Package evaluation to test PyBoltz on Julia 1.11.7 (58327cce5e*) started at 2025-10-28T19:31:55.592


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.2s


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

Installing PyBoltz...
   Resolving package versions...
    Updating `~/.julia/environments/v1.11/Project.toml`
  [0bca4874] + PyBoltz v0.2.2
    Updating `~/.julia/environments/v1.11/Manifest.toml`
  [34da2185] + Compat v4.18.1
  [992eb4ea] + CondaPkg v0.2.33
  [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 v1.2.1
  [21216c6a] + Preferences v1.5.0
  [0bca4874] + PyBoltz v0.2.2
  [6099a3de] + PythonCall v0.9.28
  [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 v1.6.0
  [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 5.21s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 190.87s


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

     Testing PyBoltz
      Status `/tmp/jl_jsGvCC/Project.toml`
  [00701ae9] BioAlignments v3.1.0
  [7e6ae17a] BioSequences v3.5.0
  [de9282ab] BioStructures v4.7.0
  [0bca4874] PyBoltz v0.2.2
  [6e960f36] TMscore v0.1.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_jsGvCC/Manifest.toml`
  [00701ae9] BioAlignments v3.1.0
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.5.0
  [de9282ab] BioStructures v4.7.0
  [3c28c6f8] BioSymbols v5.2.0
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.18.1
  [992eb4ea] CondaPkg v0.2.33
  [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 v1.2.1
  [21216c6a] Preferences v1.5.0
  [0bca4874] PyBoltz v0.2.2
  [6099a3de] PythonCall v0.9.28
  [3cdcf5f2] RecipesBase v1.3.4
  [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 v1.6.0
  [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/PGqPe/CondaPkg.toml
    CondaPkg Found dependencies: /home/pkgeval/.julia/packages/PythonCall/mkWc2/CondaPkg.toml
    CondaPkg Found dependencies: /home/pkgeval/.julia/packages/CondaPkg/0UqYV/CondaPkg.toml
    CondaPkg Resolving changes
             + boltz (pip)
             + libstdcxx
             + libstdcxx-ng
             + python
             + uv
    CondaPkg Initialising pixi
             │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_jsGvCC/.CondaPkg
✔ Created /tmp/jl_jsGvCC/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_jsGvCC/.CondaPkg/pixi.toml
             │ [dependencies]
             │ libstdcxx = ">=3.4,<14.0"
             │ uv = ">=0.4"
             │ libstdcxx-ng = ">=3.4,<14.0"
             │ 
             │     [dependencies.python]
             │     channel = "conda-forge"
             │     build = "*cp*"
             │     version = ">=3.10,<3.13, >=3.9,<4"
             │ 
             │ [project]
             │ name = ".CondaPkg"
             │ platforms = ["linux-64"]
             │ channels = ["conda-forge"]
             │ channel-priority = "strict"
             │ description = "automatically generated by CondaPkg.jl"
             │ 
             │ [pypi-dependencies.boltz]
             │ extras = ["cuda"]
             └ version = "~=2.2"
    CondaPkg Installing packages
             │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ install
             └ --manifest-path /tmp/jl_jsGvCC/.CondaPkg/pixi.toml
✔ The default environment has been installed.
Precompiling BioAlignments...
  10461.9 ms  ✓ BioSequences
   3584.5 ms  ✓ BioAlignments
  2 dependencies successfully precompiled in 14 seconds. 11 already precompiled.
Precompiling BioStructuresBioSequencesExt...
   1491.5 ms  ✓ BioStructures → BioStructuresBioSequencesExt
  1 dependency successfully precompiled in 2 seconds. 26 already precompiled.
Precompiling BioStructuresBioAlignmentsExt...
   2250.8 ms  ✓ BioStructures → BioStructuresBioAlignmentsExt
  1 dependency successfully precompiled in 2 seconds. 29 already precompiled.
Precompiling TMscore...
   1115.8 ms  ✓ TMscore_jll
   1009.8 ms  ✓ TMscore
  2 dependencies successfully precompiled in 2 seconds. 26 already precompiled.
Precompiling BioStructuresExt...
   1847.7 ms  ✓ TMscore → BioStructuresExt
  1 dependency successfully precompiled in 4 seconds. 67 already precompiled.
[ Info: Downloading file from PDB: 1TIT
Running on CPU, this will be slow. Consider using a GPU.
/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/__init__.py:1617: UserWarning: Please use the new API settings to control TF32 behavior, such as torch.backends.cudnn.conv.fp32_precision = 'tf32' or torch.backends.cuda.matmul.fp32_precision = 'ieee'. Old settings, e.g, torch.backends.cuda.matmul.allow_tf32 = True, torch.backends.cudnn.allow_tf32 = True, allowTF32CuDNN() and allowTF32CuBLAS() will be deprecated after Pytorch 2.9. Please see https://pytorch.org/docs/main/notes/cuda.html#tensorfloat-32-tf32-on-ampere-and-later-devices (Triggered internally at /pytorch/aten/src/ATen/Context.cpp:80.)
  _C._set_float32_matmul_precision(precision)
Seed set to 0
Downloading the CCD data to /home/pkgeval/.julia/scratchspaces/0bca4874-a2b8-4dca-bc03-d2d86e344f1f/boltz_cache/mols.tar. This may take a bit of time. You may change the cache directory with the --cache flag.
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,  3.35it/s]
100%|██████████| 1/1 [00:00<00:00,  3.34it/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_jsGvCC/.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_jsGvCC/.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_jsGvCC/.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_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/utils/data/dataloader.py:668: 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 154 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:522
poptask at ./task.jl:1012
wait at ./task.jl:1021
task_done_hook at ./task.jl:694
jfptr_task_done_hook_66679.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
jl_finish_task at /source/src/task.c:319
start_task at /source/src/task.c:1213
unknown function (ip: (nil))

