0b] Sockets `@stdlib/Sockets`
[2f01184e] SparseArrays `@stdlib/SparseArrays`
[10745b16] Statistics `@stdlib/Statistics`
[4607b0f0] SuiteSparse `@stdlib/SuiteSparse`
[fa267f1f] TOML v1.0.0 `@stdlib/TOML`
[a4e569a6] Tar v1.10.1 `@stdlib/Tar`
[8dfed614] Test `@stdlib/Test`
[cf7118a7] UUIDs `@stdlib/UUIDs`
[4ec0a83e] Unicode `@stdlib/Unicode`
[e66e0078] CompilerSupportLibraries_jll v1.0.1+0 `@stdlib/CompilerSupportLibraries_jll`
[deac9b47] LibCURL_jll v7.84.0+0 `@stdlib/LibCURL_jll`
[29816b5a] LibSSH2_jll v1.10.2+0 `@stdlib/LibSSH2_jll`
[c8ffd9c3] MbedTLS_jll v2.28.0+0 `@stdlib/MbedTLS_jll`
[14a3606d] MozillaCACerts_jll v2022.2.1 `@stdlib/MozillaCACerts_jll`
[4536629a] OpenBLAS_jll v0.3.20+0 `@stdlib/OpenBLAS_jll`
[05823500] OpenLibm_jll v0.8.1+0 `@stdlib/OpenLibm_jll`
[efcefdf7] PCRE2_jll v10.40.0+0 `@stdlib/PCRE2_jll`
[bea87d4a] SuiteSparse_jll v5.10.1+0 `@stdlib/SuiteSparse_jll`
[83775a58] Zlib_jll v1.2.12+3 `@stdlib/Zlib_jll`
[8e850b90] libblastrampoline_jll v5.1.1+0 `@stdlib/libblastrampoline_jll`
[8e850ede] nghttp2_jll v1.48.0+0 `@stdlib/nghttp2_jll`
[3f19e933] p7zip_jll v17.4.0+0 `@stdlib/p7zip_jll`
Info Packages marked with ⌃ and ⌅ have new versions available, but those with ⌅ are restricted by compatibility constraints from upgrading.
Precompiling project...
✗ PETSc
0 dependencies successfully precompiled in 2 seconds. 179 already precompiled.
1 dependency errored. To see a full report either run `import Pkg; Pkg.precompile()` or load the package
Testing Running tests...
[cli_0]: write_line error; fd=4 buf=:cmd=init pmi_version=1 pmi_subversion=1
:
system msg for write_line failure : Bad file descriptor
[cli_0]: Unable to write to PMI_fd
[cli_0]: write_line error; fd=4 buf=:cmd=get_appnum
:
system msg for write_line failure : Bad file descriptor
cmd=init pmi_version=1 pmi_subversion=1
[cli_2]: Error reading initack on 13
Error on readline:: Bad file descriptor
cmd=abort exitcode=-1
[cli_2]: readline failed
cmd=abort exitcode=-1
[cli_2]: readline failed
cmd=get_maxes
[cli_2]: readline failed
cmd=get_appnum
[cli_2]: readline failed
[cli_1]: Error reading initack on 7
Error on readline:: Bad file descriptor
[cli_1]: readline failed
[cli_1]: readline failed
[cli_1]: readline failed
[cli_1]: readline failed
Fatal error in internal_Init_thread: Other MPI error, error stack:
internal_Init_thread(60): MPI_Init_thread(argc=0x0, argv=0x0, required=2, provided=0x10e6e74c0) failed
MPII_Init_thread(209)...:
MPID_Init(72)...........:
init_local(135).........: channel initialization failed
init_pg(332)............:
MPIR_pmi_init(111)......: PMI_Get_appnum returned -1
[cli_0]: write_line error; fd=4 buf=:cmd=abort exitcode=136957711
:
system msg for write_line failure : Bad file descriptor
Fatal error in internal_Init_thread: Other MPI error, error stack:
internal_Init_thread(60): MPI_Init_thread(argc=0x0, argv=0x0, required=2, provided=0x10d9234c0) failed
MPII_Init_thread(209)...:
MPID_Init(72)...........:
init_local(135).........: channel initialization failed
init_pg(332)............:
MPIR_pmi_init(111)......: PMI_Get_appnum returned -1
[cli_1]: readline failed
Fatal error in internal_Init_thread: Other MPI error, error stack:
internal_Init_thread(60): MPI_Init_thread(argc=0x0, argv=0x0, required=2, provided=0x10da134c0) failed
