AlphaFold3 をテンプレートにして作成
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開始行:
本家様 [[https://github.com/google-deepmind/alphafold3>+h...
12月にリリースかなと思ったのですが11月上旬にリリース.
ここでは rockylinux9での構築をしてみます.
AlphaFold2と同じようにdockerコンテナで実行できるようにす...
まずは下記記載のドキュメント通りに作ってみます
[[https://github.com/google-deepmind/alphafold3/blob/main...
Toolkit for alphafold3 input and output files [[https://g...
***対象マシン [#jf44ec1a]
インストール対象マシンは下記の感じです
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.5 (Blue Onyx)
[root@rockylinux9 ~]# getenforce
Enforcing
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 570.153.0...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]# nvidia-smi -L
GPU 0: NVIDIA GeForce GTX 1070 (UUID: GPU-a49de51b-de1e-5...
[root@rockylinux9 ~]# ls -l /usr/local/cuda
ls: cannot access '/usr/local/cuda': No such file or dire...
[root@rockylinux9 ~]#
}}
***docker構築 [#eb777c91]
#code(nonumber){{
[root@rockylinux9 ~]# dnf -y install dnf-plugins-core
[root@rockylinux9 ~]# dnf config-manager --add-repo https...
Adding repo from: https://download.docker.com/linux/rhel/...
[root@rockylinux9 ~]# ls /etc/yum.repos.d/
docker-ce.repo rocky-addons.repo rocky-devel.repo rock...
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# sed -i s'/enabled=1/enabled=0/' /et...
}}
使用するリポジトリは「docker-ce-stable」となる. 詳細は「d...
#code(nonumber){{
[root@rockylinux9 ~]# dnf --enablerepo=docker-ce-stable i...
docker-ce, docker-ce-cli, docker-buildx-plugin, docker-ce...
っで起動
[root@rockylinux9 ~]# systemctl enable docker --now
}}
「systemctl status docker」の中身を見ると「/usr/bin/docke...
別の場所に変えたいなら「--data-root」を使って変更します. ...
次にNVIDIA Container Toolkitをインストールします
#code(nonumber){{
[root@rockylinux9 ~]# curl -s -L https://nvidia.github.io...
[root@rockylinux9 ~]# sed -i s'/enabled=1/enabled=0/' /et...
}}
追加したリポジトリ「nvidia-container-toolkit」の詳細は「d...
っでインストールします
#code(nonumber){{
[root@rockylinux9 ~]# dnf --enablerepo=nvidia-container-t...
nvidia-container-toolkit, libnvidia-container-tools, libn...
dockerを再起動させて有効にします
[root@rockylinux9 ~]# systemctl restart docker
}}
っでテスト
#code(nonumber){{
[root@rockylinux9 ~]# nvidia-container-cli info
NVRM version: 570.153.02
CUDA version: 12.8
Device Index: 0
Device Minor: 0
Model: NVIDIA GeForce GTX 1070
Brand: GeForce
GPU UUID: GPU-a49de51b-de1e-52f3-1e3f-ce704e159713
Bus Location: 00000000:06:10.0
Architecture: 6.1
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# docker run --gpus all --rm nvidia/c...
:
GPU 0: NVIDIA GeForce GTX 1070 (UUID: GPU-a49de51b-de1e-5...
[root@rockylinux9 ~]#
}}
これでdockerの構築が完了.
そのままでは一般ユーザがdockerを使えない. 一般ユーザでdoc...
利用ユーザが「dockerd-rootless-setuptool.sh --skip-iptabl...
#code(nonumber){{
[saber@rockylinux9 ~]$ dockerd-rootless-setuptool.sh --sk...
:
[INFO] Installed docker.service successfully.
[INFO] To control docker.service, run: `systemctl --user ...
[INFO] To run docker.service on system startup, run: `sud...
:
[INFO] Some applications may require the following enviro...
export DOCKER_HOST=unix:///run/user/1000/docker.sock
:
[saber@rockylinux9 ~]$ ps -ef |grep docker
(この段階でユーザアカウントのdockerが動いてます. ログアウ...
