cryoTIGER 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/turonova/cryoTIGER/>+https://...
Tilt Interpolation Generator for Enhanced Reconstruction ...
(deepL様翻訳)
クライオ電子トモグラフィにおける再構成のための傾斜補間ジ...
***環境 [#mb265b38]
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.5 (Blue Onyx)
[root@rockylinux9 ~]# uname -r
5.14.0-503.21.1.el9_5.x86_64
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 570.144 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]# ls /usr/local/cuda
ls: cannot access '/usr/local/cuda': No such file or dire...
[root@rockylinux9 ~]#
}}
***pyenv-anaconda [#icfbed2c]
ここではpyenv を敷いて、その上に anacondaやminiforgeらを...
すでにconda環境があればその環境を読み込んでください
#code(nonumber){{
[root@rockylinux9 ~]# source /apps/pyenv/versions/anacond...
}}
もしなければ構築してください。
#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 --list <--これでanaconda,minic...
pyenv install anaconda3-2024.10-1
}}
その上で
#code(nonumber){{
source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profi...
}}
とします
***インストール [#ceb018b0]
[[https://github.com/turonova/cryoTIGER/>+https://github....
「environment.yml」を使います
#code(nonumber){{
[root@rockylinux9 ~]# cd /apps/
[root@rockylinux9 apps]# git clone https://github.com/tur...
[root@rockylinux9 apps]# cd cryoTIGER/
[root@rockylinux9 cryoTIGER]# conda env create -f environ...
[root@rockylinux9 cryoTIGER]# conda activate cryoTIGER
(cryoTIGER) [root@rockylinux9 cryoTIGER]# conda list
:
cudatoolkit 11.2.2 hc23eb0c_13...
cudnn 8.1.0.77 h90431f1_0...
:
ipykernel 6.29.3 pypi_0...
ipython 8.18.1 pypi_0...
:
jupyter 1.0.0 pypi_0...
:
jupyterlab 4.1.5 pypi_0...
:
keras 2.11.0 pypi_0...
:
python 3.9.18 h0755675_1_cpyt...
:
tensorflow 2.11.0 pypi_0...
:
(cryoTIGER) [root@rockylinux9 cryoTIGER]#
}}
***Pre-trained Models [#g2e01a3e]
モデルファイルを取得して /apps/cryoTIGER に置く. gitで紹...
#code(nonumber){{
[root@rockylinux9 ~]# ls -l /apps/cryoTIGER/cryoTIGER_mod...
total 3144
drwxr-xr-x. 2 root root 6 May 2 15:39 assets
-rw-r--r--. 1 root root 208595 Sep 14 2024 keras_metada...
-rw-r--r--. 1 root root 3010009 Sep 14 2024 saved_model.pb
drwxr-xr-x. 2 root root 66 May 2 15:39 variables
[root@rockylinux9 ~]# ls -l /apps/cryoTIGER/pre-trained_V...
total 2756
drwxr-xr-x. 2 root root 6 May 2 15:42 assets
-rw-r--r--. 1 root root 212168 Jan 12 2022 keras_metada...
-rw-r--r--. 1 root root 2606292 Jan 12 2022 saved_model.pb
drwxr-xr-x. 2 root root 66 May 2 15:42 variables
[root@rockylinux9 ~]#
}}
***environment-modules [#ld8314c9]
「/apps/modulefiles/cryoTIGER」
#code(nonumber){{
#%Module1.0
set root /apps/pyenv/versions/anaconda3-2024.10-1/envs/cr...
prepend-path PATH $root/bin
}}
***つかう [#bde76c1f]
jupyter notebookを使うそうな
#code(nonumber){{
[saber@rockylinux9 ~]$ module use /apps/modulefiles/
[saber@rockylinux9 ~]$ module load cryoTIGER
[saber@rockylinux9 ~]$ jupyter --version
Selected Jupyter core packages...
IPython : 8.18.1
ipykernel : 6.29.3
ipywidgets : 8.1.2
jupyter_client : 8.6.1
jupyter_core : 5.7.2
jupyter_server : 2.13.0
jupyterlab : 4.1.5
nbclient : 0.10.0
nbconvert : 7.16.2
nbformat : 5.10.3
notebook : 7.1.2
qtconsole : 5.5.1
traitlets : 5.14.2
[saber@rockylinux9 ~]$
[saber@rockylinux9 ~]$ jupyter notebook --generate-config
Writing default config to: /home/saber/.jupyter/jupyter_n...
[saber@rockylinux9 ~]$ vi /home/saber/.jupyter/jupyter_no...
# c.ServerApp.ip = 'localhost'
↓
c.ServerApp.ip = '*'
[saber@rockylinux9 ~]$
[saber@rockylinux9 ~]$ jupyter notebook
:
[I 2025-05-03 01:03:02.654 ServerApp] Jupyter Server 2.13...
[I 2025-05-03 01:03:02.655 ServerApp] http://localhost:88...
[I 2025-05-03 01:03:02.655 ServerApp] http://127.0.0....
:
}}
ブラウザを開いて、このホストの「8888」にアクセスします
終了行:
本家様 [[https://github.com/turonova/cryoTIGER/>+https://...
Tilt Interpolation Generator for Enhanced Reconstruction ...
