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#author("2025-04-12T19:16:25+00:00","default:sysosa","sysosa") #author("2025-04-13T12:22:38+00:00;2025-04-12T19:16:25+00:00","default:sysosa","sysosa") 本家様 [[https://github.com/MPI-Dortmund/tomotwin-cryoet>+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>+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 #code(nonumber){{ 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 #code(nonumber){{ 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 #code(nonumber){{ [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 #code(nonumber){{ [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 #code(nonumber){{ [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 &size(10){内容的には crYOLO の napari_boxmanager と同じ}; #code(nonumber){{ [root@rockylinux9 ~]# source activate tomotwin [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 #code(nonumber){{ [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 }} ***environment-modules [#i50917fb] #code(nonumber){{ [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 ~]# }} ***memo [#gefdc8ee] インストールドキュメントには #code(nonumber){{ 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 #code(yaml,nonumber){{ 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
