Alphafold をテンプレートにして作成
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開始行:
Alphafold. タンパク質立体構造予測プログラム.
本家様 [[https://github.com/deepmind/alphafold>+https://g...
ここでは version 2.3.0 を構築します. オリジナルは[[docker...
&size(10){dockeを使用しないで自家に作る alphafold_non_doc...
&size(10){dockerの代わりに同じコンテナ技術の Singularity ...
[[docker]]はdocker-ce でそれに NVIDIA Container Toolkit ...
***dockerを用意する [#t385d419]
まずはインストールする計算機の紹介.
nvidiaドライバーは入っているけど、cudaライブラリは入れて...
#code(nonumber){{
[root@alphafold ~]# cat /etc/redhat-release
Rocky Linux release 9.1 (Blue Onyx)
[root@alphafold ~]# getenforce
Enforcing
[root@alphafold ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 525.60.11...
GCC version: gcc version 11.3.1 20220421 (Red Hat 11.3.1...
[root@alphafold ~]# nvidia-smi -L
GPU 0: NVIDIA RTX A2000 (UUID: GPU-23cc3ee7-31d3-a068-2f6...
[root@alphafold ~]# ls -l /usr/local/cuda
ls: cannot access '/usr/local/cuda': No such file or dire...
[root@alphafold ~]#
}}
っでdocker-ceのリポジトリを入れます
#code(nonumber){{
[root@alphafold ~]# dnf config-manager --add-repo https:/...
Adding repo from: https://download.docker.com/linux/cento...
[root@alphafold ~]# head /etc/yum.repos.d/docker-ce.repo ...
[docker-ce-stable]
name=Docker CE Stable - $basearch
baseurl=https://download.docker.com/linux/centos/$release...
enabled=1
gpgcheck=1
gpgkey=https://download.docker.com/linux/centos/gpg
[docker-ce-stable-debuginfo]
name=Docker CE Stable - Debuginfo $basearch
baseurl=https://download.docker.com/linux/centos/$release...
[root@alphafold ~]#
(docker-ceをインストール)
[root@alphafold ~]# dnf -y install docker-ce docker-ce-cl...
[root@alphafold ~]# systemctl status docker
○ docker.service - Docker Application Container Engine
Loaded: loaded (/usr/lib/systemd/system/docker.servi...
Active: inactive (dead)
TriggeredBy: ○ docker.socket
Docs: https://docs.docker.com
[root@alphafold ~]#
(dokcer-ceをデーモンとして起動)
[root@alphafold ~]# systemctl enable docker --now
Created symlink /etc/systemd/system/multi-user.target.wan...
[root@alphafold ~]#
}}
***NVIDIA Container Toolkitのインストール [#j5029af7]
[[https://docs.nvidia.com/datacenter/cloud-native/contain...
取得するリポジトリを選びます. rockylinux9.1なので「rhel9....
#code(nonumber){{
[root@alphafold ~]# curl -s -o /etc/yum.repos.d/nvidia-do...
(中身確認)
[root@alphafold ~]# head /etc/yum.repos.d/nvidia-docker.r...
[libnvidia-container]
name=libnvidia-container
baseurl=https://nvidia.github.io/libnvidia-container/stab...
repo_gpgcheck=1
gpgcheck=0
enabled=1
gpgkey=https://nvidia.github.io/libnvidia-container/gpgkey
sslverify=1
sslcacert=/etc/pki/tls/certs/ca-bundle.crt
[root@alphafold ~]# dnf install nvidia-docker2 (以前...
[root@alphafold ~]# systemctl restart docker
}}
テスト
#code(nonumber){{
[root@alphafold ~]# nvidia-container-cli info
NVRM version: 525.60.11
CUDA version: 12.0
Device Index: 0
Device Minor: 0
Model: NVIDIA RTX A2000
Brand: NvidiaRTX
GPU UUID: GPU-23cc3ee7-31d3-a068-2f61-5aa00052d084
Bus Location: 00000000:0b:00.0
Architecture: 8.6
[root@alphafold ~]#
[root@alphafold ~]# docker run --gpus all --rm nvidia/cud...
Unable to find image 'nvidia/cuda:11.8.0-base-ubuntu22.04...
11.8.0-base-ubuntu22.04: Pulling from nvidia/cuda
6e3729cf69e0: Pull complete
33effac16366: Pull complete
49118e74c29b: Pull complete
b40dd12f6d8e: Pull complete
23773815605e: Pull complete
Digest: sha256:7d667ce4e95c299f701074715138bce548a3c51b07...
Status: Downloaded newer image for nvidia/cuda:11.8.0-bas...
