本家様 https://github.com/RosettaCommons/RFdiffusion

[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.1 (Blue Onyx)
 
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module  525.105.17  Tue Mar 28 18:02:59 UTC 2023
GCC version:  gcc version 11.3.1 20220421 (Red Hat 11.3.1-2) (GCC)
 
[root@rockylinux9 ~]# nvidia-smi -L
GPU 0: NVIDIA RTX A2000 (UUID: GPU-23cc3ee7-31d3-a068-2f61-5aa00052d084)
 
[root@rockylinux9 ~]# ls -l /usr/local/cuda
ls: cannot access '/usr/local/cuda': No such file or directory
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# cd /apps/
[root@rockylinux9 apps]# git clone https://github.com/RosettaCommons/RFdiffusion.git
[root@rockylinux9 apps]# cd RFdiffusion/
[root@rockylinux9 RFdiffusion]# ls -lF
total 64
drwxr-xr-x. 3 root root    23 Apr  5 03:20 config/
drwxr-xr-x. 3 root root    45 Apr  5 03:20 env/
drwxr-xr-x. 5 root root  4096 Apr  5 03:20 examples/
drwxr-xr-x. 2 root root    50 Apr  5 03:20 helper_scripts/
drwxr-xr-x. 2 root root  4096 Apr  5 03:20 img/
-rw-r--r--. 1 root root  1631 Apr  5 03:20 LICENSE
-rw-r--r--. 1 root root 42734 Apr  5 03:20 README.md
drwxr-xr-x. 4 root root  4096 Apr  5 03:20 rfdiffusion/
drwxr-xr-x. 2 root root    30 Apr  5 03:20 scripts/
-rw-r--r--. 1 root root   394 Apr  5 03:20 setup.py
 
[root@rockylinux9 RFdiffusion]# mkdir models && cd models
[root@rockylinux9 models]#

modelsフォルダの中で下記を実行

wget http://files.ipd.uw.edu/pub/RFdiffusion/6f5902ac237024bdd0c176cb93063dc4/Base_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/e29311f6f1bf1af907f9ef9f44b8328b/Complex_base_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/60f09a193fb5e5ccdc4980417708dbab/Complex_Fold_base_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/74f51cfb8b440f50d70878e05361d8f0/InpaintSeq_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/76d00716416567174cdb7ca96e208296/InpaintSeq_Fold_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/5532d2e1f3a4738decd58b19d633b3c3/ActiveSite_ckpt.pt
wget http://files.ipd.uw.edu/pub/RFdiffusion/12fc204edeae5b57713c5ad7dcb97d39/Base_epoch8_ckpt.pt
 
wget http://files.ipd.uw.edu/pub/RFdiffusion/f572d396fae9206628714fb2ce00f72e/Complex_beta_ckpt.pt

っで

[root@rockylinux9 models]# ls -l
total 3778064
-rw-r--r--. 1 root root 483616107 Mar 30 10:31 ActiveSite_ckpt.pt
-rw-r--r--. 1 root root 483616107 Mar 30 10:31 Base_ckpt.pt
-rw-r--r--. 1 root root 483616427 Mar 30 10:30 Base_epoch8_ckpt.pt
-rw-r--r--. 1 root root 483619179 Mar 30 10:30 Complex_base_ckpt.pt
-rw-r--r--. 1 root root 483380617 Mar 30 12:36 Complex_beta_ckpt.pt
-rw-r--r--. 1 root root 483626923 Mar 30 10:30 Complex_Fold_base_ckpt.pt
-rw-r--r--. 1 root root 483619243 Mar 30 10:30 InpaintSeq_ckpt.pt
-rw-r--r--. 1 root root 483626987 Mar 30 10:30 InpaintSeq_Fold_ckpt.pt
[root@rockylinux9 models]#