}}
その後にrootで「/etc/nvidia-container-runtime/config.toml...
&size(10){systemのbootに合わせて、ログインの有無にかかわ...
っで本題へ.
***AlphaFold3構築 [#ldb5f755]
せっかくdockerをrootlessで作ったので一般ユーザでalphafold...
#code(nonumber){{
[saber@rockylinux9 ~]$ git clone https://github.com/googl...
[saber@rockylinux9 ~]$ cd alphafold3/
[saber@rockylinux9 alphafold3]$ git log -1
commit 64723739f52944274485118cab935d53d66b5aec (HEAD -> ...
Author: Augustin Zidek <augustinzidek@google.com>
Date: Fri May 30 09:23:19 2025 -0700
Update to Ubuntu 24.04 / CUDA 12.6.3 base image and u...
PiperOrigin-RevId: 765219906
Change-Id: I271f442012ee30356ef316eda87abd231319a673
[saber@rockylinux9 alphafold3]$ ls -CF
CMakeLists.txt legal/ requirement...
dev-requirements.txt LICENSE run_alphafo...
docker/ OUTPUT_TERMS_OF_USE.md run_alphafo...
docs/ pyproject.toml run_alphafo...
fetch_databases.sh README.md src/
[saber@rockylinux9 alphafold3]$
[saber@rockylinux9 alphafold3]$ docker build -t alphafold...
:
:
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID ...
alphafold3 latest 15d0b075bc01 ...
nvidia/cuda 11.8.0-runtime-ubuntu22.04 d8fb74ecc8b2 ...
[saber@rockylinux9 alphafold3]$
}}
docker imageの作成に成功しました.
***データベースの準備 [#uffa3404]
「fetch_databases.sh」が提供されている. 中身を読むと「sto...
#code(nonumber){{
[saber@rockylinux9 alphafold3]$ bash ./fetch_databases.sh...
:
(ティータイム)
:
Complete
[saber@rockylinux9 alphafold3]$
[saber@rockylinux9 alphafold3]$ ls -lh /Public/alphafold3
total 394G
-rw-r--r--. 1 1001 2001 17G Jun 1 16:06 bfd-first_non_c...
-rw-r--r--. 1 1001 2001 120G Jun 1 19:45 mgy_clusters_20...
drwxr-x---. 2 1001 2001 4.3M Oct 11 2024 mmcif_files
-rw-r--r--. 1 1001 2001 76G Jun 1 18:14 nt_rna_2023_02_...
-rw-r--r--. 1 1001 2001 223M Jun 1 14:44 pdb_seqres_2022...
-rw-r--r--. 1 1001 2001 218M Jun 1 14:45 rfam_14_9_clust...
-rw-r--r--. 1 1001 2001 13G Jun 1 15:31 rnacentral_acti...
-rw-r--r--. 1 1001 2001 102G Jun 1 19:27 uniprot_all_202...
-rw-r--r--. 1 1001 2001 67G Jun 1 18:31 uniref90_2022_0...
[saber@rockylinux9 alphafold3]$
}}
***モデルパラメータの取得 [#daac8f1d]
下記申請フォームに記載して取得します
[[https://forms.gle/svvpY4u2jsHEwWYS6>+https://forms.gle/...
Google DeepMind 側の裁量があるようです. &size(10){申請し...
「$HOME/af3-models」にでも配置しておきます
***実行 [#c4b7f1ba]
&color(red){未実施};
#code(nonumber){{
mkdir $HOME/af_input $HOME/af_output
docker run -it \
--volume $HOME/af_input:/root/af_input \
--volume $HOME/af_output:/root/af_output \
--volume $HOME/af3-models:/root/models \
--volume /Public/alphafold3:/root/public_databases \
--gpus all \
alphafold3 \
python run_alphafold.py \
--json_path=/root/af_input/fold_input.json \
--model_dir=/root/models \
--output_dir=/root/af_output
}}
***Singularityへ [#oa96eb9e]
作ったdokcerイメージを Singularity image file に変換してd...
singularityのインストール
#code(nonumber){{
[root@rockylinux9 ~]# dnf install epel-release -y
[root@rockylinux9 ~]# dnf install singularity-ce -y
}}
#code(nonumber){{
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREATED STATUS PO...