Fri Dec 16 10:19:19 2022
+--------------------------------------------------------...
| NVIDIA-SMI 525.60.11 Driver Version: 525.60.11 CU...
|-------------------------------+----------------------+-...
| GPU Name Persistence-M| Bus-Id Disp.A | ...
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | ...
| | | ...
|===============================+======================+=...
| 0 NVIDIA RTX A2000 Off | 00000000:0B:00.0 Off | ...
| 30% 52C P0 N/A / 70W | 0MiB / 6138MiB | ...
| | | ...
+-------------------------------+----------------------+-...
+--------------------------------------------------------...
| Processes: ...
| GPU GI CI PID Type Process name ...
| ID ID ...
|========================================================...
| No running processes found ...
+--------------------------------------------------------...
[root@alphafold ~]#
}}
上出来.
proxyでそのままではお外に出れない場合は
#code(nonumber){{
[root@alphafold ~]# EDITOR=vim systemctl edit docker.serv...
[Service]
Environment = 'http_proxy=http://proxy.sybyl.local:10080'...
[root@alphafold ~]# systemctl restart docker
}}
とする
っでdockerを利用するユーザを group の docker に加える
#code(nonumber){{
[root@alphafold ~]# useradd -m illya
[root@alphafold ~]# usermod -aG docker illya
[root@alphafold ~]# id illya
uid=1000(illya) gid=1000(illya) groups=1000(illya),986(do...
[root@alphafold ~]# su - illya
[illya@alphafold ~]$ docker run --gpus all --rm nvidia/cu...
GPU 0: NVIDIA RTX A2000 (UUID: GPU-23cc3ee7-31d3-a068-2f6...
[illya@alphafold ~]$
}}
っでok
***alphafoldのdockerを作成 [#bfda754e]
#code(nonumber){{
[root@alphafold ~]# mkdir /apps
[root@alphafold ~]# cd /apps
[root@alphafold apps]# git clone https://github.com/deepm...
[root@alphafold apps]# cd alphafold/
[root@alphafold alphafold]# ls -CF
afdb/ CONTRIBUTING.md docs/ LICENSE README.md...
alphafold/ docker/ imgs/ notebooks/ requireme...
[root@alphafold alphafold]#
[root@alphafold alphafold]# docker build -f docker/Docker...
:
:
[root@alphafold alphafold]# docker images
REPOSITORY TAG IMAGE I...
alphafold latest fcc5a16...
nvidia/cuda 11.8.0-base-ubuntu22.04 06a52e1...
nvidia/cuda 11.1.1-cudnn8-runtime-ubuntu18.04 cd35858...
[root@alphafold alphafold]#
}}
***「Genetic databases」と「model parameters」を取得 [#r8...
この辺は[[Alphafold/database]]を参照. ここでは「/Alphafol...
***実行環境を作る [#k5b43a5c]
前段でalphafoldを実行するコンテナが作れた. 次にそのコンテ...
OSの上に直接構築してもいいのですが、[[EnvironmentModules]...
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2022.05
pyenv global anaconda3-2022.05
export PATH=$PYENV_ROOT/versions/anaconda3-2022.05/bin/:$...
conda update --all
}}
下準備を終わらせて、alphafold向けの環境を作ります
#code(nonumber){{
[root@alphafold alphafold]# conda create -n alphafold-doc...
[root@alphafold alphafold]# source activate alphafold-doc...
(alphafold-docker) [root@alphafold alphafold]# cat /apps/...
# Dependencies necessary to execute run_docker.py
absl-py==1.0.0
docker==5.0.0
(alphafold-docker) [root@alphafold alphafold]# pip instal...
(alphafold-docker) [root@alphafold alphafold]# conda deac...
[root@alphafold alphafold]#
[root@centos7 ~]#
}}
っで[[EnvironmentModules]]向けにmodulefileを作ります「/et...
#code(nonumber){{
[root@alphafold ~]# mkdir -p /apps/modulefiles
[root@alphafold ~]# vi /apps/modulefiles/alphafold-docker
#%Module1.0
set root /apps/pyenv/versions/anaconda3-2022.05/...
prepend-path PATH $root/bin
[root@alphafold ~]#
}}
***使ってみる [#f4495cb0]
#code(nonumber){{
[illya@alphafold ~]$ vi query.fasta
>dummy_sequence
GWSTELEKHREELKEFLKKEGITNVEIRIDNGRLEVRVEGGTERLKRFLEELRQKLE...
