ModuleNotFoundError: No module named 'vortex.model'

[slives-lab]

Error after running:
python ./test/test_evo2.py --model_name evo2_7b

ModuleNotFoundError: No module named 'vortex.model'

vortex and torch versions are not consistent in requirements.txt and other files.

vortex/requirements.txt
torch>=2.6.0
rich
ruff
pre-commit

vortex/pyproject.toml
name = "vortex"
version = "0.0.2"
description = "Reference implementation of operators for deep signal processing architectures"
readme = "README.md"
license = {file = "LICENSE"}
authors = [{ name = "Michael Poli"}]
requires-python = ">=3.11"
dependencies = [
"torch==2.5.1",
"rich==13.9.2",
"ruff==0.1.1",
"numpy",
"pre-commit==4.0.1",
"einops==0.8.0",
"packaging",
"pip",
"build",
"wheel",
"tqdm",
"setuptools",
]

vortex/setup.py
setup(
name="vortex",
version="1.0.0",
description="Inference and utilities for convolutional multi-hybrid models",
long_description=readme,
long_description_content_type="text/markdown",
author="Michael Poli",
url="http://github.com/zymrael/vortex",
license="Apache-2.0",
packages=find_packages(where="vortex"),
install_requires=requirements,
)

[a96123155]

yes, I also faced this problem.
conda create -n py311_evo2 python=3.11 conda activate py311_evo2 cd evo2
I got the error:
`
(py311_evo2) yanyichu@GPU724A:~/evo2$ pip install .
Processing /home/yanyichu/evo2
Preparing metadata (setup.py) ... done
Collecting biopython (from evo2==0.1.0)
Using cached biopython-1.85-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
Collecting huggingface_hub (from evo2==0.1.0)
Using cached huggingface_hub-0.29.1-py3-none-any.whl.metadata (13 kB)
Collecting numpy (from biopython->evo2==0.1.0)
Using cached numpy-2.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Collecting filelock (from huggingface_hub->evo2==0.1.0)
Using cached filelock-3.17.0-py3-none-any.whl.metadata (2.9 kB)
Collecting fsspec>=2023.5.0 (from huggingface_hub->evo2==0.1.0)
Using cached fsspec-2025.2.0-py3-none-any.whl.metadata (11 kB)
Collecting packaging>=20.9 (from huggingface_hub->evo2==0.1.0)
Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pyyaml>=5.1 (from huggingface_hub->evo2==0.1.0)
Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting requests (from huggingface_hub->evo2==0.1.0)
Using cached requests-2.32.3-py3-none-any.whl.metadata (4.6 kB)
Collecting tqdm>=4.42.1 (from huggingface_hub->evo2==0.1.0)
Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
Collecting typing-extensions>=3.7.4.3 (from huggingface_hub->evo2==0.1.0)
Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting charset-normalizer<4,>=2 (from requests->huggingface_hub->evo2==0.1.0)
Using cached charset_normalizer-3.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (35 kB)
Collecting idna<4,>=2.5 (from requests->huggingface_hub->evo2==0.1.0)
Using cached idna-3.10-py3-none-any.whl.metadata (10 kB)
Collecting urllib3<3,>=1.21.1 (from requests->huggingface_hub->evo2==0.1.0)
Using cached urllib3-2.3.0-py3-none-any.whl.metadata (6.5 kB)
Collecting certifi>=2017.4.17 (from requests->huggingface_hub->evo2==0.1.0)
Using cached certifi-2025.1.31-py3-none-any.whl.metadata (2.5 kB)
Using cached biopython-1.85-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.3 MB)
Using cached huggingface_hub-0.29.1-py3-none-any.whl (468 kB)
Using cached fsspec-2025.2.0-py3-none-any.whl (184 kB)
Using cached packaging-24.2-py3-none-any.whl (65 kB)
Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
Using cached tqdm-4.67.1-py3-none-any.whl (78 kB)
Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Using cached filelock-3.17.0-py3-none-any.whl (16 kB)
Using cached numpy-2.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.4 MB)
Using cached requests-2.32.3-py3-none-any.whl (64 kB)
Using cached certifi-2025.1.31-py3-none-any.whl (166 kB)
Using cached charset_normalizer-3.4.1-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (143 kB)
Using cached idna-3.10-py3-none-any.whl (70 kB)
Using cached urllib3-2.3.0-py3-none-any.whl (128 kB)
Building wheels for collected packages: evo2
Building wheel for evo2 (setup.py) ... error
error: subprocess-exited-with-error

