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PETSc error in tests in v0.3.0 on a clean install due the environment not being instantiated. #204

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ViralBShah opened this issue Oct 28, 2024 · 7 comments
Closed

PETSc error in tests in v0.3.0 on a clean install due the environment not being instantiated. #204

ViralBShah opened this issue Oct 28, 2024 · 7 comments

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@ViralBShah
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ViralBShah commented Oct 28, 2024 •
edited
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I didn't see this error in CI, but getting this when running tests locally on v0.3.0. The tests were running fine before I made the release.

(@v1.11) pkg> test PETSc
     Testing PETSc
      Status `/private/var/folders/p9/shj83ry93_9g13vt_0m23d240000gn/T/jl_pAB2dr/Project.toml`
  [f6369f11] ForwardDiff v0.10.36
  [da04e1cc] MPI v0.20.22
  [3da0fdf6] MPIPreferences v0.1.11
  [ace2c81b] PETSc v0.3.0 `~/.julia/dev/PETSc`
  [91a5bcdd] Plots v1.40.8
  [47a9eef4] SparseDiffTools v2.23.0
  [b8865327] UnicodePlots v3.7.0
  [8fa3689e] PETSc_jll v3.22.0+0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [de0858da] Printf v1.11.0
  [2f01184e] SparseArrays v1.11.0
  [8dfed614] Test v1.11.0
      Status `/private/var/folders/p9/shj83ry93_9g13vt_0m23d240000gn/T/jl_pAB2dr/Manifest.toml`
  [47edcb42] ADTypes v1.9.0
  [7d9f7c33] Accessors v0.1.38
  [79e6a3ab] Adapt v4.1.0
  [ec485272] ArnoldiMethod v0.4.0
  [4fba245c] ArrayInterface v7.16.0
  [d1d4a3ce] BitFlags v0.1.9
  [944b1d66] CodecZlib v0.7.6
  [35d6a980] ColorSchemes v3.27.0
⌅ [3da002f7] ColorTypes v0.11.5
  [c3611d14] ColorVectorSpace v0.10.0
⌅ [5ae59095] Colors v0.12.11
  [bbf7d656] CommonSubexpressions v0.3.1
  [f70d9fcc] CommonWorldInvalidations v1.0.0
  [34da2185] Compat v4.16.0
  [a33af91c] CompositionsBase v0.1.2
  [f0e56b4a] ConcurrentUtilities v2.4.2
  [187b0558] ConstructionBase v1.5.8
  [d38c429a] Contour v0.6.3
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.18.20
  [8bb1440f] DelimitedFiles v1.9.1
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [ffbed154] DocStringExtensions v0.9.3
  [460bff9d] ExceptionUnwrapping v0.1.10
  [c87230d0] FFMPEG v0.4.2
  [6a86dc24] FiniteDiff v2.26.0
  [53c48c17] FixedPointNumbers v0.8.5
  [1fa38f19] Format v1.3.7
  [f6369f11] ForwardDiff v0.10.36
  [28b8d3ca] GR v0.73.8
  [86223c79] Graphs v1.12.0
  [42e2da0e] Grisu v1.0.2
  [cd3eb016] HTTP v1.10.9
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.5
  [3587e190] InverseFunctions v0.1.17
  [92d709cd] IrrationalConstants v0.2.2
  [1019f520] JLFzf v0.1.8
  [692b3bcd] JLLWrappers v1.6.1
  [682c06a0] JSON v0.21.4
  [b964fa9f] LaTeXStrings v1.4.0
  [23fbe1c1] Latexify v0.16.5
  [2ab3a3ac] LogExpFunctions v0.3.28
  [e6f89c97] LoggingExtras v1.1.0
  [da04e1cc] MPI v0.20.22
  [3da0fdf6] MPIPreferences v0.1.11
  [1914dd2f] MacroTools v0.5.13
  [299715c1] MarchingCubes v0.1.10
  [739be429] MbedTLS v1.1.9
  [442fdcdd] Measures v0.3.2
  [e1d29d7a] Missings v1.2.0
  [77ba4419] NaNMath v1.0.2
  [4d8831e6] OpenSSL v1.4.3
  [bac558e1] OrderedCollections v1.6.3
  [ace2c81b] PETSc v0.3.0 `~/.julia/dev/PETSc`
  [65ce6f38] PackageExtensionCompat v1.0.2
  [69de0a69] Parsers v2.8.1
  [b98c9c47] Pipe v1.3.0
  [eebad327] PkgVersion v0.3.3
  [ccf2f8ad] PlotThemes v3.2.0
  [995b91a9] PlotUtils v1.4.2
  [91a5bcdd] Plots v1.40.8
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [3cdcf5f2] RecipesBase v1.3.4
  [01d81517] RecipesPipeline v0.6.12
  [189a3867] Reexport v1.2.2
  [05181044] RelocatableFolders v1.0.1
  [ae029012] Requires v1.3.0
  [c0aeaf25] SciMLOperators v0.3.11
  [6c6a2e73] Scratch v1.2.1
  [efcf1570] Setfield v1.1.1
  [992d4aef] Showoff v1.0.3
  [777ac1f9] SimpleBufferStream v1.2.0
  [699a6c99] SimpleTraits v0.9.4
  [a2af1166] SortingAlgorithms v1.2.1
  [47a9eef4] SparseDiffTools v2.23.0
