Package evaluation of PyQHA on Julia 1.13.0-DEV.853 (3e868b27cf*) started at 2025-07-17T00:12:42.478 ################################################################################ # Set-up # Set-up completed after 0.22s ################################################################################ # Installation # Installing PyQHA... Resolving package versions... Installed Conda ── v1.10.2 Installed PyCall ─ v1.96.4 Updating `~/.julia/environments/v1.13/Project.toml` [5a1273f0] + PyQHA v0.1.1 Updating `~/.julia/environments/v1.13/Manifest.toml` [8f4d0f93] + Conda v1.10.2 [682c06a0] + JSON v0.21.4 [1914dd2f] + MacroTools v0.5.16 [69de0a69] + Parsers v2.8.3 [aea7be01] + PrecompileTools v1.3.2 [21216c6a] + Preferences v1.4.3 [438e738f] + PyCall v1.96.4 [5a1273f0] + PyQHA v0.1.1 [81def892] + VersionParsing v1.3.0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.7.0 [7b1f6079] + FileWatching v1.11.0 [b27032c2] + LibCURL v0.6.4 [8f399da3] + Libdl v1.11.0 [37e2e46d] + LinearAlgebra v1.12.0 [a63ad114] + Mmap v1.11.0 [ca575930] + NetworkOptions v1.3.0 [de0858da] + Printf v1.11.0 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization v1.11.0 [fa267f1f] + TOML v1.0.3 [cf7118a7] + UUIDs v1.11.0 [4ec0a83e] + Unicode v1.11.0 [e66e0078] + CompilerSupportLibraries_jll v1.3.0+1 [deac9b47] + LibCURL_jll v8.14.1+1 [29816b5a] + LibSSH2_jll v1.11.3+1 [14a3606d] + MozillaCACerts_jll v2025.5.20 [4536629a] + OpenBLAS_jll v0.3.29+0 [458c3c95] + OpenSSL_jll v3.5.1+0 [83775a58] + Zlib_jll v1.3.1+2 [8e850b90] + libblastrampoline_jll v5.13.1+0 [8e850ede] + nghttp2_jll v1.65.0+0 Building Conda ─→ `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/b19db3927f0db4151cb86d073689f2428e524576/build.log` Building PyCall → `~/.julia/scratchspaces/44cfe95a-1eb2-52ea-b672-e2afdf69b78f/9816a3826b0ebf49ab4926e2b18842ad8b5c8f04/build.log` Installation completed after 41.12s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... No packages added to or removed from `~/.julia/environments/pkgeval/Project.toml` No packages added to or removed from `~/.julia/environments/pkgeval/Manifest.toml` Precompiling package dependencies... Precompiling packages... 74099.5 ms ✓ PyQHA 1 dependency successfully precompiled in 74 seconds. 25 already precompiled. 1 dependency had output during precompilation: ┌ PyQHA │ [ Info: Running `conda config --set pip_interop_enabled true --file /home/pkgeval/.julia/conda/3/x86_64/condarc-julia.yml` in root environment │ [ Info: Running `pip install git+https://github.com/MineralsCloud/qha.git@v1.0.20` in root environment │ Collecting git+https://github.com/MineralsCloud/qha.git@v1.0.20 │ Cloning https://github.com/MineralsCloud/qha.git (to revision v1.0.20) to /tmp/pip-req-build-xmzs3496 │ Running command git clone --filter=blob:none --quiet https://github.com/MineralsCloud/qha.git /tmp/pip-req-build-xmzs3496 │ Running command git checkout -q 4f02797c5cb659be6c030a8a4a4c19c5491d1132 │ Resolved https://github.com/MineralsCloud/qha.git to commit 4f02797c5cb659be6c030a8a4a4c19c5491d1132 │ Preparing metadata (setup.py): started │ Preparing metadata (setup.py): finished with status 'done' │ Collecting lazy_property (from qha==1.0.20) │ Downloading lazy_property-0.0.1-py2.py3-none-any.whl.metadata (273 bytes) │ Collecting numba (from qha==1.0.20) │ Downloading numba-0.61.2-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (2.8 kB) │ Collecting mpmath (from qha==1.0.20) │ Downloading mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB) │ Requirement already satisfied: numpy in ./.julia/conda/3/x86_64/lib/python3.12/site-packages (from qha==1.0.20) (2.3.1) │ Collecting pandas (from qha==1.0.20) │ Downloading pandas-2.3.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (91 kB) │ Collecting scientific-string (from qha==1.0.20) │ Downloading scientific_string-0.1.0-py3-none-any.whl.metadata (292 bytes) │ Collecting scipy (from qha==1.0.20) │ Downloading scipy-1.16.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl.metadata (61 kB) │ Collecting text-stream (from qha==1.0.20) │ Downloading text_stream-0.2.0.tar.gz (3.3 kB) │ Preparing metadata (setup.py): started │ Preparing metadata (setup.py): finished with status 'done' │ Collecting pyyaml (from qha==1.0.20) │ Downloading PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB) │ Collecting matplotlib (from qha==1.0.20) │ Downloading matplotlib-3.10.