次にpyenv/anaconda環境でconda実行環境を作ります
まずはそのpyenv/anaconda環境の準備

git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2023.03
pyenv global anaconda3-2023.03
export PATH=$PYENV_ROOT/versions/anaconda3-2023.03/bin/:$PATH
conda update conda
 
 
(すでにpyenv/anaconda環境があるなら)
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
export PATH=$PYENV_ROOT/versions/anaconda3-2023.03/bin/:$PATH

っで

[root@rockylinux9 ~]# cd /apps/RFdiffusion/
[root@rockylinux9 RFdiffusion]# cat env/SE3nv.yml
name: SE3nv
channels:
  - defaults
  - conda-forge
  - pytorch
  - dglteam
  - nvidia
dependencies:
  - python=3.9
  - pytorch=1.9
  - torchaudio
  - torchvision
  - cudatoolkit=11.1
  - dgl-cuda11.1
  - icecream
  - pip
  - pip:
    - hydra-core
    - pyrsistent
 
[root@rockylinux9 RFdiffusion]# conda env create -f env/SE3nv.yml
 
[root@rockylinux9 RFdiffusion]# source activate SE3nv
(SE3nv) [root@rockylinux9 RFdiffusion]#
(SE3nv) [root@rockylinux9 RFdiffusion]# cd env/SE3Transformer
(SE3nv) [root@rockylinux9 SE3Transformer]# ls -l
total 56
-rw-r--r--. 1 root root  2276 Apr  5 03:20 Dockerfile
drwxr-xr-x. 2 root root    33 Apr  5 03:20 images
-rw-r--r--. 1 root root  1071 Apr  5 03:20 LICENSE
-rw-r--r--. 1 root root   280 Apr  5 03:20 NOTICE
-rw-r--r--. 1 root root 35388 Apr  5 03:20 README.md
-rw-r--r--. 1 root root   110 Apr  5 03:20 requirements.txt
drwxr-xr-x. 2 root root   158 Apr  5 03:20 scripts
drwxr-xr-x. 5 root root    73 Apr  5 03:20 se3_transformer
-rw-r--r--. 1 root root   307 Apr  5 03:20 setup.py
drwxr-xr-x. 2 root root    69 Apr  5 03:20 tests
 
(SE3nv) [root@rockylinux9 SE3Transformer]# cat requirements.txt
e3nn==0.3.3
wandb==0.12.0
pynvml==11.0.0
git+https://github.com/NVIDIA/dllogger#egg=dllogger
decorator==5.1.0
 
(SE3nv) [root@rockylinux9 SE3Transformer]#
(SE3nv) [root@rockylinux9 SE3Transformer]# pip install --no-cache-dir -r requirements.txt
 
(SE3nv) [root@rockylinux9 SE3Transformer]# which python
/apps/pyenv/versions/anaconda3-2023.03/envs/SE3nv/bin/python
 
(SE3nv) [root@rockylinux9 SE3Transformer]# python setup.py install
 
(SE3nv) [root@rockylinux9 SE3Transformer]# cd ../..
(SE3nv) [root@rockylinux9 RFdiffusion]# pwd
/apps/RFdiffusion
 
(SE3nv) [root@rockylinux9 RFdiffusion]# 
(SE3nv) [root@rockylinux9 RFdiffusion]# pip install -e .
 
[追加]
(SE3nv) [root@rockylinux9 RFdiffusion]# pip install torch==1.9.1+cu111 torchvision==0.10.1+cu111 torchaudio==0.9.1 -f https://download.pytorch.org/whl/torch_stable.html
 
 
(SE3nv) [root@rockylinux9 RFdiffusion]# conda deactivate
[root@rockylinux9 RFdiffusion]#

EnvironmentModules

[root@rockylinux9 ~]# vi /apps/modulefiles/RFdiffusion
#%Module
set          root /apps/pyenv/versions/anaconda3-2023.03/envs/SE3nv
prepend-path PATH $root/bin:/apps/RFdiffusion/scripts
 
