Ticket #16218: install_log.txt

File install_log.txt, 32.0 KB (added by Tom Goddard, 14 months ago)

Install log from my test run that shows OpenMM installs without errors.

Line 
1+ set -e
2+ pip install --no-warn-conflicts 'colabfold[alphafold-minus-jax] @ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72'
3Collecting colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72 (from colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
4 Cloning https://github.com/sokrypton/ColabFold (to revision 29395e7dee2c2895eaf585ef6b6cde932fd95e72) to /tmp/pip-install-_qen4b6y/colabfold_c0dd8ad74f034fe8be2cd75edd520a77
5 Running command git clone --filter=blob:none --quiet https://github.com/sokrypton/ColabFold /tmp/pip-install-_qen4b6y/colabfold_c0dd8ad74f034fe8be2cd75edd520a77
6 Running command git rev-parse -q --verify 'sha^29395e7dee2c2895eaf585ef6b6cde932fd95e72'
7 Running command git fetch -q https://github.com/sokrypton/ColabFold 29395e7dee2c2895eaf585ef6b6cde932fd95e72
8 Running command git checkout -q 29395e7dee2c2895eaf585ef6b6cde932fd95e72
9 Resolved https://github.com/sokrypton/ColabFold to commit 29395e7dee2c2895eaf585ef6b6cde932fd95e72
10 Installing build dependencies: started
11 Installing build dependencies: finished with status 'done'
12 Getting requirements to build wheel: started
13 Getting requirements to build wheel: finished with status 'done'
14 Preparing metadata (pyproject.toml): started
15 Preparing metadata (pyproject.toml): finished with status 'done'
16Requirement already satisfied: absl-py<2.0.0,>=1.0.0 in /usr/local/lib/python3.10/dist-packages (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.4.0)
17Collecting appdirs<2.0.0,>=1.4.4 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
18 Downloading appdirs-1.4.4-py2.py3-none-any.whl.metadata (9.0 kB)
19Collecting dm-haiku<0.0.10,>=0.0.9 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
20 Downloading dm_haiku-0.0.9-py3-none-any.whl.metadata (18 kB)
21Collecting importlib-metadata<5.0.0,>=4.8.2 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
22 Downloading importlib_metadata-4.13.0-py3-none-any.whl.metadata (4.9 kB)
23Requirement already satisfied: matplotlib<4.0.0,>=3.2.2 in /usr/local/lib/python3.10/dist-packages (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.7.1)
24Requirement already satisfied: numpy<2.0.0,>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.26.4)
25Collecting pandas<2.0.0,>=1.3.4 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
26 Downloading pandas-1.5.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (11 kB)
27Collecting py3Dmol<3.0.0,>=2.0.1 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
28 Downloading py3Dmol-2.4.0-py2.py3-none-any.whl.metadata (1.9 kB)
29Requirement already satisfied: requests<3.0.0,>=2.26.0 in /usr/local/lib/python3.10/dist-packages (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (2.32.3)
30Collecting tensorflow-cpu<3.0.0,>=2.11.0 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
31 Downloading tensorflow_cpu-2.18.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (4.1 kB)
32Requirement already satisfied: tqdm<5.0.0,>=4.62.2 in /usr/local/lib/python3.10/dist-packages (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (4.66.5)
33Collecting alphafold-colabfold==v2.3.5 (from colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
34 Downloading alphafold_colabfold-2.3.5-py3-none-any.whl.metadata (1.3 kB)
35Collecting biopython (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
36 Downloading biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (12 kB)
37Requirement already satisfied: chex in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.1.87)
38Requirement already satisfied: dm-tree in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.1.8)
39Collecting docker (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
40 Downloading docker-7.1.0-py3-none-any.whl.metadata (3.8 kB)
41Requirement already satisfied: immutabledict in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (4.2.0)
42Requirement already satisfied: jax in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.4.33)
43Collecting ml-collections (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
44 Downloading ml_collections-0.1.1.tar.gz (77 kB)
45 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.9/77.9 kB 7.6 MB/s eta 0:00:00
46 Preparing metadata (setup.py): started
47 Preparing metadata (setup.py): finished with status 'done'
48Requirement already satisfied: scipy in /usr/local/lib/python3.10/dist-packages (from alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.13.1)
49Collecting jmp>=0.0.2 (from dm-haiku<0.0.10,>=0.0.9->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
50 Downloading jmp-0.0.4-py3-none-any.whl.metadata (8.9 kB)
51Requirement already satisfied: tabulate>=0.8.9 in /usr/local/lib/python3.10/dist-packages (from dm-haiku<0.0.10,>=0.0.9->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.9.0)
52Requirement already satisfied: zipp>=0.5 in /usr/local/lib/python3.10/dist-packages (from importlib-metadata<5.0.0,>=4.8.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.20.2)
53Requirement already satisfied: contourpy>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.3.0)
54Requirement already satisfied: cycler>=0.10 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.12.1)
55Requirement already satisfied: fonttools>=4.22.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (4.54.1)
56Requirement already satisfied: kiwisolver>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.4.7)
57Requirement already satisfied: packaging>=20.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (24.1)
58Requirement already satisfied: pillow>=6.2.0 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (10.4.0)
59Requirement already satisfied: pyparsing>=2.3.1 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.2.0)
60Requirement already satisfied: python-dateutil>=2.7 in /usr/local/lib/python3.10/dist-packages (from matplotlib<4.0.0,>=3.2.2->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (2.8.2)
61Requirement already satisfied: pytz>=2020.1 in /usr/local/lib/python3.10/dist-packages (from pandas<2.0.0,>=1.3.4->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (2024.2)
62Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests<3.0.0,>=2.26.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.4.0)
63Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests<3.0.0,>=2.26.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.10)
64Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests<3.0.0,>=2.26.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (2.2.3)
65Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests<3.0.0,>=2.26.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (2024.8.30)
66Requirement already satisfied: astunparse>=1.6.0 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.6.3)
67Requirement already satisfied: flatbuffers>=24.3.25 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (24.3.25)
68Requirement already satisfied: gast!=0.5.0,!=0.5.1,!=0.5.2,>=0.2.1 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.6.0)
69Requirement already satisfied: google-pasta>=0.1.1 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.2.0)
70Requirement already satisfied: libclang>=13.0.0 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (18.1.1)
71Requirement already satisfied: opt-einsum>=2.3.2 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.4.0)
72Requirement already satisfied: protobuf!=4.21.0,!=4.21.1,!=4.21.2,!=4.21.3,!=4.21.4,!=4.21.5,<6.0.0dev,>=3.20.3 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.20.3)
73Requirement already satisfied: setuptools in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (75.1.0)
74Requirement already satisfied: six>=1.12.0 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.16.0)
75Requirement already satisfied: termcolor>=1.1.0 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (2.5.0)
76Requirement already satisfied: typing-extensions>=3.6.6 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (4.12.2)
77Requirement already satisfied: wrapt>=1.11.0 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.16.0)
78Requirement already satisfied: grpcio<2.0,>=1.24.3 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (1.64.1)
79Collecting tensorboard<2.19,>=2.18 (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
80 Downloading tensorboard-2.18.0-py3-none-any.whl.metadata (1.6 kB)
81Collecting keras>=3.5.0 (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
82 Downloading keras-3.6.0-py3-none-any.whl.metadata (5.8 kB)
83Requirement already satisfied: h5py>=3.11.0 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.11.0)
84Requirement already satisfied: ml-dtypes<0.5.0,>=0.4.0 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.4.1)
85Requirement already satisfied: tensorflow-io-gcs-filesystem>=0.23.1 in /usr/local/lib/python3.10/dist-packages (from tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.37.1)
