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]#

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

[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]#

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

[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 .
 
(SE3nv) [root@rockylinux9 RFdiffusion]# conda deactivate
[root@rockylinux9 RFdiffusion]#

[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 ~]#

[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]$