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB) │ Collecting seaborn (from qha==1.0.20) │ Downloading seaborn-0.13.2-py3-none-any.whl.metadata (5.4 kB) │ Collecting contourpy>=1.0.1 (from matplotlib->qha==1.0.20) │ Downloading contourpy-1.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.5 kB) │ Collecting cycler>=0.10 (from matplotlib->qha==1.0.20) │ Downloading cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB) │ Collecting fonttools>=4.22.0 (from matplotlib->qha==1.0.20) │ Downloading fonttools-4.59.0-cp312-cp312-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl.metadata (107 kB) │ Collecting kiwisolver>=1.3.1 (from matplotlib->qha==1.0.20) │ Downloading kiwisolver-1.4.8-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.2 kB) │ Requirement already satisfied: packaging>=20.0 in ./.julia/conda/3/x86_64/lib/python3.12/site-packages (from matplotlib->qha==1.0.20) (25.0) │ Collecting pillow>=8 (from matplotlib->qha==1.0.20) │ Downloading pillow-11.3.0-cp312-cp312-manylinux_2_27_x86_64.manylinux_2_28_x86_64.whl.metadata (9.0 kB) │ Collecting pyparsing>=2.3.1 (from matplotlib->qha==1.0.20) │ Downloading pyparsing-3.2.3-py3-none-any.whl.metadata (5.0 kB) │ Collecting python-dateutil>=2.7 (from matplotlib->qha==1.0.20) │ Downloading python_dateutil-2.9.0.post0-py2.py3-none-any.whl.metadata (8.4 kB) │ Collecting six>=1.5 (from python-dateutil>=2.7->matplotlib->qha==1.0.20) │ Downloading six-1.17.0-py2.py3-none-any.whl.metadata (1.7 kB) │ Collecting llvmlite<0.45,>=0.44.0dev0 (from numba->qha==1.0.20) │ Downloading llvmlite-0.44.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.0 kB) │ Collecting numpy (from qha==1.0.20) │ Downloading numpy-2.2.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB) │ Collecting pytz>=2020.1 (from pandas->qha==1.0.20) │ Downloading pytz-2025.2-py2.py3-none-any.whl.metadata (22 kB) │ Collecting tzdata>=2022.7 (from pandas->qha==1.0.20) │ Downloading tzdata-2025.2-py2.py3-none-any.whl.metadata (1.4 kB) │ Downloading lazy_property-0.0.1-py2.py3-none-any.whl (2.4 kB) │ Downloading matplotlib-3.10.3-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (8.6 MB) │ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 8.6/8.6 MB 87.8 MB/s eta 0:00:00 │ Downloading contourpy-1.3.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (323 kB) │ Downloading cycler-0.12.1-py3-none-any.whl (8.3 kB) │ Downloading fonttools-4.59.0-cp312-cp312-manylinux1_x86_64.manylinux2014_x86_64.manylinux_2_17_x86_64.manylinux_2_5_x86_64.whl (4.9 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llvmlite-0.44.0-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (42.4 MB) │ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 42.4/42.4 MB 117.1 MB/s eta 0:00:00 │ Downloading numpy-2.2.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.5 MB) │ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 16.5/16.5 MB 89.8 MB/s eta 0:00:00 │ Downloading pandas-2.3.1-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.0 MB) │ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.0/12.0 MB 136.0 MB/s eta 0:00:00 │ Downloading pytz-2025.2-py2.py3-none-any.whl (509 kB) │ Downloading tzdata-2025.2-py2.py3-none-any.whl (347 kB) │ Downloading PyYAML-6.0.2-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (767 kB) │ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 767.5/767.5 kB 45.6 MB/s eta 0:00:00 │ Downloading scientific_string-0.1.0-py3-none-any.whl (4.0 kB) │ Downloading scipy-1.16.0-cp312-cp312-manylinux2014_x86_64.manylinux_2_17_x86_64.whl (35.1 MB) │ ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 35.1/35.1 MB 80.9 MB/s eta 0:00:00 │ Downloading seaborn-0.13.2-py3-none-any.whl (294 kB) │ Building wheels for collected packages: qha, text-stream │ DEPRECATION: Building 'qha' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'qha'. Discussion can be found at https://github.com/pypa/pip/issues/6334 │ Building wheel for qha (setup.py): started │ Building wheel for qha (setup.py): finished with status 'done' │ Created wheel for qha: filename=qha-1.0.20-py3-none-any.whl