× python setup.py bdist_wheel did not run successfully.
│ exit code: 1
╰─> [250 lines of output]
running bdist_wheel
running egg_info
writing evo2.egg-info/PKG-INFO
writing dependency_links to evo2.egg-info/dependency_links.txt
writing requirements to evo2.egg-info/requires.txt
writing top-level names to evo2.egg-info/top_level.txt
reading manifest file 'evo2.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'pyproject.toml'
warning: no previously-included files matching '.pyc' found under directory 'vortex/vortex'
warning: no previously-included files matching '' found under directory 'vortex/vortex/pycache'
adding license file 'LICENSE'
adding license file 'NOTICE'
adding license file 'AUTHORS'
writing manifest file 'evo2.egg-info/SOURCES.txt'
running build
Updating git submodules...
Running 'make setup-full' in /home/yanyichu/evo2/vortex with PYTHON=/home/yanyichu/miniconda/envs/py311_evo2/bin/python ...
Detected Conda environment "py311_evo2"
git submodule update --init --recursive
pip install ninja cmake pybind11 numpy psutil
Collecting ninja
Using cached ninja-1.11.1.3-py3-none-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (5.3 kB)
Collecting cmake
Using cached cmake-3.31.4-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (6.5 kB)
Collecting pybind11
Using cached pybind11-2.13.6-py3-none-any.whl.metadata (9.5 kB)
Collecting numpy
Using cached numpy-2.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (62 kB)
Collecting psutil
Using cached psutil-7.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (22 kB)
Using cached ninja-1.11.1.3-py3-none-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (422 kB)
Using cached cmake-3.31.4-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (27.8 MB)
Using cached pybind11-2.13.6-py3-none-any.whl (243 kB)
Using cached numpy-2.2.3-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (16.4 MB)
Using cached psutil-7.0.0-cp36-abi3-manylinux_2_12_x86_64.manylinux2010_x86_64.manylinux_2_17_x86_64.manylinux2014_x86_64.whl (277 kB)
Installing collected packages: pybind11, psutil, numpy, ninja, cmake
Successfully installed cmake-3.31.4 ninja-1.11.1.3 numpy-2.2.3 psutil-7.0.0 pybind11-2.13.6
pip install -e .
Obtaining file:///home/yanyichu/evo2/vortex
Installing build dependencies: started
Installing build dependencies: finished with status 'done'
Checking if build backend supports build_editable: started
Checking if build backend supports build_editable: finished with status 'done'
Getting requirements to build editable: started
Getting requirements to build editable: finished with status 'done'
Preparing editable metadata (pyproject.toml): started
Preparing editable metadata (pyproject.toml): finished with status 'done'
Collecting torch==2.5.1 (from vortex==0.0.2)
Using cached torch-2.5.1-cp311-cp311-manylinux1_x86_64.whl.metadata (28 kB)
Collecting rich==13.9.2 (from vortex==0.0.2)
Using cached rich-13.9.2-py3-none-any.whl.metadata (18 kB)
Collecting ruff==0.1.1 (from vortex==0.0.2)
Using cached ruff-0.1.1-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Requirement already satisfied: numpy in /home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages (from vortex==0.0.2) (2.2.3)
Collecting pre-commit==4.0.1 (from vortex==0.0.2)
Using cached pre_commit-4.0.1-py2.py3-none-any.whl.metadata (1.3 kB)
Collecting einops==0.8.0 (from vortex==0.0.2)
Using cached einops-0.8.0-py3-none-any.whl.metadata (12 kB)
Collecting packaging (from vortex==0.0.2)
Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Requirement already satisfied: pip in /home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages (from vortex==0.0.2) (25.0)
Collecting build (from vortex==0.0.2)
Using cached build-1.2.2.post1-py3-none-any.whl.metadata (6.5 kB)
Requirement already satisfied: wheel in /home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages (from vortex==0.0.2) (0.45.1)
Collecting tqdm (from vortex==0.0.2)
Using cached tqdm-4.67.1-py3-none-any.whl.metadata (57 kB)
Requirement already satisfied: setuptools in /home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages (from vortex==0.0.2) (75.8.0)
Collecting cfgv>=2.0.0 (from pre-commit==4.0.1->vortex==0.0.2)
Using cached cfgv-3.4.0-py2.py3-none-any.whl.metadata (8.5 kB)
Collecting identify>=1.0.0 (from pre-commit==4.0.1->vortex==0.0.2)
Using cached identify-2.6.7-py2.py3-none-any.whl.metadata (4.4 kB)
Collecting nodeenv>=0.11.1 (from pre-commit==4.0.1->vortex==0.0.2)
Using cached nodeenv-1.9.1-py2.py3-none-any.whl.metadata (21 kB)
Collecting pyyaml>=5.1 (from pre-commit==4.0.1->vortex==0.0.2)
Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.1 kB)
Collecting virtualenv>=20.10.0 (from pre-commit==4.0.1->vortex==0.0.2)
Using cached virtualenv-20.29.2-py3-none-any.whl.metadata (4.5 kB)
Collecting markdown-it-py>=2.2.0 (from rich==13.9.2->vortex==0.0.2)
Using cached markdown_it_py-3.0.0-py3-none-any.whl.metadata (6.9 kB)
Collecting pygments<3.0.0,>=2.13.0 (from rich==13.9.2->vortex==0.0.2)
Using cached pygments-2.19.1-py3-none-any.whl.metadata (2.5 kB)
Collecting filelock (from torch==2.5.1->vortex==0.0.2)
Using cached filelock-3.17.0-py3-none-any.whl.metadata (2.9 kB)
Collecting typing-extensions>=4.8.0 (from torch==2.5.1->vortex==0.0.2)
Using cached typing_extensions-4.12.2-py3-none-any.whl.metadata (3.0 kB)
Collecting networkx (from torch==2.5.1->vortex==0.0.2)
Using cached networkx-3.4.2-py3-none-any.whl.metadata (6.3 kB)
Collecting jinja2 (from torch==2.5.1->vortex==0.0.2)
Using cached jinja2-3.1.5-py3-none-any.whl.metadata (2.6 kB)
Collecting fsspec (from torch==2.5.1->vortex==0.0.2)
Using cached fsspec-2025.2.0-py3-none-any.whl.metadata (11 kB)
Collecting nvidia-cuda-nvrtc-cu12==12.4.127 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_cuda_nvrtc_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-cuda-runtime-cu12==12.4.127 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_cuda_runtime_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-cuda-cupti-cu12==12.4.127 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_cuda_cupti_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-cudnn-cu12==9.1.0.70 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_cudnn_cu12-9.1.0.70-py3-none-manylinux2014_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-cublas-cu12==12.4.5.8 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_cublas_cu12-12.4.5.8-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-cufft-cu12==11.2.1.3 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_cufft_cu12-11.2.1.3-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-curand-cu12==10.3.5.147 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_curand_cu12-10.3.5.147-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)
Collecting nvidia-cusolver-cu12==11.6.1.9 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_cusolver_cu12-11.6.1.9-py3-none-manylinux2014_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-cusparse-cu12==12.3.1.170 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_cusparse_cu12-12.3.1.170-py3-none-manylinux2014_x86_64.whl.metadata (1.6 kB)
Collecting nvidia-nccl-cu12==2.21.5 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_nccl_cu12-2.21.5-py3-none-manylinux2014_x86_64.whl.metadata (1.8 kB)
Collecting nvidia-nvtx-cu12==12.4.127 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_nvtx_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl.metadata (1.7 kB)
Collecting nvidia-nvjitlink-cu12==12.4.127 (from torch==2.5.1->vortex==0.0.2)
Using cached nvidia_nvjitlink_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl.metadata (1.5 kB)
Collecting triton==3.1.0 (from torch==2.5.1->vortex==0.0.2)
Using cached triton-3.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.3 kB)
Collecting sympy==1.13.1 (from torch==2.5.1->vortex==0.0.2)
Using cached sympy-1.13.1-py3-none-any.whl.metadata (12 kB)
Collecting mpmath<1.4,>=1.1.0 (from sympy==1.13.1->torch==2.5.1->vortex==0.0.2)
Using cached mpmath-1.3.0-py3-none-any.whl.metadata (8.6 kB)
Collecting pyproject_hooks (from build->vortex==0.0.2)
Using cached pyproject_hooks-1.2.0-py3-none-any.whl.metadata (1.3 kB)
Collecting mdurl~=0.1 (from markdown-it-py>=2.2.0->rich==13.9.2->vortex==0.0.2)
Using cached mdurl-0.1.2-py3-none-any.whl.metadata (1.6 kB)
Collecting distlib<1,>=0.3.7 (from virtualenv>=20.10.0->pre-commit==4.0.1->vortex==0.0.2)
Using cached distlib-0.3.9-py2.py3-none-any.whl.metadata (5.2 kB)
Collecting platformdirs<5,>=3.9.1 (from virtualenv>=20.10.0->pre-commit==4.0.1->vortex==0.0.2)
Using cached platformdirs-4.3.6-py3-none-any.whl.metadata (11 kB)
Collecting MarkupSafe>=2.0 (from jinja2->torch==2.5.1->vortex==0.0.2)
Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.0 kB)
Using cached einops-0.8.0-py3-none-any.whl (43 kB)
Using cached pre_commit-4.0.1-py2.py3-none-any.whl (218 kB)
Using cached rich-13.9.2-py3-none-any.whl (242 kB)
Using cached ruff-0.1.1-py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (6.2 MB)
Using cached torch-2.5.1-cp311-cp311-manylinux1_x86_64.whl (906.5 MB)
Using cached nvidia_cublas_cu12-12.4.5.8-py3-none-manylinux2014_x86_64.whl (363.4 MB)
Using cached nvidia_cuda_cupti_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl (13.8 MB)