  [276daf66] SpecialFunctions v2.4.0
  [860ef19b] StableRNGs v1.0.2
  [aedffcd0] Static v1.1.1
  [0d7ed370] StaticArrayInterface v1.8.0
  [90137ffa] StaticArrays v1.9.8
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.3
  [62fd8b95] TensorCore v0.1.1
  [3bb67fe8] TranscodingStreams v0.11.3
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1cfade01] UnicodeFun v0.4.1
  [b8865327] UnicodePlots v3.7.0
  [1986cc42] Unitful v1.21.0
  [45397f5d] UnitfulLatexify v1.6.4
  [41fe7b60] Unzip v0.2.0
  [19fa3120] VertexSafeGraphs v0.2.0
  [6e34b625] Bzip2_jll v1.0.8+2
  [83423d85] Cairo_jll v1.18.2+1
  [ee1fde0b] Dbus_jll v1.14.10+0
  [2702e6a9] EpollShim_jll v0.0.20230411+0
  [2e619515] Expat_jll v2.6.2+0
⌅ [b22a6f82] FFMPEG_jll v4.4.4+1
  [a3f928ae] Fontconfig_jll v2.13.96+0
  [d7e528f0] FreeType2_jll v2.13.2+0
  [559328eb] FriBidi_jll v1.0.14+0
  [0656b61e] GLFW_jll v3.4.0+1
  [d2c73de3] GR_jll v0.73.8+0
  [78b55507] Gettext_jll v0.21.0+0
  [7746bdde] Glib_jll v2.80.5+0
  [3b182d85] Graphite2_jll v1.3.14+0
  [2e76f6c2] HarfBuzz_jll v8.3.1+0
  [e33a78d0] Hwloc_jll v2.11.2+0
  [aacddb02] JpegTurbo_jll v3.0.4+0
  [c1c5ebd0] LAME_jll v3.100.2+0
  [88015f11] LERC_jll v4.0.0+0
  [1d63c593] LLVMOpenMP_jll v18.1.7+0
  [dd4b983a] LZO_jll v2.10.2+1
⌅ [e9f186c6] Libffi_jll v3.2.2+1
  [d4300ac3] Libgcrypt_jll v1.11.0+0
  [7e76a0d4] Libglvnd_jll v1.6.0+0
  [7add5ba3] Libgpg_error_jll v1.50.0+0
  [94ce4f54] Libiconv_jll v1.17.0+1
  [4b2f31a3] Libmount_jll v2.40.1+0
  [89763e89] Libtiff_jll v4.7.0+0
  [38a345b3] Libuuid_jll v2.40.1+0
  [7cb0a576] MPICH_jll v4.2.3+0
  [f1f71cc9] MPItrampoline_jll v5.5.1+0
  [9237b28f] MicrosoftMPI_jll v10.1.4+2
  [e7412a2a] Ogg_jll v1.3.5+1
  [656ef2d0] OpenBLAS32_jll v0.3.28+3
  [fe0851c0] OpenMPI_jll v5.0.5+0
  [458c3c95] OpenSSL_jll v3.0.15+1
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [91d4177d] Opus_jll v1.3.3+0
  [8fa3689e] PETSc_jll v3.22.0+0
  [36c8627f] Pango_jll v1.54.1+0
  [30392449] Pixman_jll v0.43.4+0
  [c0090381] Qt6Base_jll v6.7.1+1
  [629bc702] Qt6Declarative_jll v6.7.1+2
  [ce943373] Qt6ShaderTools_jll v6.7.1+1
  [e99dba38] Qt6Wayland_jll v6.7.1+1
  [aabda75e] SCALAPACK32_jll v2.2.1+1
  [a44049a8] Vulkan_Loader_jll v1.3.243+0
  [a2964d1f] Wayland_jll v1.21.0+1
  [2381bf8a] Wayland_protocols_jll v1.31.0+0
  [02c8fc9c] XML2_jll v2.13.4+0
  [aed1982a] XSLT_jll v1.1.41+0
  [ffd25f8a] XZ_jll v5.6.3+0
  [f67eecfb] Xorg_libICE_jll v1.1.1+0
  [c834827a] Xorg_libSM_jll v1.2.4+0
  [4f6342f7] Xorg_libX11_jll v1.8.6+0
  [0c0b7dd1] Xorg_libXau_jll v1.0.11+0
  [935fb764] Xorg_libXcursor_jll v1.2.0+4
  [a3789734] Xorg_libXdmcp_jll v1.1.4+0
  [1082639a] Xorg_libXext_jll v1.3.6+0
  [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 v0.9.11+0
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.1+0
  [c7cfdc94] Xorg_libxcb_jll v1.17.0+0
  [cc61e674] Xorg_libxkbfile_jll v1.1.2+0
  [e920d4aa] Xorg_xcb_util_cursor_jll v0.1.4+0
  [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 v1.4.6+0
  [33bec58e] Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] Xorg_xtrans_jll v1.5.0+0
  [3161d3a3] Zstd_jll v1.5.6+1
  [35ca27e7] eudev_jll v3.2.9+0
  [214eeab7] fzf_jll v0.53.0+0
  [1a1c6b14] gperf_jll v3.1.1+0
  [a4ae2306] libaom_jll v3.9.0+0
  [0ac62f75] libass_jll v0.15.2+0
  [1183f4f0] libdecor_jll v0.2.2+0
  [2db6ffa8] libevdev_jll v1.11.0+0
  [f638f0a6] libfdk_aac_jll v2.0.3+0
  [36db933b] libinput_jll v1.18.0+0
  [b53b4c65] libpng_jll v1.6.44+0
  [f27f6e37] libvorbis_jll v1.3.7+2
  [009596ad] mtdev_jll v1.1.6+0
⌅ [1270edf5] x264_jll v2021.5.5+0
⌅ [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+1
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [4af54fe1] LazyArtifacts v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.11.0
  [de0858da] Printf v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [1a1011a3] SharedArrays v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays v1.11.0
  [f489334b] StyledStrings v1.11.0