==============================================================
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/v1.11/Profile/src/Profile.jl:1240
Overhead ╎ [+additional indent] Count File:Line; Function
=========================================================
Thread 1 Task 0x00007bf1ed997080 Total snapshots: 357. Utilization: 0%
   ╎357 @Base/task.jl:694; task_done_hook(t::Task)
   ╎ 357 @Base/task.jl:1021; wait()
356╎  357 @Base/task.jl:1012; poptask(W::Base.IntrusiveLinkedListSynchronized{T…


======================================================================================
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:522
poptask at ./task.jl:1012
wait at ./task.jl:1021
#wait#733 at ./condition.jl:130
wait at ./condition.jl:125 [inlined]
wait at ./process.jl:694
wait at ./process.jl:687
unknown function (ip: 0x7bd73b52dd92)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
subprocess_handler at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2146
#131 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2086
withenv at ./env.jl:265
#118 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1935
with_temp_env at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1793
#116 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1902
#mktempdir#28 at ./file.jl:819
unknown function (ip: 0x7bd73b525e1d)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
mktempdir at ./file.jl:815
mktempdir at ./file.jl:815 [inlined]
#sandbox#115 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1849 [inlined]
sandbox at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:1841
unknown function (ip: 0x7bd73b51a3a6)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
#test#128 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2067
test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/Operations.jl:2011 [inlined]
#test#146 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:481
test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:460
unknown function (ip: 0x7bd73b51a0ad)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
#test#77 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:159
unknown function (ip: 0x7bd73b519a7d)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:148
#test#75 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined]
test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:147 [inlined]
#test#74 at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:146 [inlined]
test at /source/usr/share/julia/stdlib/v1.11/Pkg/src/API.jl:146
unknown function (ip: 0x7bd73b515f16)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
do_call at /source/src/interpreter.c:126
eval_value at /source/src/interpreter.c:223
eval_stmt_value at /source/src/interpreter.c:174 [inlined]
eval_body at /source/src/interpreter.c:670
eval_body at /source/src/interpreter.c:539
eval_body at /source/src/interpreter.c:539
jl_interpret_toplevel_thunk at /source/src/interpreter.c:824
jl_toplevel_eval_flex at /source/src/toplevel.c:943
jl_toplevel_eval_flex at /source/src/toplevel.c:886
ijl_toplevel_eval_in at /source/src/toplevel.c:994
eval at ./boot.jl:430 [inlined]
include_string at ./loading.jl:2775
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
_include at ./loading.jl:2835
include at ./Base.jl:562
jfptr_include_47022.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
exec_options at ./client.jl:316
_start at ./client.jl:524
jfptr__start_73678.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
true_main at /source/src/jlapi.c:900
jl_repl_entrypoint at /source/src/jlapi.c:1059
main at /source/cli/loader_exe.c:58
unknown function (ip: 0x7bd73c9fe249)
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8)
unknown function (ip: (nil))

