tomotwin-cryoet をテンプレートにして作成
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開始行:
本家様 [[https://github.com/MPI-Dortmund/tomotwin-cryoet>...
Particle picking in Tomograms using triplet networks and ...
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/ma...
読むとcondaの代わりにmambaを使ってねとあるが、パラレルで...
っでconda環境を作ります. ここでは pyenvの上にanaconda3を...
#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/profi...
}}
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/profi...
}}
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 570.133.0...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]# nvidia-smi -L
GPU 0: NVIDIA GeForce GTX 1070 (UUID: GPU-a49de51b-de1e-5...
[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 htt...
[root@rockylinux9 ~]# conda activate tomotwin
(tomotwin) [root@rockylinux9 ~]# pip install tomotwin-cry...
(tomotwin) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]# conda env create -n napari-tomotwin...
[root@rockylinux9 ~]# conda activate napari-tomotwin
(napari-tomotwin) [root@rockylinux9 ~]# pip install napar...
(napari-tomotwin) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
}}
ここまでで「tomotwin」と「napari-tomotwin」の実行環境が用...
#code(nonumber){{
[root@rockylinux9 src]# conda env list
# conda environments:
#
base /apps/pyenv/versions/anaconda3-2...
napari-tomotwin /apps/pyenv/versions/anaconda3-2...
tomotwin /apps/pyenv/versions/anaconda3-2...
[root@rockylinux9 src]#
}}
っで「tomotwin」実行環境から「napari-tomotwin」のnapari_b...
&size(10){内容的には crYOLO の napari_boxmanager と同じ};
#code(nonumber){{
[root@rockylinux9 ~]# conda activate tomotwin
(tomotwin) [root@rockylinux9 ~]# tomotwin_dir=$(realpath ...
(tomotwin) [root@rockylinux9 ~]# echo $tomotwin_dir
/apps/pyenv/versions/anaconda3-2024.10-1/envs/tomotwin/bin
(tomotwin) [root@rockylinux9 ~]# napari_link_file=${tomot...
(tomotwin) [root@rockylinux9 ~]# echo $napari_link_file
/apps/pyenv/versions/anaconda3-2024.10-1/envs/tomotwin/bi...
(tomotwin) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# conda activate napari-tomotwin
(napari-tomotwin) [root@rockylinux9 ~]# echo -e "#\!/usr/...
(napari-tomotwin) [root@rockylinux9 ~]# cat $napari_link_...
#\!/usr/bin/bash
export NAPARI_EXE=/apps/pyenv/versions/anaconda3-2023.03/...
napari_exe='/apps/pyenv/versions/anaconda3-2023.03/envs/n...
${napari_exe} "${@}"
(napari-tomotwin) [root@rockylinux9 ~]# ln -rs $(which na...
(napari-tomotwin) [root@rockylinux9 ~]# chmod +x ${napari...
(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...
}}
***environment-modules [#i50917fb]
#code(nonumber){{
[root@rockylinux9 ~]# vi /apps/modulefiles/tomotwin
#%Module1.0
set root /apps/pyenv/versions/anaconda3-2024.10-...
prepend-path PATH $root/bin
[root@rockylinux9 ~]#
}}
***memo [#gefdc8ee]
インストールドキュメントには
#code(nonumber){{
mamba create -n tomotwin -c pytorch -c rapidsai -c nvidia...
matplotlib pytables cuML=23.04 cudatoolkit=11.8 'protob...
}}
とあるのだが、gitで取得したものには
#code(yaml,nonumber){{
name: tomotwin
channels:
- conda-forge
- pytorch
- rapidsai
- nvidia
- defaults
dependencies:
- pytorch==1.13.1
- torchvision
- pandas[version='<2']
- scipy
- numpy
- matplotlib
- pytables
- cuml=23.04
- cudatoolkit=11.8
- protobuf[version='>3.20']
- tensorboard
- optuna
- mysql-connector-python
}}
とある
終了行:
本家様 [[https://github.com/MPI-Dortmund/tomotwin-cryoet>...
