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#author("2026-06-14T04:46:57+00:00","default:sysosa","sysosa") #author("2026-06-14T13:05:41+00:00","default:sysosa","sysosa") &color(red){製作途中}; Proteina-Complexaをdocker/apptainerで作ってみた 本家様 [[https://github.com/NVIDIA-BioNeMo/Proteina-Complexa>+https://github.com/NVIDIA-BioNeMo/Proteina-Complexa]] 各自のホームディレクトリに Proteina-Complexa を構築して利用できるが、docker でも利用可能のご様子. まずはローカルに構築 #code(nonumber){{ [root@r9 ~]# cat /etc/redhat-release Rocky Linux release 9.7 (Blue Onyx) [root@r9 ~]# cat /proc/driver/nvidia/version NVRM version: NVIDIA UNIX Open Kernel Module for x86_64 595.80 Release Build (dvs-builder@U22-I3-AF05-29-2) Thu May 21 19:21:58 UTC 2026 GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0-11) (GCC) [root@r9 ~]# ls -l /usr/local/cuda* ls: cannot access '/usr/local/cuda*': No such file or directory [root@r9 ~]# }} #code(nonumber){{ [root@r9 ~]# git clone https://github.com/NVIDIA-Digital-Bio/Proteina-Complexa [root@r9 ~]# cd Proteina-Complexa [root@r9 Proteina-Complexa]# ./env/build_uv_env.sh : : ============================================== Installation Complete! ============================================== To activate the environment: source /root/Proteina-Complexa/.venv/bin/activate To verify installation: python -c "import torch; print(f'PyTorch: {torch.__version__}, CUDA: {torch.cuda.is_available()}')" Note: Foldseek and MMseqs2 are not included in the public build. Install them separately if needed: wget https://mmseqs.com/foldseek/foldseek-linux-gpu.tar.gz wget https://mmseqs.com/latest/mmseqs-linux-gpu.tar.gz [root@r9 Proteina-Complexa]# }} ちょいと確認 #code(nonumber){{ [root@r9 Proteina-Complexa]# ls /root/.local/bin/ uv uvx [root@r9 Proteina-Complexa]# source .venv/bin/activate (complexa) [root@r9 Proteina-Complexa]# which python /root/Proteina-Complexa/.venv/bin/python (complexa) [root@r9 Proteina-Complexa]# python -c "import torch; print(f'PyTorch: {torch.__version__}, CUDA: {torch.cuda.is_available()}')" PyTorch: 2.7.0+cu126, CUDA: True (complexa) [root@r9 Proteina-Complexa]# deactivate [root@r9 Proteina-Complexa]# }} インストール後のセットアップ #code(nonumber){{ [root@r9 Proteina-Complexa]# source .venv/bin/activate (complexa) [root@r9 Proteina-Complexa]# complexa init uv Created .env from /root/Proteina-Complexa/.env_example Location: /root/Proteina-Complexa/.env Next steps: 1. Edit .env and fill in your credentials and paths 2. Run: complexa init <uv|docker> (complexa) [root@r9 Proteina-Complexa]# vi .env : HF_TOKEN=xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx LOCAL_CODE_PATH=/root/Proteina-Complexa LOCAL_DATA_PATH=/apps/PFM_data : (complexa) [root@r9 Proteina-Complexa]# (complexa) [root@r9 Proteina-Complexa]# complexa download : What would you like to download? Complexa Models: p) Download Complexa Protein weights (protein binder design) l) Download Complexa Ligand weights (ligand binder design) e) Download Complexa AME weights (enzyme/motif scaffolding) a) Download all Complexa weights (protein + ligand + AME) Community Models: 1) Download all community weights (ProteinMPNN + LigandMPNN + AF2 + ESM2 + RF3) 2) Download ProteinMPNN weights only (~50MB) 3) Download LigandMPNN weights only (~500MB) 4) Download AlphaFold2 weights only (~5GB) 5) Download ESM2 weights only (~2.6GB) [requires HF_TOKEN if rate limited] 6) Download RoseTTAFold3 weights (~2.5GB) 7) Download everything (all Complexa + community) Other: s) Check installation status q) Quit Enter your choice [p, l, e, a, 1-7, s, q]: a }} (complexa) [root@r9 Proteina-Complexa]# complexa init uv (complexa) [root@r9 Proteina-Complexa]# vi ***dockerの準備 [#x7dab182] #code(nonumber){{ [root@r9 ~]# cat /etc/redhat-release Rocky Linux release 9.7 (Blue Onyx) [root@r9 ~]# cat /proc/driver/nvidia/version NVRM version: NVIDIA UNIX Open Kernel Module for x86_64 595.58.03 Release Build (dvs-builder@U22-I3-AM25-28-3) Tue Mar 17 19:55:10 UTC 2026 GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0-11) (GCC) [root@r9 ~]# }} #code(nonumber){{ [root@r9 ~]# dnf config-manager --add-repo https://download.docker.com/linux/centos/docker-ce.repo Adding repo from: https://download.docker.com/linux/centos/docker-ce.repo [root@r9 ~]# dnf install docker-ce docker-ce-cli containerd.io [root@r9 ~]# systemctl enable docker --now Created symlink /etc/systemd/system/multi-user.target.wants/docker.service → /usr/lib/systemd/system/docker.service. [root@r9 ~]# dnf config-manager --disable docker-ce-stable [root@r9 ~]# docker --version Docker version 29.5.3, build d1c06ef [root@r9 ~]# [root@r9 ~]# curl -s -o /etc/yum.repos.d/nvidia-container-toolkit.repo https://nvidia.github.io/libnvidia-container/stable/rpm/nvidia-container-toolkit.repo [root@r9 ~]# dnf install nvidia-container-toolkit -y [root@r9 ~]# nvidia-ctk runtime configure --runtime=docker INFO[0000] Config file does not exist; using empty config INFO[0000] Wrote updated config to /etc/docker/daemon.json INFO[0000] It is recommended that docker daemon be restarted. [root@r9 ~]# [root@r9 ~]# systemctl restart docker [root@r9 ~]# dnf config-manager --disable nvidia-container-toolkit [root@r9 ~]# nvidia-container-cli info NVRM version: 595.58.03 CUDA version: 13.2 Device Index: 0 Device Minor: 0 Model: NVIDIA RTX PRO 2000 Blackwell Brand: NvidiaRTX GPU UUID: GPU-40660e37-0d35-d4f4-294a-eee3fe83049e Bus Location: 00000000:06:10.0 Architecture: 12.0 [root@r9 ~]# }} ***コンテナ作成 [#t2467896] #code(nonumber){{ [root@r9 ~]# git clone https://github.com/NVIDIA-BioNeMo/Proteina-Complexa [root@r9 ~]# cd Proteina-Complexa/ [root@r9 Proteina-Complexa]# [root@r9 Proteina-Complexa]# docker build -t proteina-complexa -f env/docker/Dockerfile . }}
