Package evaluation of PyBoltz on Julia 1.13.0-DEV.974 (7bbb213719*) started at 2025-08-12T15:14:50.828


################################################################################
# Set-up
#

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 9.87s


################################################################################
# Installation
#

Installing PyBoltz...
   Resolving package versions...
    Updating `~/.julia/environments/v1.13/Project.toml`
  [0bca4874] + PyBoltz v0.2.0
    Updating `~/.julia/environments/v1.13/Manifest.toml`
  [34da2185] + Compat v4.18.0
  [992eb4ea] + CondaPkg v0.2.29
  [9a962f9c] + DataAPI v1.16.0
  [e2d170a0] + DataValueInterfaces v1.0.0
  [82899510] + IteratorInterfaceExtensions v1.0.0
  [692b3bcd] + JLLWrappers v1.7.1
  [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 v1.3.2
  [21216c6a] + Preferences v1.5.0
  [0bca4874] + PyBoltz v0.2.0
  [6099a3de] + PythonCall v0.9.26
  [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 v1.5.12+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 v1.7.0
  [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
  [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
  [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 v8.15.0+1
  [e37daf67] + LibGit2_jll v1.9.1+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.7.15
  [458c3c95] + OpenSSL_jll v3.5.2+0
  [efcefdf7] + PCRE2_jll v10.45.0+0
  [83775a58] + Zlib_jll v1.3.1+2
  [3161d3a3] + Zstd_jll v1.5.7+1
  [8e850ede] + nghttp2_jll v1.65.0+0
  [3f19e933] + p7zip_jll v17.5.0+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 4.62s


################################################################################
# Precompilation
#

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 194.31s


################################################################################
# Testing
#

     Testing PyBoltz
      Status `/tmp/jl_DSEgn8/Project.toml`
  [00701ae9] BioAlignments v3.1.0
  [7e6ae17a] BioSequences v3.5.0
  [de9282ab] BioStructures v4.6.0
  [0bca4874] PyBoltz v0.2.0
  [6e960f36] TMscore v0.1.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_DSEgn8/Manifest.toml`
  [00701ae9] BioAlignments v3.1.0
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.5.0
  [de9282ab] BioStructures v4.6.0
  [3c28c6f8] BioSymbols v5.2.0
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.18.0
  [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 v1.7.1
  [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 v1.3.2
  [21216c6a] Preferences v1.5.0
  [0bca4874] PyBoltz v0.2.0
  [6099a3de] PythonCall v0.9.26
  [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 v1.5.12+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 v1.7.0
  [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 v1.13.0
  [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
  [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 v8.15.0+1
  [e37daf67] LibGit2_jll v1.9.1+0
  [29816b5a] LibSSH2_jll v1.11.3+1
  [14a3606d] MozillaCACerts_jll v2025.7.15
  [4536629a] OpenBLAS_jll v0.3.29+0
  [458c3c95] OpenSSL_jll v3.5.2+0
  [efcefdf7] PCRE2_jll v10.45.0+0
  [83775a58] Zlib_jll v1.3.1+2
  [3161d3a3] Zstd_jll v1.5.7+1
  [8e850b90] libblastrampoline_jll v5.13.1+0
  [8e850ede] nghttp2_jll v1.65.0+0
  [3f19e933] p7zip_jll v17.5.0+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/avYrV/CondaPkg.toml
    CondaPkg Resolving changes
             + boltz (pip)
             + openssl
             + python
             + uv
    CondaPkg Initialising pixi
             │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_DSEgn8/.CondaPkg
✔ Created /tmp/jl_DSEgn8/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_DSEgn8/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ uv = ">=0.4"
             │ 
             │     [dependencies.python]
             │     version = ">=3.8,<4"
             │     build = "*cpython*"
             │     channel = "conda-forge"
             │ 
             │ [pypi-dependencies]
             │ boltz = "~=2.1.1"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ description = "automatically generated by CondaPkg.jl"
             │ platforms = ["linux-64"]
             │ channel-priority = "strict"
             └ channels = ["conda-forge"]
    CondaPkg Installing packages
             │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /tmp/jl_DSEgn8/.CondaPkg/pixi.toml
✔ The default environment has been installed.
Precompiling packages...
   9641.1 ms  ✓ BioSequences
   3517.7 ms  ✓ BioAlignments
  2 dependencies successfully precompiled in 13 seconds. 11 already precompiled.
Precompiling packages...
   1680.5 ms  ✓ BioStructures → BioStructuresBioSequencesExt
  1 dependency successfully precompiled in 2 seconds. 27 already precompiled.
Precompiling packages...
   2213.8 ms  ✓ BioStructures → BioStructuresBioAlignmentsExt
  1 dependency successfully precompiled in 2 seconds. 30 already precompiled.
Precompiling packages...
   1445.3 ms  ✓ TMscore_jll
   1139.7 ms  ✓ TMscore
  2 dependencies successfully precompiled in 3 seconds. 29 already precompiled.
Precompiling packages...
   2129.8 ms  ✓ TMscore → BioStructuresExt
  1 dependency successfully precompiled in 4 seconds. 71 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<?, ?it/s]Found explicit empty MSA for some proteins, will run these in single sequence mode. Keep in mind that the model predictions will be suboptimal without an MSA.

