Proteina-Complexa/container

[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 ~]#

[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]#

[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]#

[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

[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 ~]#

[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 ~]#

[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 .