[illya@alphafold ~]$
}}
#code(nonumber){{
[illya@alphafold ~]$ mkdir /tmp/alphafold <-- 初回だけ
[illya@alphafold ~]$ module use --append /apps/modulefiles/
[illya@alphafold ~]$ module load alphafold-docker
[illya@alphafold ~]$ which python
/apps/pyenv/versions/anaconda3-2022.05/envs/alphafold-doc...
[illya@alphafold ~]$ python /apps/alphafold/docker/run_do...
FATAL Flags parsing error:
flag --data_dir=None: Flag --data_dir must have a value...
flag --fasta_paths=None: Flag --fasta_paths must have a...
flag --max_template_date=None: Flag --max_template_date...
Pass --helpshort or --helpfull to see help on flags.
[illya@alphafold ~]$
[illya@alphafold ~]$ python /apps/alphafold/docker/run_do...
}}
結果は「/tmp/alphafold/」に置かれる. 特定の場所に結果を書...
計算中のログを残したい場合はコマンド行の末尾に「2>&1 | te...
複数サブユニットでの予測は
#code(nonumber){{
[illya@centos7 ~]$ cat dimaer.fasta
>XP_009313165.1
MRAAFAEARAALAEGEVPVGCVLVPVDASCAANAQLAADDDDDENKSKGSSNSNNSK...
RNATNREHHALAHAEFVAVEALLRELAANGQQRPASLAGYVLYVVVEPCIMCAAMLL...
PRFGGNGTVLAVHTAAGCSAPGYESSGGHRADEAVALLQEFYRHENTNAPGHKRRRK...
>XP_009313165.2
MRAAFAEARAALAEGEVPVGCVLVPVDASCAANAQLAADDDDDENKSKGSSNSNNSK...
RNATNREHHALAHAEFVAVEALLRELAANGQQRPASLAGYVLYVVVEPCIMCAAMLL...
PRFGGNGTVLAVHTAAGCSAPGYESSGGHRADEAVALLQEFYRHENTNAPGHKRRRK...
[illya@centos7 ~]$ mkdir dimaer
[illya@centos7 ~]$ python /apps/alphafold/docker/run_dock...
}}
&size(10){出力先を予め作る必要がある};
***memo [#abb2cb76]
作ったdocker imageの中身を探索してみる. 「alphafold/docke...
#code(nonumber){{
docker run -it --rm --entrypoint /bin/bash alphafold:latest
}}
として中身を見ることができる.
終了行:
Alphafold. タンパク質立体構造予測プログラム.
本家様 [[https://github.com/deepmind/alphafold>+https://g...
ここでは version 2.3.0 を構築します. オリジナルは[[docker...
&size(10){dockeを使用しないで自家に作る alphafold_non_doc...
&size(10){dockerの代わりに同じコンテナ技術の Singularity ...
[[docker]]はdocker-ce でそれに NVIDIA Container Toolkit ...
***dockerを用意する [#t385d419]
まずはインストールする計算機の紹介.
nvidiaドライバーは入っているけど、cudaライブラリは入れて...
#code(nonumber){{
[root@alphafold ~]# cat /etc/redhat-release
Rocky Linux release 9.1 (Blue Onyx)
[root@alphafold ~]# getenforce
Enforcing
[root@alphafold ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 525.60.11...
GCC version: gcc version 11.3.1 20220421 (Red Hat 11.3.1...
[root@alphafold ~]# nvidia-smi -L
GPU 0: NVIDIA RTX A2000 (UUID: GPU-23cc3ee7-31d3-a068-2f6...
[root@alphafold ~]# ls -l /usr/local/cuda
ls: cannot access '/usr/local/cuda': No such file or dire...
[root@alphafold ~]#
}}
っでdocker-ceのリポジトリを入れます
#code(nonumber){{
[root@alphafold ~]# dnf config-manager --add-repo https:/...
Adding repo from: https://download.docker.com/linux/cento...
[root@alphafold ~]# head /etc/yum.repos.d/docker-ce.repo ...
[docker-ce-stable]
name=Docker CE Stable - $basearch
baseurl=https://download.docker.com/linux/centos/$release...
enabled=1
gpgcheck=1
gpgkey=https://download.docker.com/linux/centos/gpg
[docker-ce-stable-debuginfo]
name=Docker CE Stable - Debuginfo $basearch
baseurl=https://download.docker.com/linux/centos/$release...
[root@alphafold ~]#
(docker-ceをインストール)
[root@alphafold ~]# dnf -y install docker-ce docker-ce-cl...
[root@alphafold ~]# systemctl status docker
○ docker.service - Docker Application Container Engine
Loaded: loaded (/usr/lib/systemd/system/docker.servi...