86Requirement already satisfied: wheel<1.0,>=0.23.0 in /usr/local/lib/python3.10/dist-packages (from astunparse>=1.6.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.44.0)
87Requirement already satisfied: rich in /usr/local/lib/python3.10/dist-packages (from keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (13.9.3)
88Requirement already satisfied: namex in /usr/local/lib/python3.10/dist-packages (from keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.0.8)
89Requirement already satisfied: optree in /usr/local/lib/python3.10/dist-packages (from keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.13.0)
90Requirement already satisfied: markdown>=2.6.8 in /usr/local/lib/python3.10/dist-packages (from tensorboard<2.19,>=2.18->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.7)
91Requirement already satisfied: tensorboard-data-server<0.8.0,>=0.7.0 in /usr/local/lib/python3.10/dist-packages (from tensorboard<2.19,>=2.18->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.7.2)
92Requirement already satisfied: werkzeug>=1.0.1 in /usr/local/lib/python3.10/dist-packages (from tensorboard<2.19,>=2.18->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.0.6)
93Requirement already satisfied: jaxlib>=0.4.27 in /usr/local/lib/python3.10/dist-packages (from chex->alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.4.33)
94Requirement already satisfied: toolz>=0.9.0 in /usr/local/lib/python3.10/dist-packages (from chex->alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.12.1)
95Requirement already satisfied: PyYAML in /usr/local/lib/python3.10/dist-packages (from ml-collections->alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (6.0.2)
96Collecting contextlib2 (from ml-collections->alphafold-colabfold==v2.3.5->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72)
97 Downloading contextlib2-21.6.0-py2.py3-none-any.whl.metadata (4.1 kB)
98Requirement already satisfied: MarkupSafe>=2.1.1 in /usr/local/lib/python3.10/dist-packages (from werkzeug>=1.0.1->tensorboard<2.19,>=2.18->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.0.2)
99Requirement already satisfied: markdown-it-py>=2.2.0 in /usr/local/lib/python3.10/dist-packages (from rich->keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (3.0.0)
100Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /usr/local/lib/python3.10/dist-packages (from rich->keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (2.18.0)
101Requirement already satisfied: mdurl~=0.1 in /usr/local/lib/python3.10/dist-packages (from markdown-it-py>=2.2.0->rich->keras>=3.5.0->tensorflow-cpu<3.0.0,>=2.11.0->colabfold@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72->colabfold[alphafold-minus-jax]@ git+https://github.com/sokrypton/ColabFold@29395e7dee2c2895eaf585ef6b6cde932fd95e72) (0.1.2)
102Downloading alphafold_colabfold-2.3.5-py3-none-any.whl (242 kB)
103 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 242.0/242.0 kB 20.8 MB/s eta 0:00:00
104Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
105Downloading dm_haiku-0.0.9-py3-none-any.whl (352 kB)
106 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 352.1/352.1 kB 29.3 MB/s eta 0:00:00
107Downloading importlib_metadata-4.13.0-py3-none-any.whl (23 kB)
108Downloading pandas-1.5.3-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.1 MB)
109 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 12.1/12.1 MB 97.6 MB/s eta 0:00:00
110Downloading py3Dmol-2.4.0-py2.py3-none-any.whl (7.0 kB)
111Downloading tensorflow_cpu-2.18.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (230.0 MB)
112 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 230.0/230.0 MB 5.0 MB/s eta 0:00:00
113Downloading jmp-0.0.4-py3-none-any.whl (18 kB)
114Downloading keras-3.6.0-py3-none-any.whl (1.2 MB)
115 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 1.2/1.2 MB 35.8 MB/s eta 0:00:00
116Downloading tensorboard-2.18.0-py3-none-any.whl (5.5 MB)
117 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.5/5.5 MB 66.0 MB/s eta 0:00:00
118Downloading biopython-1.84-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.2 MB)
119 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.2/3.2 MB 65.5 MB/s eta 0:00:00
120Downloading docker-7.1.0-py3-none-any.whl (147 kB)
121 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 147.8/147.8 kB 10.2 MB/s eta 0:00:00
122Downloading contextlib2-21.6.0-py2.py3-none-any.whl (13 kB)
123Building wheels for collected packages: colabfold, ml-collections
124 Building wheel for colabfold (pyproject.toml): started
125 Building wheel for colabfold (pyproject.toml): finished with status 'done'