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.7.2+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [4536629a] OpenBLAS_jll v0.3.27+1
  [05823500] OpenLibm_jll v0.8.1+2
  [efcefdf7] PCRE2_jll v10.42.0+1
  [bea87d4a] SuiteSparse_jll v7.7.0+0
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.59.0+0
  [3f19e933] p7zip_jll v17.4.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
┌ Info: Testing PETSc.jl with
│   MPIPreferences.binary = "MPICH_jll"
│   MPIPreferences.abi = "MPICH"
└   PETSc_jll.host_platform = macOS aarch64 {cxxstring_abi=cxx11, julia_version=1.11.1, libgfortran_version=5.0.0, mpi=mpich}
Test Summary: | Pass  Total  Time
DMDACreate1D  |  460    460  1.5s
Test Summary: | Pass  Total  Time
DMDACreate2D  | 2624   2624  0.3s
Test Summary: |  Pass  Total  Time
DMDACreate3D  | 12096  12096  1.8s
Test Summary: | Pass  Total  Time
creatematrix  |   40     40  0.5s
Test Summary:              | Pass  Total  Time
DM Vectors and Coordinates |  380    380  0.4s
Test Summary: | Total   Time
mpi examples  |     0  17.3s
Test Summary: | Pass  Total  Time
options tests |  144    144  0.6s
Test Summary:       | Pass  Total  Time
parse_options tests |    1      1  3.6s
Test Summary: | Pass  Total  Time
DMDACreate1D  |  460    460  1.1s
Test Summary: | Pass  Total  Time
DMDACreate2D  | 2624   2624  0.4s
Test Summary: |  Pass  Total  Time
DMDACreate3D  | 12096  12096  2.8s
Test Summary: | Pass  Total  Time
creatematrix  |   40     40  0.5s
Test Summary:              | Pass  Total  Time
DM Vectors and Coordinates |  360    360  0.4s
[0]PETSC ERROR: --------------------- Error Message --------------------------------------------------------------
[0]PETSC ERROR: Object is in wrong state
[0]PETSC ERROR: Vector has been unlocked from read-only access too many times
[0]PETSC ERROR: See https://petsc.org/release/faq/ for trouble shooting.
[0]PETSC ERROR: Petsc Release Version 3.22.0, Sep 28, 2024 
[0]PETSC ERROR: Unknown Name with 1 MPI process(es) and PETSC_ARCH  on Virals-MacBook-Pro.local by viralshah Mon Oct 28 14:07:50 2024
[0]PETSC ERROR: Configure options: --prefix=/workspace/destdir/lib/petsc/double_real_Int64 --CC=mpicc --FC=mpif90 --CXX=mpicxx --COPTFLAGS=-O3 -g --CXXOPTFLAGS=-O3 -g --FOPTFLAGS=-O3 --with-blaslapack-lib=/workspace/destdir/lib/libopenblas.dylib --with-blaslapack-suffix= --CFLAGS=-fno-stack-protector --FFLAGS=" " --LDFLAGS=-L/workspace/destdir/lib --CC_LINKER_FLAGS= --with-64-bit-indices=1 --with-debugging=0 --with-batch --with-mpi=1 --with-mpi-lib="[/workspace/destdir/lib/libmpifort.dylib,/workspace/destdir/lib/libmpi.dylib]" --with-mpi-include=/workspace/destdir/include --with-sowing=0 --with-precision=double --with-scalar-type=real --with-pthread=0 --PETSC_ARCH=aarch64-apple-darwin20_double_real_Int64 --with-scalapack-lib=/workspace/destdir/lib/libscalapack32.dylib --with-scalapack-include=/workspace/destdir/include --download-suitesparse=1 --download-suitesparse-shared=0 --download-superlu_dist=1 --download-superlu_dist-shared=0 --download-hypre=1 --download-hypre-shared=0 --download-hypre-configure-arguments="--host --build" --download-mumps=1 --download-mumps-shared=0 --download-tetgen=1 --download-triangle=1 --SOSUFFIX=double_real_Int64 --with-shared-libraries=1 --with-clean=1
[0]PETSC ERROR: #1 VecLockReadPop() at /workspace/srcdir/petsc-3.22.0/src/vec/vec/interface/rvector.c:4032
[0]PETSC ERROR: #2 MatMult() at /workspace/srcdir/petsc-3.22.0/src/mat/interface/matrix.c:2670
ERROR: LoadError: Some tests did not pass: 19 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /Users/viralshah/.julia/dev/PETSc/test/old_test.jl:6
in expression starting at /Users/viralshah/.julia/dev/PETSc/test/runtests.jl:32
ERROR: Package PETSc errored during testing
@boriskaus
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I initially encountered the same on my local machine, but did not notice it anymore after the last push before 0.3.0