MPII_Init_thread(209)...:
MPID_Init(72)...........:
init_local(135).........: channel initialization failed
init_pg(332)............:
MPIR_pmi_init(111)......: PMI_Get_appnum returned -1
cmd=abort exitcode=271175439
[cli_2]: readline failed
[cli_3]: write_line error; fd=17 buf=:cmd=init pmi_version=1 pmi_subversion=1
:
system msg for write_line failure : Bad file descriptor
[cli_3]: Unable to write to PMI_fd
[cli_3]: write_line error; fd=17 buf=:cmd=get_appnum
:
system msg for write_line failure : Bad file descriptor
Fatal error in internal_Init_thread: Other MPI error, error stack:
internal_Init_thread(60): MPI_Init_thread(argc=0x0, argv=0x0, required=2, provided=0x109a274c0) failed
MPII_Init_thread(209)...:
MPID_Init(72)...........:
init_local(135).........: channel initialization failed
init_pg(332)............:
MPIR_pmi_init(111)......: PMI_Get_appnum returned -1
[cli_3]: write_line error; fd=17 buf=:cmd=abort exitcode=942264079
:
system msg for write_line failure : Bad file descriptor
ERROR: LoadError: ERROR: LoadError: ERROR: LoadError: ERROR: LoadError: Failed to precompile PETSc [ace2c81b-2b5f-4b1e-a30d-d662738edfe0] to /Users/r/.julia/compiled/v1.8/PETSc/jl_8eObYL.
Stacktrace:
[1] error(s::Failed to precompile PETSc [ace2c81b-2b5f-4b1e-a30d-d662738edfe0] to /Users/r/.julia/compiled/v1.8/PETSc/jl_PM71Ms.
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
in expression starting at /Users/r/.julia/packages/PETSc/LSdRz/test/dmda.jl:2
Failed to precompile PETSc [ace2c81b-2b5f-4b1e-a30d-d662738edfe0] to /Users/r/.julia/compiled/v1.8/PETSc/jl_R8vl3k.
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
in expression starting at /Users/r/.julia/packages/PETSc/LSdRz/test/dmda.jl:2
String)
@ Base ./error.jl:35
[2] compilecache(pkg::Base.PkgId, path::String, internal_stderr::IO, internal_stdout::IO, Failed to precompile PETSc [ace2c81b-2b5f-4b1e-a30d-d662738edfe0] to /Users/r/.julia/compiled/v1.8/PETSc/jl_Zsv0g5.keep_loaded_modules::
Stacktrace:Bool
)
@ Base[1] ./errorloading.jl:1707(s
:: [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
in expression starting at /Users/r/.julia/packages/PETSc/LSdRz/test/dmda.jl:2
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
in expression starting at /Users/r/.julia/packages/PETSc/LSdRz/test/dmda.jl:2
mpi tests: Test Failed at /Users/r/.julia/packages/PETSc/LSdRz/test/runtests.jl:8
Expression: mpiexec() do mpi_cmd
cmd = `$mpi_cmd -n 4 $(Base.julia_cmd()) --project dmda.jl`
success(pipeline(cmd, stderr = stderr))
end
Stacktrace:
[1] macro expansion
@ ~/.julia/juliaup/julia-1.8.5+0.aarch64.apple.darwin14/share/julia/stdlib/v1.8/Test/src/Test.jl:464 [inlined]
[2] macro expansion
@ ~/.julia/packages/PETSc/LSdRz/test/runtests.jl:8 [inlined]
[3] macro expansion
@ ~/.julia/juliaup/julia-1.8.5+0.aarch64.apple.darwin14/share/julia/stdlib/v1.8/Test/src/Test.jl:1363 [inlined]
[4] top-level scope
@ ~/.julia/packages/PETSc/LSdRz/test/runtests.jl:8
Test Summary: | Fail Total Time
mpi tests | 1 1 1.7s
ERROR: LoadError: Some tests did not pass: 0 passed, 1 failed, 0 errored, 0 broken.
in expression starting at /Users/r/.julia/packages/PETSc/LSdRz/test/runtests.jl:6
ERROR: Package PETSc errored during testing