Particle picking in Tomograms using triplet networks and ...
ここにインストール方法が記載されている
[[https://github.com/MPI-Dortmund/tomotwin-cryoet/blob/ma...
読むとcondaの代わりにmambaを使ってねとあるが、パラレルで...
っでconda環境を作ります. ここでは pyenvの上にanaconda3を...
#code(nonumber){{
git clone https://github.com/yyuu/pyenv.git /apps/pyenv
export PYENV_ROOT=/apps/pyenv
export PATH=$PYENV_ROOT/bin:$PATH
pyenv install anaconda3-2024.10-1
pyenv global anaconda3-2024.10-1
source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profi...
}}
として環境を作ります. 既に環境があるなら
#code(nonumber){{
source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profi...
}}
とPATHの定義を行います.
っでモノを作ります
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.5 (Blue Onyx)
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 570.133.0...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]# nvidia-smi -L
GPU 0: NVIDIA GeForce GTX 1070 (UUID: GPU-a49de51b-de1e-5...
[root@rockylinux9 ~]#
}}
環境はこんな感じで nvidia ドライバー装備です
っで
#code(nonumber){{
[root@rockylinux9 ~]# conda env create -n tomotwin -f htt...
[root@rockylinux9 ~]# conda activate tomotwin
(tomotwin) [root@rockylinux9 ~]# pip install tomotwin-cry...
(tomotwin) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]# conda env create -n napari-tomotwin...
[root@rockylinux9 ~]# conda activate napari-tomotwin
(napari-tomotwin) [root@rockylinux9 ~]# pip install napar...
(napari-tomotwin) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
}}
ここまでで「tomotwin」と「napari-tomotwin」の実行環境が用...
#code(nonumber){{
[root@rockylinux9 src]# conda env list
# conda environments:
#
base /apps/pyenv/versions/anaconda3-2...
napari-tomotwin /apps/pyenv/versions/anaconda3-2...
tomotwin /apps/pyenv/versions/anaconda3-2...
[root@rockylinux9 src]#
}}
っで「tomotwin」実行環境から「napari-tomotwin」のnapari_b...
&size(10){内容的には crYOLO の napari_boxmanager と同じ};
#code(nonumber){{
[root@rockylinux9 ~]# conda activate tomotwin
(tomotwin) [root@rockylinux9 ~]# tomotwin_dir=$(realpath ...
(tomotwin) [root@rockylinux9 ~]# echo $tomotwin_dir
/apps/pyenv/versions/anaconda3-2024.10-1/envs/tomotwin/bin
(tomotwin) [root@rockylinux9 ~]# napari_link_file=${tomot...
(tomotwin) [root@rockylinux9 ~]# echo $napari_link_file
/apps/pyenv/versions/anaconda3-2024.10-1/envs/tomotwin/bi...
(tomotwin) [root@rockylinux9 ~]# conda deactivate
[root@rockylinux9 ~]#
[root@rockylinux9 ~]# conda activate napari-tomotwin
(napari-tomotwin) [root@rockylinux9 ~]# echo -e "#\!/usr/...
(napari-tomotwin) [root@rockylinux9 ~]# cat $napari_link_...
#\!/usr/bin/bash
export NAPARI_EXE=/apps/pyenv/versions/anaconda3-2023.03/...
napari_exe='/apps/pyenv/versions/anaconda3-2023.03/envs/n...
${napari_exe} "${@}"
(napari-tomotwin) [root@rockylinux9 ~]# ln -rs $(which na...
(napari-tomotwin) [root@rockylinux9 ~]# chmod +x ${napari...
(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...
}}
***environment-modules [#i50917fb]
#code(nonumber){{
[root@rockylinux9 ~]# vi /apps/modulefiles/tomotwin
#%Module1.0
set root /apps/pyenv/versions/anaconda3-2024.10-...
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...
matplotlib pytables cuML=23.04 cudatoolkit=11.8 'protob...
}}
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
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