Package evaluation of PyBoltz on Julia 1.11.5 (32ac370b68*) started at 2025-06-29T09:21:21.805 ################################################################################ # Set-up # Installing PkgEval dependencies (TestEnv)... Set-up completed after 8.33s ################################################################################ # Installation # Installing PyBoltz... Resolving package versions... Updating `~/.julia/environments/v1.11/Project.toml` [0bca4874] + PyBoltz v0.2.0 Updating `~/.julia/environments/v1.11/Manifest.toml` [34da2185] + Compat v4.16.0 [992eb4ea] + CondaPkg v0.2.29 [9a962f9c] + DataAPI v1.16.0 [e2d170a0] + DataValueInterfaces v1.0.0 [82899510] + IteratorInterfaceExtensions v1.0.0 [692b3bcd] + JLLWrappers v1.7.0 [0f8b85d8] + JSON3 v1.14.3 [1914dd2f] + MacroTools v0.5.16 [0b3b1443] + MicroMamba v0.1.14 [bac558e1] + OrderedCollections v1.8.1 [69de0a69] + Parsers v2.8.3 [fa939f87] + Pidfile v1.3.0 ⌅ [aea7be01] + PrecompileTools v1.2.1 [21216c6a] + Preferences v1.4.3 [0bca4874] + PyBoltz v0.2.0 [6099a3de] + PythonCall v0.9.25 [ae029012] + Requires v1.3.1 [6c6a2e73] + Scratch v1.3.0 [69024149] + StringEncodings v0.3.7 [856f2bd8] + StructTypes v1.11.0 [3783bdb8] + TableTraits v1.0.1 [bd369af6] + Tables v1.12.1 [e17b2a0c] + UnsafePointers v1.0.0 [ddb6d928] + YAML v0.4.14 [94ce4f54] + Libiconv_jll v1.18.0+0 [f8abcde7] + micromamba_jll v1.5.8+0 [4d7b5844] + pixi_jll v0.41.3+0 [0dad84c5] + ArgTools v1.1.2 [56f22d72] + Artifacts v1.11.0 [2a0f44e3] + Base64 v1.11.0 [ade2ca70] + Dates v1.11.0 [f43a241f] + Downloads v1.6.0 [7b1f6079] + FileWatching 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 [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 [9a3f8284] + Random v1.11.0 [ea8e919c] + SHA v0.7.0 [9e88b42a] + Serialization 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 [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 [83775a58] + Zlib_jll v1.2.13+1 [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. To see why use `status --outdated -m` Installation completed after 4.19s ################################################################################ # Precompilation # Precompiling PkgEval dependencies... Precompiling package dependencies... Precompilation completed after 147.15s ################################################################################ # Testing # Testing PyBoltz Status `/tmp/jl_n0odfL/Project.toml` [00701ae9] BioAlignments v3.1.0 [7e6ae17a] BioSequences v3.4.1 [de9282ab] BioStructures v4.6.0 [0bca4874] PyBoltz v0.2.0 [6e960f36] TMscore v0.1.0 [8dfed614] Test v1.11.0 Status `/tmp/jl_n0odfL/Manifest.toml` [00701ae9] BioAlignments v3.1.0 [47718e42] BioGenerics v0.1.5 [7e6ae17a] BioSequences v3.4.1 [de9282ab] BioStructures v4.6.0 [3c28c6f8] BioSymbols v5.2.0 [944b1d66] CodecZlib v0.7.8 [34da2185] Compat v4.16.0 [992eb4ea] CondaPkg v0.2.29 [9a962f9c] DataAPI v1.16.0 [e2d170a0] DataValueInterfaces v1.0.0 [1fa38f19] Format v1.3.7 [524e6230] IntervalTrees v1.1.0 [82899510] IteratorInterfaceExtensions v1.0.0 [692b3bcd] JLLWrappers v1.7.0 [0f8b85d8] JSON3 v1.14.3 [1914dd2f] MacroTools v0.5.16 [0b3b1443] MicroMamba v0.1.14 [bac558e1] OrderedCollections v1.8.1 [69de0a69] Parsers v2.8.3 [fa939f87] Pidfile v1.3.0 ⌅ [aea7be01] PrecompileTools v1.2.1 [21216c6a] Preferences v1.4.3 [0bca4874] PyBoltz v0.2.0 [6099a3de] PythonCall v0.9.25 [3cdcf5f2] RecipesBase v1.3.4 [ae029012] Requires v1.3.1 [6c6a2e73] Scratch v1.3.0 [10745b16] Statistics v1.11.1 [69024149] StringEncodings v0.3.7 [856f2bd8] StructTypes v1.11.0 [6e960f36] TMscore v0.1.0 [3783bdb8] TableTraits v1.0.1 [bd369af6] Tables v1.12.1 [3bb67fe8] TranscodingStreams v0.11.3 [7200193e] Twiddle v1.1.2 [e17b2a0c] UnsafePointers v1.0.0 [ddb6d928] YAML v0.4.14 [94ce4f54] Libiconv_jll v1.18.0+0 [1d8dad79] TMscore_jll v1.0.0+0 [f8abcde7] micromamba_jll v1.5.8+0 [4d7b5844] pixi_jll v0.41.3+0 [0dad84c5] ArgTools v1.1.2 [56f22d72] Artifacts v1.11.0 [2a0f44e3] Base64 v1.11.0 [ade2ca70] Dates v1.11.0 [f43a241f] Downloads v1.6.0 [7b1f6079] FileWatching 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 [9a3f8284] Random v1.11.0 [ea8e919c] SHA v0.7.0 [9e88b42a] Serialization 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 [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... CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PyBoltz/MeWga/CondaPkg.toml CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/L4cjh/CondaPkg.toml CondaPkg Resolving changes + boltz (pip) + libstdcxx-ng + python + uv CondaPkg Initialising pixi │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ init │ --format pixi └ /tmp/jl_n0odfL/.CondaPkg ✔ Created /tmp/jl_n0odfL/.CondaPkg/pixi.toml CondaPkg Wrote /tmp/jl_n0odfL/.CondaPkg/pixi.toml │ [dependencies] │ uv = ">=0.4" │ libstdcxx-ng = ">=3.4,<14.0" │ │ [dependencies.python] │ channel = "conda-forge" │ build = "*cpython*" │ version = ">=3.8,<4" │ │ [project] │ name = ".CondaPkg" │ platforms = ["linux-64"] │ channels = ["conda-forge"] │ channel-priority = "strict" │ description = "automatically generated by CondaPkg.jl" │ │ [pypi-dependencies] └ boltz = "~=2.1.1" CondaPkg Installing packages │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi │ install └ --manifest-path /tmp/jl_n0odfL/.CondaPkg/pixi.toml ✔ The default environment has been installed. Precompiling BioStructuresExt... 