size=57150 sha256=46667522a1b4cc81e99c0a88a5c49bf121dc378bd5989b50b593efd2b151e074 │ Stored in directory: /tmp/pip-ephem-wheel-cache-klqfq4fy/wheels/a4/27/cc/373477d94235056992d8c6b9be80cd77bd6b507c84b1657ce1 │ DEPRECATION: Building 'text-stream' using the legacy setup.py bdist_wheel mechanism, which will be removed in a future version. pip 25.3 will enforce this behaviour change. A possible replacement is to use the standardized build interface by setting the `--use-pep517` option, (possibly combined with `--no-build-isolation`), or adding a `pyproject.toml` file to the source tree of 'text-stream'. Discussion can be found at https://github.com/pypa/pip/issues/6334 │ Building wheel for text-stream (setup.py): started │ Building wheel for text-stream (setup.py): finished with status 'done' │ Created wheel for text-stream: filename=text_stream-0.2.0-py3-none-any.whl size=4099 sha256=ddd1b5cc861431b4760d4cdeb627e23a8574f283efcbb7637adcbca7bc58c996 │ Stored in directory: /home/pkgeval/.cache/pip/wheels/13/5a/ee/2701513b92267f7da734705913d5bd744dd7582a075167db3f │ Successfully built qha text-stream │ Installing collected packages: text-stream, scientific-string, pytz, mpmath, lazy_property, tzdata, six, pyyaml, pyparsing, pillow, numpy, llvmlite, kiwisolver, fonttools, cycler, scipy, python-dateutil, numba, contourpy, pandas, matplotlib, seaborn, qha │ Attempting uninstall: numpy │ Found existing installation: numpy 2.3.1 │ Uninstalling numpy-2.3.1: │ Successfully uninstalled numpy-2.3.1 │ │ Successfully installed contourpy-1.3.2 cycler-0.12.1 fonttools-4.59.0 kiwisolver-1.4.8 lazy_property-0.0.1 llvmlite-0.44.0 matplotlib-3.10.3 mpmath-1.3.0 numba-0.61.2 numpy-2.2.6 pandas-2.3.1 pillow-11.3.0 pyparsing-3.2.3 python-dateutil-2.9.0.post0 pytz-2025.2 pyyaml-6.0.2 qha-1.0.20 scientific-string-0.1.0 scipy-1.16.0 seaborn-0.13.2 six-1.17.0 text-stream-0.2.0 tzdata-2025.2 └ Precompilation completed after 45.31s ################################################################################ # Loading # Loading PyQHA... ERROR: InitError: PyError (PyImport_ImportModule) TypingError('Failed in nopython mode pipeline (step: nopython frontend)\n\x1b[1m\x1b[1mUntyped global name \'ho_free_energy\':\x1b[0m \x1b[1m\x1b[1mCannot determine Numba type of \x1b[0m\n\x1b[1m\nFile ".julia/conda/3/x86_64/lib/python3.12/site-packages/qha/single_configuration.py", line 45:\x1b[0m\n\x1b[1mdef free_energy(temperature: Scalar, q_weights: Vector, static_energies: Vector, frequencies: Array3D,\n \n scaled_q_weights: Vector = q_weights / np.sum(q_weights)\n\x1b[1m vibrational_energies: Vector = np.dot(ho_free_energy(temperature, frequencies).sum(axis=2), scaled_q_weights)\n\x1b[0m \x1b[1m^\x1b[0m\x1b[0m\n\x1b[0m\n\x1b[0m\x1b[1mDuring: Pass nopython_type_inference\x1b[0m') File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/qha/calculator.py", line 20, in import qha.multi_configurations.different_phonon_dos as different_phonon_dos File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/qha/multi_configurations/different_phonon_dos.py", line 17, in from qha.single_configuration import free_energy File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/qha/single_configuration.py", line 20, in @jit(float64[:](float64, float64[:], float64[:], float64[:, :, :], boolean), cache=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/decorators.py", line 232, in wrapper disp.compile(sig) File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/dispatcher.py", line 904, in compile cres = self._compiler.compile(args, return_type) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/dispatcher.py", line 84, in compile raise retval File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/dispatcher.py", line 94, in _compile_cached retval = self._compile_core(args, return_type) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/dispatcher.py", line 107, in _compile_core cres = compiler.compile_extra(self.targetdescr.typing_context, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/compiler.py", line 739, in compile_extra return pipeline.compile_extra(func) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/compiler.py", line 439, in compile_extra return