Package evaluation of PyBoltz on Julia 1.12.0-rc1.2 (995ff9db19*) started at 2025-07-14T14:44:31.610


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

Installing PkgEval dependencies (TestEnv)...

Set-up completed after 8.75s


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

Installing PyBoltz...
   Resolving package versions...
    Updating `~/.julia/environments/v1.12/Project.toml`
  [0bca4874] + PyBoltz v0.2.0
    Updating `~/.julia/environments/v1.12/Manifest.toml`
  [34da2185] + Compat v4.17.0
  [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 v1.3.2
  [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
  [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
  [deac9b47] + LibCURL_jll v8.11.1+1
  [e37daf67] + LibGit2_jll v1.9.0+0
  [29816b5a] + LibSSH2_jll v1.11.3+1
  [14a3606d] + MozillaCACerts_jll v2025.5.20
  [458c3c95] + OpenSSL_jll v3.5.1+0
  [83775a58] + Zlib_jll v1.3.1+2
  [8e850ede] + nghttp2_jll v1.64.0+1
  [3f19e933] + p7zip_jll v17.5.0+2

Installation completed after 4.38s


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

Precompiling PkgEval dependencies...

Precompiling package dependencies...

Precompilation completed after 157.35s


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

     Testing PyBoltz
      Status `/tmp/jl_zNIjhD/Project.toml`
  [00701ae9] BioAlignments v3.1.0
  [7e6ae17a] BioSequences v3.4.2
  [de9282ab] BioStructures v4.6.0
  [0bca4874] PyBoltz v0.2.0
  [6e960f36] TMscore v0.1.0
  [8dfed614] Test v1.11.0
      Status `/tmp/jl_zNIjhD/Manifest.toml`
  [00701ae9] BioAlignments v3.1.0
  [47718e42] BioGenerics v0.1.5
  [7e6ae17a] BioSequences v3.4.2
  [de9282ab] BioStructures v4.6.0
  [3c28c6f8] BioSymbols v5.2.0
  [944b1d66] CodecZlib v0.7.8
  [34da2185] Compat v4.17.0
  [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 v1.3.2
  [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
  [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
  [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 v8.11.1+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 v3.5.1+0
  [83775a58] Zlib_jll v1.3.1+2
  [8e850b90] libblastrampoline_jll v5.13.1+0
  [8e850ede] nghttp2_jll v1.64.0+1
  [3f19e933] p7zip_jll v17.5.0+2
     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
             + openssl
             + python
             + uv
    CondaPkg Initialising pixi
             │ /home/pkgeval/.julia/artifacts/cefba4912c2b400756d043a2563ef77a0088866b/bin/pixi
             │ init
             │ --format pixi
             └ /tmp/jl_zNIjhD/.CondaPkg
✔ Created /tmp/jl_zNIjhD/.CondaPkg/pixi.toml
    CondaPkg Wrote /tmp/jl_zNIjhD/.CondaPkg/pixi.toml
             │ [dependencies]
             │ openssl = ">=3, <3.6"
             │ uv = ">=0.4"
             │ libstdcxx-ng = ">=3.4,<15.0"
             │ 
             │     [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_zNIjhD/.CondaPkg/pixi.toml
✔ The default environment has been installed.
Precompiling packages...
   2042.2 ms  ✓ TMscore → BioStructuresExt
  1 dependency successfully precompiled in 2 seconds. 70 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,  3.51it/s]