(deepL様翻訳)
クライオ電子トモグラフィにおける再構成のための傾斜補間ジ...
***環境 [#mb265b38]
#code(nonumber){{
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.5 (Blue Onyx)
[root@rockylinux9 ~]# uname -r
5.14.0-503.21.1.el9_5.x86_64
[root@rockylinux9 ~]# cat /proc/driver/nvidia/version
NVRM version: NVIDIA UNIX x86_64 Kernel Module 570.144 ...
GCC version: gcc version 11.5.0 20240719 (Red Hat 11.5.0...
[root@rockylinux9 ~]# ls /usr/local/cuda
ls: cannot access '/usr/local/cuda': No such file or dire...
[root@rockylinux9 ~]#
}}
***pyenv-anaconda [#icfbed2c]
ここではpyenv を敷いて、その上に anacondaやminiforgeらを...
すでにconda環境があればその環境を読み込んでください
#code(nonumber){{
[root@rockylinux9 ~]# source /apps/pyenv/versions/anacond...
}}
もしなければ構築してください。
#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 --list <--これでanaconda,minic...
pyenv install anaconda3-2024.10-1
}}
その上で
#code(nonumber){{
source /apps/pyenv/versions/anaconda3-2024.10-1/etc/profi...
}}
とします
***インストール [#ceb018b0]
[[https://github.com/turonova/cryoTIGER/>+https://github....
「environment.yml」を使います
#code(nonumber){{
[root@rockylinux9 ~]# cd /apps/
[root@rockylinux9 apps]# git clone https://github.com/tur...
[root@rockylinux9 apps]# cd cryoTIGER/
[root@rockylinux9 cryoTIGER]# conda env create -f environ...
[root@rockylinux9 cryoTIGER]# conda activate cryoTIGER
(cryoTIGER) [root@rockylinux9 cryoTIGER]# conda list
:
cudatoolkit 11.2.2 hc23eb0c_13...
cudnn 8.1.0.77 h90431f1_0...
:
ipykernel 6.29.3 pypi_0...
ipython 8.18.1 pypi_0...
:
jupyter 1.0.0 pypi_0...
:
jupyterlab 4.1.5 pypi_0...
:
keras 2.11.0 pypi_0...
:
python 3.9.18 h0755675_1_cpyt...
:
tensorflow 2.11.0 pypi_0...
:
(cryoTIGER) [root@rockylinux9 cryoTIGER]#
}}
***Pre-trained Models [#g2e01a3e]
モデルファイルを取得して /apps/cryoTIGER に置く. gitで紹...
#code(nonumber){{
[root@rockylinux9 ~]# ls -l /apps/cryoTIGER/cryoTIGER_mod...
total 3144
drwxr-xr-x. 2 root root 6 May 2 15:39 assets
-rw-r--r--. 1 root root 208595 Sep 14 2024 keras_metada...
-rw-r--r--. 1 root root 3010009 Sep 14 2024 saved_model.pb
drwxr-xr-x. 2 root root 66 May 2 15:39 variables
[root@rockylinux9 ~]# ls -l /apps/cryoTIGER/pre-trained_V...
total 2756
drwxr-xr-x. 2 root root 6 May 2 15:42 assets
-rw-r--r--. 1 root root 212168 Jan 12 2022 keras_metada...
-rw-r--r--. 1 root root 2606292 Jan 12 2022 saved_model.pb
drwxr-xr-x. 2 root root 66 May 2 15:42 variables
[root@rockylinux9 ~]#
}}
***environment-modules [#ld8314c9]
「/apps/modulefiles/cryoTIGER」
#code(nonumber){{
#%Module1.0
set root /apps/pyenv/versions/anaconda3-2024.10-1/envs/cr...
prepend-path PATH $root/bin
}}
***つかう [#bde76c1f]
jupyter notebookを使うそうな
#code(nonumber){{
[saber@rockylinux9 ~]$ module use /apps/modulefiles/
[saber@rockylinux9 ~]$ module load cryoTIGER
[saber@rockylinux9 ~]$ jupyter --version
Selected Jupyter core packages...
IPython : 8.18.1
ipykernel : 6.29.3
ipywidgets : 8.1.2
jupyter_client : 8.6.1
jupyter_core : 5.7.2
jupyter_server : 2.13.0
jupyterlab : 4.1.5
nbclient : 0.10.0
nbconvert : 7.16.2
nbformat : 5.10.3
notebook : 7.1.2
qtconsole : 5.5.1
traitlets : 5.14.2
[saber@rockylinux9 ~]$
[saber@rockylinux9 ~]$ jupyter notebook --generate-config
Writing default config to: /home/saber/.jupyter/jupyter_n...
[saber@rockylinux9 ~]$ vi /home/saber/.jupyter/jupyter_no...
# c.ServerApp.ip = 'localhost'
↓
c.ServerApp.ip = '*'
[saber@rockylinux9 ~]$
[saber@rockylinux9 ~]$ jupyter notebook
:
[I 2025-05-03 01:03:02.654 ServerApp] Jupyter Server 2.13...
[I 2025-05-03 01:03:02.655 ServerApp] http://localhost:88...
[I 2025-05-03 01:03:02.655 ServerApp] http://127.0.0....
:
}}
ブラウザを開いて、このホストの「8888」にアクセスします
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