@ViralBShah
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ViralBShah commented Oct 28, 2024 •
edited
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I deleted all my dev files so that it pulled in the latest released version, and now I get a package related error with MPI. I can't quite figure out why this suddenly started happening now.

@v1.11) pkg> add PETSc
   Resolving package versions...
    Updating `~/.julia/environments/v1.11/Project.toml`
  [ace2c81b] + PETSc v0.3.0
    Updating `~/.julia/environments/v1.11/Manifest.toml`
  [ffbed154] + DocStringExtensions v0.9.3
  [692b3bcd] + JLLWrappers v1.6.1
  [da04e1cc] + MPI v0.20.22
  [3da0fdf6] + MPIPreferences v0.1.11
  [ace2c81b] + PETSc v0.3.0
  [eebad327] + PkgVersion v0.3.3
  [aea7be01] + PrecompileTools v1.2.1
  [21216c6a] + Preferences v1.4.3
  [ae029012] + Requires v1.3.0
  [e33a78d0] + Hwloc_jll v2.11.2+0
  [7cb0a576] + MPICH_jll v4.2.3+0
  [f1f71cc9] + MPItrampoline_jll v5.5.1+0
  [9237b28f] + MicrosoftMPI_jll v10.1.4+2
  [656ef2d0] + OpenBLAS32_jll v0.3.28+3
  [fe0851c0] + OpenMPI_jll v5.0.5+0
  [8fa3689e] + PETSc_jll v3.22.0+0
  [aabda75e] + SCALAPACK32_jll v2.2.1+1
  [0dad84c5] + ArgTools v1.1.2
  [56f22d72] + Artifacts v1.11.0
  [2a0f44e3] + Base64 v1.11.0
  [ade2ca70] + Dates v1.11.0
  [8ba89e20] + Distributed v1.11.0
  [f43a241f] + Downloads v1.6.0
  [7b1f6079] + FileWatching v1.11.0
  [4af54fe1] + LazyArtifacts v1.11.0
  [b27032c2] + LibCURL v0.6.4
  [76f85450] + LibGit2 v1.11.0
  [8f399da3] + Libdl v1.11.0
  [37e2e46d] + LinearAlgebra v1.11.0
  [56ddb016] + Logging v1.11.0
  [d6f4376e] + Markdown v1.11.0
  [ca575930] + NetworkOptions v1.2.0
  [44cfe95a] + Pkg v1.11.0
  [de0858da] + Printf v1.11.0
  [9a3f8284] + Random v1.11.0
  [ea8e919c] + SHA v0.7.0
  [9e88b42a] + Serialization v1.11.0
  [6462fe0b] + Sockets v1.11.0
  [2f01184e] + SparseArrays v1.11.0
  [fa267f1f] + TOML v1.0.3
  [a4e569a6] + Tar v1.10.0
  [cf7118a7] + UUIDs v1.11.0
  [4ec0a83e] + Unicode v1.11.0
  [e66e0078] + CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] + LibCURL_jll v8.6.0+0
  [e37daf67] + LibGit2_jll v1.7.2+0
  [29816b5a] + LibSSH2_jll v1.11.0+1
  [c8ffd9c3] + MbedTLS_jll v2.28.6+0
  [14a3606d] + MozillaCACerts_jll v2023.12.12
  [4536629a] + OpenBLAS_jll v0.3.27+1
  [bea87d4a] + SuiteSparse_jll v7.7.0+0
  [83775a58] + Zlib_jll v1.2.13+1
  [8e850b90] + libblastrampoline_jll v5.11.0+0
  [8e850ede] + nghttp2_jll v1.59.0+0
  [3f19e933] + p7zip_jll v17.4.0+2