100%|██████████| 1/1 [00:00<00:00,  3.51it/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_zNIjhD/.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_zNIjhD/.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_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/utils/data/dataloader.py:626: 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_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/utils/data/dataloader.py:665: 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:457
poptask at ./task.jl:1187
wait at ./task.jl:1199
task_done_hook at ./task.jl:839
jfptr_task_done_hook_104661.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
jl_apply at /source/src/julia.h:2375 [inlined]
jl_finish_task at /source/src/task.c:345
start_task at /source/src/task.c:1260
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
poptask at ./task.jl:1187
wait at ./task.jl:1199
#wait#398 at ./condition.jl:141
wait at ./condition.jl:136 [inlined]
wait at ./process.jl:694
wait at ./process.jl:687
jfptr_wait_84416.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
subprocess_handler at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2476
unknown function (ip: 0x7f3b8fd86c33) at (unknown file)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
#213 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2416
withenv at ./env.jl:265
#198 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2237
with_temp_env at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2087
#194 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2196
#mktempdir#21 at ./file.jl:899
unknown function (ip: 0x7f3b8fd7a28c) at (unknown file)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
mktempdir at ./file.jl:895
mktempdir at ./file.jl:895
#sandbox#190 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2143 [inlined]
sandbox at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2135
unknown function (ip: 0x7f3b8fd71561) at (unknown file)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
#test#201 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2401
test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/Operations.jl:2313 [inlined]
#test#170 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:511
test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:490
unknown function (ip: 0x7f3b8fd70761) at (unknown file)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
#test#84 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:164
unknown function (ip: 0x7f3b8fd67de8) at (unknown file)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:153
#test#82 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:152
test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:152 [inlined]
#test#81 at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:151 [inlined]
test at /source/usr/share/julia/stdlib/v1.12/Pkg/src/API.jl:151
unknown function (ip: 0x7f3b8fd65a7f) at (unknown file)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
jl_apply at /source/src/julia.h:2375 [inlined]
do_call at /source/src/interpreter.c:123
eval_value at /source/src/interpreter.c:243
eval_stmt_value at /source/src/interpreter.c:194 [inlined]
eval_body at /source/src/interpreter.c:693
eval_body at /source/src/interpreter.c:558
eval_body at /source/src/interpreter.c:558
jl_interpret_toplevel_thunk at /source/src/interpreter.c:898
jl_toplevel_eval_flex at /source/src/toplevel.c:1035
jl_toplevel_eval_flex at /source/src/toplevel.c:975
ijl_toplevel_eval at /source/src/toplevel.c:1047
ijl_toplevel_eval_in at /source/src/toplevel.c:1092
