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本家様 https://github.com/MPI-Dortmund/tomotwin-cryoet
Particle picking in Tomograms using triplet networks and metric learning
ここにインストール方法が記載されている
https://github.com/MPI-Dortmund/tomotwin-cryoet/blob/main/docs/installation.rst
読むとcondaの代わりにmambaを使ってねとあるが、パラレルでパッケージをダウンロードしてインストールは現行のcondaでも機能しているのでcondaのままでいいかなと..
っでconda環境を作ります. ここでは pyenvの上にanaconda3を敷いてcondaを使ってましてpyenv/anaconda環境が用意されてないなら
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
pyenv global anaconda3-2024.10-1
source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profile.d/conda.shとして環境を作ります. 既に環境があるなら
source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profile.d/conda.shとPATHの定義を行います.
っでモノを作ります
[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 ~]# nvidia-smi -L
GPU 0: NVIDIA GeForce GTX 1070 (UUID: GPU-a49de51b-de1e-52f3-1e3f-ce704e159713)
[root@rockylinux9 ~]#環境はこんな感じで nvidia ドライバー装備です
っで
[root@rockylinux9 ~]# conda env create -n tomotwin -f https://raw.githubusercontent.com/MPI-Dortmund/tomotwin-cryoet/main/conda_env_tomotwin.yml
[root@rockylinux9 ~]# conda activate tomotwin
(tomotwin) [root@rockylinux9 ~]# pip install tomotwin-cryoet
(tomotwin) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]# conda env create -n napari-tomotwin -f https://raw.githubusercontent.com/MPI-Dortmund/napari-tomotwin/main/conda_env.yml
[root@rockylinux9 ~]# conda activate napari-tomotwin
(napari-tomotwin) [root@rockylinux9 ~]# pip install napari-tomotwin
(napari-tomotwin) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#ここまでで「tomotwin」と「napari-tomotwin」の実行環境が用意されました
[root@rockylinux9 src]# conda env list
# conda environments:
#
base /apps/pyenv/versions/anaconda3-2024.10-1
napari-tomotwin /apps/pyenv/versions/anaconda3-2024.10-1/envs/napari-tomotwin
tomotwin /apps/pyenv/versions/anaconda3-2024.10-1/envs/tomotwin
[root@rockylinux9 src]#っで「tomotwin」実行環境から「napari-tomotwin」のnapari_boxmanagerを引けるようにlinkを貼ります
内容的には crYOLO の napari_boxmanager と同じ
[root@rockylinux9 ~]# conda activate tomotwin
(tomotwin) [root@rockylinux9 ~]# tomotwin_dir=$(realpath $(dirname $(which tomotwin_embed.py)))
(tomotwin) [root@rockylinux9 ~]# echo $tomotwin_dir
/apps/pyenv/versions/anaconda3-2024.10-1/envs/tomotwin/bin
(tomotwin) [root@rockylinux9 ~]# napari_link_file=${tomotwin_dir}/napari_boxmanager
(tomotwin) [root@rockylinux9 ~]# echo $napari_link_file
/apps/pyenv/versions/anaconda3-2024.10-1/envs/tomotwin/bin/napari_boxmanager
(tomotwin) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# conda activate napari-tomotwin
(napari-tomotwin) [root@rockylinux9 ~]# echo -e "#\!/usr/bin/bash\nexport NAPARI_EXE=$(which napari)\nnapari_exe='$(which napari_boxmanager)'\n\${napari_exe} \"\${@}\""> ${napari_link_file}
(napari-tomotwin) [root@rockylinux9 ~]# cat $napari_link_file
#\!/usr/bin/bash
export NAPARI_EXE=/apps/pyenv/versions/anaconda3-2023.03/envs/napari-tomotwin/bin/napari
napari_exe='/apps/pyenv/versions/anaconda3-2023.03/envs/napari-tomotwin/bin/napari_boxmanager'
${napari_exe} "${@}"
(napari-tomotwin) [root@rockylinux9 ~]# ln -rs $(which napari) ${tomotwin_dir}
(napari-tomotwin) [root@rockylinux9 ~]# chmod +x ${napari_link_file}
(napari-tomotwin) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#あと
[root@rockylinux9 ~]# mkdir /apps/tomotwin-cryoet
[root@rockylinux9 ~]# cd /apps/tomotwin-cryoet
[root@rockylinux9 tomotwin-cryoet]# wget https://ftp.gwdg.de/pub/misc/sphire/TomoTwin/models/tomotwin_model_p120_052022_loss.pth[root@rockylinux9 ~]# vi /apps/modulefiles/tomotwin
#%Module1.0
set root /apps/pyenv/versions/anaconda3-2024.10-1/envs/tomotwin
prepend-path PATH $root/bin
[root@rockylinux9 ~]#インストールドキュメントには
mamba create -n tomotwin -c pytorch -c rapidsai -c nvidia -c conda-forge python=3.10 pytorch==1.13.1 torchvision pandas scipy numpy \
matplotlib pytables cuML=23.04 cudatoolkit=11.8 'protobuf>3.20' tensorboard optuna mysql-connector-pythonとあるのだが、gitで取得したものには
name: tomotwin
channels:
- conda-forge
- pytorch
- rapidsai
- nvidia
- defaults
dependencies:
- pytorch==1.13.1
- torchvision
- pandas[version='<2']
- scipy
- numpy
- matplotlib
- pytables
- cuml=23.04
- cudatoolkit=11.8
- protobuf[version='>3.20']
- tensorboard
- optuna
- mysql-connector-pythonとある
