Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in / Register
Toggle navigation
Menu
Open sidebar
ModelZoo
Uni-Fold_pytorch
Commits
7f269210
Commit
7f269210
authored
Oct 30, 2024
by
yuhai
Browse files
Update README.md
parent
67decff0
Changes
1
Hide whitespace changes
Inline
Side-by-side
Showing
1 changed file
with
21 additions
and
11 deletions
+21
-11
README.md
README.md
+21
-11
No files found.
README.md
View file @
7f269210
...
...
@@ -18,22 +18,30 @@
提供
[
光源
](
https://www.sourcefind.cn/#/service-details
)
拉取的训练的docker镜像:
```
docker pull image.sourcefind.cn:5000/dcu/admin/base/custom:unifold-latest
docker run -it -v /path/your_code_data/:/path/your_code_data/ --shm-size=32G --privileged=true --device=/dev/kfd --device=/dev/dri/ --group-add video --name docker_name imageID bash
等待上传镜像
cd /root/Uni-Fold-main
```
docker run -it --network=host -v <unifold代码路径>:<容器内路径> --shm-size=32G --privileged=true --device=/dev/kfd --device=/dev/dri/ --group-add video -v /opt/hyhal:/opt/hyhal:ro -v /opt/dtk-24.04.2-runtime/:/opt/dtk/:ro --name <镜像名称> <上面获得的镜像ID> bash
安装requirement.txt中的工具,镜像中已经安装好,加载方式
cd /root/Uni-Fold
//进行homosearch需要挂载AF2数据集至容器内`/alphafold`。若只为测试,本镜像无需挂载AF2数据集
//因为本镜像在昆山K100AI节点测试,dtk24.04.2不能正常使用,测试时挂载dtk-24.04.2-runtime至/opt/dtk。若确认dtk能正常使用可以选择不挂载,并修改/root目录下的///env.sh及Uni-Fold目录中的/opt/dtk为/opt/dtk-24.04.2
```
export PATH=/root/software/hmmer/bin${PATH:+:${PATH}}
export PATH=/root/software/hh-suite-master/bin${PATH:+:${PATH}}
镜像版本依赖:
*
DTK驱动:dtk24.04.2
*
Pytorch: 2.1.0
*
unifold: 2.2.0
*
unicore: 0.0.1
*
python: python3.10
export PATH=/root/software/kalign/bin${PATH:+:${PATH}}
测试目录:
`/root/Uni-Fold`
安装requirement.txt中的工具,镜像中已经安装好,加载方式
export LD_LIBRARY_PATH=/root/software/hh-suite-master/lib${LD_LIBRARY_PATH:+:${LD_LIBRARY_PATH}}
```
source /root/env.sh
```
## 数据集
...
...
@@ -91,8 +99,6 @@ bash scripts/download/download_all_data.sh /path/to/database/directory
```
cd Uni-Core-main
export CUDA_HOME=/opt/dtk-22.04.2
python3 setup.py install
```
...
...
@@ -102,6 +108,10 @@ pip install -e .
```
### 多卡测试
如果没有挂载AF2数据集,会出现多体、单体测试脚本运行homosearch中报错
`ValueError: Could not find hmmsearch database /alphafold/pdb_seqres/pdb_seqres.txt`
并停止搜索、直接进行推理的情况,由于单本镜像内置了部分序列的搜索结果,因此可以无视此报错进行正常推理。
内置搜索结果的目录见
`/root/Uni-Fold/data`
,其中有H1036、H1072、T1024的搜索结果,若要选择其他序列进行推理,请挂载AF2数据集并进行homosearch(非常耗时)。
#### 多聚体参考脚本,需要根据实际情况修改路径配置
```
sh run_multimer.sh
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment