CryoSamba

[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.5 (Blue Onyx)
 
 
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module  570.133.07  Fri Mar 14 13:12:07 UTC 2025
GCC version:  gcc version 11.5.0 20240719 (Red Hat 11.5.0-2) (GCC)
 
 
[root@rockylinux9 ~]# /usr/local/cuda/bin/nvcc --version
-bash: /usr/local/cuda/bin/nvcc: No such file or directory
 
[root@rockylinux9 ~]#

source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profile.d/conda.sh

git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2024.10-1
 
source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profile.d/conda.sh
conda update conda

[root@rockylinux9 ~]# cd /apps/
[root@rockylinux9 apps]# git clone https://github.com/kirchhausenlab/Cryosamba.git CryoSamba
[root@rockylinux9 apps]# cd CryoSamba/
[root@rockylinux9 CryoSamba]# ls
advanced_instructions.md  automate  Dockerfile       inference.py  LICENSE            README.md         setup.py  train.py
assets                    core      environment.yml  __init__.py   logging_config.py  run_cryosamba.py  tests
[root@rockylinux9 CryoSamba]#

[root@rockylinux9 CryoSamba]# conda create --name cryosamba python=3.11
 
[root@rockylinux9 CryoSamba]# conda activate cryosamba
(cryosamba) [root@rockylinux9 CryoSamba]# pip install torch==2.3.1 torchvision==0.18.1 torchaudio==2.3.1 --index-url https://download.pytorch.org/whl/cu118
 
(cryosamba) [root@rockylinux9 CryoSamba]# pip install tifffile mrcfile easydict loguru tensorboard cupy-cuda11x streamlit typer
 
(cryosamba) [root@rockylinux9 CryoSamba]# conda deactivate
[root@rockylinux9 CryoSamba]#

#%Module
set root   /apps/pyenv/versions/anaconda3-2024.10-1/envs/cryosamba
prepend-path PATH $root/bin

[saber@rockylinux9 ~]$ module use /apps/modulefiles
 
[saber@rockylinux9 ~]$ module load CryoSamba
 
[saber@rockylinux9 ~]$ python /apps/CryoSamba/run_cryosamba.py
 
(略
 
Welcome to CryoSamba v1.0
by Kirchhausen Lab (https://kirchhausen.hms.harvard.edu/)
 
Please read the instructions carefully. If you experience any issues reach out to
Jose Costa-Filho @ joseinacio@tklab.hms.harvard.edu
Arkash Jain @ arkash@tklab.hms.harvard.edu
We appreciate all feedback!
 
*** MAIN MENU ***
 
|1| Manage experiments (start here!)
|2| Run training
|3| Run inference
|4| Exit
 
Choose an option [1/2/3/4]:

[saber@rockylinux9 ~]$ module use /apps/modulefiles
 
[saber@rockylinux9 ~]$ module load CryoSamba
 
[saber@rockylinux9 ~]$ python /apps/CryoSamba/run_cryosamba.py
 
[saber@rockylinux9 ~]$ streamlit run /apps/CryoSamba/automate/main.py
 
  You can now view your Streamlit app in your browser.
 
  Local URL: http://localhost:8501
  Network URL: http://192.168.0.160:8501
  External URL: http://153.232.45.169:8501