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
alphafold3 latest dea05120089d 7 minutes ago 6.7...
[saber@rockylinux9 alphafold3]$ docker run -d -p 5000:500...
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
alphafold3 latest dea05120089d 8 minutes ago 6.7...
registry 2 26b2eb03618e 20 months ago 25....
[saber@rockylinux9 alphafold3]$ docker ps
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 34 s...
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 47 s...
[saber@rockylinux9 alphafold3]$
[saber@rockylinux9 alphafold3]$ docker tag alphafold3 loc...
[saber@rockylinux9 alphafold3]$ docker ps -a (「docker...
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 3 mi...
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREA...
alphafold3 latest dea05120089d 11 m...
localhost:5000/alphafold3 latest dea05120089d 11 m...
registry 2 26b2eb03618e 20 m...
[saber@rockylinux9 alphafold3]$ docker push localhost:500...
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 10 m...
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREA...
alphafold3 latest dea05120089d 5 ho...
localhost:5000/alphafold3 latest dea05120089d 5 ho...
registry 2 26b2eb03618e 20 m...
[saber@rockylinux9 alphafold3]$
(変換)
[saber@rockylinux9 alphafold3]$ SINGULARITY_NOHTTPS=1 sin...
:
INFO: Extracting OCI image...
INFO: Inserting Singularity configuration...
INFO: Creating SIF file...
INFO: Build complete: alphafold3.sif
[saber@rockylinux9 alphafold3]$ ls -lh alphafold3.sif
-rwxr-xr-x. 1 saber saber 2.8G Jun 1 15:17 alphafold3.sif
[saber@rockylinux9 alphafold3]$
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREA...
alphafold3 latest dea05120089d 5 ho...
localhost:5000/alphafold3 latest dea05120089d 5 ho...
registry 2 26b2eb03618e 20 m...
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 16 m...
[saber@rockylinux9 alphafold3]$
}}
後始末
#code(nonumber){{
[saber@rockylinux9 alphafold3]$ docker stop registry
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 17 m...
[saber@rockylinux9 alphafold3]$ docker rm registry
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREATED STATUS PO...
[saber@rockylinux9 alphafold3]$
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREA...
alphafold3 latest dea05120089d 5 ho...
localhost:5000/alphafold3 latest dea05120089d 5 ho...
registry 2 26b2eb03618e 20 m...
[saber@rockylinux9 alphafold3]$ docker rmi localhost:5000...
[saber@rockylinux9 alphafold3]$ docker rmi dea05120089d
}}
***job [#f5333338]
配列構造データベースが「/Public/alphafold3」にあって
取得したmodelファイルが「/Public/af3-model」にあるとして
slurmな環境なら今いるディレクトリに「af_input」と「af_out...
「af_input/fold_input.json」のインプットファイルを作って
下記batchを動かす
#code(nonumber){{
#!/bin/bash
#SBATCH -J af3-test
#SBATCH -o %j.out
#SBATCH -e %j.err
#SBATCH -p workq
#SBATCH -n 8
#SBATCH --gres=gpu:1
cd $SLURM_SUBMIT_DIR
MODEL_DIR=/Public/af3-model
DB_DIR=/Public/alphafold3
singularity exec \
--nv \
--bind $SLURM_SUBMIT_DIR/af_input:/root/af_input \
--bind $SLURM_SUBMIT_DIR/af_output:/root/af_output \
--bind $MODEL_DIR:/root/models \
--bind $DB_DIR:/root/public_databases \
/apps/alphafold3.sif \
python /app/alphafold/run_alphafold.py \
--json_path=/root/af_input/fold_input.json \
--model_dir=/root/models \
--db_dir=/root/public_databases \
--output_dir=/root/af_output
}}
終了行:
本家様 [[https://github.com/google-deepmind/alphafold3>+h...
12月にリリースかなと思ったのですが11月上旬にリリース.