Active: inactive (dead)
TriggeredBy: ○ docker.socket
Docs: https://docs.docker.com
[root@alphafold ~]#
(dokcer-ceをデーモンとして起動)
[root@alphafold ~]# systemctl enable docker --now
Created symlink /etc/systemd/system/multi-user.target.wan...
[root@alphafold ~]#
}}
***NVIDIA Container Toolkitのインストール [#j5029af7]
[[https://docs.nvidia.com/datacenter/cloud-native/contain...
取得するリポジトリを選びます. rockylinux9.1なので「rhel9....
#code(nonumber){{
[root@alphafold ~]# curl -s -o /etc/yum.repos.d/nvidia-do...
(中身確認)
[root@alphafold ~]# head /etc/yum.repos.d/nvidia-docker.r...
[libnvidia-container]
name=libnvidia-container
baseurl=https://nvidia.github.io/libnvidia-container/stab...
repo_gpgcheck=1
gpgcheck=0
enabled=1
gpgkey=https://nvidia.github.io/libnvidia-container/gpgkey
sslverify=1
sslcacert=/etc/pki/tls/certs/ca-bundle.crt
[root@alphafold ~]# dnf install nvidia-docker2 (以前...
[root@alphafold ~]# systemctl restart docker
}}
テスト
#code(nonumber){{
[root@alphafold ~]# nvidia-container-cli info
NVRM version: 525.60.11
CUDA version: 12.0
Device Index: 0
Device Minor: 0
Model: NVIDIA RTX A2000
Brand: NvidiaRTX
GPU UUID: GPU-23cc3ee7-31d3-a068-2f61-5aa00052d084
Bus Location: 00000000:0b:00.0
Architecture: 8.6
[root@alphafold ~]#
[root@alphafold ~]# docker run --gpus all --rm nvidia/cud...
Unable to find image 'nvidia/cuda:11.8.0-base-ubuntu22.04...
11.8.0-base-ubuntu22.04: Pulling from nvidia/cuda
6e3729cf69e0: Pull complete
33effac16366: Pull complete
49118e74c29b: Pull complete
b40dd12f6d8e: Pull complete
23773815605e: Pull complete
Digest: sha256:7d667ce4e95c299f701074715138bce548a3c51b07...
Status: Downloaded newer image for nvidia/cuda:11.8.0-bas...
Fri Dec 16 10:19:19 2022
+--------------------------------------------------------...
| NVIDIA-SMI 525.60.11 Driver Version: 525.60.11 CU...
|-------------------------------+----------------------+-...
| GPU Name Persistence-M| Bus-Id Disp.A | ...
| Fan Temp Perf Pwr:Usage/Cap| Memory-Usage | ...
| | | ...
|===============================+======================+=...
| 0 NVIDIA RTX A2000 Off | 00000000:0B:00.0 Off | ...
| 30% 52C P0 N/A / 70W | 0MiB / 6138MiB | ...
| | | ...
+-------------------------------+----------------------+-...
+--------------------------------------------------------...
| Processes: ...
| GPU GI CI PID Type Process name ...
| ID ID ...
|========================================================...
| No running processes found ...
+--------------------------------------------------------...
[root@alphafold ~]#
}}
上出来.
proxyでそのままではお外に出れない場合は
#code(nonumber){{
[root@alphafold ~]# EDITOR=vim systemctl edit docker.serv...
[Service]
Environment = 'http_proxy=http://proxy.sybyl.local:10080'...
[root@alphafold ~]# systemctl restart docker
}}
とする
っでdockerを利用するユーザを group の docker に加える
#code(nonumber){{
[root@alphafold ~]# useradd -m illya
[root@alphafold ~]# usermod -aG docker illya
[root@alphafold ~]# id illya
uid=1000(illya) gid=1000(illya) groups=1000(illya),986(do...
[root@alphafold ~]# su - illya
[illya@alphafold ~]$ docker run --gpus all --rm nvidia/cu...
GPU 0: NVIDIA RTX A2000 (UUID: GPU-23cc3ee7-31d3-a068-2f6...
[illya@alphafold ~]$
}}
っでok
***alphafoldのdockerを作成 [#bfda754e]
#code(nonumber){{
[root@alphafold ~]# mkdir /apps
[root@alphafold ~]# cd /apps
[root@alphafold apps]# git clone https://github.com/deepm...
[root@alphafold apps]# cd alphafold/
[root@alphafold alphafold]# ls -CF
afdb/ CONTRIBUTING.md docs/ LICENSE README.md...
alphafold/ docker/ imgs/ notebooks/ requireme...
[root@alphafold alphafold]#
[root@alphafold alphafold]# docker build -f docker/Docker...