Using cached nvidia_cuda_nvrtc_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl (24.6 MB)
Using cached nvidia_cuda_runtime_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl (883 kB)
Using cached nvidia_cudnn_cu12-9.1.0.70-py3-none-manylinux2014_x86_64.whl (664.8 MB)
Using cached nvidia_cufft_cu12-11.2.1.3-py3-none-manylinux2014_x86_64.whl (211.5 MB)
Using cached nvidia_curand_cu12-10.3.5.147-py3-none-manylinux2014_x86_64.whl (56.3 MB)
Using cached nvidia_cusolver_cu12-11.6.1.9-py3-none-manylinux2014_x86_64.whl (127.9 MB)
Using cached nvidia_cusparse_cu12-12.3.1.170-py3-none-manylinux2014_x86_64.whl (207.5 MB)
Using cached nvidia_nccl_cu12-2.21.5-py3-none-manylinux2014_x86_64.whl (188.7 MB)
Using cached nvidia_nvjitlink_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl (21.1 MB)
Using cached nvidia_nvtx_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl (99 kB)
Using cached sympy-1.13.1-py3-none-any.whl (6.2 MB)
Using cached triton-3.1.0-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (209.5 MB)
Using cached build-1.2.2.post1-py3-none-any.whl (22 kB)
Using cached packaging-24.2-py3-none-any.whl (65 kB)
Using cached tqdm-4.67.1-py3-none-any.whl (78 kB)
Using cached cfgv-3.4.0-py2.py3-none-any.whl (7.2 kB)
Using cached identify-2.6.7-py2.py3-none-any.whl (99 kB)
Using cached markdown_it_py-3.0.0-py3-none-any.whl (87 kB)
Using cached nodeenv-1.9.1-py2.py3-none-any.whl (22 kB)
Using cached pygments-2.19.1-py3-none-any.whl (1.2 MB)
Using cached PyYAML-6.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (762 kB)
Using cached typing_extensions-4.12.2-py3-none-any.whl (37 kB)
Using cached virtualenv-20.29.2-py3-none-any.whl (4.3 MB)
Using cached filelock-3.17.0-py3-none-any.whl (16 kB)
Using cached fsspec-2025.2.0-py3-none-any.whl (184 kB)
Using cached jinja2-3.1.5-py3-none-any.whl (134 kB)
Using cached networkx-3.4.2-py3-none-any.whl (1.7 MB)
Using cached pyproject_hooks-1.2.0-py3-none-any.whl (10 kB)
Using cached distlib-0.3.9-py2.py3-none-any.whl (468 kB)
Using cached MarkupSafe-3.0.2-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (23 kB)
Using cached mdurl-0.1.2-py3-none-any.whl (10.0 kB)
Using cached mpmath-1.3.0-py3-none-any.whl (536 kB)
Using cached platformdirs-4.3.6-py3-none-any.whl (18 kB)
Building wheels for collected packages: vortex
Building editable for vortex (pyproject.toml): started
Building editable for vortex (pyproject.toml): finished with status 'done'
Created wheel for vortex: filename=vortex-0.0.2-0.editable-py3-none-any.whl size=12428 sha256=4896e4f67a6283901a768ff135cab4c0b87e60cec26b70ed2f3346dfc656f90c
Stored in directory: /tmp/pip-ephem-wheel-cache-j80xuo15/wheels/02/1d/a6/a2ddd8755e82b4e19a844fe73226e7137de38b6f3de154b49f
Successfully built vortex
Installing collected packages: mpmath, distlib, typing-extensions, tqdm, sympy, ruff, pyyaml, pyproject_hooks, pygments, platformdirs, packaging, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, nodeenv, networkx, mdurl, MarkupSafe, identify, fsspec, filelock, einops, cfgv, virtualenv, triton, nvidia-cusparse-cu12, nvidia-cudnn-cu12, markdown-it-py, jinja2, build, rich, pre-commit, nvidia-cusolver-cu12, torch, vortex
Successfully installed MarkupSafe-3.0.2 build-1.2.2.post1 cfgv-3.4.0 distlib-0.3.9 einops-0.8.0 filelock-3.17.0 fsspec-2025.2.0 identify-2.6.7 jinja2-3.1.5 markdown-it-py-3.0.0 mdurl-0.1.2 mpmath-1.3.0 networkx-3.4.2 nodeenv-1.9.1 nvidia-cublas-cu12-12.4.5.8 nvidia-cuda-cupti-cu12-12.4.127 nvidia-cuda-nvrtc-cu12-12.4.127 nvidia-cuda-runtime-cu12-12.4.127 nvidia-cudnn-cu12-9.1.0.70 nvidia-cufft-cu12-11.2.1.3 nvidia-curand-cu12-10.3.5.147 nvidia-cusolver-cu12-11.6.1.9 nvidia-cusparse-cu12-12.3.1.170 nvidia-nccl-cu12-2.21.5 nvidia-nvjitlink-cu12-12.4.127 nvidia-nvtx-cu12-12.4.127 packaging-24.2 platformdirs-4.3.6 pre-commit-4.0.1 pygments-2.19.1 pyproject_hooks-1.2.0 pyyaml-6.0.2 rich-13.9.2 ruff-0.1.1 sympy-1.13.1 torch-2.5.1 tqdm-4.67.1 triton-3.1.0 typing-extensions-4.12.2 virtualenv-20.29.2 vortex-0.0.2
pip install transformer_engine[pytorch] --no-build-isolation
Collecting transformer_engine[pytorch]
Using cached transformer_engine-1.13.0-py3-none-any.whl.metadata (16 kB)
Collecting transformer_engine_cu12==1.13.0 (from transformer_engine[pytorch])
Using cached transformer_engine_cu12-1.13.0-py3-none-manylinux_2_28_x86_64.whl.metadata (16 kB)
Collecting transformer_engine_torch==1.13.0 (from transformer_engine[pytorch])
Using cached transformer_engine_torch-1.13.0.tar.gz (121 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
error: subprocess-exited-with-error