ここでは rockylinux9での構築をしてみます.
AlphaFold2と同じようにdockerコンテナで実行できるようにす...
まずは下記記載のドキュメント通りに作ってみます
[[https://github.com/google-deepmind/alphafold3/blob/main...
Toolkit for alphafold3 input and output files [[https://g...
***対象マシン [#jf44ec1a]
インストール対象マシンは下記の感じです
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.5 (Blue Onyx)
[root@rockylinux9 ~]# getenforce
Enforcing
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 570.153.0...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]# nvidia-smi -L
GPU 0: NVIDIA GeForce GTX 1070 (UUID: GPU-a49de51b-de1e-5...
[root@rockylinux9 ~]# ls -l /usr/local/cuda
ls: cannot access '/usr/local/cuda': No such file or dire...
[root@rockylinux9 ~]#
}}
***docker構築 [#eb777c91]
#code(nonumber){{
[root@rockylinux9 ~]# dnf -y install dnf-plugins-core
[root@rockylinux9 ~]# dnf config-manager --add-repo https...
Adding repo from: https://download.docker.com/linux/rhel/...
[root@rockylinux9 ~]# ls /etc/yum.repos.d/
docker-ce.repo rocky-addons.repo rocky-devel.repo rock...
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# sed -i s'/enabled=1/enabled=0/' /et...
}}
使用するリポジトリは「docker-ce-stable」となる. 詳細は「d...
#code(nonumber){{
[root@rockylinux9 ~]# dnf --enablerepo=docker-ce-stable i...
docker-ce, docker-ce-cli, docker-buildx-plugin, docker-ce...
っで起動
[root@rockylinux9 ~]# systemctl enable docker --now
}}
「systemctl status docker」の中身を見ると「/usr/bin/docke...
別の場所に変えたいなら「--data-root」を使って変更します. ...
次にNVIDIA Container Toolkitをインストールします
#code(nonumber){{
[root@rockylinux9 ~]# curl -s -L https://nvidia.github.io...
[root@rockylinux9 ~]# sed -i s'/enabled=1/enabled=0/' /et...
}}
追加したリポジトリ「nvidia-container-toolkit」の詳細は「d...
っでインストールします
#code(nonumber){{
[root@rockylinux9 ~]# dnf --enablerepo=nvidia-container-t...
nvidia-container-toolkit, libnvidia-container-tools, libn...
dockerを再起動させて有効にします
[root@rockylinux9 ~]# systemctl restart docker
}}
っでテスト
#code(nonumber){{
[root@rockylinux9 ~]# nvidia-container-cli info
NVRM version: 570.153.02
CUDA version: 12.8
Device Index: 0
Device Minor: 0
Model: NVIDIA GeForce GTX 1070
Brand: GeForce
GPU UUID: GPU-a49de51b-de1e-52f3-1e3f-ce704e159713
Bus Location: 00000000:06:10.0
Architecture: 6.1
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# docker run --gpus all --rm nvidia/c...
:
GPU 0: NVIDIA GeForce GTX 1070 (UUID: GPU-a49de51b-de1e-5...
[root@rockylinux9 ~]#
}}
これでdockerの構築が完了.
そのままでは一般ユーザがdockerを使えない. 一般ユーザでdoc...
利用ユーザが「dockerd-rootless-setuptool.sh --skip-iptabl...
#code(nonumber){{
[saber@rockylinux9 ~]$ dockerd-rootless-setuptool.sh --sk...
:
[INFO] Installed docker.service successfully.
[INFO] To control docker.service, run: `systemctl --user ...
[INFO] To run docker.service on system startup, run: `sud...
:
[INFO] Some applications may require the following enviro...
export DOCKER_HOST=unix:///run/user/1000/docker.sock
:
[saber@rockylinux9 ~]$ ps -ef |grep docker
(この段階でユーザアカウントのdockerが動いてます. ログアウ...
}}
その後にrootで「/etc/nvidia-container-runtime/config.toml...
&size(10){systemのbootに合わせて、ログインの有無にかかわ...
