list index out of range

[NanoDesign2025]

pxdesign pipeline --preset extended -i ./examples/PDL1_quick_start.yaml -o ./examples/test_run --N_sample 10 --dtype bf16 --use_fast_ln True --use_deepspeed_evo_attention True
[2025-12-17 08:37:46,586] [INFO] [real_accelerator.py:219:get_accelerator] Setting ds_accelerator to cuda (auto detect)
Traceback (most recent call last):
File "/home/miniconda/envs/torch11/bin/pxdesign", line 8, in
sys.exit(cli())
^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/click/core.py", line 1442, in call
return self.main(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/click/core.py", line 1363, in main
rv = self.invoke(ctx)
^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/click/core.py", line 1830, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/click/core.py", line 1226, in invoke
return ctx.invoke(self.callback, **ctx.params)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/click/core.py", line 794, in invoke
return callback(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/pxdesign/runner/cli.py", line 162, in wrapper
return func(*args, common=common, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/click/decorators.py", line 34, in new_func
return f(get_current_context(), *args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/pxdesign/runner/cli.py", line 280, in pipeline
from . import pipeline as _pipeline
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/pxdesign/runner/pipeline.py", line 58, in
from pxdesign.runner.inference import InferenceRunner
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/pxdesign/runner/inference.py", line 33, in
from pxdesign.utils.infer import (
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/pxdesign/utils/infer.py", line 34, in
from pxdesign.configs.configs_infer import inference_configs
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/pxdesign/configs/configs_infer.py", line 24, in
"seeds": ListValue([], dtype=int),
^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/miniconda/envs/torch11/lib/python3.11/site-packages/protenix/config/extend_types.py", line 42, in init
self.dtype = type(value[0])
~~~~~^^^
IndexError: list index out of range

[xinshi-chen]

Hi @NanoDesign2025 ,

It appears that the error is caused by a pre-existing protenix installation in your current environment, that does not match the protenix version specified in our install.sh script.

Could you try the following steps to install PXDesign in a fresh, clean environment?

1. exit all current environments:
   while [ "$CONDA_SHLVL" -gt 0 ]; do conda deactivate; done

2. run the installation script again (example):
   bash -x install.sh --env pxdesign --pkg_manager conda --cuda-version 12.1

[NanoDesign2025]

Thanks for quick reply, but pip install revision v0.5.0+pxd failed
pip install --no-cache-dir "git+https://github.com/bytedance/Protenix.git@v0.5.0+pxd"

Collecting git+https://github.com/bytedance/Protenix.git@v0.5.0+pxd
Cloning https://github.com/bytedance/Protenix.git (to revision v0.5.0+pxd) to /tmp/pip-req-build-sd0uw8t0
Running command git clone --filter=blob:none --quiet https://github.com/bytedance/Protenix.git /tmp/pip-req-build-sd0uw8t0
error: RPC failed; curl 56 Recv failure: Connection reset by peer
error: 8837 bytes of body are still expected
fetch-pack: unexpected disconnect while reading sideband packet
fatal: early EOF
fatal: fetch-pack: invalid index-pack output
fatal: could not fetch f825ce9d3365170dec807d097ceb6cf4fb1f0c07 from promisor remote
warning: Clone succeeded, but checkout failed.
You can inspect what was checked out with 'git status'
and retry with 'git restore --source=HEAD :/'

[JinyuanSun]

This error (RPC failed; curl 56 Recv failure) looks like a network connection issue, likely due to an unstable connection to GitHub or a proxy timeout during the clone. You may retry it or change network environment.