    × python setup.py egg_info did not run successfully.
    │ exit code: 1
    ╰─> [9 lines of output]
        Traceback (most recent call last):
          File "<string>", line 2, in <module>
          File "<pip-setuptools-caller>", line 34, in <module>
          File "/tmp/pip-install-mvxiigfj/transformer-engine-torch_7aa7e7f8dc7e43858755ebda293d57a9/setup.py", line 15, in <module>
            from torch.utils.cpp_extension import BuildExtension
          File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/torch/__init__.py", line 367, in <module>
            from torch._C import *  # noqa: F403
            ^^^^^^^^^^^^^^^^^^^^^^
        ImportError: /home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/torch/lib/../../nvidia/cusparse/lib/libcusparse.so.12: undefined symbol: __nvJitLinkComplete_12_4, version libnvJitLink.so.12
        [end of output]
  
    note: This error originates from a subprocess, and is likely not a problem with pip.
  error: metadata-generation-failed
  
  × Encountered error while generating package metadata.
  ╰─> See above for output.
  
  note: This is an issue with the package mentioned above, not pip.
  hint: See above for details.
  make: *** [Makefile:61: setup-full] Error 1
  Traceback (most recent call last):
    File "<string>", line 2, in <module>
    File "<pip-setuptools-caller>", line 34, in <module>
    File "/home/yanyichu/evo2/setup.py", line 78, in <module>
      setup(
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/setuptools/__init__.py", line 117, in setup
      return distutils.core.setup(**attrs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 186, in setup
      return run_commands(dist)
             ^^^^^^^^^^^^^^^^^^
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
      dist.run_commands()
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 983, in run_commands
      self.run_command(cmd)
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/setuptools/dist.py", line 999, in run_command
      super().run_command(command)
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
      cmd_obj.run()
    File "/home/yanyichu/evo2/setup.py", line 58, in run
      _bdist_wheel.run(self)
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/setuptools/command/bdist_wheel.py", line 379, in run
      self.run_command("build")
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/setuptools/_distutils/cmd.py", line 339, in run_command
      self.distribution.run_command(command)
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/setuptools/dist.py", line 999, in run_command
      super().run_command(command)
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1002, in run_command
      cmd_obj.run()
    File "/home/yanyichu/evo2/setup.py", line 45, in run
      run_make_setup_full()
    File "/home/yanyichu/evo2/setup.py", line 36, in run_make_setup_full
      subprocess.check_call(['make', 'setup-full'], env=env)
    File "/home/yanyichu/miniconda/envs/py311_evo2/lib/python3.11/subprocess.py", line 413, in check_call
      raise CalledProcessError(retcode, cmd)
  subprocess.CalledProcessError: Command '['make', 'setup-full']' returned non-zero exit status 2.
  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for evo2
Running setup.py clean for evo2
Failed to build evo2
ERROR: Failed to build installable wheels for some pyproject.toml based projects (evo2)
`

[mtgh0909]

yes, I also faced this problem.

[jwilber]

If you're having issues, try starting from a fresh env, import the submodules, cd directly into vortex and run make there:

 conda create -n evo2 python=3.11
 conda activate evo2
 git clone https://github.com/ArcInstitute/evo2.git
 cd evo2
 git submodule update --init --recursive
 pip install -r requirements.txt 
 cd vortex/
 make setup-full

[onionpork]

I had the same problem, and then following your solution leads to a second one.

note: This error originates from a subprocess, and is likely not a problem with pip.
  ERROR: Failed building wheel for transformer_engine_torch
  Running setup.py clean for transformer_engine_torch
Failed to build transformer_engine_torch
ERROR: Failed to build installable wheels for some pyproject.toml based projects (transformer_engine_torch)

[slives-lab]

If you're having issues, try starting from a fresh env, import the submodules, cd directly into vortex and run make there:

 conda create -n evo2 python=3.11
 conda activate evo2
 git clone https://github.com/ArcInstitute/evo2.git
 cd evo2
 git submodule update --init --recursive
 pip install -r requirements.txt 
 cd vortex/
 make setup-full

This strategy does not work, here is the resulting error:

note: This error originates from a subprocess, and is likely not a problem with pip.
ERROR: Failed building wheel for transformer_engine_torch
Running setup.py clean for transformer_engine_torch
Failed to build transformer_engine_torch
ERROR: Failed to build installable wheels for some pyproject.toml based projects (transformer_engine_torch)

[zli12321]

Also got this error. What is transformer_engine_torch? I never saw this package before.

[JunSeok94]

done

conda create -n evo2 python=3.11                                                                                                                     
conda activate evo2                                                                                                                                  
                                                                                                                                                     
# torch 2.5.1 and cuda >= 12.0 because of vortex                                                                                                     
conda install pytorch==2.5.1 torchvision==0.20.1 torchaudio==2.5.1 pytorch-cuda=12.4 -c pytorch -c nvidia                                            
# and need to set cuda symlink to that version because of vortex                                                                                     
                                                                                                                                                     
git clone https://github.com/ArcInstitute/evo2.git                                                                                                   
cd evo2                                                                                                                                              
git submodule update --init --recursive                                                                                                              
    
pip install sympy==1.13.1                                                                                                                            
pip install -r requirements.txt                                                                                                                      

# Install cuDNN 9.3+ #################################
cd vortex/                                                                                                                                           
make setup-full
pip install transformer_engine[pytorch]==1.13
cd ..
python
from evo2 import Evo2

[grpinto]

I have this mistake :

Installing collected packages: local_flash_attn
  DEPRECATION: Legacy editable install of local_flash_attn==0.0.0 from file:///ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/ops/attn (setup.py develop) is deprecated. pip 25.3 will enforce this behaviour change. A possible replacement is to add a pyproject.toml or enable --use-pep517, and use setuptools >= 64. If the resulting installation is not behaving as expected, try using --config-settings editable_mode=compat. Please consult the setuptools documentation for more information. Discussion can be found at https://github.com/pypa/pip/issues/11457
  Running setup.py develop for local_flash_attn
    Running command python setup.py develop
    error: pathspec 'csrc/cutlass' did not match any file(s) known to git
    /ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
    !!

            ********************************************************************************
            Requirements should be satisfied by a PEP 517 installer.
            If you are using pip, you can try `pip install --use-pep517`.

            By 2025-Oct-31, you need to update your project and remove deprecated calls
            or your builds will no longer be supported.
            ********************************************************************************

    !!
      dist.fetch_build_eggs(dist.setup_requires)


    torch.__version__  = 2.5.1


    CUDA_HOME = /usr/local/cuda
    running develop
    /ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:90: DevelopDeprecationWarning: develop command is deprecated.
    !!

            ********************************************************************************
            Please avoid running ``setup.py`` and ``develop``.
            Instead, use standards-based tools like pip or uv.

            By 2025-Oct-31, you need to update your project and remove deprecated calls
            or your builds will no longer be supported.