==============================================================
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/v1.11/Profile/src/Profile.jl:1240
Overhead ╎ [+additional indent] Count File:Line; Function
=========================================================
Thread 1 Task 0x00007bd72fbfc010 Total snapshots: 125. Utilization: 0%
   ╎125 @Base/client.jl:524; _start()
   ╎ 125 @Base/client.jl:316; exec_options(opts::Base.JLOptions)
   ╎  125 @Base/Base.jl:562; include(mod::Module, _path::String)
   ╎   125 @Base/loading.jl:2835; _include(mapexpr::Function, mod::Module, _pat…
   ╎    125 @Base/loading.jl:2775; include_string(mapexpr::typeof(identity), mo…
   ╎     125 @Base/boot.jl:430; eval
   ╎    ╎ 125 @Pkg/src/API.jl:146; kwcall(::@NamedTuple{julia_args::Cmd}, ::typ…
   ╎    ╎  125 @Pkg/src/API.jl:146; #test#74
   ╎    ╎   125 @Pkg/src/API.jl:147; test
   ╎    ╎    125 @Pkg/src/API.jl:147; #test#75
   ╎    ╎     125 @Pkg/src/API.jl:148; kwcall(::@NamedTuple{julia_args::Cmd}, :…
   ╎    ╎    ╎ 125 @Pkg/src/API.jl:159; test(pkgs::Vector{Pkg.Types.PackageSpec…
   ╎    ╎    ╎  125 @Pkg/src/API.jl:460; kwcall(::@NamedTuple{julia_args::Cmd, …
   ╎    ╎    ╎   125 @Pkg/src/API.jl:481; test(ctx::Pkg.Types.Context, pkgs::Ve…
   ╎    ╎    ╎    125 …rc/Operations.jl:2011; test
   ╎    ╎    ╎     125 …rc/Operations.jl:2067; test(ctx::Pkg.Types.Context, pkg…
   ╎    ╎    ╎    ╎ 125 …c/Operations.jl:1841; kwcall(::@NamedTuple{preferences…
   ╎    ╎    ╎    ╎  125 …c/Operations.jl:1849; #sandbox#115
   ╎    ╎    ╎    ╎   125 @Base/file.jl:815; mktempdir
   ╎    ╎    ╎    ╎    125 @Base/file.jl:815; mktempdir(fn::Function, parent::S…
   ╎    ╎    ╎    ╎     125 @Base/file.jl:819; mktempdir(fn::Pkg.Operations.var…
   ╎    ╎    ╎    ╎    ╎ 125 …Operations.jl:1902; (::Pkg.Operations.var"#116#12…
   ╎    ╎    ╎    ╎    ╎  125 …Operations.jl:1793; with_temp_env(fn::Pkg.Operat…
   ╎    ╎    ╎    ╎    ╎   125 …Operations.jl:1935; (::Pkg.Operations.var"#118#…
   ╎    ╎    ╎    ╎    ╎    125 @Base/env.jl:265; withenv(::Pkg.Operations.var"…
   ╎    ╎    ╎    ╎    ╎     125 …perations.jl:2086; (::Pkg.Operations.var"#131…
   ╎    ╎    ╎    ╎    ╎    ╎ 125 …erations.jl:2146; subprocess_handler(cmd::Cm…
   ╎    ╎    ╎    ╎    ╎    ╎  125 …/process.jl:687; wait(x::Base.Process)
   ╎    ╎    ╎    ╎    ╎    ╎   125 …/process.jl:694; wait(x::Base.Process, syn…
   ╎    ╎    ╎    ╎    ╎    ╎    125 …ondition.jl:125; wait
   ╎    ╎    ╎    ╎    ╎    ╎     125 …ondition.jl:130; wait(c::Base.GenericCon…
   ╎    ╎    ╎    ╎    ╎    ╎    ╎ 125 …ase/task.jl:1021; wait()
124╎    ╎    ╎    ╎    ╎    ╎    ╎  125 …ase/task.jl:1012; poptask(W::Base.Intr…


[154] signal 15: Terminated
in expression starting at /home/pkgeval/.julia/packages/PyBoltz/PGqPe/test/runtests.jl:13
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:522

