Package evaluation of AdFem on Julia 1.13.0-DEV.748 (36a4616fc2*) started at 2025-06-17T19:23:15.382 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 7.93s ################################################################################ # Installation # Installing AdFem... Resolving package versions... Installed Conda ── v1.10.2 Installed CMake ── v1.2.0 Installed PyCall ─ v1.96.4 Installed HDF5 ─── v0.13.6 Installed ADCME ── v0.6.7 Installed AdFem ── v0.1.1 Updating `~/.julia/environments/v1.13/Project.toml` [c10abcb9] + AdFem v0.1.1 Updating `~/.julia/environments/v1.13/Manifest.toml` ⌅ [07b341a0] + ADCME v0.6.7 [621f4979] + AbstractFFTs v1.5.0 [c10abcb9] + AdFem v0.1.1 [9e28174c] + BinDeps v1.0.2 [a74b3585] + Blosc v0.7.3 [e1450e63] + BufferedStreams v1.2.2 [631607c0] + CMake v1.2.0 [944b1d66] + CodecZlib v0.7.8 ⌅ [3da002f7] + ColorTypes v0.11.5 ⌃ [5ae59095] + Colors v0.12.11 [8f4d0f93] + Conda v1.10.2 [7a1cc6ca] + FFTW v1.9.0 [53c48c17] + FixedPointNumbers v0.8.5 ⌅ [f67ccb44] + HDF5 v0.13.6 [692b3bcd] + JLLWrappers v1.7.0 [682c06a0] + JSON v0.21.4 [b964fa9f] + LaTeXStrings v1.4.0 ⌅ [23992714] + MAT v0.8.1 [3da0fdf6] + MPIPreferences v0.1.11 [1914dd2f] + MacroTools v0.5.16 [bac558e1] + OrderedCollections v1.8.1 [d96e819e] + Parameters v0.12.3 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [438e738f] + PyCall v1.96.4 [d330b81b] + PyPlot v2.11.6 ⌅ [189a3867] + Reexport v0.2.0 ⌅ [276daf66] + SpecialFunctions v0.10.3 [10745b16] + Statistics v1.11.1 [3bb67fe8] + TranscodingStreams v0.11.3 [30578b45] + URIParser v0.4.1 [3a884ed6] + UnPack v1.0.2 [81def892] + VersionParsing v1.3.0 [0b7ba130] + Blosc_jll v1.21.7+0 [f5851436] + FFTW_jll v3.3.11+0 [0234f1f7] + HDF5_jll v1.14.6+0 [e33a78d0] + Hwloc_jll v2.12.1+0 [1d5cc7b8] + IntelOpenMP_jll v2025.0.4+0 [5ced341a] + Lz4_jll v1.10.1+0 [856f044c] + MKL_jll v2025.0.1+1 [7cb0a576] + MPICH_jll v4.3.0+1 [f1f71cc9] + MPItrampoline_jll v5.5.3+0 [9237b28f] + MicrosoftMPI_jll v10.1.4+3 [fe0851c0] + OpenMPI_jll v5.0.8+0 [efe28fd5] + OpenSpecFun_jll v0.5.6+0 [477f73a3] + libaec_jll v1.1.3+0 [1317d2d5] + oneTBB_jll v2022.0.0+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b77e0a4c] + InteractiveUtils v1.11.0 [ac6e5ff7] + JuliaSyntaxHighlighting v1.12.0 [4af54fe1] + LazyArtifacts v1.11.0 [b27032c2] + LibCURL v0.6.4 [76f85450] + LibGit2 v1.11.0 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [56ddb016] + Logging v1.11.0 [d6f4376e] + Markdown v1.11.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [44cfe95a] + Pkg v1.13.0 [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 v1.12.0 [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 v1.3.0+1 [deac9b47] + LibCURL_jll v8.14.1+1 [e37daf67] + LibGit2_jll v1.9.0+0 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.0+0 [bea87d4a] + SuiteSparse_jll v7.10.1+0 [83775a58] + Zlib_jll v1.3.1+2 [3161d3a3] + Zstd_jll v1.5.7+1 [8e850b90] + libblastrampoline_jll v5.12.0+0 [8e850ede] + nghttp2_jll v1.65.0+0 [3f19e933] + p7zip_jll v17.5.0+2 Info Packages marked with ⌃ and ⌅ have new versions available. Those with ⌃ may be upgradable, but those with ⌅ are restricted by compatibility constraints from upgrading. To see why use `status --outdated -m` Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log` Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9816a3826b0ebf49ab4926e2b18842ad8b5c8f04/build.log` Building HDF5 ──→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/0713cbabdf855852dfab3ce6447c87145f3d9ea8/build.log` Building CMake ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/50a8b41d2c562fccd9ab841085fc7d1e2706da82/build.log` Building ADCME ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/0da04753658d14abee2062cee67209eb12e62df3/build.log` Building AdFem ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/de766a129f0ef5ca65af57e4e2b5bbac6d212f86/build.log` Installation failed after 1356.83s ERROR: LoadError: Error building `AdFem`: WARNING: method definition for #newton_raphson#39 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:453 declares type variable T but does not use it. WARNING: method definition for #newton_raphson_with_grad#49 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:607 declares type variable T but does not use it. WARNING: method definition for NonlinearConstrainedProblem at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:681 declares type variable T but does not use it. WARNING: Method definition size(PyCall.PyObject) in module PyCall at /home/pkgeval/.julia/packages/PyCall/1gn3u/src/PyCall.jl:820 overwritten in module ADCME at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/variable.jl:214. ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. WARNING: method definition for #newton_raphson#39 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:453 declares type variable T but does not use it. WARNING: method definition for #newton_raphson_with_grad#49 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:607 declares type variable T but does not use it. WARNING: method definition for NonlinearConstrainedProblem at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:681 declares type variable T but does not use it. OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids. OMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info OMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 109 OMP: Info #156: KMP_AFFINITY: 1 available OS procs OMP: Info #157: KMP_AFFINITY: Uniform topology OMP: Info #159: KMP_AFFINITY: 1 packages x 1 cores/pkg x 1 threads/core (1 total cores) OMP: Info #214: KMP_AFFINITY: OS proc to physical thread map: OMP: Info #171: KMP_AFFINITY: OS proc 109 maps to package 1 OMP: Info #250: KMP_AFFINITY: pid 10897 tid 10897 thread 0 bound to OS proc set 109 -- The C compiler identification is GNU 5.4.0 -- The CXX compiler identification is GNU 5.4.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /home/pkgeval/.julia/adcme/bin/x86_64-conda_cos6-linux-gnu-gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /home/pkgeval/.julia/adcme/bin/x86_64-conda_cos6-linux-gnu-g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done JULIA=/opt/julia/bin/julia Precompiling packages... 914.7 ms ✓ Reexport 41411.0 ms ✓ FFTW Info Given ADCME was explicitly requested, output will be shown live  WARNING: method definition for #newton_raphson#39 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:453 declares type variable T but does not use it. WARNING: method definition for #newton_raphson_with_grad#49 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:607 declares type variable T but does not use it. WARNING: method definition for NonlinearConstrainedProblem at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:681 declares type variable T but does not use it. WARNING: Method definition size(PyCall.PyObject) in module PyCall at /home/pkgeval/.julia/packages/PyCall/1gn3u/src/PyCall.jl:820 overwritten in module ADCME at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/variable.jl:214. ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. 9288.3 ms ? ADCME 2 dependencies successfully precompiled in 52 seconds. 68 already precompiled. 1 dependencies failed but may be precompilable after restarting julia 1 dependency had output during precompilation: ┌ ADCME │ [Output was shown above] └ WARNING: method definition for #newton_raphson#39 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:453 declares type variable T but does not use it. WARNING: method definition for #newton_raphson_with_grad#49 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:607 declares type variable T but does not use it. WARNING: method definition for NonlinearConstrainedProblem at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:681 declares type variable T but does not use it. WARNING: Method definition size(PyCall.PyObject) in module PyCall at /home/pkgeval/.julia/packages/PyCall/1gn3u/src/PyCall.jl:820 overwritten in module ADCME at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/variable.jl:214. ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. WARNING: method definition for #newton_raphson#39 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:453 declares type variable T but does not use it. WARNING: method definition for #newton_raphson_with_grad#49 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:607 declares type variable T but does not use it. WARNING: method definition for NonlinearConstrainedProblem at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:681 declares type variable T but does not use it. OMP: Info #212: KMP_AFFINITY: decoding x2APIC ids. OMP: Info #210: KMP_AFFINITY: Affinity capable, using global cpuid leaf 11 info OMP: Info #154: KMP_AFFINITY: Initial OS proc set respected: 109 OMP: Info #156: KMP_AFFINITY: 1 available OS procs OMP: Info #157: KMP_AFFINITY: Uniform topology OMP: Info #159: KMP_AFFINITY: 1 packages x 1 cores/pkg x 1 threads/core (1 total cores) OMP: Info #214: KMP_AFFINITY: OS proc to physical thread map: OMP: Info #171: KMP_AFFINITY: OS proc 109 maps to package 1 OMP: Info #250: KMP_AFFINITY: pid 10970 tid 10970 thread 0 bound to OS proc set 109 ┌ Warning: Cannot load /home/pkgeval/.julia/packages/ADCME/hCmEo/deps/CustomOps/build/libadcme.so. Please recompile the shared library by `ADCME.precompile()` for using custom operators. └ @ ADCME ~/.julia/packages/ADCME/hCmEo/src/ADCME.jl:76 Python path=/home/pkgeval/.julia/adcme/bin/python PREFIXDIR=/home/pkgeval/.julia/adcme/lib/Libraries TF_INC=/home/pkgeval/.julia/adcme/lib/python3.7/site-packages/tensorflow_core/include TF_ABI=1 TF_LIB_FILE=/home/pkgeval/.julia/adcme/lib/python3.7/site-packages/tensorflow_core/libtensorflow_framework.so.1 Use openblas library /home/pkgeval/.julia/adcme/lib/libopenblas.so -- Configuring done -- Generating done -- Build files have been written to: /home/pkgeval/.julia/adcme/lib/Libraries/Adept-2/adept/build [1/12] Building CXX object CMakeFiles/adept.dir/StackStorageOrig.cpp.o [2/12] Building CXX object CMakeFiles/adept.dir/cppblas.cpp.o [3/12] Building CXX object CMakeFiles/adept.dir/settings.cpp.o [4/12] Building CXX object CMakeFiles/adept.dir/Storage.cpp.o [5/12] Building CXX object CMakeFiles/adept.dir/index.cpp.o [6/12] Building CXX object CMakeFiles/adept.dir/Array.cpp.o [7/12] Building CXX object CMakeFiles/adept.dir/Stack.cpp.o [8/12] Building CXX object CMakeFiles/adept.dir/inv.cpp.o [9/12] Building CXX object CMakeFiles/adept.dir/vector_utilities.cpp.o [10/12] Building CXX object CMakeFiles/adept.dir/jacobian.cpp.o [11/12] Building CXX object CMakeFiles/adept.dir/solve.cpp.o [12/12] Linking CXX shared library /home/pkgeval/.julia/adcme/lib/libadept.so Precompiling packages... 848.1 ms ✓ Reexport 30556.6 ms ✓ FFTW Info Given ADCME was explicitly requested, output will be shown live  WARNING: method definition for #newton_raphson#39 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:453 declares type variable T but does not use it. WARNING: method definition for #newton_raphson_with_grad#49 at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:607 declares type variable T but does not use it. WARNING: method definition for NonlinearConstrainedProblem at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/optim.jl:681 declares type variable T but does not use it. WARNING: Method definition size(PyCall.PyObject) in module PyCall at /home/pkgeval/.julia/packages/PyCall/1gn3u/src/PyCall.jl:820 overwritten in module ADCME at /home/pkgeval/.julia/packages/ADCME/hCmEo/src/variable.jl:214. ERROR: Method overwriting is not permitted during Module precompilation. Use `__precompile__(false)` to opt-out of precompilation. 9444.4 ms ? ADCME 2 dependencies successfully precompiled in 41 seconds. 68 already precompiled. 1 dependencies failed but may be precompilable after restarting julia 1 dependency had output during precompilation: ┌ ADCME │ [Output was shown above] └ ┌ Warning: Cannot load /home/pkgeval/.julia/packages/ADCME/hCmEo/deps/CustomOps/build/libadcme.so. Please recompile the shared library by `ADCME.precompile()` for using custom operators. └ @ ADCME ~/.julia/packages/ADCME/hCmEo/src/ADCME.jl:76 [ Info: Changed to directory /home/pkgeval/.julia/adcme/lib/Libraries [ Info: Cloning from https://github.com/ADCMEMarket/Adept-2 to Adept-2... [ Info: Cloned https://github.com/ADCMEMarket/Adept-2 to Adept-2 [ Info: Made directory directory [ Info: Changed to directory build [ Info: Changed to directory /home/pkgeval/.julia/adcme/lib/Libraries [ Info: Downloading https://github.com/kailaix/mfem/archive/shared-msvc-dev.zip -> mfem.zip ERROR: LoadError: RequestError: HTTP/2 503 while requesting https://github.com/kailaix/mfem/archive/shared-msvc-dev.zip Stacktrace: [1] (::Downloads.var"#7#8"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Nothing, String})(output::IOStream) @ Downloads /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:285 [2] open(f::Downloads.var"#7#8"{Nothing, Vector{Pair{String, String}}, Float64, Nothing, Bool, Nothing, Nothing, String}, args::String; kwargs::@Kwargs{write::Bool, lock::Bool}) @ Base ./io.jl:420 [3] open_nolock @ /opt/julia/share/julia/stdlib/v1.13/ArgTools/src/ArgTools.jl:35 [inlined] [4] arg_write(f::Function, arg::String) @ ArgTools /opt/julia/share/julia/stdlib/v1.13/ArgTools/src/ArgTools.jl:103 [5] #download#5 @ /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:272 [inlined] [6] download(url::String, output::String) @ Downloads /opt/julia/share/julia/stdlib/v1.13/Downloads/src/Downloads.jl:252 [7] do_download(url::String, path::String) @ Base ./download.jl:24 [8] download @ ./download.jl:19 [inlined] [9] (::ADCME.var"#http_file##0#http_file##1"{String, String})() @ ADCME ~/.julia/packages/ADCME/hCmEo/src/toolchain.jl:37 [10] require_file(f::ADCME.var"#http_file##0#http_file##1"{String, String}, file::String) @ ADCME ~/.julia/packages/ADCME/hCmEo/src/toolchain.jl:101 [11] http_file @ ~/.julia/packages/ADCME/hCmEo/src/toolchain.jl:35 [inlined] [12] install_mfem() @ ADCME ~/.julia/packages/ADCME/hCmEo/src/install.jl:83 [13] top-level scope @ ~/.julia/packages/AdFem/UvDr4/deps/build.jl:4 [14] include(mapexpr::Function, mod::Module, _path::String) @ Base ./Base.jl:310 [15] top-level scope @ none:5 [16] eval(m::Module, e::Any) @ Core ./boot.jl:489 [17] exec_options(opts::Base.JLOptions) @ Base ./client.jl:290 [18] _start() @ Base ./client.jl:557 in expression starting at /home/pkgeval/.julia/packages/AdFem/UvDr4/deps/build.jl:4 Stacktrace: [1] pkgerror(msg::String) @ Pkg.Types /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Types.jl:68 [2] (::Pkg.Operations.var"#137#138"{Bool, Pkg.Types.Context, String, PackageSpec, String})() @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1457 [3] withenv(::Pkg.Operations.var"#137#138"{Bool, Pkg.Types.Context, String, PackageSpec, String}, ::Pair{String, String}, ::Vararg{Pair{String}}) @ Base ./env.jl:265 [4] (::Pkg.Operations.var"#197#198"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#137#138"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec})() @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2200 [5] with_temp_env(fn::Pkg.Operations.var"#197#198"{String, Pkg.Types.EnvCache, Bool, Bool, Bool, Pkg.Operations.var"#137#138"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec}, temp_env::String) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2058 [6] (::Pkg.Operations.var"#193#194"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#137#138"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec, String, String})(tmp::String) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2167 [7] mktempdir(fn::Pkg.Operations.var"#193#194"{Dict{String, Any}, Bool, Bool, Bool, Pkg.Operations.var"#137#138"{Bool, Pkg.Types.Context, String, PackageSpec, String}, Pkg.Types.Context, PackageSpec, String, String}, parent::String; prefix::String) @ Base.Filesystem ./file.jl:899 [8] mktempdir(fn::Function, parent::String) @ Base.Filesystem ./file.jl:895 [9] #sandbox#189 @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:2114 [inlined] [10] build_versions(ctx::Pkg.Types.Context, uuids::Set{UUID}; verbose::Bool) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1438 [11] build_versions @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1356 [inlined] [12] add(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}, new_git::Set{UUID}; allow_autoprecomp::Bool, preserve::PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol) @ Pkg.Operations /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1733 [13] add @ /opt/julia/share/julia/stdlib/v1.13/Pkg/src/Operations.jl:1680 [inlined] [14] add(ctx::Pkg.Types.Context, pkgs::Vector{PackageSpec}; preserve::PreserveLevel, platform::Base.BinaryPlatforms.Platform, target::Symbol, allow_autoprecomp::Bool, kwargs::@Kwargs{io::IOContext{IO}}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:328 [15] add(pkgs::Vector{PackageSpec}; io::IOContext{IO}, kwargs::@Kwargs{}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:164 [16] add(pkgs::Vector{PackageSpec}) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:153 [17] add(pkg::PackageSpec) @ Pkg.API /opt/julia/share/julia/stdlib/v1.13/Pkg/src/API.jl:151 [18] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:112 [19] include(mod::Module, _path::String) @ Base ./Base.jl:309 [20] exec_options(opts::Base.JLOptions) @ Base ./client.jl:324 [21] _start() @ Base ./client.jl:557 in expression starting at /PkgEval.jl/scripts/evaluate.jl:109 PkgEval skipped after 1455.64s: package could not be installed