            See https://github.com/pypa/setuptools/issues/917 for details.
            ********************************************************************************

    !!
      self.initialize_options()
    Obtaining file:///ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/ops/attn
      Installing build dependencies: started
      Installing build dependencies: finished with status 'done'
      Checking if build backend supports build_editable: started
      Checking if build backend supports build_editable: finished with status 'done'
      Getting requirements to build editable: started
      Getting requirements to build editable: finished with status 'error'
      error: subprocess-exited-with-error

      × Getting requirements to build editable did not run successfully.
      │ exit code: 1
      ╰─> [23 lines of output]
          Traceback (most recent call last):
            File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
              main()
            File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
              json_out["return_val"] = hook(**hook_input["kwargs"])
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 157, in get_requires_for_build_editable
              return hook(config_settings)
                     ^^^^^^^^^^^^^^^^^^^^^
            File "/tmp/pip-build-env-jc0r2z4l/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 473, in get_requires_for_build_editable
              return self.get_requires_for_build_wheel(config_settings)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            File "/tmp/pip-build-env-jc0r2z4l/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 331, in get_requires_for_build_wheel
              return self._get_build_requires(config_settings, requirements=[])
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            File "/tmp/pip-build-env-jc0r2z4l/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 301, in _get_build_requires
              self.run_setup()
            File "/tmp/pip-build-env-jc0r2z4l/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 512, in run_setup
              super().run_setup(setup_script=setup_script)
            File "/tmp/pip-build-env-jc0r2z4l/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 317, in run_setup
              exec(code, locals())
            File "<string>", line 17, in <module>
          ModuleNotFoundError: No module named 'torch'
          [end of output]

      note: This error originates from a subprocess, and is likely not a problem with pip.
    error: subprocess-exited-with-error

    × Getting requirements to build editable did not run successfully.
    │ exit code: 1
    ╰─> See above for output.

    note: This error originates from a subprocess, and is likely not a problem with pip.
    Traceback (most recent call last):
      File "<string>", line 2, in <module>
      File "<pip-setuptools-caller>", line 35, in <module>
      File "/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/ops/attn/setup.py", line 208, in <module>
        setup(
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/__init__.py", line 115, in setup
        return distutils.core.setup(**attrs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 186, in setup
        return run_commands(dist)
               ^^^^^^^^^^^^^^^^^^
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
        dist.run_commands()
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands
        self.run_command(cmd)
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/dist.py", line 1102, in run_command
        super().run_command(command)
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
        cmd_obj.run()
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/command/develop.py", line 39, in run
        subprocess.check_call(cmd)
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/subprocess.py", line 413, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/bin/python3.11', '-m', 'pip', 'install', '-e', '.', '--use-pep517', '--no-deps']' returned non-zero exit status 1.
    error: subprocess-exited-with-error
    
    × python setup.py develop did not run successfully.
    │ exit code: 1
    ╰─> See above for output.
    
    note: This error originates from a subprocess, and is likely not a problem with pip.
    full command: /ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/bin/python3.11 -c '
    exec(compile('"'"''"'"''"'"'
    # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
    #
    # - It imports setuptools before invoking setup.py, to enable projects that directly
    #   import from `distutils.core` to work with newer packaging standards.
    # - It provides a clear error message when setuptools is not installed.
    # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
    #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
    #     manifest_maker: standard file '"'"'-c'"'"' not found".
    # - It generates a shim setup.py, for handling setup.cfg-only projects.
    import os, sys, tokenize, traceback
    
    try:
        import setuptools
    except ImportError:
        print(
            "ERROR: Can not execute `setup.py` since setuptools failed to import in "
            "the build environment with exception:",
            file=sys.stderr,
        )
        traceback.print_exc()
        sys.exit(1)
    
    __file__ = %r
    sys.argv[0] = __file__
    
    if os.path.exists(__file__):
        filename = __file__
        with tokenize.open(__file__) as f:
            setup_py_code = f.read()
    else:
        filename = "<auto-generated setuptools caller>"
        setup_py_code = "from setuptools import setup; setup()"
    
    exec(compile(setup_py_code, filename, "exec"))
    '"'"''"'"''"'"' % ('"'"'/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/ops/attn/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' develop --no-deps
    cwd: /ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/ops/attn/
error: subprocess-exited-with-error

× python setup.py develop did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
make: *** [Makefile:62: setup-full] Error 1

I tried to install vortex using :

make setup-vortex-ops

Which worked, but I could not do the command make setup-full work.

Python 3.11.13 | packaged by conda-forge | (main, Jun  4 2025, 14:48:23) [GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from evo2 import Evo2
[06/05/25 11:28:20] INFO     root - INFO - Could not find package __init__.py:39
                             transformer_engine_jax. Install                    
                             transformer-engine using 'pip                      
                             install                                            
                             transformer-engine[jax]==VERSION'                  
[06/05/25 11:28:21] INFO     root - INFO - Could not find package __init__.py:38
                             transformer_engine_paddle. Install                 
                             transformer-engine using 'pip                      
                             install                                            
                             transformer-engine[paddle]==VERSION'               
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/evo2/__init__.py", line 1, in <module>
    from .models import Evo2
  File "/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/evo2/models.py", line 12, in <module>
    from vortex.model.model import StripedHyena
  File "/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/model/model.py", line 14, in <module>
    from vortex.model.layers import (
  File "/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/model/layers.py", line 10, in <module>
    from transformer_engine.pytorch import Linear
  File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/transformer_engine/pytorch/__init__.py", line 63, in <module>
    _load_library()
  File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/transformer_engine/pytorch/__init__.py", line 58, in _load_library
    solib = importlib.util.module_from_spec(spec)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: /ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/transformer_engine/transformer_engine_torch.cpython-311-x86_64-linux-gnu.so: undefined symbol: _ZN3c108ListType3getERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS_4Type24SingletonOrSharedTypePtrIS9_EE

from the previous post here. How can I fix this ? Great model btw. Thanks.