1693.9 ms ✓ TMscore → BioStructuresExt 1 dependency successfully precompiled in 2 seconds. 68 already precompiled. [ Info: Downloading file from PDB: 1TIT Error while loading libcue_ops.so: libcuda.so.1: cannot open shared object file: No such file or directory Running on CPU, this will be slow. Consider using a GPU. Seed set to 0 Downloading and extracting the CCD data to /home/pkgeval/.julia/scratchspaces/0bca4874-a2b8-4dca-bc03-d2d86e344f1f/boltz_cache/mols. This may take a bit of time. You may change the cache directory with the --cache flag. Downloading the Boltz-2 weights to /home/pkgeval/.julia/scratchspaces/0bca4874-a2b8-4dca-bc03-d2d86e344f1f/boltz_cache/boltz2_conf.ckpt. You may change the cache directory with the --cache flag. Downloading the Boltz-2 affinity weights to /home/pkgeval/.julia/scratchspaces/0bca4874-a2b8-4dca-bc03-d2d86e344f1f/boltz_cache/boltz2_aff.ckpt. You may change the cache directory with the --cache flag. Checking input data. Processing 1 inputs with 1 threads. 0%| | 0/1 [00:00 sys.exit(cli()) ^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 1157, in __call__ return self.main(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) ^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, **ctx.params) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 783, in invoke return __callback(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/main.py", line 1190, in predict trainer.predict( File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/trainer/trainer.py", line 859, in predict return call._call_and_handle_interrupt( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/trainer/call.py", line 47, in _call_and_handle_interrupt return trainer_fn(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/trainer/trainer.py", line 898, in _predict_impl results = self._run(model, ckpt_path=ckpt_path) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/trainer/trainer.py", line 982, in _run results = self._run_stage() ^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/trainer/trainer.py", line 1021, in _run_stage return self.predict_loop.run() ^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/loops/utilities.py", line 179, in _decorator return loop_run(self, *args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/loops/prediction_loop.py", line 125, in run jfptr_print_48490.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 showerror at ./errorshow.jl:152 unknown function (ip: 0x7132cf570a46) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 self._predict_step(batch, batch_idx, dataloader_idx, dataloader_iter) File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/loops/prediction_loop.py", line 255, in _predict_step predictions = call._call_strategy_hook(trainer, "predict_step", *step_args) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/trainer/call.py", line 323, in _call_strategy_hook output = fn(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/strategies/strategy.py", line 438, in predict_step return self.lightning_module.predict_step(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/tmp/jl_n0odfL/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/models/boltz2.py", line 1124, in predict_step raise {"exception": True} TypeError: exceptions must derive from BaseException poptask at ./task.jl:1012 _atexit at ./initdefs.jl:454 wait at ./task.jl:1021 jfptr__atexit_69651.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] ijl_atexit_hook at /source/src/init.c:271 jl_exit_thread0_cb at /source/src/signals-unix.c:517 uv_write at ./stream.jl:1081 unsafe_write at ./stream.jl:1154 write at ./strings/io.jl:248 [inlined] print at ./strings/io.jl:250 jfptr_print_48490.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 showerror at ./errorshow.jl:152 unknown function (ip: 0x7f4192146866) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 _atexit at ./initdefs.jl:454 jfptr__atexit_69651.1 at /opt/julia/lib/julia/sys.so (unknown line) _jl_invoke at /source/src/gf.c:2948 [inlined] ijl_apply_generic at /source/src/gf.c:3125 jl_apply at /source/src/julia.h:2157 [inlined] ijl_atexit_hook at /source/src/init.c:271 jl_exit_thread0_cb at /source/src/signals-unix.c:517 PkgEval terminated after 2737.65s: test duration exceeded the time limit