っで本題へ.
***AlphaFold3構築 [#ldb5f755]
せっかくdockerをrootlessで作ったので一般ユーザでalphafold...
#code(nonumber){{
[saber@rockylinux9 ~]$ git clone https://github.com/googl...
[saber@rockylinux9 ~]$ cd alphafold3/
[saber@rockylinux9 alphafold3]$ git log -1
commit 64723739f52944274485118cab935d53d66b5aec (HEAD -> ...
Author: Augustin Zidek <augustinzidek@google.com>
Date: Fri May 30 09:23:19 2025 -0700
Update to Ubuntu 24.04 / CUDA 12.6.3 base image and u...
PiperOrigin-RevId: 765219906
Change-Id: I271f442012ee30356ef316eda87abd231319a673
[saber@rockylinux9 alphafold3]$ ls -CF
CMakeLists.txt legal/ requirement...
dev-requirements.txt LICENSE run_alphafo...
docker/ OUTPUT_TERMS_OF_USE.md run_alphafo...
docs/ pyproject.toml run_alphafo...
fetch_databases.sh README.md src/
[saber@rockylinux9 alphafold3]$
[saber@rockylinux9 alphafold3]$ docker build -t alphafold...
:
:
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID ...
alphafold3 latest 15d0b075bc01 ...
nvidia/cuda 11.8.0-runtime-ubuntu22.04 d8fb74ecc8b2 ...
[saber@rockylinux9 alphafold3]$
}}
docker imageの作成に成功しました.
***データベースの準備 [#uffa3404]
「fetch_databases.sh」が提供されている. 中身を読むと「sto...
#code(nonumber){{
[saber@rockylinux9 alphafold3]$ bash ./fetch_databases.sh...
:
(ティータイム)
:
Complete
[saber@rockylinux9 alphafold3]$
[saber@rockylinux9 alphafold3]$ ls -lh /Public/alphafold3
total 394G
-rw-r--r--. 1 1001 2001 17G Jun 1 16:06 bfd-first_non_c...
-rw-r--r--. 1 1001 2001 120G Jun 1 19:45 mgy_clusters_20...
drwxr-x---. 2 1001 2001 4.3M Oct 11 2024 mmcif_files
-rw-r--r--. 1 1001 2001 76G Jun 1 18:14 nt_rna_2023_02_...
-rw-r--r--. 1 1001 2001 223M Jun 1 14:44 pdb_seqres_2022...
-rw-r--r--. 1 1001 2001 218M Jun 1 14:45 rfam_14_9_clust...
-rw-r--r--. 1 1001 2001 13G Jun 1 15:31 rnacentral_acti...
-rw-r--r--. 1 1001 2001 102G Jun 1 19:27 uniprot_all_202...
-rw-r--r--. 1 1001 2001 67G Jun 1 18:31 uniref90_2022_0...
[saber@rockylinux9 alphafold3]$
}}
***モデルパラメータの取得 [#daac8f1d]
下記申請フォームに記載して取得します
[[https://forms.gle/svvpY4u2jsHEwWYS6>+https://forms.gle/...
Google DeepMind 側の裁量があるようです. &size(10){申請し...
「$HOME/af3-models」にでも配置しておきます
***実行 [#c4b7f1ba]
&color(red){未実施};
#code(nonumber){{
mkdir $HOME/af_input $HOME/af_output
docker run -it \
--volume $HOME/af_input:/root/af_input \
--volume $HOME/af_output:/root/af_output \
--volume $HOME/af3-models:/root/models \
--volume /Public/alphafold3:/root/public_databases \
--gpus all \
alphafold3 \
python run_alphafold.py \
--json_path=/root/af_input/fold_input.json \
--model_dir=/root/models \
--output_dir=/root/af_output
}}
***Singularityへ [#oa96eb9e]
作ったdokcerイメージを Singularity image file に変換してd...
singularityのインストール
#code(nonumber){{
[root@rockylinux9 ~]# dnf install epel-release -y
[root@rockylinux9 ~]# dnf install singularity-ce -y
}}
#code(nonumber){{
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREATED STATUS PO...