[TLyan-ze]

I have this mistake :

Installing collected packages: local_flash_attn
  DEPRECATION: Legacy editable install of local_flash_attn==0.0.0 from file:///ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/ops/attn (setup.py develop) is deprecated. pip 25.3 will enforce this behaviour change. A possible replacement is to add a pyproject.toml or enable --use-pep517, and use setuptools >= 64. If the resulting installation is not behaving as expected, try using --config-settings editable_mode=compat. Please consult the setuptools documentation for more information. Discussion can be found at https://github.com/pypa/pip/issues/11457
  Running setup.py develop for local_flash_attn
    Running command python setup.py develop
    error: pathspec 'csrc/cutlass' did not match any file(s) known to git
    /ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/__init__.py:92: _DeprecatedInstaller: setuptools.installer and fetch_build_eggs are deprecated.
    !!

            ********************************************************************************
            Requirements should be satisfied by a PEP 517 installer.
            If you are using pip, you can try `pip install --use-pep517`.

            By 2025-Oct-31, you need to update your project and remove deprecated calls
            or your builds will no longer be supported.
            ********************************************************************************

    !!
      dist.fetch_build_eggs(dist.setup_requires)


    torch.__version__  = 2.5.1


    CUDA_HOME = /usr/local/cuda
    running develop
    /ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/_distutils/cmd.py:90: DevelopDeprecationWarning: develop command is deprecated.
    !!

            ********************************************************************************
            Please avoid running ``setup.py`` and ``develop``.
            Instead, use standards-based tools like pip or uv.

            By 2025-Oct-31, you need to update your project and remove deprecated calls
            or your builds will no longer be supported.

            See https://github.com/pypa/setuptools/issues/917 for details.
            ********************************************************************************

    !!
      self.initialize_options()
    Obtaining file:///ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/ops/attn
      Installing build dependencies: started
      Installing build dependencies: finished with status 'done'
      Checking if build backend supports build_editable: started
      Checking if build backend supports build_editable: finished with status 'done'
      Getting requirements to build editable: started
      Getting requirements to build editable: finished with status 'error'
      error: subprocess-exited-with-error

      × Getting requirements to build editable did not run successfully.
      │ exit code: 1
      ╰─> [23 lines of output]
          Traceback (most recent call last):
            File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 389, in <module>
              main()
            File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 373, in main
              json_out["return_val"] = hook(**hook_input["kwargs"])
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 157, in get_requires_for_build_editable
              return hook(config_settings)
                     ^^^^^^^^^^^^^^^^^^^^^
            File "/tmp/pip-build-env-jc0r2z4l/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 473, in get_requires_for_build_editable
              return self.get_requires_for_build_wheel(config_settings)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            File "/tmp/pip-build-env-jc0r2z4l/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 331, in get_requires_for_build_wheel
              return self._get_build_requires(config_settings, requirements=[])
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
            File "/tmp/pip-build-env-jc0r2z4l/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 301, in _get_build_requires
              self.run_setup()
            File "/tmp/pip-build-env-jc0r2z4l/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 512, in run_setup
              super().run_setup(setup_script=setup_script)
            File "/tmp/pip-build-env-jc0r2z4l/overlay/lib/python3.11/site-packages/setuptools/build_meta.py", line 317, in run_setup
              exec(code, locals())
            File "<string>", line 17, in <module>
          ModuleNotFoundError: No module named 'torch'
          [end of output]

      note: This error originates from a subprocess, and is likely not a problem with pip.
    error: subprocess-exited-with-error

    × Getting requirements to build editable did not run successfully.
    │ exit code: 1
    ╰─> See above for output.

    note: This error originates from a subprocess, and is likely not a problem with pip.
    Traceback (most recent call last):
      File "<string>", line 2, in <module>
      File "<pip-setuptools-caller>", line 35, in <module>
      File "/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/ops/attn/setup.py", line 208, in <module>
        setup(
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/__init__.py", line 115, in setup
        return distutils.core.setup(**attrs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 186, in setup
        return run_commands(dist)
               ^^^^^^^^^^^^^^^^^^
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/_distutils/core.py", line 202, in run_commands
        dist.run_commands()
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1002, in run_commands
        self.run_command(cmd)
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/dist.py", line 1102, in run_command
        super().run_command(command)
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/_distutils/dist.py", line 1021, in run_command
        cmd_obj.run()
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/setuptools/command/develop.py", line 39, in run
        subprocess.check_call(cmd)
      File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/subprocess.py", line 413, in check_call
        raise CalledProcessError(retcode, cmd)
    subprocess.CalledProcessError: Command '['/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/bin/python3.11', '-m', 'pip', 'install', '-e', '.', '--use-pep517', '--no-deps']' returned non-zero exit status 1.
    error: subprocess-exited-with-error
    
    × python setup.py develop did not run successfully.
    │ exit code: 1
    ╰─> See above for output.
    
    note: This error originates from a subprocess, and is likely not a problem with pip.
    full command: /ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/bin/python3.11 -c '
    exec(compile('"'"''"'"''"'"'
    # This is <pip-setuptools-caller> -- a caller that pip uses to run setup.py
    #
    # - It imports setuptools before invoking setup.py, to enable projects that directly
    #   import from `distutils.core` to work with newer packaging standards.
    # - It provides a clear error message when setuptools is not installed.
    # - It sets `sys.argv[0]` to the underlying `setup.py`, when invoking `setup.py` so
    #   setuptools doesn'"'"'t think the script is `-c`. This avoids the following warning:
    #     manifest_maker: standard file '"'"'-c'"'"' not found".
    # - It generates a shim setup.py, for handling setup.cfg-only projects.
    import os, sys, tokenize, traceback
    
    try:
        import setuptools
    except ImportError:
        print(
            "ERROR: Can not execute `setup.py` since setuptools failed to import in "
            "the build environment with exception:",
            file=sys.stderr,
        )
        traceback.print_exc()
        sys.exit(1)
    