:
:
[root@alphafold alphafold]# docker images
REPOSITORY TAG IMAGE I...
alphafold latest fcc5a16...
nvidia/cuda 11.8.0-base-ubuntu22.04 06a52e1...
nvidia/cuda 11.1.1-cudnn8-runtime-ubuntu18.04 cd35858...
[root@alphafold alphafold]#
}}
***「Genetic databases」と「model parameters」を取得 [#r8...
この辺は[[Alphafold/database]]を参照. ここでは「/Alphafol...
***実行環境を作る [#k5b43a5c]
前段でalphafoldを実行するコンテナが作れた. 次にそのコンテ...
OSの上に直接構築してもいいのですが、[[EnvironmentModules]...
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2022.05
pyenv global anaconda3-2022.05
export PATH=$PYENV_ROOT/versions/anaconda3-2022.05/bin/:$...
conda update --all
}}
下準備を終わらせて、alphafold向けの環境を作ります
#code(nonumber){{
[root@alphafold alphafold]# conda create -n alphafold-doc...
[root@alphafold alphafold]# source activate alphafold-doc...
(alphafold-docker) [root@alphafold alphafold]# cat /apps/...
# Dependencies necessary to execute run_docker.py
absl-py==1.0.0
docker==5.0.0
(alphafold-docker) [root@alphafold alphafold]# pip instal...
(alphafold-docker) [root@alphafold alphafold]# conda deac...
[root@alphafold alphafold]#
[root@centos7 ~]#
}}
っで[[EnvironmentModules]]向けにmodulefileを作ります「/et...
#code(nonumber){{
[root@alphafold ~]# mkdir -p /apps/modulefiles
[root@alphafold ~]# vi /apps/modulefiles/alphafold-docker
#%Module1.0
set root /apps/pyenv/versions/anaconda3-2022.05/...
prepend-path PATH $root/bin
[root@alphafold ~]#
}}
***使ってみる [#f4495cb0]
#code(nonumber){{
[illya@alphafold ~]$ vi query.fasta
>dummy_sequence
GWSTELEKHREELKEFLKKEGITNVEIRIDNGRLEVRVEGGTERLKRFLEELRQKLE...
[illya@alphafold ~]$
}}
#code(nonumber){{
[illya@alphafold ~]$ mkdir /tmp/alphafold <-- 初回だけ
[illya@alphafold ~]$ module use --append /apps/modulefiles/
[illya@alphafold ~]$ module load alphafold-docker
[illya@alphafold ~]$ which python
/apps/pyenv/versions/anaconda3-2022.05/envs/alphafold-doc...
[illya@alphafold ~]$ python /apps/alphafold/docker/run_do...
FATAL Flags parsing error:
flag --data_dir=None: Flag --data_dir must have a value...
flag --fasta_paths=None: Flag --fasta_paths must have a...
flag --max_template_date=None: Flag --max_template_date...
Pass --helpshort or --helpfull to see help on flags.
[illya@alphafold ~]$
[illya@alphafold ~]$ python /apps/alphafold/docker/run_do...
}}
結果は「/tmp/alphafold/」に置かれる. 特定の場所に結果を書...
計算中のログを残したい場合はコマンド行の末尾に「2>&1 | te...
複数サブユニットでの予測は
#code(nonumber){{
[illya@centos7 ~]$ cat dimaer.fasta
>XP_009313165.1
MRAAFAEARAALAEGEVPVGCVLVPVDASCAANAQLAADDDDDENKSKGSSNSNNSK...
RNATNREHHALAHAEFVAVEALLRELAANGQQRPASLAGYVLYVVVEPCIMCAAMLL...
PRFGGNGTVLAVHTAAGCSAPGYESSGGHRADEAVALLQEFYRHENTNAPGHKRRRK...
>XP_009313165.2
MRAAFAEARAALAEGEVPVGCVLVPVDASCAANAQLAADDDDDENKSKGSSNSNNSK...
RNATNREHHALAHAEFVAVEALLRELAANGQQRPASLAGYVLYVVVEPCIMCAAMLL...
PRFGGNGTVLAVHTAAGCSAPGYESSGGHRADEAVALLQEFYRHENTNAPGHKRRRK...
[illya@centos7 ~]$ mkdir dimaer
[illya@centos7 ~]$ python /apps/alphafold/docker/run_dock...
}}
&size(10){出力先を予め作る必要がある};
***memo [#abb2cb76]
作ったdocker imageの中身を探索してみる. 「alphafold/docke...
#code(nonumber){{
docker run -it --rm --entrypoint /bin/bash alphafold:latest
}}
として中身を見ることができる.
ページ名:
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