(@v1.11) pkg> test PETSc
     Testing PETSc
      Status `/private/var/folders/p9/shj83ry93_9g13vt_0m23d240000gn/T/jl_HWoJUL/Project.toml`
  [f6369f11] ForwardDiff v0.10.36
  [da04e1cc] MPI v0.20.22
  [3da0fdf6] MPIPreferences v0.1.11
  [ace2c81b] PETSc v0.3.0
  [91a5bcdd] Plots v1.40.8
  [47a9eef4] SparseDiffTools v2.23.0
  [b8865327] UnicodePlots v3.7.0
  [8fa3689e] PETSc_jll v3.22.0+0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [de0858da] Printf v1.11.0
  [2f01184e] SparseArrays v1.11.0
  [8dfed614] Test v1.11.0
      Status `/private/var/folders/p9/shj83ry93_9g13vt_0m23d240000gn/T/jl_HWoJUL/Manifest.toml`
  [47edcb42] ADTypes v1.9.0
  [7d9f7c33] Accessors v0.1.38
  [79e6a3ab] Adapt v4.1.0
  [ec485272] ArnoldiMethod v0.4.0
  [4fba245c] ArrayInterface v7.16.0
  [d1d4a3ce] BitFlags v0.1.9
  [944b1d66] CodecZlib v0.7.6
  [35d6a980] ColorSchemes v3.27.0
⌅ [3da002f7] ColorTypes v0.11.5
  [c3611d14] ColorVectorSpace v0.10.0
⌅ [5ae59095] Colors v0.12.11
  [bbf7d656] CommonSubexpressions v0.3.1
  [f70d9fcc] CommonWorldInvalidations v1.0.0
  [34da2185] Compat v4.16.0
  [a33af91c] CompositionsBase v0.1.2
  [f0e56b4a] ConcurrentUtilities v2.4.2
  [187b0558] ConstructionBase v1.5.8
  [d38c429a] Contour v0.6.3
  [a8cc5b0e] Crayons v4.1.1
  [9a962f9c] DataAPI v1.16.0
  [864edb3b] DataStructures v0.18.20
  [8bb1440f] DelimitedFiles v1.9.1
  [163ba53b] DiffResults v1.1.0
  [b552c78f] DiffRules v1.15.1
  [ffbed154] DocStringExtensions v0.9.3
  [460bff9d] ExceptionUnwrapping v0.1.10
  [c87230d0] FFMPEG v0.4.2
  [6a86dc24] FiniteDiff v2.26.0
  [53c48c17] FixedPointNumbers v0.8.5
  [1fa38f19] Format v1.3.7
  [f6369f11] ForwardDiff v0.10.36
  [28b8d3ca] GR v0.73.8
  [86223c79] Graphs v1.12.0
  [42e2da0e] Grisu v1.0.2
  [cd3eb016] HTTP v1.10.9
  [615f187c] IfElse v0.1.1
  [d25df0c9] Inflate v0.1.5
  [3587e190] InverseFunctions v0.1.17
  [92d709cd] IrrationalConstants v0.2.2
  [1019f520] JLFzf v0.1.8
  [692b3bcd] JLLWrappers v1.6.1
  [682c06a0] JSON v0.21.4
  [b964fa9f] LaTeXStrings v1.4.0
  [23fbe1c1] Latexify v0.16.5
  [2ab3a3ac] LogExpFunctions v0.3.28
  [e6f89c97] LoggingExtras v1.1.0
  [da04e1cc] MPI v0.20.22
  [3da0fdf6] MPIPreferences v0.1.11
  [1914dd2f] MacroTools v0.5.13
  [299715c1] MarchingCubes v0.1.10
  [739be429] MbedTLS v1.1.9
  [442fdcdd] Measures v0.3.2
  [e1d29d7a] Missings v1.2.0
  [77ba4419] NaNMath v1.0.2
  [4d8831e6] OpenSSL v1.4.3
  [bac558e1] OrderedCollections v1.6.3
  [ace2c81b] PETSc v0.3.0
  [65ce6f38] PackageExtensionCompat v1.0.2
  [69de0a69] Parsers v2.8.1
  [b98c9c47] Pipe v1.3.0
  [eebad327] PkgVersion v0.3.3
  [ccf2f8ad] PlotThemes v3.2.0
  [995b91a9] PlotUtils v1.4.2
  [91a5bcdd] Plots v1.40.8
  [aea7be01] PrecompileTools v1.2.1
  [21216c6a] Preferences v1.4.3
  [3cdcf5f2] RecipesBase v1.3.4
  [01d81517] RecipesPipeline v0.6.12
  [189a3867] Reexport v1.2.2
  [05181044] RelocatableFolders v1.0.1
  [ae029012] Requires v1.3.0
  [c0aeaf25] SciMLOperators v0.3.11
  [6c6a2e73] Scratch v1.2.1
  [efcf1570] Setfield v1.1.1
  [992d4aef] Showoff v1.0.3
  [777ac1f9] SimpleBufferStream v1.2.0
  [699a6c99] SimpleTraits v0.9.4
  [a2af1166] SortingAlgorithms v1.2.1
  [47a9eef4] SparseDiffTools v2.23.0
  [276daf66] SpecialFunctions v2.4.0
  [860ef19b] StableRNGs v1.0.2
  [aedffcd0] Static v1.1.1
  [0d7ed370] StaticArrayInterface v1.8.0
  [90137ffa] StaticArrays v1.9.8
  [1e83bf80] StaticArraysCore v1.4.3
  [10745b16] Statistics v1.11.1
  [82ae8749] StatsAPI v1.7.0
  [2913bbd2] StatsBase v0.34.3
  [62fd8b95] TensorCore v0.1.1
  [3bb67fe8] TranscodingStreams v0.11.3
  [5c2747f8] URIs v1.5.1
  [3a884ed6] UnPack v1.0.2
  [1cfade01] UnicodeFun v0.4.1
  [b8865327] UnicodePlots v3.7.0
  [1986cc42] Unitful v1.21.0
  [45397f5d] UnitfulLatexify v1.6.4
  [41fe7b60] Unzip v0.2.0
  [19fa3120] VertexSafeGraphs v0.2.0
  [6e34b625] Bzip2_jll v1.0.8+2
  [83423d85] Cairo_jll v1.18.2+1
  [ee1fde0b] Dbus_jll v1.14.10+0
  [2702e6a9] EpollShim_jll v0.0.20230411+0
  [2e619515] Expat_jll v2.6.2+0
⌅ [b22a6f82] FFMPEG_jll v4.4.4+1
  [a3f928ae] Fontconfig_jll v2.13.96+0
  [d7e528f0] FreeType2_jll v2.13.2+0
  [559328eb] FriBidi_jll v1.0.14+0
  [0656b61e] GLFW_jll v3.4.0+1
  [d2c73de3] GR_jll v0.73.8+0
  [78b55507] Gettext_jll v0.21.0+0
  [7746bdde] Glib_jll v2.80.5+0
  [3b182d85] Graphite2_jll v1.3.14+0
  [2e76f6c2] HarfBuzz_jll v8.3.1+0
  [e33a78d0] Hwloc_jll v2.11.2+0
  [aacddb02] JpegTurbo_jll v3.0.4+0
  [c1c5ebd0] LAME_jll v3.100.2+0
  [88015f11] LERC_jll v4.0.0+0
  [1d63c593] LLVMOpenMP_jll v18.1.7+0
  [dd4b983a] LZO_jll v2.10.2+1
⌅ [e9f186c6] Libffi_jll v3.2.2+1
  [d4300ac3] Libgcrypt_jll v1.11.0+0
  [7e76a0d4] Libglvnd_jll v1.6.0+0
  [7add5ba3] Libgpg_error_jll v1.50.0+0
  [94ce4f54] Libiconv_jll v1.17.0+1