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
alphafold3 latest dea05120089d 7 minutes ago 6.7...
[saber@rockylinux9 alphafold3]$ docker run -d -p 5000:500...
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREATED SIZE
alphafold3 latest dea05120089d 8 minutes ago 6.7...
registry 2 26b2eb03618e 20 months ago 25....
[saber@rockylinux9 alphafold3]$ docker ps
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 34 s...
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 47 s...
[saber@rockylinux9 alphafold3]$
[saber@rockylinux9 alphafold3]$ docker tag alphafold3 loc...
[saber@rockylinux9 alphafold3]$ docker ps -a (「docker...
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 3 mi...
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREA...
alphafold3 latest dea05120089d 11 m...
localhost:5000/alphafold3 latest dea05120089d 11 m...
registry 2 26b2eb03618e 20 m...
[saber@rockylinux9 alphafold3]$ docker push localhost:500...
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 10 m...
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREA...
alphafold3 latest dea05120089d 5 ho...
localhost:5000/alphafold3 latest dea05120089d 5 ho...
registry 2 26b2eb03618e 20 m...
[saber@rockylinux9 alphafold3]$
(変換)
[saber@rockylinux9 alphafold3]$ SINGULARITY_NOHTTPS=1 sin...
:
INFO: Extracting OCI image...
INFO: Inserting Singularity configuration...
INFO: Creating SIF file...
INFO: Build complete: alphafold3.sif
[saber@rockylinux9 alphafold3]$ ls -lh alphafold3.sif
-rwxr-xr-x. 1 saber saber 2.8G Jun 1 15:17 alphafold3.sif
[saber@rockylinux9 alphafold3]$
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREA...
alphafold3 latest dea05120089d 5 ho...
localhost:5000/alphafold3 latest dea05120089d 5 ho...
registry 2 26b2eb03618e 20 m...
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 16 m...
[saber@rockylinux9 alphafold3]$
}}
後始末
#code(nonumber){{
[saber@rockylinux9 alphafold3]$ docker stop registry
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREA...
9d6e05c348fb registry:2 "/entrypoint.sh /etc…" 17 m...
[saber@rockylinux9 alphafold3]$ docker rm registry
[saber@rockylinux9 alphafold3]$ docker ps -a
CONTAINER ID IMAGE COMMAND CREATED STATUS PO...
[saber@rockylinux9 alphafold3]$
[saber@rockylinux9 alphafold3]$ docker images
REPOSITORY TAG IMAGE ID CREA...
alphafold3 latest dea05120089d 5 ho...
localhost:5000/alphafold3 latest dea05120089d 5 ho...
registry 2 26b2eb03618e 20 m...
[saber@rockylinux9 alphafold3]$ docker rmi localhost:5000...
[saber@rockylinux9 alphafold3]$ docker rmi dea05120089d
}}
***job [#f5333338]
配列構造データベースが「/Public/alphafold3」にあって
取得したmodelファイルが「/Public/af3-model」にあるとして
slurmな環境なら今いるディレクトリに「af_input」と「af_out...
「af_input/fold_input.json」のインプットファイルを作って
下記batchを動かす
#code(nonumber){{
#!/bin/bash
#SBATCH -J af3-test
#SBATCH -o %j.out
#SBATCH -e %j.err
#SBATCH -p workq
#SBATCH -n 8
#SBATCH --gres=gpu:1
cd $SLURM_SUBMIT_DIR
MODEL_DIR=/Public/af3-model
DB_DIR=/Public/alphafold3
singularity exec \
--nv \
--bind $SLURM_SUBMIT_DIR/af_input:/root/af_input \
--bind $SLURM_SUBMIT_DIR/af_output:/root/af_output \
--bind $MODEL_DIR:/root/models \
--bind $DB_DIR:/root/public_databases \
/apps/alphafold3.sif \
python /app/alphafold/run_alphafold.py \
--json_path=/root/af_input/fold_input.json \
--model_dir=/root/models \
--db_dir=/root/public_databases \
--output_dir=/root/af_output
}}
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