eval at ./boot.jl:489
include_string at ./loading.jl:2837
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
_include at ./loading.jl:2897
include at ./Base.jl:305
exec_options at ./client.jl:321
_start at ./client.jl:554
jfptr__start_81451.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
jl_apply at /source/src/julia.h:2375 [inlined]
true_main at /source/src/jlapi.c:971
jl_repl_entrypoint at /source/src/jlapi.c:1139
main at /source/cli/loader_exe.c:58
unknown function (ip: 0x7f3ba5fd8249) at /lib/x86_64-linux-gnu/libc.so.6
__libc_start_main at /lib/x86_64-linux-gnu/libc.so.6 (unknown line)
unknown function (ip: 0x4010b8) at /workspace/srcdir/glibc-2.17/csu/../sysdeps/x86_64/start.S
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/v1.12/Profile/src/Profile.jl:1362
Overhead ╎ [+additional indent] Count File:Line  Function
=========================================================
Thread 1 (default) Task 0x00007f3b8b600010 Total snapshots: 71. Utilization: 0%
  ╎71 @Base/client.jl:554  _start()
  ╎ 71 @Base/client.jl:321  exec_options(opts::Base.JLOptions)
  ╎  71 @Base/Base.jl:305  include(mod::Module, _path::String)
  ╎   71 @Base/loading.jl:2897  _include(mapexpr::Function, mod::Module, _path:…
  ╎    71 @Base/loading.jl:2837  include_string(mapexpr::typeof(identity), mod:…
  ╎     71 @Base/boot.jl:489  eval(m::Module, e::Any)
  ╎    ╎ 71 @Pkg/src/API.jl:151  kwcall(::@NamedTuple{julia_args::Cmd}, ::typeo…
  ╎    ╎  71 @Pkg/src/API.jl:151  #test#81
  ╎    ╎   71 @Pkg/src/API.jl:152  test
  ╎    ╎    71 @Pkg/src/API.jl:152  test(pkgs::Vector{String}; kwargs::Base.Pai…
  ╎    ╎     71 @Pkg/src/API.jl:153  kwcall(::@NamedTuple{julia_args::Cmd}, ::t…
  ╎    ╎    ╎ 71 @Pkg/src/API.jl:164  test(pkgs::Vector{PackageSpec}; io::IOCon…
  ╎    ╎    ╎  71 @Pkg/src/API.jl:490  kwcall(::@NamedTuple{julia_args::Cmd, io…
  ╎    ╎    ╎   71 @Pkg/src/API.jl:511  test(ctx::Pkg.Types.Context, pkgs::Vect…
  ╎    ╎    ╎    71 @Pkg/…perations.jl:2313  test
  ╎    ╎    ╎     71 @Pkg/…perations.jl:2401  test(ctx::Pkg.Types.Context, pkgs…
  ╎    ╎    ╎    ╎ 71 @Pkg/…erations.jl:2135  kwcall(::@NamedTuple{preferences:…
  ╎    ╎    ╎    ╎  71 @Pkg/…erations.jl:2143  #sandbox#190
  ╎    ╎    ╎    ╎   71 @Base/file.jl:895  mktempdir(fn::Function)
  ╎    ╎    ╎    ╎    71 @Base/file.jl:895  mktempdir(fn::Function, parent::Str…
  ╎    ╎    ╎    ╎     71 @Base/file.jl:899  mktempdir(fn::Pkg.Operations.var"#…
  ╎    ╎    ╎    ╎    ╎ 71 @Pkg/…ations.jl:2196  (::Pkg.Operations.var"#194#195…
  ╎    ╎    ╎    ╎    ╎  71 @Pkg/…ations.jl:2087  with_temp_env(fn::Pkg.Operati…
  ╎    ╎    ╎    ╎    ╎   71 @Pkg/…tions.jl:2237  (::Pkg.Operations.var"#198#19…
  ╎    ╎    ╎    ╎    ╎    71 @Base/env.jl:265  withenv(::Pkg.Operations.var"#2…
  ╎    ╎    ╎    ╎    ╎     71 @Pkg/…tions.jl:2416  (::Pkg.Operations.var"#213#…
  ╎    ╎    ╎    ╎    ╎    ╎ 71 @Pkg/…ions.jl:2476  subprocess_handler(cmd::Cmd…
  ╎    ╎    ╎    ╎    ╎    ╎  71 @Base/…ess.jl:687  wait(x::Base.Process)
  ╎    ╎    ╎    ╎    ╎    ╎   71 @Base/…ess.jl:694  wait(x::Base.Process, sync…
  ╎    ╎    ╎    ╎    ╎    ╎    71 @Base/…on.jl:136  wait
  ╎    ╎    ╎    ╎    ╎    ╎     71 @Base/…on.jl:141  wait(c::Base.GenericCondi…
  ╎    ╎    ╎    ╎    ╎    ╎    ╎ 71 @Base/…sk.jl:1199  wait()
70╎    ╎    ╎    ╎    ╎    ╎    ╎  71 @Base/…sk.jl:1187  poptask(W::Base.Intrus…