  [4b2f31a3] Libmount_jll v2.40.1+0
  [89763e89] Libtiff_jll v4.7.0+0
  [38a345b3] Libuuid_jll v2.40.1+0
  [7cb0a576] MPICH_jll v4.2.3+0
  [f1f71cc9] MPItrampoline_jll v5.5.1+0
  [9237b28f] MicrosoftMPI_jll v10.1.4+2
  [e7412a2a] Ogg_jll v1.3.5+1
  [656ef2d0] OpenBLAS32_jll v0.3.28+3
  [fe0851c0] OpenMPI_jll v5.0.5+0
  [458c3c95] OpenSSL_jll v3.0.15+1
  [efe28fd5] OpenSpecFun_jll v0.5.5+0
  [91d4177d] Opus_jll v1.3.3+0
  [8fa3689e] PETSc_jll v3.22.0+0
  [36c8627f] Pango_jll v1.54.1+0
  [30392449] Pixman_jll v0.43.4+0
  [c0090381] Qt6Base_jll v6.7.1+1
  [629bc702] Qt6Declarative_jll v6.7.1+2
  [ce943373] Qt6ShaderTools_jll v6.7.1+1
  [e99dba38] Qt6Wayland_jll v6.7.1+1
  [aabda75e] SCALAPACK32_jll v2.2.1+1
  [a44049a8] Vulkan_Loader_jll v1.3.243+0
  [a2964d1f] Wayland_jll v1.21.0+1
  [2381bf8a] Wayland_protocols_jll v1.31.0+0
  [02c8fc9c] XML2_jll v2.13.4+0
  [aed1982a] XSLT_jll v1.1.41+0
  [ffd25f8a] XZ_jll v5.6.3+0
  [f67eecfb] Xorg_libICE_jll v1.1.1+0
  [c834827a] Xorg_libSM_jll v1.2.4+0
  [4f6342f7] Xorg_libX11_jll v1.8.6+0
  [0c0b7dd1] Xorg_libXau_jll v1.0.11+0
  [935fb764] Xorg_libXcursor_jll v1.2.0+4
  [a3789734] Xorg_libXdmcp_jll v1.1.4+0
  [1082639a] Xorg_libXext_jll v1.3.6+0
  [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 v0.9.11+0
  [14d82f49] Xorg_libpthread_stubs_jll v0.1.1+0
  [c7cfdc94] Xorg_libxcb_jll v1.17.0+0
  [cc61e674] Xorg_libxkbfile_jll v1.1.2+0
  [e920d4aa] Xorg_xcb_util_cursor_jll v0.1.4+0
  [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 v1.4.6+0
  [33bec58e] Xorg_xkeyboard_config_jll v2.39.0+0
  [c5fb5394] Xorg_xtrans_jll v1.5.0+0
  [3161d3a3] Zstd_jll v1.5.6+1
  [35ca27e7] eudev_jll v3.2.9+0
  [214eeab7] fzf_jll v0.53.0+0
  [1a1c6b14] gperf_jll v3.1.1+0
  [a4ae2306] libaom_jll v3.9.0+0
  [0ac62f75] libass_jll v0.15.2+0
  [1183f4f0] libdecor_jll v0.2.2+0
  [2db6ffa8] libevdev_jll v1.11.0+0
  [f638f0a6] libfdk_aac_jll v2.0.3+0
  [36db933b] libinput_jll v1.18.0+0
  [b53b4c65] libpng_jll v1.6.44+0
  [f27f6e37] libvorbis_jll v1.3.7+2
  [009596ad] mtdev_jll v1.1.6+0
⌅ [1270edf5] x264_jll v2021.5.5+0
⌅ [dfaa095f] x265_jll v3.5.0+0
  [d8fb68d0] xkbcommon_jll v1.4.1+1
  [0dad84c5] ArgTools v1.1.2
  [56f22d72] Artifacts v1.11.0
  [2a0f44e3] Base64 v1.11.0
  [ade2ca70] Dates v1.11.0
  [8ba89e20] Distributed v1.11.0
  [f43a241f] Downloads v1.6.0
  [7b1f6079] FileWatching v1.11.0
  [9fa8497b] Future v1.11.0
  [b77e0a4c] InteractiveUtils v1.11.0
  [4af54fe1] LazyArtifacts v1.11.0
  [b27032c2] LibCURL v0.6.4
  [76f85450] LibGit2 v1.11.0
  [8f399da3] Libdl v1.11.0
  [37e2e46d] LinearAlgebra v1.11.0
  [56ddb016] Logging v1.11.0
  [d6f4376e] Markdown v1.11.0
  [a63ad114] Mmap v1.11.0
  [ca575930] NetworkOptions v1.2.0
  [44cfe95a] Pkg v1.11.0
  [de0858da] Printf v1.11.0
  [3fa0cd96] REPL v1.11.0
  [9a3f8284] Random v1.11.0
  [ea8e919c] SHA v0.7.0
  [9e88b42a] Serialization v1.11.0
  [1a1011a3] SharedArrays v1.11.0
  [6462fe0b] Sockets v1.11.0
  [2f01184e] SparseArrays v1.11.0
  [f489334b] StyledStrings v1.11.0
  [fa267f1f] TOML v1.0.3
  [a4e569a6] Tar v1.10.0
  [8dfed614] Test v1.11.0
  [cf7118a7] UUIDs v1.11.0
  [4ec0a83e] Unicode v1.11.0
  [e66e0078] CompilerSupportLibraries_jll v1.1.1+0
  [deac9b47] LibCURL_jll v8.6.0+0
  [e37daf67] LibGit2_jll v1.7.2+0
  [29816b5a] LibSSH2_jll v1.11.0+1
  [c8ffd9c3] MbedTLS_jll v2.28.6+0
  [14a3606d] MozillaCACerts_jll v2023.12.12
  [4536629a] OpenBLAS_jll v0.3.27+1
  [05823500] OpenLibm_jll v0.8.1+2
  [efcefdf7] PCRE2_jll v10.42.0+1
  [bea87d4a] SuiteSparse_jll v7.7.0+0
  [83775a58] Zlib_jll v1.2.13+1
  [8e850b90] libblastrampoline_jll v5.11.0+0
  [8e850ede] nghttp2_jll v1.59.0+0
  [3f19e933] p7zip_jll v17.4.0+2
        Info Packages marked with ⌅ have new versions available but compatibility constraints restrict them from upgrading.
     Testing Running tests...
┌ Info: Testing PETSc.jl with
│   MPIPreferences.binary = "MPICH_jll"
│   MPIPreferences.abi = "MPICH"
└   PETSc_jll.host_platform = macOS aarch64 {cxxstring_abi=cxx11, julia_version=1.11.1, libgfortran_version=5.0.0, mpi=mpich}
Test Summary: | Pass  Total  Time
DMDACreate1D  |  460    460  1.5s
Test Summary: | Pass  Total  Time
DMDACreate2D  | 2624   2624  0.4s
Test Summary: |  Pass  Total  Time
DMDACreate3D  | 12096  12096  1.9s
Test Summary: | Pass  Total  Time
creatematrix  |   40     40  0.6s
Test Summary:              | Pass  Total  Time
DM Vectors and Coordinates |  380    380  0.4s
Test Summary: | Total   Time
mpi examples  |     0  17.4s
Test Summary: | Pass  Total  Time
options tests |  144    144  0.6s
ERROR: LoadError: ArgumentError: Package MPI [da04e1cc-30fd-572f-bb4f-1f8673147195] is required but does not seem to be installed:
 - Run `Pkg.instantiate()` to install all recorded dependencies.