126 Created wheel for colabfold: filename=colabfold-1.5.3-py3-none-any.whl size=61553 sha256=6d7228b96fbbe94d6f7afdb014227d4cb84c1ff14690d07f9eb67724122c2d37
127 Stored in directory: /root/.cache/pip/wheels/0a/84/5a/d55512132cfd5a14ace505b83af68d378992924dd8ea760c72
128 Building wheel for ml-collections (setup.py): started
129 Building wheel for ml-collections (setup.py): finished with status 'done'
130 Created wheel for ml-collections: filename=ml_collections-0.1.1-py3-none-any.whl size=94508 sha256=96f9c8d5ef8bbcffb1eb73289a1ad46bb57fe46029d7f2a9407b79d2ac7e0aaf
131 Stored in directory: /root/.cache/pip/wheels/7b/89/c9/a9b87790789e94aadcfc393c283e3ecd5ab916aed0a31be8fe
132Successfully built colabfold ml-collections
133Installing collected packages: py3Dmol, appdirs, jmp, importlib-metadata, contextlib2, biopython, tensorboard, pandas, ml-collections, docker, dm-haiku, keras, tensorflow-cpu, colabfold, alphafold-colabfold
134 Attempting uninstall: importlib-metadata
135 Found existing installation: importlib_metadata 8.5.0
136 Uninstalling importlib_metadata-8.5.0:
137 Successfully uninstalled importlib_metadata-8.5.0
138 Attempting uninstall: tensorboard
139 Found existing installation: tensorboard 2.17.0
140 Uninstalling tensorboard-2.17.0:
141 Successfully uninstalled tensorboard-2.17.0
142 Attempting uninstall: pandas
143 Found existing installation: pandas 2.2.2
144 Uninstalling pandas-2.2.2:
145 Successfully uninstalled pandas-2.2.2
146 Attempting uninstall: keras
147 Found existing installation: keras 3.4.1
148 Uninstalling keras-3.4.1:
149 Successfully uninstalled keras-3.4.1
150Successfully installed alphafold-colabfold-2.3.5 appdirs-1.4.4 biopython-1.84 colabfold-1.5.3 contextlib2-21.6.0 dm-haiku-0.0.9 docker-7.1.0 importlib-metadata-4.13.0 jmp-0.0.4 keras-3.6.0 ml-collections-0.1.1 pandas-1.5.3 py3Dmol-2.4.0 tensorboard-2.18.0 tensorflow-cpu-2.18.0
151+ pip install --upgrade dm-haiku
152Requirement already satisfied: dm-haiku in /usr/local/lib/python3.10/dist-packages (0.0.9)
153Collecting dm-haiku
154 Downloading dm_haiku-0.0.13-py3-none-any.whl.metadata (19 kB)
155Requirement already satisfied: absl-py>=0.7.1 in /usr/local/lib/python3.10/dist-packages (from dm-haiku) (1.4.0)
156Requirement already satisfied: jmp>=0.0.2 in /usr/local/lib/python3.10/dist-packages (from dm-haiku) (0.0.4)
157Requirement already satisfied: numpy>=1.18.0 in /usr/local/lib/python3.10/dist-packages (from dm-haiku) (1.26.4)
158Requirement already satisfied: tabulate>=0.8.9 in /usr/local/lib/python3.10/dist-packages (from dm-haiku) (0.9.0)
159Downloading dm_haiku-0.0.13-py3-none-any.whl (373 kB)
160 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 373.9/373.9 kB 29.4 MB/s eta 0:00:00
161Installing collected packages: dm-haiku
162 Attempting uninstall: dm-haiku
163 Found existing installation: dm-haiku 0.0.9
164 Uninstalling dm-haiku-0.0.9:
165 Successfully uninstalled dm-haiku-0.0.9
166ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts.
167colabfold 1.5.3 requires dm-haiku<0.0.10,>=0.0.9, but you have dm-haiku 0.0.13 which is incompatible.
168Successfully installed dm-haiku-0.0.13
169+ sed -i 's/weights = jax.nn.softmax(logits)/logits=jnp.clip(logits,-1e8,1e8);weights=jax.nn.softmax(logits)/g' /usr/local/lib/python3.10/dist-packages/alphafold/model/modules.py
170+ pip install biopython==1.81
171Collecting biopython==1.81
172 Downloading biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (13 kB)
173Requirement already satisfied: numpy in /usr/local/lib/python3.10/dist-packages (from biopython==1.81) (1.26.4)
174Downloading biopython-1.81-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (3.1 MB)
175 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 79.6 MB/s eta 0:00:00
176Installing collected packages: biopython
177 Attempting uninstall: biopython
178 Found existing installation: biopython 1.84
179 Uninstalling biopython-1.84:
180 Successfully uninstalled biopython-1.84
181Successfully installed biopython-1.81
182+ touch COLABFOLD_READY
183+ set -e
184+ wget -qnc https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
185+ bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local
186+ rm Miniconda3-latest-Linux-x86_64.sh
187+ touch CONDA_READY
188+ set -e
189+ conda install -y -q -c conda-forge openmm=7.7.0 python=3.10 pdbfixer
190+ ln -s /usr/local/lib/python3.10/site-packages/simtk .
191+ ln -s /usr/local/lib/python3.10/site-packages/openmm .
192+ ln -s /usr/local/lib/python3.10/site-packages/pdbfixer .
193+ touch AMBER_READY