100%|██████████| 1/1 [00:00<00:00,  3.70it/s]
100%|██████████| 1/1 [00:00<00:00,  3.69it/s]
Using bfloat16 Automatic Mixed Precision (AMP)
GPU available: False, used: False
TPU available: False, using: 0 TPU cores
HPU available: False, using: 0 HPUs
/tmp/jl_DSEgn8/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/trainer/connectors/logger_connector/logger_connector.py:76: Starting from v1.9.0, `tensorboardX` has been removed as a dependency of the `pytorch_lightning` package, due to potential conflicts with other packages in the ML ecosystem. For this reason, `logger=True` will use `CSVLogger` as the default logger, unless the `tensorboard` or `tensorboardX` packages are found. Please `pip install lightning[extra]` or one of them to enable TensorBoard support by default
Running structure prediction for 1 input.
/tmp/jl_DSEgn8/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/utilities/migration/utils.py:56: The loaded checkpoint was produced with Lightning v2.5.0.post0, which is newer than your current Lightning version: v2.5.0
/tmp/jl_DSEgn8/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/utils/data/dataloader.py:627: UserWarning: This DataLoader will create 2 worker processes in total. Our suggested max number of worker in current system is 1, which is smaller than what this DataLoader is going to create. Please be aware that excessive worker creation might get DataLoader running slow or even freeze, lower the worker number to avoid potential slowness/freeze if necessary.
  warnings.warn(
/tmp/jl_DSEgn8/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/utils/data/dataloader.py:666: UserWarning: 'pin_memory' argument is set as true but no accelerator is found, then device pinned memory won't be used.
  warnings.warn(warn_msg)

Predicting: |          | 0/? [00:00<?, ?it/s]
Predicting:   0%|          | 0/1 [00:00<?, ?it/s]
Predicting DataLoader 0:   0%|          | 0/1 [00:00<?, ?it/s]
======================================================================================
Information request received. A stacktrace will print followed by a 1.0 second profile
======================================================================================

cmd: /opt/julia/bin/julia 179 running 0 of 1

signal (10): User defined signal 1
epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404
uv_run at /workspace/srcdir/libuv/src/unix/core.c:430
ijl_task_get_next at /source/src/scheduler.c:457
wait at ./task.jl:1192
wait_forever at ./task.jl:1129
jfptr_wait_forever_70431.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:4015 [inlined]
ijl_apply_generic at /source/src/gf.c:4212
jl_apply at /source/src/julia.h:2375 [inlined]
start_task at /source/src/task.c:1253
unknown function (ip: (nil)) at (unknown file)

==============================================================
Profile collected. A report will print at the next yield point
==============================================================


======================================================================================
Information request received. A stacktrace will print followed by a 1.0 second profile
======================================================================================

cmd: /opt/julia/bin/julia 1 running 0 of 1

signal (10): User defined signal 1
epoll_pwait at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
uv__io_poll at /workspace/srcdir/libuv/src/unix/linux.c:1404
uv_run at /workspace/srcdir/libuv/src/unix/core.c:430
ijl_task_get_next at /source/src/scheduler.c:457
wait at ./task.jl:1192
wait_forever at ./task.jl:1129
jfptr_wait_forever_70431.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:4015 [inlined]
ijl_apply_generic at /source/src/gf.c:4212
jl_apply at /source/src/julia.h:2375 [inlined]
start_task at /source/src/task.c:1253
unknown function (ip: (nil)) at (unknown file)

==============================================================
Profile collected. A report will print at the next yield point
==============================================================

┌ Warning: There were no samples collected in one or more groups.
│ This may be due to idle threads, or you may need to run your
│ program longer (perhaps by running it multiple times),
│ or adjust the delay between samples with `Profile.init()`.
└ @ Profile /opt/julia/share/julia/stdlib/v1.13/Profile/src/Profile.jl:1362
Overhead ╎ [+additional indent] Count File:Line  Function
=========================================================
Thread 1 (default) Task 0x000074e57870d2d0 Total snapshots: 139. Utilization: 0%
   ╎139 @Base/task.jl:1129  wait_forever()
138╎ 139 @Base/task.jl:1192  wait()

[rank: 0] Received SIGTERM: 15

[179] signal 15: Terminated
in expression starting at /home/pkgeval/.julia/packages/PyBoltz/MeWga/test/runtests.jl:13

PkgEval terminated after 2727.7s: test duration exceeded the time limit