Stacktrace:
  [1] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2438
  [2] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2315
  [3] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
  [4] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
  [5] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2302
  [6] macro expansion
    @ ./loading.jl:2241 [inlined]
  [7] macro expansion
    @ ./lock.jl:273 [inlined]
  [8] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2198
  [9] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [10] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [11] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2191
 [12] include
    @ ./Base.jl:557 [inlined]
 [13] 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, UInt128}}, source::Nothing)
    @ Base ./loading.jl:2790
 [14] top-level scope
    @ stdin:5
in expression starting at /Users/viralshah/.julia/packages/PETSc/DgE0D/src/PETSc.jl:3
in expression starting at stdin:5
ERROR: Failed to precompile PETSc [ace2c81b-2b5f-4b1e-a30d-d662738edfe0] to "/Users/viralshah/.julia/compiled/v1.11/PETSc/jl_ZJNFTf".
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; flags::Cmd, cacheflags::Base.CacheFlags, reasons::Dict{String, Int64}, isext::Bool)
    @ Base ./loading.jl:3085
  [3] (::Base.var"#1082#1083"{Base.PkgId})()
    @ Base ./loading.jl:2492
  [4] mkpidlock(f::Base.var"#1082#1083"{Base.PkgId}, at::String, pid::Int32; kwopts::@Kwargs{stale_age::Int64, wait::Bool})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.11.1+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:95
  [5] #mkpidlock#6
    @ ~/.julia/juliaup/julia-1.11.1+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:90 [inlined]
  [6] trymkpidlock(::Function, ::Vararg{Any}; kwargs::@Kwargs{stale_age::Int64})
    @ FileWatching.Pidfile ~/.julia/juliaup/julia-1.11.1+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/FileWatching/src/pidfile.jl:116
  [7] #invokelatest#2
    @ ./essentials.jl:1057 [inlined]
  [8] invokelatest
    @ ./essentials.jl:1052 [inlined]
  [9] maybe_cachefile_lock(f::Base.var"#1082#1083"{Base.PkgId}, pkg::Base.PkgId, srcpath::String; stale_age::Int64)
    @ Base ./loading.jl:3609
 [10] maybe_cachefile_lock
    @ ./loading.jl:3606 [inlined]
 [11] _require(pkg::Base.PkgId, env::String)
    @ Base ./loading.jl:2488
 [12] __require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2315
 [13] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [14] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [15] _require_prelocked(uuidkey::Base.PkgId, env::String)
    @ Base ./loading.jl:2302
 [16] macro expansion
    @ ./loading.jl:2241 [inlined]
 [17] macro expansion
    @ ./lock.jl:273 [inlined]
 [18] __require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2198
 [19] #invoke_in_world#3
    @ ./essentials.jl:1089 [inlined]
 [20] invoke_in_world
    @ ./essentials.jl:1086 [inlined]
 [21] require(into::Module, mod::Symbol)
    @ Base ./loading.jl:2191
parse_options tests: Error During Test at /Users/viralshah/.julia/packages/PETSc/DgE0D/test/options.jl:89
  Test threw exception
  Expression: begin
    #= /Users/viralshah/.julia/packages/PETSc/DgE0D/test/options.jl:90 =#
    julia = joinpath(Sys.BINDIR, Base.julia_exename())
    #= /Users/viralshah/.julia/packages/PETSc/DgE0D/test/options.jl:91 =#
    run(`$(julia) --startup-file=no --project -e "using PETSc
                                 using Test
                                 opts = PETSc.parse_options(ARGS)
                                 @test length(opts) == 4
                                 @test opts.ksp_monitor === nothing
                                 @test opts.ksp_view === nothing
                                 @test opts.pc_type === \"mg\"
                                 @test opts.da_grid_x === \"100\"
                                 @test_throws ErrorException opts.bad_opt
                                 "
                                 --
                                 -ksp_monitor
                                 -da_grid_x 100
                                 -ksp_view
                                 -pc_type mg`)
    #= /Users/viralshah/.julia/packages/PETSc/DgE0D/test/options.jl:106 =#
    true
end
  failed process: Process(`/Users/viralshah/.julia/juliaup/julia-1.11.1+0.aarch64.apple.darwin14/bin/julia --startup-file=no --project -e 'using PETSc
                                   using Test
                                   opts = PETSc.parse_options(ARGS)
                                   @test length(opts) == 4
                                   @test opts.ksp_monitor === nothing
                                   @test opts.ksp_view === nothing
                                   @test opts.pc_type === "mg"
                                   @test opts.da_grid_x === "100"
                                   @test_throws ErrorException opts.bad_opt
                                   ' -- -ksp_monitor -da_grid_x 100 -ksp_view -pc_type mg`, ProcessExited(1)) [1]
  