    __file__ = %r
    sys.argv[0] = __file__
    
    if os.path.exists(__file__):
        filename = __file__
        with tokenize.open(__file__) as f:
            setup_py_code = f.read()
    else:
        filename = "<auto-generated setuptools caller>"
        setup_py_code = "from setuptools import setup; setup()"
    
    exec(compile(setup_py_code, filename, "exec"))
    '"'"''"'"''"'"' % ('"'"'/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/ops/attn/setup.py'"'"',), "<pip-setuptools-caller>", "exec"))' develop --no-deps
    cwd: /ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/ops/attn/
error: subprocess-exited-with-error

× python setup.py develop did not run successfully.
│ exit code: 1
╰─> See above for output.

note: This error originates from a subprocess, and is likely not a problem with pip.
make: *** [Makefile:62: setup-full] Error 1

I tried to install vortex using :

make setup-vortex-ops

Which worked, but I could not do the command make setup-full work.

Python 3.11.13 | packaged by conda-forge | (main, Jun  4 2025, 14:48:23) [GCC 13.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from evo2 import Evo2
[06/05/25 11:28:20] INFO     root - INFO - Could not find package __init__.py:39
                             transformer_engine_jax. Install                    
                             transformer-engine using 'pip                      
                             install                                            
                             transformer-engine[jax]==VERSION'                  
[06/05/25 11:28:21] INFO     root - INFO - Could not find package __init__.py:38
                             transformer_engine_paddle. Install                 
                             transformer-engine using 'pip                      
                             install                                            
                             transformer-engine[paddle]==VERSION'               
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/evo2/__init__.py", line 1, in <module>
    from .models import Evo2
  File "/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/evo2/models.py", line 12, in <module>
    from vortex.model.model import StripedHyena
  File "/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/model/model.py", line 14, in <module>
    from vortex.model.layers import (
  File "/ictstr01/groups/ml01/workspace/goncalo.pinto/evo2/vortex/vortex/model/layers.py", line 10, in <module>
    from transformer_engine.pytorch import Linear
  File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/transformer_engine/pytorch/__init__.py", line 63, in <module>
    _load_library()
  File "/ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/transformer_engine/pytorch/__init__.py", line 58, in _load_library
    solib = importlib.util.module_from_spec(spec)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
ImportError: /ictstr01/home/icb/goncalo.pinto/tools/apps/mamba/envs/evo2/lib/python3.11/site-packages/transformer_engine/transformer_engine_torch.cpython-311-x86_64-linux-gnu.so: undefined symbol: _ZN3c108ListType3getERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEENS_4Type24SingletonOrSharedTypePtrIS9_EE

from the previous post here. How can I fix this ? Great model btw. Thanks.

I have the same problem. May I ask if you have solved it

[jvdp1]

I get the same problem. Any solutions?

[JunSeok94]

@grpinto @TLyan-ze @jvdp1 try this?

##################################################################
torch 2.5.1, cuda 12.0+, cuDNN 9.3+, GCC 9+

Edit use_fp8_input_projections to False in evo2/configs files on other than H100 servers.
##################################################################

First, remove all envs related to evo2

conda create -n evo2 python=3.11
conda activate evo2
conda install pytorch==2.5.1 torchvision==0.20.1 torchaudio==2.5.1 pytorch-cuda=12.x -c pytorch -c nvidia

git clone https://github.com/ArcInstitute/evo2.git
cd evo2
git submodule update --init --recursive

pip install sympy==1.13.1
pip install -r requirements.txt
cd vortex/

vi Makefile

Edit all cuda to cuda-{$VERSION} i.e. /usr/local/cuda-12.x

Save and exit

make setup-full ######### cuDNN 9.3+ needed
pip install transformer_engine[pytorch]==1.13

[wowwowooo]

I got the same problem

[jvdp1]

Thank you @JunSeok94 . I could compile it using your instructions

[grpinto]

Now I am having this mistake when I get to make setup-full :

Collecting transformer_engine_torch==2.4.0 (from transformer_engine[pytorch])
  Using cached transformer_engine_torch-2.4.0.tar.gz (156 kB)
  Preparing metadata (setup.py) ... error
  error: subprocess-exited-with-error
  
  × python setup.py egg_info did not run successfully.
  │ exit code: 1
  ╰─> [12 lines of output]
      Traceback (most recent call last):
        File "<string>", line 2, in <module>
        File "<pip-setuptools-caller>", line 35, in <module>
        File "/tmp/pip-install-x4sgfyvz/transformer-engine-torch_05f5dfb28bcc4d319ba01ecfe260c103/setup.py", line 46, in <module>
          setup_pytorch_extension(
        File "/tmp/pip-install-x4sgfyvz/transformer-engine-torch_05f5dfb28bcc4d319ba01ecfe260c103/build_tools/pytorch.py", line 45, in setup_pytorch_extension
          version = cuda_version()
                    ^^^^^^^^^^^^^^
        File "/tmp/pip-install-x4sgfyvz/transformer-engine-torch_05f5dfb28bcc4d319ba01ecfe260c103/build_tools/utils.py", line 275, in cuda_version
          version_str = version("nvidia-cuda-runtime-cu12")
                        ^^^^^^^
      UnboundLocalError: cannot access local variable 'version' where it is not associated with a value
      [end of output]
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
make: *** [Makefile:61: setup-full] Error 1

How can I fix this ?

[JunSeok94]

@grpinto Edit Vortex Makefile cuda version? i.e. cuda-12.4