Proteina-Complexa/container をテンプレートにして作成
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開始行:
&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-Compl...
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 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@r9 ~]# ls -l /usr/local/cuda*
ls: cannot access '/usr/local/cuda*': No such file or dir...
[root@r9 ~]#
}}
#code(nonumber){{
[root@r9 ~]# git clone https://github.com/NVIDIA-Digital-...
[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.__vers...
Note: Foldseek and MMseqs2 are not included in the public...
Install them separately if needed:
wget https://mmseqs.com/foldseek/foldseek-linux-gpu.tar...
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...
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 de...
l) Download Complexa Ligand weights (ligand binder desi...
e) Download Complexa AME weights (enzyme/motif scaffold...
a) Download all Complexa weights (protein + ligand + AME)
Community Models:
1) Download all community weights (ProteinMPNN + Ligand...
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_TOK...
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 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@r9 ~]#
}}
#code(nonumber){{
[root@r9 ~]# dnf config-manager --add-repo https://downlo...
Adding repo from: https://download.docker.com/linux/cento...
[root@r9 ~]# dnf install docker-ce docker-ce-cli containe...
[root@r9 ~]# systemctl enable docker --now
Created symlink /etc/systemd/system/multi-user.target.wan...
[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...
[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 restar...
[root@r9 ~]#
[root@r9 ~]# systemctl restart docker
[root@r9 ~]# dnf config-manager --disable nvidia-contain...
[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/...
[root@r9 ~]# cd Proteina-Complexa/
[root@r9 Proteina-Complexa]#
[root@r9 Proteina-Complexa]# docker build -t proteina-com...
}}
終了行:
&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-Compl...
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 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@r9 ~]# ls -l /usr/local/cuda*
ls: cannot access '/usr/local/cuda*': No such file or dir...
[root@r9 ~]#
}}
#code(nonumber){{
[root@r9 ~]# git clone https://github.com/NVIDIA-Digital-...
[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.__vers...
Note: Foldseek and MMseqs2 are not included in the public...
Install them separately if needed:
wget https://mmseqs.com/foldseek/foldseek-linux-gpu.tar...
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...
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 de...
l) Download Complexa Ligand weights (ligand binder desi...
e) Download Complexa AME weights (enzyme/motif scaffold...
a) Download all Complexa weights (protein + ligand + AME)
Community Models:
1) Download all community weights (ProteinMPNN + Ligand...
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_TOK...
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 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@r9 ~]#
}}
#code(nonumber){{
[root@r9 ~]# dnf config-manager --add-repo https://downlo...
Adding repo from: https://download.docker.com/linux/cento...
[root@r9 ~]# dnf install docker-ce docker-ce-cli containe...
[root@r9 ~]# systemctl enable docker --now
Created symlink /etc/systemd/system/multi-user.target.wan...
[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...
[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 restar...
[root@r9 ~]#
[root@r9 ~]# systemctl restart docker
[root@r9 ~]# dnf config-manager --disable nvidia-contain...
[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/...
[root@r9 ~]# cd Proteina-Complexa/
[root@r9 Proteina-Complexa]#
[root@r9 Proteina-Complexa]# docker build -t proteina-com...
}}
ページ名:
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