[root@rockylinux9 ~]#

使ってみる

[saber@rockylinux9 ~]$ module use /apps/modulefiles/
[saber@rockylinux9 ~]$ module load RFdiffusion
 
[saber@rockylinux9 ~]$ mkdir -p test/RFdiffusion
[saber@rockylinux9 ~]$ cd test/RFdiffusion
[saber@rockylinux9 RFdiffusion]$
 
 
[saber@rockylinux9 RFdiffusion]$ ls -CF /apps/RFdiffusion/examples
design_cyclic_oligos.sh*                design_nickel.sh*                    design_tetrahedral_oligos.sh*  target_folds/
design_dihedral_oligos.sh*              design_partialdiffusion.sh*          design_timbarrel.sh*           tim_barrel_scaffold/
design_enzyme.sh*                       design_partialdiffusion_withseq.sh*  design_unconditional.sh*
design_motifscaffolding_inpaintseq.sh*  design_ppi_scaffolded.sh*            input_pdbs/
design_motifscaffolding.sh*             design_ppi.sh*                       ppi_scaffolds_subset.tar.gz
 
[saber@rockylinux9 RFdiffusion]$ cp  -r /apps/RFdiffusion/examples .
 
[saber@rockylinux9 RFdiffusion]$ ls -l
total 4
drwxr-xr-x. 5 saber saber 4096 Apr  5 03:50 examples
 
[saber@rockylinux9 RFdiffusion]$ tar xf examples/ppi_scaffolds_subset.tar.gz -C examples/
[saber@rockylinux9 RFdiffusion]$ ls -CF examples/
design_cyclic_oligos.sh*                design_nickel.sh*                    design_tetrahedral_oligos.sh*  ppi_scaffolds_subset.tar.gz
design_dihedral_oligos.sh*              design_partialdiffusion.sh*          design_timbarrel.sh*           target_folds/
design_enzyme.sh*                       design_partialdiffusion_withseq.sh*  design_unconditional.sh*       tim_barrel_scaffold/
design_motifscaffolding_inpaintseq.sh*  design_ppi_scaffolded.sh*            input_pdbs/
design_motifscaffolding.sh*             design_ppi.sh*                       ppi_scaffolds/
 
[saber@rockylinux9 RFdiffusion]$
 
[saber@rockylinux9 RFdiffusion]$ run_inference.py 'contigmap.contigs=[150-150]' inference.output_prefix=test_outputs/test inference.num_designs=10 inference.schedule_directory_path=./schedules
 :
 :
 :
[saber@rockylinux9 RFdiffusion]$ ls -l
total 8
drwxr-xr-x. 6 saber saber 4096 Apr  5 03:51 examples
drwxr-xr-x. 3 saber saber   24 Apr  5 03:57 outputs
drwxr-xr-x. 3 saber saber 4096 Apr  5 04:11 test_outputs
 
[saber@rockylinux9 RFdiffusion]$
[saber@rockylinux9 RFdiffusion]$ ls -l test_outputs/
total 764
-rw-r--r--. 1 saber saber 40200 Apr  5 04:01 test_0.pdb
-rw-r--r--. 1 saber saber 33308 Apr  5 04:01 test_0.trb
-rw-r--r--. 1 saber saber 40200 Apr  5 04:02 test_1.pdb
-rw-r--r--. 1 saber saber 33308 Apr  5 04:02 test_1.trb
 :
 :
-rw-r--r--. 1 saber saber 40200 Apr  5 04:11 test_9.pdb
-rw-r--r--. 1 saber saber 33308 Apr  5 04:11 test_9.trb
drwxr-xr-x. 2 saber saber  4096 Apr  5 04:11 traj
[saber@rockylinux9 RFdiffusion]$

inference.schedule_directory_path=./schedules」と自分が書ける場所にフォルダを用意できるように定義を加える必要あり.

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Last-modified: 2024-02-18 (日) 00:50:06