[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:457
poptask at ./task.jl:1187
wait at ./task.jl:1199
#wait#398 at ./condition.jl:141
wait at ./condition.jl:136 [inlined]
_trywait at ./asyncevent.jl:185
profile_printing_listener at ./Base.jl:331
#start_profile_listener##0 at ./Base.jl:351
jfptr_YY.start_profile_listenerYY.YY.0_48105.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
jl_apply at /source/src/julia.h:2375 [inlined]
start_task at /source/src/task.c:1249
unknown function (ip: (nil)) at (unknown file)
Allocations: 21413506 (Pool: 21413007; Big: 499); GC: 18

[154] signal 15: Terminated
in expression starting at /home/pkgeval/.julia/packages/PyBoltz/MeWga/test/runtests.jl:13
widenreturn at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3905
unknown function (ip: 0x7ce5f39fd1df) at (unknown file)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_invoke at /source/src/gf.c:4107
tojlinvoke122171.1 at /opt/julia/lib/julia/sys.so (unknown line)
j_widenreturn_120037.1 at /opt/julia/lib/julia/sys.so (unknown line)
widenreturn at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3887 [inlined]
widenreturn at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:3883 [inlined]
update_bestguess! at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4067
typeinf_local at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4301
jfptr_typeinf_local_120374.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
typeinf at ./../usr/share/julia/Compiler/src/abstractinterpretation.jl:4493
typeinf_ext at ./../usr/share/julia/Compiler/src/typeinfer.jl:1259
typeinf_ext_toplevel at ./../usr/share/julia/Compiler/src/typeinfer.jl:1442 [inlined]
typeinf_ext_toplevel at ./../usr/share/julia/Compiler/src/typeinfer.jl:1451
jfptr_typeinf_ext_toplevel_121101.1 at /opt/julia/lib/julia/sys.so (unknown line)
[rank: 0] Received SIGTERM: 15
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
jl_apply at /source/src/julia.h:2375 [inlined]
jl_type_infer at /source/src/gf.c:462
jl_compile_method_internal at /source/src/gf.c:3602
_jl_invoke at /source/src/gf.c:4092 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
tree_format at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1067
print_tree at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1255
tree at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:1309
print_group at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:389
#print#5 at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:331
print at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:271 [inlined]
print at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:271 [inlined]
print at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:271
_peek_report at /source/usr/share/julia/stdlib/v1.12/Profile/src/Profile.jl:94
unknown function (ip: 0x7ce60fc4531f) at (unknown file)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
jl_apply at /source/src/julia.h:2375 [inlined]
jl_f_invokelatest at /source/src/builtins.c:875
profile_printing_listener at ./Base.jl:333
#start_profile_listener##0 at ./Base.jl:351
jfptr_YY.start_profile_listenerYY.YY.0_48105.1 at /opt/julia/lib/julia/sys.so (unknown line)
_jl_invoke at /source/src/gf.c:4100 [inlined]
ijl_apply_generic at /source/src/gf.c:4300
jl_apply at /source/src/julia.h:2375 [inlined]
start_task at /source/src/task.c:1249
unknown function (ip: (nil)) at (unknown file)
Allocations: 27209122 (Pool: 27208861; Big: 261); GC: 15
Traceback (most recent call last):
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/models/boltz2.py", line 1055, in predict_step
    out = self(
          ^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/models/boltz2.py", line 529, in forward
    struct_out = self.structure_module.sample(
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/modules/diffusionv2.py", line 376, in sample
    atom_coords_denoised_chunk = self.preconditioned_network_forward(
                                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.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_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.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_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/modules/transformersv2.py", line 129, in forward
    a = layer(
        ^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/modules/transformersv2.py", line 205, in forward
    a = a + self.transition(a, s)
            ^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/modules/transformersv2.py", line 61, in forward
    a = self.adaln(a, s)
        ^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/model/modules/transformersv2.py", line 30, in forward
    a = sigmoid(self.s_scale(s)) * a + self.s_bias(s)
                ^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1751, in _wrapped_call_impl
    return self._call_impl(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/module.py", line 1762, in _call_impl
    return forward_call(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/torch/nn/modules/linear.py", line 125, in forward
    return F.linear(input, self.weight, self.bias)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.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 255) is killed by signal: Terminated. 

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/bin/boltz", line 10, in <module>
    sys.exit(cli())
             ^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.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_zNIjhD/.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_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/tmp/jl_zNIjhD/.CondaPkg/.pixi/envs/default/lib/python3.12/site-packages/boltz/main.py", line 1190, in predict
    trainer.predict(
  File "/tmp/jl_zNIjhD/.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_zNIjhD/.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_zNIjhD/.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_zNIjhD/.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_zNIjhD/.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_zNIjhD/.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_zNIjhD/.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_zNIjhD/.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_zNIjhD/.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_zNIjhD/.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_zNIjhD/.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

Predicting DataLoader 0:   0%|          | 0/1 [36:45<?, ?it/s]
PkgEval terminated after 2733.59s: test duration exceeded the time limit