  Stacktrace:
   [1] pipeline_error
     @ ./process.jl:598 [inlined]
   [2] run(::Cmd; wait::Bool)
     @ Base ./process.jl:513
   [3] run(::Cmd)
     @ Base ./process.jl:510
   [4] macro expansion
     @ ~/.julia/packages/PETSc/DgE0D/test/options.jl:91 [inlined]
   [5] macro expansion
     @ ~/.julia/juliaup/julia-1.11.1+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/Test/src/Test.jl:676 [inlined]
   [6] macro expansion
     @ ~/.julia/packages/PETSc/DgE0D/test/options.jl:89 [inlined]
   [7] macro expansion
     @ ~/.julia/juliaup/julia-1.11.1+0.aarch64.apple.darwin14/share/julia/stdlib/v1.11/Test/src/Test.jl:1700 [inlined]
   [8] top-level scope
     @ ~/.julia/packages/PETSc/DgE0D/test/options.jl:89
Test Summary:       | Error  Total  Time
parse_options tests |     1      1  2.2s
ERROR: LoadError: Some tests did not pass: 0 passed, 0 failed, 1 errored, 0 broken.
in expression starting at /Users/viralshah/.julia/packages/PETSc/DgE0D/test/options.jl:88
in expression starting at /Users/viralshah/.julia/packages/PETSc/DgE0D/test/runtests.jl:30
ERROR: Package PETSc errored during testing

@ViralBShah ViralBShah changed the title PETSc error in tests PETSc error in tests in v0.3.0 Oct 28, 2024
@ViralBShah
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This doesn't happen in the CI because Pkg.instantiate() get's called. Also, if you call instantiate() and set it up once, then it doesn't happen again.

For first time users of the package, however, the tests are likely to fail with this issue.

@ViralBShah ViralBShah changed the title PETSc error in tests in v0.3.0 PETSc error in tests in v0.3.0 on a clean install due the environment not being instantiated. Oct 28, 2024
@boriskaus
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will it help if we instantiate the package at the beginning of the tests?

PETSc.jl/test/runtests.jl

Line 8 in e6f8a88

@ViralBShah
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I think it would be valuable to have that. To test it, you have to make sure you remove all development copies and instantiated environments. Otherwise it is pretty easy to never see it unless you install PETSc.jl on a new machine.

@boriskaus boriskaus mentioned this issue Oct 29, 2024
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@boriskaus
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I was able to reproduce the issue on a local machine and addressed this in PR #205, but it would be good if you an try this as well as it is possible I spoiled the machine while testing

@ViralBShah
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JuliaRegistries/General#118383

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