[1] signal 15: Terminated
in expression starting at /PkgEval.jl/scripts/evaluate.jl:210
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:522
[rank: 0] Received SIGTERM: 15
poptask at ./task.jl:1012
poptask at ./task.jl:1012
wait at ./task.jl:1021
wait at ./task.jl:1021
#wait#733 at ./condition.jl:130
#wait#733 at ./condition.jl:130
wait at ./condition.jl:125 [inlined]
_trywait at ./asyncevent.jl:145
wait at ./condition.jl:125 [inlined]
_trywait at ./asyncevent.jl:145
profile_printing_listener at ./Base.jl:582
profile_printing_listener at ./Base.jl:582
#1192 at ./Base.jl:622
#1192 at ./Base.jl:622
jfptr_YY.1192_76252.1 at /opt/julia/lib/julia/sys.so (unknown line)
jfptr_YY.1192_76252.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
start_task at /source/src/task.c:1202
unknown function (ip: (nil))
Allocations: 18876775 (Pool: 18876023; Big: 752); GC: 17
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
jl_apply at /source/src/julia.h:2157 [inlined]
start_task at /source/src/task.c:1202
unknown function (ip: (nil))
Allocations: 20860715 (Pool: 20859960; Big: 755); GC: 21
val already in a list
atexit hook threw an error: ErrorException("schedule: Task not runnable")
error at ./error.jl:35
#schedule#763 at ./task.jl:884
schedule at ./task.jl:876 [inlined]
uv_writecb_task at ./stream.jl:1200
jfptr_uv_writecb_task_67129.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
val already in a list
atexit hook threw an error: ErrorException("schedule: Task not runnable")
jlcapi_uv_writecb_task_67593.1 at /opt/julia/lib/julia/sys.so (unknown line)
uv__write_callbacks at /workspace/srcdir/libuv/src/unix/stream.c:926
uv__stream_io at /workspace/srcdir/libuv/src/unix/stream.c:1227
uv__run_pending at /workspace/srcdir/libuv/src/unix/core.c:824
uv_run at /workspace/srcdir/libuv/src/unix/core.c:420
ijl_task_get_next at /source/src/scheduler.c:522
error at ./error.jl:35
poptask at ./task.jl:1012
#schedule#763 at ./task.jl:884
wait at ./task.jl:1021
Traceback (most recent call last):
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/bin/boltz", line 10, in <module>
    sys.exit(cli())
             ^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.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_jsGvCC/.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_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/main.py", line 1329, in predict
    trainer.predict(
  File "/tmp/jl_jsGvCC/.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_jsGvCC/.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_jsGvCC/.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_jsGvCC/.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_jsGvCC/.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_jsGvCC/.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_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/pytorch_lightning/loops/prediction_loop.py", line 125, in run
    self._predict_step(batch, batch_idx, dataloader_idx, dataloader_iter)
  File "/tmp/jl_jsGvCC/.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_jsGvCC/.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_jsGvCC/.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_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/models/boltz2.py", line 1130, in predict_step
    raise e
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/models/boltz2.py", line 1059, in predict_step
    out = self(
          ^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1775, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1786, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/models/boltz2.py", line 533, in forward
schedule at ./task.jl:876 [inlined]
uv_writecb_task at ./stream.jl:1200
    struct_out = self.structure_module.sample(
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/modules/diffusionv2.py", line 388, in sample
    atom_coords_denoised_chunk = self.preconditioned_network_forward(
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/modules/diffusionv2.py", line 264, in preconditioned_network_forward
    r_update = self.score_model(
               ^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1775, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1786, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/modules/diffusionv2.py", line 154, in forward
    a = self.token_transformer(
        ^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1775, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1786, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/modules/transformersv2.py", line 129, in forward
    a = layer(
        ^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1775, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1786, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/modules/transformersv2.py", line 192, in forward
    b = self.pair_bias_attn(
        ^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1775, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1786, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/layers/attentionv2.py", line 90, in forward
    q = self.proj_q(s).view(B, -1, self.num_heads, self.head_dim)
        ^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1775, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1786, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/linear.py", line 134, in forward
    return F.linear(input, self.weight, self.bias)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_jsGvCC/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/utils/data/_utils/signal_handling.py", line 73, in handler
    _error_if_any_worker_fails()
RuntimeError: DataLoader worker (pid 278) is killed by signal: Terminated. 
uv_write at ./stream.jl:1081
jfptr_uv_writecb_task_67129.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
unsafe_write at ./stream.jl:1154
jlcapi_uv_writecb_task_67593.1 at /opt/julia/lib/julia/sys.so (unknown line)
uv__write_callbacks at /workspace/srcdir/libuv/src/unix/stream.c:926
uv__stream_io at /workspace/srcdir/libuv/src/unix/stream.c:1227
write at ./strings/io.jl:248 [inlined]
print at ./strings/io.jl:250
uv__run_pending at /workspace/srcdir/libuv/src/unix/core.c:824
uv_run at /workspace/srcdir/libuv/src/unix/core.c:420
ijl_task_get_next at /source/src/scheduler.c:522
poptask at ./task.jl:1012
jfptr_print_48479.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
showerror at ./errorshow.jl:152
unknown function (ip: 0x7bd73b53aeb6)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
wait at ./task.jl:1021
_atexit at ./initdefs.jl:454
uv_write at ./stream.jl:1081
jfptr__atexit_69637.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
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
unsafe_write at ./stream.jl:1154
write at ./strings/io.jl:248 [inlined]
print at ./strings/io.jl:250
jfptr_print_48479.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128
showerror at ./errorshow.jl:152
unknown function (ip: 0x7bf1da994986)
_jl_invoke at /source/src/gf.c:2951 [inlined]
ijl_apply_generic at /source/src/gf.c:3128

PkgEval terminated after 2724.55s: test duration exceeded the time limit