self._compile_bytecode() ^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/compiler.py", line 505, in _compile_bytecode return self._compile_core() ^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/compiler.py", line 484, in _compile_core raise e File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/compiler.py", line 473, in _compile_core pm.run(self.state) File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/compiler_machinery.py", line 367, in run raise patched_exception File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/compiler_machinery.py", line 356, in run self._runPass(idx, pass_inst, state) File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/compiler_lock.py", line 35, in _acquire_compile_lock return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/compiler_machinery.py", line 311, in _runPass mutated |= check(pss.run_pass, internal_state) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/compiler_machinery.py", line 272, in check mangled = func(compiler_state) ^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/typed_passes.py", line 112, in run_pass typemap, return_type, calltypes, errs = type_inference_stage( ^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/typed_passes.py", line 91, in type_inference_stage infer.build_constraint() File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/typeinfer.py", line 1027, in build_constraint self.constrain_statement(inst) File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/typeinfer.py", line 1389, in constrain_statement self.typeof_assign(inst) File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/typeinfer.py", line 1464, in typeof_assign self.typeof_global(inst, inst.target, value) File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/typeinfer.py", line 1564, in typeof_global typ = self.resolve_value_type(inst, gvar.value) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/pkgeval/.julia/conda/3/x86_64/lib/python3.12/site-packages/numba/core/typeinfer.py", line 1485, in resolve_value_type raise TypingError(msg, loc=inst.loc) Stacktrace: [1] pyimport(name::String) @ PyCall ~/.julia/packages/PyCall/1gn3u/src/PyCall.jl:558 [2] __init__() @ PyQHA ~/.julia/packages/PyQHA/S6CTK/src/PyQHA.jl:22 [3] run_module_init(mod::Module, i::Int64) @ Base ./loading.jl:1417 [4] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String) @ Base ./loading.jl:1405 [5] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::Nothing, depmods::Vector{Any}; register::Bool) @ Base ./loading.jl:1293 [6] _include_from_serialized @ ./loading.jl:1247 [inlined] [7] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128, stalecheck::Bool; reasons::Dict{String, Int64}, DEPOT_PATH::Vector{String}) @ Base ./loading.jl:2089 [8] __require_prelocked(pkg::Base.PkgId, env::String) @ Base ./loading.jl:2602 [9] _require_prelocked(uuidkey::Base.PkgId, env::String) @ Base ./loading.jl:2468 [10] macro expansion @ ./loading.jl:2396 [inlined] [11] macro expansion @ ./lock.jl:376 [inlined] [12] __require(into::Module, mod::Symbol) @ Base ./loading.jl:2360 [13] require @ ./loading.jl:2336 [inlined] [14] eval_import_path @ ./module.jl:36 [inlined] [15] eval_import_path_all(at::Module, path::Expr, keyword::String) @ Base ./module.jl:60 [16] _eval_using(to::Module, path::Expr) @ Base ./module.jl:137 [17] top-level scope @ none:1 [18] eval(m::Module, e::Any) @ Core ./boot.jl:489 [19] exec_options(opts::Base.JLOptions) @ Base ./client.jl:286 [20] _start() @ Base ./client.jl:553 during initialization of module PyQHA Loading failed after 13.7s ERROR: LoadError: failed process: Process(`/opt/julia/bin/julia -C native -J/opt/julia/lib/julia/sys.so -g1 --check-bounds=yes --inline=yes --pkgimages=existing -e 'using PyQHA'`, ProcessExited(1)) [1] Stacktrace: [1] pipeline_error @ ./process.jl:602 [inlined] [2] run(::Cmd; wait::Bool) @ Base ./process.jl:517 [3] run(::Cmd) @ Base ./process.jl:514 [4] top-level scope @ /PkgEval.jl/scripts/evaluate.jl:193 [5] include(mod::Module, _path::String) @ Base ./Base.jl:309 [6] exec_options(opts::Base.JLOptions) @ Base ./client.jl:320 [7] _start() @ Base ./client.jl:553 in expression starting at /PkgEval.jl/scripts/evaluate.jl:184 PkgEval failed after 173.74s: there were unidentified errors